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This page was generated on 2024-02-28 11:37:02 -0500 (Wed, 28 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1320/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
msa 1.34.0  (landing page)
Ulrich Bodenhofer
Snapshot Date: 2024-02-27 14:05:07 -0500 (Tue, 27 Feb 2024)
git_url: https://git.bioconductor.org/packages/msa
git_branch: RELEASE_3_18
git_last_commit: 2df795c
git_last_commit_date: 2023-10-24 10:43:22 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

BUILD BIN results for msa on palomino4


To the developers/maintainers of the msa package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/msa.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: msa
Version: 1.34.0
Command: rm -rf msa.buildbin-libdir && mkdir msa.buildbin-libdir && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL --build --library=msa.buildbin-libdir msa_1.34.0.tar.gz
StartedAt: 2024-02-28 08:50:12 -0500 (Wed, 28 Feb 2024)
EndedAt: 2024-02-28 08:59:28 -0500 (Wed, 28 Feb 2024)
EllapsedTime: 556.0 seconds
RetCode: 0
Status:   OK  
PackageFile: msa_1.34.0.zip
PackageFileSize: 2.036 MiB

Command output

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###
### Running command:
###
###   rm -rf msa.buildbin-libdir && mkdir msa.buildbin-libdir && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL --build --library=msa.buildbin-libdir msa_1.34.0.tar.gz
###
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* installing *source* package 'msa' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I"./gc-8.2.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -Wno-deprecated   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_msa.cpp -o R_init_msa.o
In file included from ./Muscle/RMuscle.h:4,
                 from R_init_msa.cpp:3:
./Muscle/muscle.h:54: warning: "assert" redefined
   54 | #define assert(exp)     ((void)0)
      | 
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\cassert:44,
                 from F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include/Rcpp/utils/tinyformat/tinyformat.h:137,
                 from F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include/Rcpp/utils/tinyformat.h:40,
                 from F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include/RcppCommon.h:73,
                 from F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from ./ClustalOmega/src/RClustalOmega.h:4,
                 from R_init_msa.cpp:1:
c:\rtools43\x86_64-w64-mingw32.static.posix\include\assert.h:42: note: this is the location of the previous definition
   42 | #define assert(_Expression) ((void)0)
      | 
In file included from ./Muscle/muscle.h:38:
./Muscle/intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I"./gc-8.2.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -Wno-deprecated   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SplitCharVector2List.cpp -o SplitCharVector2List.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -I"./gc-8.2.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -Wno-deprecated   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SplitCharVector2Matrix.cpp -o SplitCharVector2Matrix.o
make --file=msaMakefile.win --directory=gc-8.2.2 AR="ar"
make[1]: Entering directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/gc-8.2.2'
export PKG_LIBS=" -I./include -I./include/private -I."; \
export PKG_CFLAGS="-fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I."; \
export PKG_CXXFLAGS="-fcommon  -DALL_INTERIOR_POINTERS -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I."; \
F:/biocbuild/bbs-3.18-bioc/R/bin/x64/R.exe CMD SHLIB -o gc82.dll *.c; \
F:/biocbuild/bbs-3.18-bioc/R/bin/x64/R.exe CMD SHLIB -o gccpp82.dll -L. -lgc82 *.cpp; \
ar rcs libGC.a allchblk.o alloc.o backgraph.o blacklst.o checksums.o darwin_stop_world.o dbg_mlc.o dyn_load.o finalize.o fnlz_mlc.o gcj_mlc.o gc_dlopen.o headers.o mach_dep.o malloc.o mallocx.o mark.o mark_rts.o misc.o new_hblk.o obj_map.o os_dep.o pthread_start.o pthread_stop_world.o pthread_support.o ptr_chck.o reclaim.o specific.o thread_local_alloc.o typd_mlc.o win32_threads.o; \
ar rcs libGCcpp.a gc_cpp.o; \
cp libGC*.a ../
using C compiler: 'gcc.exe (GCC) 12.3.0'
make[2]: Entering directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/gc-8.2.2'
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c allchblk.c -o allchblk.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c alloc.c -o alloc.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c backgraph.c -o backgraph.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c blacklst.c -o blacklst.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c checksums.c -o checksums.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c darwin_stop_world.c -o darwin_stop_world.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dbg_mlc.c -o dbg_mlc.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dyn_load.c -o dyn_load.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c finalize.c -o finalize.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fnlz_mlc.c -o fnlz_mlc.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gc_dlopen.c -o gc_dlopen.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gcj_mlc.c -o gcj_mlc.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c headers.c -o headers.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mach_dep.c -o mach_dep.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c malloc.c -o malloc.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mallocx.c -o mallocx.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mark.c -o mark.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mark_rts.c -o mark_rts.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c misc.c -o misc.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c new_hblk.c -o new_hblk.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c obj_map.c -o obj_map.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c os_dep.c -o os_dep.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pthread_start.c -o pthread_start.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pthread_stop_world.c -o pthread_stop_world.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pthread_support.c -o pthread_support.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ptr_chck.c -o ptr_chck.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c reclaim.c -o reclaim.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c specific.c -o specific.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c thread_local_alloc.c -o thread_local_alloc.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c typd_mlc.c -o typd_mlc.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c win32_threads.c -o win32_threads.o
g++ -std=gnu++17 -shared -s -static-libgcc -o gc82.dll tmp.def allchblk.o alloc.o backgraph.o blacklst.o checksums.o darwin_stop_world.o dbg_mlc.o dyn_load.o finalize.o fnlz_mlc.o gc_dlopen.o gcj_mlc.o headers.o mach_dep.o malloc.o mallocx.o mark.o mark_rts.o misc.o new_hblk.o obj_map.o os_dep.o pthread_start.o pthread_stop_world.o pthread_support.o ptr_chck.o reclaim.o specific.o thread_local_alloc.o typd_mlc.o win32_threads.o -I./include -I./include/private -I. -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
make[2]: Leaving directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/gc-8.2.2'
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
make[2]: Entering directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/gc-8.2.2'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gc_badalc.cc -o gc_badalc.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -fcommon  -DALL_INTERIOR_POINTERS -DALL_INTERIOR_POINTERS -DGC_DLL -DGC_THREADS -D_CRT_SECURE_NO_DEPRECATE -I./libatomic_ops/src -I./include -I./include/private -I.   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gc_cpp.cc -o gc_cpp.o
g++ -std=gnu++17 -shared -s -static-libgcc -o gccpp82.dll tmp.def gc_badalc.o gc_cpp.o -L. -lgc82 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
make[2]: Leaving directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/gc-8.2.2'
make[1]: Leaving directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/gc-8.2.2'
----------------------------------------
------------------ GC  -----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile.win --directory=Muscle AR="ar"
make[1]: Entering directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/Muscle'
export PKG_LIBS=" -L"../gc-8.2.2/" -lgc82 -lgccpp82"
export PKG_CXXFLAGS="-c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1  -I../gc-8.2.2./include/"
F:/biocbuild/bbs-3.18-bioc/R/bin/x64/R.exe CMD SHLIB -o Muscle.dll aligngivenpath.cpp aligngivenpathsw.cpp aligntwomsas.cpp aligntwoprofs.cpp aln.cpp alpha.cpp anchors.cpp bittraceback.cpp blosum62.cpp blosumla.cpp clust.cpp cluster.cpp clwwt.cpp color.cpp cons.cpp diaglist.cpp diffobjscore.cpp diffpaths.cpp difftrees.cpp difftreese.cpp distcalc.cpp distfunc.cpp distpwkimura.cpp domuscle.cpp dosp.cpp dpreglist.cpp drawtree.cpp edgelist.cpp enumopts.cpp enumtostr.cpp estring.cpp fasta.cpp fasta2.cpp fastclust.cpp fastdist.cpp fastdistjones.cpp fastdistkbit.cpp fastdistkmer.cpp fastdistmafft.cpp fastdistnuc.cpp fastscorepath2.cpp finddiags.cpp finddiagsn.cpp glbalign.cpp glbalign352.cpp glbaligndiag.cpp glbalignle.cpp glbalignsimple.cpp glbalignsp.cpp glbalignspn.cpp glbalignss.cpp glbalndimer.cpp globals.cpp globalslinux.cpp globalsosx.cpp globalsother.cpp globalswin32.cpp gonnet.cpp henikoffweight.cpp henikoffweightpb.cpp html.cpp hydro.cpp intmath.cpp local.cpp main.cpp makerootmsa.cpp makerootmsab.cpp maketree.cpp mhack.cpp mpam200.cpp msa.cpp msa2.cpp msadistkimura.cpp msf.cpp muscle.cpp muscleout.cpp nucmx.cpp nwdasimple.cpp nwdasimple2.cpp nwdasmall.cpp nwrec.cpp nwsmall.cpp objscore.cpp objscore2.cpp objscoreda.cpp onexception.cpp options.cpp outweights.cpp pam200mafft.cpp params.cpp phy.cpp phy2.cpp phy3.cpp phy4.cpp phyfromclust.cpp phyfromfile.cpp physeq.cpp phytofile.cpp posgap.cpp ppscore.cpp profdb.cpp profile.cpp profilefrommsa.cpp progalign.cpp progress.cpp progressivealign.cpp pwpath.cpp readmx.cpp realigndiffs.cpp realigndiffse.cpp refine.cpp refinehoriz.cpp refinesubfams.cpp refinetree.cpp refinetreee.cpp refinevert.cpp refinew.cpp savebest.cpp scoredist.cpp scoregaps.cpp scorehistory.cpp scorepp.cpp seq.cpp seqvect.cpp setblosumweights.cpp setgscweights.cpp setnewhandler.cpp spfast.cpp sptest.cpp stabilize.cpp subfam.cpp subfams.cpp sw.cpp termgaps.cpp textfile.cpp threewaywt.cpp tomhydro.cpp traceback.cpp tracebackopt.cpp tracebacksw.cpp treefrommsa.cpp typetostr.cpp upgma2.cpp usage.cpp validateids.cpp vtml2.cpp writescorefile.cpp RMuscle.cpp
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
make[2]: Entering directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/Muscle'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c aligngivenpath.cpp -o aligngivenpath.o
aligngivenpath.cpp: In function 'void AppendTplInserts(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)':
aligngivenpath.cpp:186:24: warning: unused variable 'uLengthA' [-Wunused-variable]
  186 |         const unsigned uLengthA = msaA.GetColCount();
      |                        ^~~~~~~~
aligngivenpath.cpp:187:24: warning: unused variable 'uLengthB' [-Wunused-variable]
  187 |         const unsigned uLengthB = msaB.GetColCount();
      |                        ^~~~~~~~
aligngivenpath.cpp: In function 'void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)':
aligngivenpath.cpp:335:40: warning: unused variable 'uColA' [-Wunused-variable]
  335 |                         const unsigned uColA = uPrefixLengthA - 1;
      |                                        ^~~~~
aligngivenpath.cpp:336:40: warning: unused variable 'uColB' [-Wunused-variable]
  336 |                         const unsigned uColB = uPrefixLengthB - 1;
      |                                        ^~~~~
aligngivenpath.cpp:346:40: warning: unused variable 'uColA' [-Wunused-variable]
  346 |                         const unsigned uColA = uPrefixLengthA - 1;
      |                                        ^~~~~
aligngivenpath.cpp:354:40: warning: unused variable 'uColB' [-Wunused-variable]
  354 |                         const unsigned uColB = uPrefixLengthB - 1;
      |                                        ^~~~~
In file included from muscle.h:38,
                 from aligngivenpath.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c aligngivenpathsw.cpp -o aligngivenpathsw.o
aligngivenpathsw.cpp: In function 'void AppendUnalignedTerminals(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)':
aligngivenpathsw.cpp:58:24: warning: unused variable 'uLengthA' [-Wunused-variable]
   58 |         const unsigned uLengthA = msaA.GetColCount();
      |                        ^~~~~~~~
aligngivenpathsw.cpp:59:24: warning: unused variable 'uLengthB' [-Wunused-variable]
   59 |         const unsigned uLengthB = msaB.GetColCount();
      |                        ^~~~~~~~
aligngivenpathsw.cpp: In function 'void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)':
aligngivenpathsw.cpp:204:40: warning: unused variable 'uColA' [-Wunused-variable]
  204 |                         const unsigned uColA = uPrefixLengthA - 1;
      |                                        ^~~~~
aligngivenpathsw.cpp:205:40: warning: unused variable 'uColB' [-Wunused-variable]
  205 |                         const unsigned uColB = uPrefixLengthB - 1;
      |                                        ^~~~~
aligngivenpathsw.cpp:215:40: warning: unused variable 'uColA' [-Wunused-variable]
  215 |                         const unsigned uColA = uPrefixLengthA - 1;
      |                                        ^~~~~
aligngivenpathsw.cpp:223:40: warning: unused variable 'uColB' [-Wunused-variable]
  223 |                         const unsigned uColB = uPrefixLengthB - 1;
      |                                        ^~~~~
In file included from muscle.h:38,
                 from aligngivenpathsw.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c aligntwomsas.cpp -o aligntwomsas.o
In file included from aligntwomsas.cpp:6:
timing.h:5: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
    5 | #pragma warning(disable:4035)
      | 
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
   24 | static double TicksToSecs(TICKS t)
      |               ^~~~~~~~~~~
In file included from muscle.h:38,
                 from aligntwomsas.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c aligntwoprofs.cpp -o aligntwoprofs.o
In file included from muscle.h:38,
                 from aligntwoprofs.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c aln.cpp -o aln.o
In file included from muscle.h:38,
                 from aln.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c alpha.cpp -o alpha.o
alpha.cpp: In function 'unsigned int GetAlphaSize(ALPHA)':
alpha.cpp:84:16: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
   84 |         switch (Alpha)
      |                ^
In file included from muscle.h:38,
                 from alpha.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c anchors.cpp -o anchors.o
anchors.cpp: In function 'void MergeBestCols(const SCORE*, const unsigned int*, unsigned int, unsigned int, unsigned int*, unsigned int*)':
anchors.cpp:162:34: warning: unused variable 'uWindowCenter' [-Wunused-variable]
  162 |                         unsigned uWindowCenter = uBestColIndex + uWindowLength/2;
      |                                  ^~~~~~~~~~~~~
anchors.cpp: At global scope:
anchors.cpp:105:13: warning: 'void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)' defined but not used [-Wunused-function]
  105 | static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[],
      |             ^~~~~~~~~~~~
anchors.cpp:53:13: warning: 'void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
   53 | static void FindBestColsGrade(const SCORE Score[], unsigned uCount,
      |             ^~~~~~~~~~~~~~~~~
In file included from muscle.h:38,
                 from anchors.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bittraceback.cpp -o bittraceback.o
bittraceback.cpp: In function 'void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)':
bittraceback.cpp:146:14: warning: unused variable 'Bits' [-Wunused-variable]
  146 |         char Bits = TraceBack[uLengthA][uLengthB];
      |              ^~~~
bittraceback.cpp: At global scope:
bittraceback.cpp:15:20: warning: 'const char* BitsToStr(char)' defined but not used [-Wunused-function]
   15 | static const char *BitsToStr(char Bits)
      |                    ^~~~~~~~~
In file included from muscle.h:38,
                 from bittraceback.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c blosum62.cpp -o blosum62.o
In file included from muscle.h:38,
                 from blosum62.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c blosumla.cpp -o blosumla.o
blosumla.cpp:7:14: warning: 'Blosum62LA' defined but not used [-Wunused-variable]
    7 | static float Blosum62LA[20][20] =
      |              ^~~~~~~~~~
In file included from muscle.h:38,
                 from blosumla.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c clust.cpp -o clust.o
clust.cpp: In member function 'void Clust::ChooseJoin(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:167:16: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
  167 |         switch (m_JoinStyle)
      |                ^
clust.cpp: In member function 'void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:184:24: warning: unused variable 'uClusterCount' [-Wunused-variable]
  184 |         const unsigned uClusterCount = GetClusterCount();
      |                        ^~~~~~~~~~~~~
clust.cpp: In member function 'void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)':
clust.cpp:204:24: warning: unused variable 'uClusterCount' [-Wunused-variable]
  204 |         const unsigned uClusterCount = GetClusterCount();
      |                        ^~~~~~~~~~~~~
clust.cpp: In member function 'float Clust::ComputeDist(unsigned int, unsigned int)':
clust.cpp:295:16: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch]
  295 |         switch (m_CentroidStyle)
      |                ^
clust.cpp: In member function 'float Clust::ComputeDistMAFFT(unsigned int, unsigned int)':
clust.cpp:360:21: warning: unused variable 'dDistLR' [-Wunused-variable]
  360 |         const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex);
      |                     ^~~~~~~
clust.cpp: In member function 'float Clust::ComputeMetric(unsigned int, unsigned int) const':
clust.cpp:611:16: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
  611 |         switch (m_JoinStyle)
      |                ^
In file included from muscle.h:38,
                 from clust.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cluster.cpp -o cluster.o
cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)':
cluster.cpp:284:22: warning: variable 'bFound' set but not used [-Wunused-but-set-variable]
  284 |                 bool bFound = false;
      |                      ^~~~~~
cluster.cpp:267:16: warning: unused variable 'dMaxDist' [-Wunused-variable]
  267 |         double dMaxDist = 0.0;
      |                ^~~~~~~~
In file included from muscle.h:38,
                 from cluster.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
cluster.cpp: In member function 'void ClusterTree::Create(const DistFunc&)':
cluster.cpp:308:47: warning: 'uIndexClosest2' may be used uninitialized [-Wmaybe-uninitialized]
  308 |                 ClusterNode &Child2 = m_Nodes[uIndexClosest2];
      |                                               ^~~~~~~~~~~~~~
cluster.cpp:283:26: note: 'uIndexClosest2' was declared here
  283 |                 unsigned uIndexClosest2;
      |                          ^~~~~~~~~~~~~~
cluster.cpp:307:47: warning: 'uIndexClosest1' may be used uninitialized [-Wmaybe-uninitialized]
  307 |                 ClusterNode &Child1 = m_Nodes[uIndexClosest1];
      |                                               ^~~~~~~~~~~~~~
cluster.cpp:282:26: note: 'uIndexClosest1' was declared here
  282 |                 unsigned uIndexClosest1;
      |                          ^~~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c clwwt.cpp -o clwwt.o
In file included from muscle.h:38,
                 from clwwt.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c color.cpp -o color.o
color.cpp:72:12: warning: 'int BlosumScore(char, char)' defined but not used [-Wunused-function]
   72 | static int BlosumScore(char c1, char c2)
      |            ^~~~~~~~~~~
In file included from muscle.h:38,
                 from color.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cons.cpp -o cons.o
In file included from muscle.h:38,
                 from cons.cpp:7:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c diaglist.cpp -o diaglist.o
In file included from muscle.h:38,
                 from diaglist.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
diaglist.cpp: In member function 'void DiagList::FromPath(const PWPath&)':
diaglist.cpp:51:18: warning: 'uStartPosA' is used uninitialized [-Wuninitialized]
   51 |         unsigned uStartPosA;
      |                  ^~~~~~~~~~
diaglist.cpp:52:18: warning: 'uStartPosB' is used uninitialized [-Wuninitialized]
   52 |         unsigned uStartPosB;
      |                  ^~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c diffobjscore.cpp -o diffobjscore.o
diffobjscore.cpp: In function 'SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)':
diffobjscore.cpp:76:24: warning: unused variable 'uSeqCount' [-Wunused-variable]
   76 |         const unsigned uSeqCount = msa.GetSeqCount();
      |                        ^~~~~~~~~
diffobjscore.cpp:77:24: warning: unused variable 'uColCount' [-Wunused-variable]
   77 |         const unsigned uColCount = msa.GetColCount();
      |                        ^~~~~~~~~
In file included from muscle.h:38,
                 from diffobjscore.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c diffpaths.cpp -o diffpaths.o
In file included from muscle.h:38,
                 from diffpaths.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c difftrees.cpp -o difftrees.o
difftrees.cpp: In function 'void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)':
difftrees.cpp:161:24: warning: unused variable 'uLeafCount2' [-Wunused-variable]
  161 |         const unsigned uLeafCount2 = Tree2.GetLeafCount();
      |                        ^~~~~~~~~~~
In file included from muscle.h:38,
                 from difftrees.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c difftreese.cpp -o difftreese.o
In file included from muscle.h:38,
                 from difftreese.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c distcalc.cpp -o distcalc.o
In file included from muscle.h:38,
                 from distcalc.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c distfunc.cpp -o distfunc.o
In file included from muscle.h:38,
                 from distfunc.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c distpwkimura.cpp -o distpwkimura.o
In file included from muscle.h:38,
                 from distpwkimura.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c domuscle.cpp -o domuscle.o
In file included from domuscle.cpp:9:
timing.h:5: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
    5 | #pragma warning(disable:4035)
      | 
domuscle.cpp: In function 'void DoMuscle(MuscleInput*, MuscleOutput*)':
domuscle.cpp:169:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  169 |                 if (g_bClusterOnly)
      |                 ^~
domuscle.cpp:172:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  172 |                         return;
      |                         ^~~~~~
domuscle.cpp:180:13: warning: unused variable 'PNlength' [-Wunused-variable]
  180 |         int PNlength = (msaInput->inputSeqs).Length();
      |             ^~~~~~~~
timing.h: At global scope:
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
   24 | static double TicksToSecs(TICKS t)
      |               ^~~~~~~~~~~
In file included from muscle.h:38,
                 from RMuscle.h:4,
                 from domuscle.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dosp.cpp -o dosp.o
In file included from muscle.h:38,
                 from dosp.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dpreglist.cpp -o dpreglist.o
dpreglist.cpp: In function 'void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)':
dpreglist.cpp:82:40: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable]
   82 |                         const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1;
      |                                        ^~~~~~~~~~~~~~~~~~~~
In file included from muscle.h:38,
                 from dpreglist.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c drawtree.cpp -o drawtree.o
In file included from muscle.h:38,
                 from drawtree.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c edgelist.cpp -o edgelist.o
In file included from muscle.h:38,
                 from edgelist.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c enumopts.cpp -o enumopts.o
In file included from muscle.h:38,
                 from enumopts.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c enumtostr.cpp -o enumtostr.o
In file included from muscle.h:38,
                 from enumtostr.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c estring.cpp -o estring.o
estring.cpp:464:13: warning: 'bool CanMultiplyEstrings(const short int*, const short int*)' defined but not used [-Wunused-function]
  464 | static bool CanMultiplyEstrings(const short es1[], const short es2[])
      |             ^~~~~~~~~~~~~~~~~~~
In file included from muscle.h:38,
                 from estring.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
estring.cpp: In function 'void EstringsToPath(const short int*, const short int*, PWPath&)':
estring.cpp:409:17: warning: 'cType' may be used uninitialized [-Wmaybe-uninitialized]
  409 |                 switch (cType)
      |                 ^~~~~~
estring.cpp:377:22: note: 'cType' was declared here
  377 |                 char cType;
      |                      ^~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fasta.cpp -o fasta.o
fasta.cpp: In member function 'void MSA::FromFASTAFile(TextFile&)':
fasta.cpp:15:18: warning: unused variable 'uSeqCount' [-Wunused-variable]
   15 |         unsigned uSeqCount = 0;
      |                  ^~~~~~~~~
fasta.cpp:16:18: warning: unused variable 'uColCount' [-Wunused-variable]
   16 |         unsigned uColCount = uInsane;
      |                  ^~~~~~~~~
In file included from muscle.h:38,
                 from fasta.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fasta2.cpp -o fasta2.o
In file included from muscle.h:38,
                 from fasta2.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fastclust.cpp -o fastclust.o
In file included from muscle.h:38,
                 from fastclust.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fastdist.cpp -o fastdist.o
In file included from muscle.h:38,
                 from fastdist.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fastdistjones.cpp -o fastdistjones.o
In file included from muscle.h:38,
                 from fastdistjones.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fastdistkbit.cpp -o fastdistkbit.o
In file included from muscle.h:38,
                 from fastdistkbit.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fastdistkmer.cpp -o fastdistkmer.o
fastdistkmer.cpp: In function 'void FastDistKmer(const SeqVect&, DistFunc&)':
fastdistkmer.cpp:235:32: warning: unused variable 'KD' [-Wunused-variable]
  235 |                         double KD = KimuraDist(EstimatedPctId);
      |                                ^~
In file included from muscle.h:38,
                 from fastdistkmer.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fastdistmafft.cpp -o fastdistmafft.o
fastdistmafft.cpp: In function 'void DistKmer6_6(const SeqVect&, DistFunc&)':
fastdistmafft.cpp:239:29: warning: unused variable 'pName1' [-Wunused-variable]
  239 |                 const char *pName1 = s1.GetName();
      |                             ^~~~~~
fastdistmafft.cpp: At global scope:
fastdistmafft.cpp:104:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
  104 | static void ListCount(const unsigned char Count[])
      |             ^~~~~~~~~
In file included from muscle.h:38,
                 from fastdistmafft.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fastdistnuc.cpp -o fastdistnuc.o
fastdistnuc.cpp: In function 'void DistKmer4_6(const SeqVect&, DistFunc&)':
fastdistnuc.cpp:223:29: warning: unused variable 'pName1' [-Wunused-variable]
  223 |                 const char *pName1 = s1.GetName();
      |                             ^~~~~~
fastdistnuc.cpp: At global scope:
fastdistnuc.cpp:85:13: warning: 'void ListCount(const unsigned char*)' defined but not used [-Wunused-function]
   85 | static void ListCount(const unsigned char Count[])
      |             ^~~~~~~~~
fastdistnuc.cpp:33:17: warning: 'uResidueGroupCount' defined but not used [-Wunused-variable]
   33 | static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]);
      |                 ^~~~~~~~~~~~~~~~~~
In file included from muscle.h:38,
                 from fastdistnuc.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fastscorepath2.cpp -o fastscorepath2.o
In file included from muscle.h:38,
                 from fastscorepath2.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c finddiags.cpp -o finddiags.o
finddiags.cpp:11:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
   11 | static char *TupleToStr(int t)
      |              ^~~~~~~~~~
In file included from muscle.h:38,
                 from finddiags.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c finddiagsn.cpp -o finddiagsn.o
finddiagsn.cpp: In function 'char* TupleToStr(int)':
finddiagsn.cpp:16:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
   16 |         for (int i = 0; i < K; ++i)
      |                         ~~^~~
finddiagsn.cpp: At global scope:
finddiagsn.cpp:12:14: warning: 'char* TupleToStr(int)' defined but not used [-Wunused-function]
   12 | static char *TupleToStr(int t)
      |              ^~~~~~~~~~
In file included from muscle.h:38,
                 from finddiagsn.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c glbalign.cpp -o glbalign.o
In file included from glbalign.cpp:3:
timing.h:5: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
    5 | #pragma warning(disable:4035)
      | 
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
   24 | static double TicksToSecs(TICKS t)
      |               ^~~~~~~~~~~
In file included from muscle.h:38,
                 from glbalign.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c glbalign352.cpp -o glbalign352.o
In file included from glbalign352.cpp:3:
timing.h:5: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
    5 | #pragma warning(disable:4035)
      | 
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
   24 | static double TicksToSecs(TICKS t)
      |               ^~~~~~~~~~~
In file included from muscle.h:38,
                 from glbalign352.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c glbaligndiag.cpp -o glbaligndiag.o
In file included from glbaligndiag.cpp:6:
timing.h:5: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
    5 | #pragma warning(disable:4035)
      | 
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
   24 | static double TicksToSecs(TICKS t)
      |               ^~~~~~~~~~~
In file included from muscle.h:38,
                 from glbaligndiag.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c glbalignle.cpp -o glbalignle.o
In file included from muscle.h:38,
                 from glbalignle.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
glbalignle.cpp: In function 'SCORE GlobalAlignLE(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignle.cpp:431:30: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  431 |                 iTraceBack = (int) uInsertPos - (int) uLengthB;
      |                              ^~~~~~~~~~~~~~~~
glbalignle.cpp:404:18: note: 'uInsertPos' was declared here
  404 |         unsigned uInsertPos;
      |                  ^~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c glbalignsimple.cpp -o glbalignsimple.o
glbalignsimple.cpp:52:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
   52 | static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
      |             ^~~~~~
glbalignsimple.cpp:28:13: warning: 'void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
   28 | static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB,
      |             ^~~~~~
In file included from muscle.h:38,
                 from glbalignsimple.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c glbalignsp.cpp -o glbalignsp.o
In file included from muscle.h:38,
                 from glbalignsp.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
glbalignsp.cpp: In function 'SCORE GlobalAlignSP(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignsp.cpp:366:30: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  366 |                 iTraceBack = (int) uInsertPos - (int) uLengthB;
      |                              ^~~~~~~~~~~~~~~~
glbalignsp.cpp:339:18: note: 'uInsertPos' was declared here
  339 |         unsigned uInsertPos;
      |                  ^~~~~~~~~~
glbalignsp.cpp:305:52: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  305 |                                 *ptrTraceBack_ij = (int) uInsertPos - (int) j;
      |                                                    ^~~~~~~~~~~~~~~~
glbalignsp.cpp:272:26: note: 'uInsertPos' was declared here
  272 |                 unsigned uInsertPos;
      |                          ^~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c glbalignspn.cpp -o glbalignspn.o
In file included from muscle.h:38,
                 from glbalignspn.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
glbalignspn.cpp: In function 'SCORE GlobalAlignSPN(const ProfPos*, unsigned int, const ProfPos*, unsigned int, PWPath&)':
glbalignspn.cpp:401:30: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  401 |                 iTraceBack = (int) uInsertPos - (int) uLengthB;
      |                              ^~~~~~~~~~~~~~~~
glbalignspn.cpp:374:18: note: 'uInsertPos' was declared here
  374 |         unsigned uInsertPos;
      |                  ^~~~~~~~~~
glbalignspn.cpp:340:52: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  340 |                                 *ptrTraceBack_ij = (int) uInsertPos - (int) j;
      |                                                    ^~~~~~~~~~~~~~~~
glbalignspn.cpp:307:26: note: 'uInsertPos' was declared here
  307 |                 unsigned uInsertPos;
      |                          ^~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c glbalignss.cpp -o glbalignss.o
glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)':
glbalignss.cpp:177:30: warning: unused variable 'ptrRowA' [-Wunused-variable]
  177 |                 const SCORE *ptrRowA = MxRowA[i];
      |                              ^~~~~~~
glbalignss.cpp:119:24: warning: unused variable 'uPrefixCountA' [-Wunused-variable]
  119 |         const unsigned uPrefixCountA = uLengthA + 1;
      |                        ^~~~~~~~~~~~~
glbalignss.cpp:120:24: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
  120 |         const unsigned uPrefixCountB = uLengthB + 1;
      |                        ^~~~~~~~~~~~~
glbalignss.cpp: At global scope:
glbalignss.cpp:11:14: warning: 'SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
   11 | static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j)
      |              ^~~~~
In file included from muscle.h:38,
                 from glbalignss.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
glbalignss.cpp: In function 'SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)':
glbalignss.cpp:310:30: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  310 |                 iTraceBack = (int) uInsertPos - (int) uLengthB;
      |                              ^~~~~~~~~~~~~~~~
glbalignss.cpp:283:18: note: 'uInsertPos' was declared here
  283 |         unsigned uInsertPos;
      |                  ^~~~~~~~~~
glbalignss.cpp:252:52: warning: 'uInsertPos' may be used uninitialized [-Wmaybe-uninitialized]
  252 |                                 *ptrTraceBack_ij = (int) uInsertPos - (int) j;
      |                                                    ^~~~~~~~~~~~~~~~
glbalignss.cpp:221:26: note: 'uInsertPos' was declared here
  221 |                 unsigned uInsertPos;
      |                          ^~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c glbalndimer.cpp -o glbalndimer.o
glbalndimer.cpp: In function 'SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)':
glbalndimer.cpp:123:16: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
  123 |         switch (g_PPScore)
      |                ^
glbalndimer.cpp:123:16: warning: enumeration value 'PPSCORE_SPN' not handled in switch [-Wswitch]
glbalndimer.cpp: At global scope:
glbalndimer.cpp:14:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
   14 | static const char *LocalScoreToStr(SCORE s)
      |                    ^~~~~~~~~~~~~~~
In file included from muscle.h:38,
                 from glbalndimer.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c globals.cpp -o globals.o
In file included from muscle.h:38,
                 from globals.cpp:6:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c globalslinux.cpp -o globalslinux.o
In file included from muscle.h:38,
                 from globalslinux.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c globalsosx.cpp -o globalsosx.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c globalsother.cpp -o globalsother.o
In file included from muscle.h:38,
                 from globalsother.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c globalswin32.cpp -o globalswin32.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gonnet.cpp -o gonnet.o
gonnet.cpp:137:14: warning: 'Gonnet160' defined but not used [-Wunused-variable]
  137 | static SCORE Gonnet160[20][20] =
      |              ^~~~~~~~~
In file included from muscle.h:38,
                 from gonnet.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c henikoffweight.cpp -o henikoffweight.o
In file included from muscle.h:38,
                 from henikoffweight.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c henikoffweightpb.cpp -o henikoffweightpb.o
In file included from muscle.h:38,
                 from henikoffweightpb.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c html.cpp -o html.o
In file included from muscle.h:38,
                 from html.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hydro.cpp -o hydro.o
In file included from muscle.h:38,
                 from hydro.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c intmath.cpp -o intmath.o
In file included from muscle.h:38,
                 from intmath.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c local.cpp -o local.o
In file included from muscle.h:38,
                 from local.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c main.cpp -o main.o
In file included from muscle.h:38,
                 from main.cpp:3:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c makerootmsa.cpp -o makerootmsa.o
makerootmsa.cpp: In function 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)':
makerootmsa.cpp:18:24: warning: unused variable 'uSeqLength' [-Wunused-variable]
   18 |         const unsigned uSeqLength = s.Length();
      |                        ^~~~~~~~~~
makerootmsa.cpp: In function 'short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)':
makerootmsa.cpp:94:31: warning: unused variable 'Path' [-Wunused-variable]
   94 |                 const PWPath &Path = Nodes[uNodeIndex].m_Path;
      |                               ^~~~
makerootmsa.cpp: In function 'void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)':
makerootmsa.cpp:168:24: warning: unused variable 'uTreeNodeCount' [-Wunused-variable]
  168 |         const unsigned uTreeNodeCount = GuideTree.GetNodeCount();
      |                        ^~~~~~~~~~~~~~
makerootmsa.cpp: At global scope:
makerootmsa.cpp:12:13: warning: 'void PathSeq(const Seq&, const PWPath&, bool, Seq&)' defined but not used [-Wunused-function]
   12 | static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut)
      |             ^~~~~~~
In file included from muscle.h:38,
                 from makerootmsa.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c makerootmsab.cpp -o makerootmsab.o
In file included from muscle.h:38,
                 from makerootmsab.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c maketree.cpp -o maketree.o
In file included from muscle.h:38,
                 from maketree.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mhack.cpp -o mhack.o
In file included from muscle.h:38,
                 from mhack.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mpam200.cpp -o mpam200.o
In file included from muscle.h:38,
                 from mpam200.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c msa.cpp -o msa.o
msa.cpp:419:13: warning: 'void FmtPad(unsigned int)' defined but not used [-Wunused-function]
  419 | static void FmtPad(unsigned n)
      |             ^~~~~~
msa.cpp:407:13: warning: 'void FmtInt0(unsigned int, unsigned int)' defined but not used [-Wunused-function]
  407 | static void FmtInt0(unsigned u, unsigned uWidth)
      |             ^~~~~~~
msa.cpp:392:13: warning: 'void FmtInt(unsigned int, unsigned int)' defined but not used [-Wunused-function]
  392 | static void FmtInt(unsigned u, unsigned uWidth)
      |             ^~~~~~
msa.cpp:385:13: warning: 'void FmtChar(char, unsigned int)' defined but not used [-Wunused-function]
  385 | static void FmtChar(char c, unsigned uWidth)
      |             ^~~~~~~
In file included from muscle.h:38,
                 from msa.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c msa2.cpp -o msa2.o
msa2.cpp: In function 'void SetMSAWeightsMuscle(MSA&)':
msa2.cpp:357:16: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch]
  357 |         switch (Method)
      |                ^
msa2.cpp: In function 'void MSAAppend(MSA&, const MSA&)':
msa2.cpp:476:24: warning: unused variable 'uColCountCat' [-Wunused-variable]
  476 |         const unsigned uColCountCat = uColCount1 + uColCount2;
      |                        ^~~~~~~~~~~~
In file included from muscle.h:38,
                 from msa2.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c msadistkimura.cpp -o msadistkimura.o
In file included from muscle.h:38,
                 from msadistkimura.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c msf.cpp -o msf.o
msf.cpp:24:20: warning: 'const char* strfind(const char*, const char*)' defined but not used [-Wunused-function]
   24 | static const char *strfind(const char *s, const char *t)
      |                    ^~~~~~~
In file included from muscle.h:38,
                 from msf.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c muscle.cpp -o muscle.o
In file included from muscle.h:38,
                 from muscle.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c muscleout.cpp -o muscleout.o
In file included from muscle.h:38,
                 from muscleout.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nucmx.cpp -o nucmx.o
In file included from muscle.h:38,
                 from nucmx.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nwdasimple.cpp -o nwdasimple.o
In file included from muscle.h:38,
                 from nwdasimple.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nwdasimple2.cpp -o nwdasimple2.o
In file included from muscle.h:38,
                 from nwdasimple2.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nwdasmall.cpp -o nwdasmall.o
In file included from muscle.h:38,
                 from nwdasmall.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nwrec.cpp -o nwrec.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nwsmall.cpp -o nwsmall.o
In file included from muscle.h:38,
                 from nwsmall.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c objscore.cpp -o objscore.o
In file included from objscore.cpp:5:
timing.h:5: warning: ignoring '#pragma warning ' [-Wunknown-pragmas]
    5 | #pragma warning(disable:4035)
      | 
objscore.cpp: In function 'SCORE ObjScore(const MSA&, const unsigned int*, unsigned int, const unsigned int*, unsigned int)':
objscore.cpp:31:16: warning: enumeration value 'OBJSCORE_Undefined' not handled in switch [-Wswitch]
   31 |         switch (OS)
      |                ^
objscore.cpp:31:16: warning: enumeration value 'OBJSCORE_SPM' not handled in switch [-Wswitch]
timing.h: At global scope:
timing.h:24:15: warning: 'double TicksToSecs(TICKS)' defined but not used [-Wunused-function]
   24 | static double TicksToSecs(TICKS t)
      |               ^~~~~~~~~~~
In file included from muscle.h:38,
                 from objscore.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c objscore2.cpp -o objscore2.o
objscore2.cpp: In function 'SCORE TermGapScore(bool)':
objscore2.cpp:22:16: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch]
   22 |         switch (g_TermGaps)
      |                ^
objscore2.cpp: In function 'SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)':
objscore2.cpp:62:15: warning: unused variable 'scoreGaps' [-Wunused-variable]
   62 |         SCORE scoreGaps = 0;
      |               ^~~~~~~~~
objscore2.cpp:63:14: warning: unused variable 'bGapping1' [-Wunused-variable]
   63 |         bool bGapping1 = false;
      |              ^~~~~~~~~
objscore2.cpp:64:14: warning: unused variable 'bGapping2' [-Wunused-variable]
   64 |         bool bGapping2 = false;
      |              ^~~~~~~~~
objscore2.cpp:67:14: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
   67 |         bool bLeftTermGap = false;
      |              ^~~~~~~~~~~~
objscore2.cpp:82:14: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
   82 |         bool bRightTermGap = false;
      |              ^~~~~~~~~~~~~
objscore2.cpp: In function 'SCORE ScoreSeqPairGaps(const MSA&, unsigned int, const MSA&, unsigned int)':
objscore2.cpp:140:14: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable]
  140 |         bool bLeftTermGap = false;
      |              ^~~~~~~~~~~~
objscore2.cpp:155:14: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
  155 |         bool bRightTermGap = false;
      |              ^~~~~~~~~~~~~
objscore2.cpp: In function 'SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)':
objscore2.cpp:314:24: warning: unused variable 'uColCount2' [-Wunused-variable]
  314 |         const unsigned uColCount2 = msa2.GetColCount();
      |                        ^~~~~~~~~~
objscore2.cpp: In function 'SCORE ObjScoreXP(const MSA&, const MSA&)':
objscore2.cpp:493:38: warning: unused variable 'w' [-Wunused-variable]
  493 |                         const WEIGHT w = w1*w2;
      |                                      ^
In file included from muscle.h:38,
                 from objscore2.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c objscoreda.cpp -o objscoreda.o
In file included from muscle.h:38,
                 from objscoreda.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c onexception.cpp -o onexception.o
In file included from muscle.h:38,
                 from onexception.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c options.cpp -o options.o
In file included from muscle.h:38,
                 from options.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c outweights.cpp -o outweights.o
In file included from muscle.h:38,
                 from outweights.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pam200mafft.cpp -o pam200mafft.o
pam200mafft.cpp:6:14: warning: 'PAM200' defined but not used [-Wunused-variable]
    6 | static float PAM200[23][23] =
      |              ^~~~~~
In file included from muscle.h:38,
                 from pam200mafft.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c params.cpp -o params.o
params.cpp: In function 'void SetPPScore(bool)':
params.cpp:441:16: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
  441 |         switch (g_PPScore)
      |                ^
In file included from muscle.h:38,
                 from params.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c phy.cpp -o phy.o
phy.cpp: In member function 'void Tree::RootUnrootedTree(ROOT)':
phy.cpp:665:16: warning: unused variable 'dEdgeLength' [-Wunused-variable]
  665 |         double dEdgeLength = GetEdgeLength(uNode1, uNode2);
      |                ^~~~~~~~~~~
In file included from muscle.h:38,
                 from phy.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c phy2.cpp -o phy2.o
In file included from muscle.h:38,
                 from phy2.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c phy3.cpp -o phy3.o
phy3.cpp: In function 'void CalcInfo(const Tree&, unsigned int, unsigned int, EdgeInfo**)':
phy3.cpp:125:22: warning: unused variable 'dThisDist' [-Wunused-variable]
  125 |         const double dThisDist = tree.GetEdgeLength(uNode1, uNode2);
      |                      ^~~~~~~~~
phy3.cpp: In function 'void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)':
phy3.cpp:167:24: warning: unused variable 'uLeafCount' [-Wunused-variable]
  167 |         const unsigned uLeafCount = tree.GetLeafCount();
      |                        ^~~~~~~~~~
phy3.cpp:190:16: warning: unused variable 'dAllMaxDist' [-Wunused-variable]
  190 |         double dAllMaxDist = -1e20;
      |                ^~~~~~~~~~~
phy3.cpp:191:18: warning: unused variable 'uMaxFrom' [-Wunused-variable]
  191 |         unsigned uMaxFrom = NULL_NEIGHBOR;
      |                  ^~~~~~~~
phy3.cpp:192:18: warning: unused variable 'uMaxTo' [-Wunused-variable]
  192 |         unsigned uMaxTo = NULL_NEIGHBOR;
      |                  ^~~~~~
phy3.cpp: In function 'void RootByMidLongestSpan(const Tree&, EdgeInfo**, unsigned int*, unsigned int*, double*, double*)':
phy3.cpp:263:18: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable]
  263 |         unsigned uMostDistantLeaf = NULL_NEIGHBOR;
      |                  ^~~~~~~~~~~~~~~~
phy3.cpp: At global scope:
phy3.cpp:45:13: warning: 'void ListEIs(EdgeInfo**, unsigned int)' defined but not used [-Wunused-function]
   45 | static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount)
      |             ^~~~~~~
In file included from muscle.h:38,
                 from phy3.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c phy4.cpp -o phy4.o
In file included from muscle.h:38,
                 from phy4.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c phyfromclust.cpp -o phyfromclust.o
In file included from muscle.h:38,
                 from phyfromclust.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c phyfromfile.cpp -o phyfromfile.o
In file included from muscle.h:38,
                 from phyfromfile.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c physeq.cpp -o physeq.o
physeq.cpp: In member function 'void MSA::ToPhySequentialFile(TextFile&) const':
physeq.cpp:60:41: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
   60 |                                 if (Col == ColCount)
      |                                     ~~~~^~~~~~~~~~~
physeq.cpp:71:33: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
   71 |                         if (Col == ColCount)
      |                             ~~~~^~~~~~~~~~~
physeq.cpp: In member function 'void MSA::ToPhyInterleavedFile(TextFile&) const':
physeq.cpp:112:41: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  112 |                                 if (Col == ColCount)
      |                                     ~~~~^~~~~~~~~~~
physeq.cpp:124:25: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  124 |                 if (Col == ColCount)
      |                     ~~~~^~~~~~~~~~~
In file included from muscle.h:38,
                 from physeq.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c phytofile.cpp -o phytofile.o
In file included from muscle.h:38,
                 from phytofile.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c posgap.cpp -o posgap.o
In file included from muscle.h:38,
                 from posgap.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ppscore.cpp -o ppscore.o
In file included from muscle.h:38,
                 from ppscore.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c profdb.cpp -o profdb.o
In file included from clustsetmsa.h:8,
                 from profdb.cpp:9:
msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
msadist.h:22:23: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
   22 |                 switch(m_Distance)
      |                       ^
msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
In file included from muscle.h:38,
                 from profdb.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c profile.cpp -o profile.o
In file included from muscle.h:38,
                 from profile.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c profilefrommsa.cpp -o profilefrommsa.o
profilefrommsa.cpp: In function 'void ListProfile(const ProfPos*, unsigned int, const MSA*)':
profilefrommsa.cpp:131:24: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  131 |                 if (-1 == PP.m_uResidueGroup)
      |                     ~~~^~~~~~~~~~~~~~~~~~~~~
profilefrommsa.cpp: In function 'unsigned int ResidueGroupFromFCounts(const FCOUNT*)':
profilefrommsa.cpp:230:16: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
  230 |         switch (g_Alpha)
      |                ^
profilefrommsa.cpp: In function 'ProfPos* ProfileFromMSA(const MSA&)':
profilefrommsa.cpp:245:24: warning: unused variable 'uSeqCount' [-Wunused-variable]
  245 |         const unsigned uSeqCount = a.GetSeqCount();
      |                        ^~~~~~~~~
profilefrommsa.cpp:253:18: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable]
  253 |         unsigned uHydrophobicRunLength = 0;
      |                  ^~~~~~~~~~~~~~~~~~~~~
profilefrommsa.cpp: At global scope:
profilefrommsa.cpp:15:20: warning: 'const char* LocalScoreToStr(SCORE)' defined but not used [-Wunused-function]
   15 | static const char *LocalScoreToStr(SCORE s)
      |                    ^~~~~~~~~~~~~~~
In file included from muscle.h:38,
                 from profilefrommsa.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c progalign.cpp -o progalign.o
progalign.cpp: In function 'ProgNode* ProgressiveAlignE(const SeqVect&, const Tree&, MSA&)':
progalign.cpp:41:24: warning: unused variable 'uIterCount' [-Wunused-variable]
   41 |         const unsigned uIterCount = uSeqCount - 1;
      |                        ^~~~~~~~~~
In file included from muscle.h:38,
                 from progalign.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c progress.cpp -o progress.o
In file included from muscle.h:38,
                 from progress.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c progressivealign.cpp -o progressivealign.o
In file included from muscle.h:38,
                 from progressivealign.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pwpath.cpp -o pwpath.o
pwpath.cpp: In member function 'void PWPath::Validate() const':
pwpath.cpp:80:23: warning: unused variable 'LastEdge' [-Wunused-variable]
   80 |         const PWEdge &LastEdge = GetEdge(uEdgeCount - 1);
      |                       ^~~~~~~~
pwpath.cpp: In member function 'void PWPath::FromFile(TextFile&)':
pwpath.cpp:213:18: warning: unused variable 'uEdgeIndex' [-Wunused-variable]
  213 |         unsigned uEdgeIndex = 0;
      |                  ^~~~~~~~~~
In file included from muscle.h:38,
                 from pwpath.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c readmx.cpp -o readmx.o
readmx.cpp: In function 'float (* ReadMx(TextFile&))[32][32]':
readmx.cpp:83:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
   83 |         for (int i = 0; i < MAX_ALPHA; ++i)
      |                         ~~^~~~~~~~~~~
readmx.cpp:84:35: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
   84 |                 for (int j = 0; j < MAX_ALPHA; ++j)
      |                                 ~~^~~~~~~~~~~
readmx.cpp: In function 'float (* ReadMxFromR(std::vector<std::__cxx11::basic_string<char> >, float (*)[32]))[32][32]':
readmx.cpp:184:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  184 |         for (int i = 0; i < MAX_ALPHA; ++i)
      |                         ~~^~~~~~~~~~~
readmx.cpp:185:35: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  185 |                 for (int j = 0; j < MAX_ALPHA; ++j)
      |                                 ~~^~~~~~~~~~~
readmx.cpp: At global scope:
readmx.cpp:30:17: warning: 'unsigned int MxCharToLetter(char)' defined but not used [-Wunused-function]
   30 | static unsigned MxCharToLetter(char c)
      |                 ^~~~~~~~~~~~~~
In file included from muscle.h:38,
                 from readmx.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c realigndiffs.cpp -o realigndiffs.o
In file included from muscle.h:38,
                 from realigndiffs.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c realigndiffse.cpp -o realigndiffse.o
realigndiffse.cpp: In function 'void RealignDiffsE(const MSA&, const SeqVect&, const Tree&, const Tree&, const unsigned int*, MSA&, ProgNode*)':
realigndiffse.cpp:77:34: warning: unused variable 'uNewRight' [-Wunused-variable]
   77 |                         unsigned uNewRight = NewTree.GetRight(uNewNodeIndex);
      |                                  ^~~~~~~~~
realigndiffse.cpp:80:34: warning: unused variable 'uOldRight' [-Wunused-variable]
   80 |                         unsigned uOldRight = OldTree.GetRight(uOld);
      |                                  ^~~~~~~~~
In file included from muscle.h:38,
                 from realigndiffse.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c refine.cpp -o refine.o
In file included from clustsetmsa.h:8,
                 from refine.cpp:9:
msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
msadist.h:22:23: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
   22 |                 switch(m_Distance)
      |                       ^
msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
In file included from muscle.h:38,
                 from refine.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c refinehoriz.cpp -o refinehoriz.o
In file included from muscle.h:38,
                 from refinehoriz.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
In function 'void RefineHeightParts(MSA&, const Tree&, const unsigned int*, bool, bool, unsigned int, ScoreHistory&, bool*, bool*, bool, bool)',
    inlined from 'bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)' at refinehoriz.cpp:263:21:
refinehoriz.cpp:187:58: warning: 'scoreAfter' may be used uninitialized [-Wmaybe-uninitialized]
  187 |                 SCORE scoreMax = scoreAfter > scoreBefore? scoreAfter : scoreBefore;
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
refinehoriz.cpp: In function 'bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)':
refinehoriz.cpp:174:23: note: 'scoreAfter' was declared here
  174 |                 SCORE scoreAfter;
      |                       ^~~~~~~~~~
In function 'void RefineHeightParts(MSA&, const Tree&, const unsigned int*, bool, bool, unsigned int, ScoreHistory&, bool*, bool*, bool, bool)',
    inlined from 'bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)' at refinehoriz.cpp:263:21:
refinehoriz.cpp:187:58: warning: 'scoreBefore' may be used uninitialized [-Wmaybe-uninitialized]
  187 |                 SCORE scoreMax = scoreAfter > scoreBefore? scoreAfter : scoreBefore;
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
refinehoriz.cpp: In function 'bool RefineHoriz(MSA&, const Tree&, unsigned int, bool, bool)':
refinehoriz.cpp:173:23: note: 'scoreBefore' was declared here
  173 |                 SCORE scoreBefore;
      |                       ^~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c refinesubfams.cpp -o refinesubfams.o
refinesubfams.cpp: In function 'bool RefineSubfams(MSA&, const Tree&, unsigned int)':
refinesubfams.cpp:63:24: warning: unused variable 'uNodeCount' [-Wunused-variable]
   63 |         const unsigned uNodeCount = tree.GetNodeCount();
      |                        ^~~~~~~~~~
In file included from muscle.h:38,
                 from refinesubfams.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c refinetree.cpp -o refinetree.o
In file included from muscle.h:38,
                 from refinetree.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c refinetreee.cpp -o refinetreee.o
In file included from muscle.h:38,
                 from refinetreee.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c refinevert.cpp -o refinevert.o
In file included from muscle.h:38,
                 from refinevert.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c refinew.cpp -o refinew.o
refinew.cpp: In function 'void AppendMSA(MSA&, const MSA&)':
refinew.cpp:22:24: warning: unused variable 'uColCountCat' [-Wunused-variable]
   22 |         const unsigned uColCountCat = uColCount1 + uColCount2;
      |                        ^~~~~~~~~~~~
refinew.cpp: In function 'void RefineW(const MSA&, MSA&)':
refinew.cpp:125:34: warning: unused variable 'uOutCols' [-Wunused-variable]
  125 |                         unsigned uOutCols = msaOut.GetColCount();
      |                                  ^~~~~~~~
In file included from muscle.h:38,
                 from refinew.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c savebest.cpp -o savebest.o
In file included from muscle.h:38,
                 from savebest.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c scoredist.cpp -o scoredist.o
In file included from muscle.h:38,
                 from scoredist.cpp:3:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c scoregaps.cpp -o scoregaps.o
scoregaps.cpp:80:14: warning: 'SCORE Penalty(unsigned int, bool)' defined but not used [-Wunused-function]
   80 | static SCORE Penalty(unsigned Length, bool Term)
      |              ^~~~~~~
scoregaps.cpp:37:13: warning: 'void FreeGapInfo(GAPINFO*)' defined but not used [-Wunused-function]
   37 | static void FreeGapInfo(GAPINFO *GI)
      |             ^~~~~~~~~~~
In file included from muscle.h:38,
                 from scoregaps.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c scorehistory.cpp -o scorehistory.o
In file included from muscle.h:38,
                 from scorehistory.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c scorepp.cpp -o scorepp.o
In file included from muscle.h:38,
                 from scorepp.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c seq.cpp -o seq.o
In file included from muscle.h:38,
                 from seq.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c seqvect.cpp -o seqvect.o
In file included from muscle.h:38,
                 from seqvect.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c setblosumweights.cpp -o setblosumweights.o
In file included from muscle.h:38,
                 from setblosumweights.cpp:42:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c setgscweights.cpp -o setgscweights.o
In file included from muscle.h:38,
                 from setgscweights.cpp:104:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c setnewhandler.cpp -o setnewhandler.o
In file included from muscle.h:38,
                 from setnewhandler.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c spfast.cpp -o spfast.o
spfast.cpp: In function 'SCORE ObjScoreSPDimer(const MSA&)':
spfast.cpp:252:24: warning: unused variable 'uSeqCount' [-Wunused-variable]
  252 |         const unsigned uSeqCount = msa.GetSeqCount();
      |                        ^~~~~~~~~
spfast.cpp: At global scope:
spfast.cpp:59:14: warning: 'SCORE SPColBrute(const MSA&, unsigned int)' defined but not used [-Wunused-function]
   59 | static SCORE SPColBrute(const MSA &msa, unsigned uColIndex)
      |              ^~~~~~~~~~
spfast.cpp:14:20: warning: 'const char* GapTypeToStr(int)' defined but not used [-Wunused-function]
   14 | static const char *GapTypeToStr(int GapType)
      |                    ^~~~~~~~~~~~
In file included from muscle.h:38,
                 from spfast.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sptest.cpp -o sptest.o
In file included from muscle.h:38,
                 from sptest.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c stabilize.cpp -o stabilize.o
In file included from muscle.h:38,
                 from stabilize.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c subfam.cpp -o subfam.o
subfam.cpp: In function 'void AlignSubFam(SeqVect&, const Tree&, unsigned int, MSA&)':
subfam.cpp:173:13: warning: unused variable 'NotUsed' [-Wunused-variable]
  173 |         int NotUsed = system(CmdLine);
      |             ^~~~~~~
In file included from muscle.h:38,
                 from subfam.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c subfams.cpp -o subfams.o
subfams.cpp:54:13: warning: 'void Relax(DistFunc&, unsigned int, unsigned int)' defined but not used [-Wunused-function]
   54 | static void Relax(DistFunc &DF, unsigned u, unsigned v)
      |             ^~~~~
subfams.cpp:42:13: warning: 'void InitializeSingleSource(DistFunc&, unsigned int)' defined but not used [-Wunused-function]
   42 | static void InitializeSingleSource(DistFunc &DF, unsigned uIndex)
      |             ^~~~~~~~~~~~~~~~~~~~~~
subfams.cpp:12:13: warning: 'void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)' defined but not used [-Wunused-function]
   12 | static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2)
      |             ^~~~~~~~~~~~~~~~~~
In file included from muscle.h:38,
                 from subfams.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sw.cpp -o sw.o
sw.cpp:20:13: warning: 'void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)' defined but not used [-Wunused-function]
   20 | static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB,
      |             ^~~~~~
In file included from muscle.h:38,
                 from sw.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c termgaps.cpp -o termgaps.o
In file included from muscle.h:38,
                 from termgaps.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c textfile.cpp -o textfile.o
textfile.cpp: In member function 'void TextFile::PutChar(char)':
textfile.cpp:111:13: warning: unused variable 'i' [-Wunused-variable]
  111 |         int i = fputc(c, m_ptrFile);
      |             ^
textfile.cpp: In member function 'void TextFile::PutString(const char*)':
textfile.cpp:124:13: warning: unused variable 'iError' [-Wunused-variable]
  124 |         int iError = fputs(szLine, m_ptrFile);
      |             ^~~~~~
textfile.cpp: In member function 'TEXTFILEPOS TextFile::GetPos()':
textfile.cpp:224:13: warning: unused variable 'i' [-Wunused-variable]
  224 |         int i = fgetpos(m_ptrFile, &p);
      |             ^
textfile.cpp: In member function 'void TextFile::SetPos(TEXTFILEPOS)':
textfile.cpp:237:13: warning: unused variable 'i' [-Wunused-variable]
  237 |         int i = fsetpos(m_ptrFile, &p);
      |             ^
In file included from muscle.h:38,
                 from textfile.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c threewaywt.cpp -o threewaywt.o
In file included from muscle.h:38,
                 from threewaywt.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tomhydro.cpp -o tomhydro.o
In file included from muscle.h:38,
                 from tomhydro.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c traceback.cpp -o traceback.o
traceback.cpp: In function 'SCORE TraceBack(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, PWPath&)':
traceback.cpp:21:24: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
   21 |         const unsigned uPrefixCountB = uLengthB + 1;
      |                        ^~~~~~~~~~~~~
In file included from muscle.h:38,
                 from traceback.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tracebackopt.cpp -o tracebackopt.o
In file included from muscle.h:38,
                 from tracebackopt.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tracebacksw.cpp -o tracebacksw.o
tracebacksw.cpp: In function 'void TraceBackSW(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, unsigned int, unsigned int, PWPath&)':
tracebacksw.cpp:22:24: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
   22 |         const unsigned uPrefixCountB = uLengthB + 1;
      |                        ^~~~~~~~~~~~~
tracebacksw.cpp:29:15: warning: unused variable 'scoreMax' [-Wunused-variable]
   29 |         SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB);
      |               ^~~~~~~~
In file included from muscle.h:38,
                 from tracebacksw.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c treefrommsa.cpp -o treefrommsa.o
In file included from clustsetmsa.h:8,
                 from treefrommsa.cpp:5:
msadist.h: In member function 'double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)':
msadist.h:22:23: warning: enumeration value 'DISTANCE_Undefined' not handled in switch [-Wswitch]
   22 |                 switch(m_Distance)
      |                       ^
msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer6_6' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer20_3' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer20_4' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_Kbit20_3' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_Kmer4_6' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_PWKimura' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switch [-Wswitch]
msadist.h:22:23: warning: enumeration value 'DISTANCE_Edit' not handled in switch [-Wswitch]
In file included from muscle.h:38,
                 from treefrommsa.cpp:1:
intmath.h: At global scope:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c typetostr.cpp -o typetostr.o
In file included from muscle.h:38,
                 from typetostr.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c upgma2.cpp -o upgma2.o
upgma2.cpp:68:13: warning: 'void ListState()' defined but not used [-Wunused-function]
   68 | static void ListState()
      |             ^~~~~~~~~
In file included from muscle.h:38,
                 from upgma2.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
upgma2.cpp: In function 'void UPGMA2(const DistCalc&, Tree&, LINKAGE)':
upgma2.cpp:292:36: warning: 'dtNewDist' may be used uninitialized [-Wmaybe-uninitialized]
  292 |                         g_Dist[vL] = dtNewDist;
      |                         ~~~~~~~~~~~^~~~~~~~~~~
upgma2.cpp:252:32: note: 'dtNewDist' was declared here
  252 |                         dist_t dtNewDist;
      |                                ^~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c usage.cpp -o usage.o
In file included from muscle.h:38,
                 from usage.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c validateids.cpp -o validateids.o
In file included from muscle.h:38,
                 from validateids.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c vtml2.cpp -o vtml2.o
In file included from muscle.h:38,
                 from vtml2.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c writescorefile.cpp -o writescorefile.o
In file included from muscle.h:38,
                 from writescorefile.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
In function 'double GetColScore(const MSA&, unsigned int)',
    inlined from 'void WriteScoreFile(const MSA&)' at writescorefile.cpp:59:29:
writescorefile.cpp:40:30: warning: 'Score' may be used uninitialized [-Wmaybe-uninitialized]
   40 |                         dSum += Score;
      |                         ~~~~~^~~~~~~~
writescorefile.cpp: In function 'void WriteScoreFile(const MSA&)':
writescorefile.cpp:27:32: note: 'Score' was declared here
   27 |                         double Score;
      |                                ^~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RMuscle.cpp -o RMuscle.o
In file included from muscle.h:38,
                 from RMuscle.h:4,
                 from RMuscle.cpp:1:
intmath.h:59:15: warning: 'double ScoreToDouble(SCORE)' defined but not used [-Wunused-function]
   59 | static double ScoreToDouble(SCORE Score)
      |               ^~~~~~~~~~~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o Muscle.dll tmp.def aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o RMuscle.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
make[2]: Leaving directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/Muscle'
ar rcs libMuscle.a aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o RMuscle.o
cp libMuscle.a ../
make[1]: Leaving directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/Muscle'
----------------------------------------
---------------- MUSCLE ----------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile.win --directory=ClustalW AR="ar"
make[1]: Entering directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/ClustalW'
cp windows/Makefile .; \
cp windows/m4/Makefile m4/; \
cp windows/src/Makefile src/; \
cp windows/src/clustalw_version.h src/; \
cp windows/src/config.h src/; \
cd src; \
export PKG_CXXFLAGS="-DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result"; \
F:/biocbuild/bbs-3.18-bioc/R/bin/x64/R.exe CMD SHLIB -o ClustalW.dll pairwise/FullPairwiseAlign.cpp pairwise/FastPairwiseAlign.cpp fileInput/MSFFileParser.cpp fileInput/FileReader.cpp fileInput/PIRFileParser.cpp fileInput/RSFFileParser.cpp fileInput/GDEFileParser.cpp fileInput/InFileStream.cpp fileInput/ClustalFileParser.cpp fileInput/PearsonFileParser.cpp fileInput/FileParser.cpp fileInput/EMBLFileParser.cpp tree/UPGMA/RootedClusterTree.cpp tree/UPGMA/UPGMAAlgorithm.cpp tree/UPGMA/Node.cpp tree/UPGMA/RootedGuideTree.cpp tree/UPGMA/RootedTreeOutput.cpp tree/Tree.cpp tree/ClusterTree.cpp tree/TreeInterface.cpp tree/UnRootedClusterTree.cpp tree/ClusterTreeOutput.cpp tree/RandomGenerator.cpp tree/NJTree.cpp tree/AlignmentSteps.cpp interface/CommandLineParser.cpp substitutionMatrix/SubMatrix.cpp multipleAlign/Iteration.cpp multipleAlign/MSA.cpp multipleAlign/MyersMillerProfileAlign.cpp multipleAlign/ProfileStandard.cpp multipleAlign/ProfileWithSub.cpp multipleAlign/ProfileBase.cpp multipleAlign/LowScoreSegProfile.cpp general/OutputFile.cpp general/UserParameters.cpp general/Utility.cpp general/InvalidCombination.cpp general/DebugLog.cpp general/ClustalWResources.cpp general/VectorOutOfRange.cpp general/SymMatrix.cpp general/Stats.cpp Help.cpp alignment/Alignment.cpp alignment/AlignmentOutput.cpp alignment/ObjectiveScore.cpp alignment/Sequence.cpp Clustal.cpp RClustalWMain.cpp RClustalW.cpp &&\
ar rcs libClustalW.a pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o && \
cp libClustalW.a ../../
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
make[2]: Entering directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/ClustalW/src'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pairwise/FullPairwiseAlign.cpp -o pairwise/FullPairwiseAlign.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pairwise/FastPairwiseAlign.cpp -o pairwise/FastPairwiseAlign.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fileInput/MSFFileParser.cpp -o fileInput/MSFFileParser.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fileInput/FileReader.cpp -o fileInput/FileReader.o
fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readCharacterSeqs(clustalw::Alignment*, int, std::string*, ClustalWInput*)':
fileInput/FileReader.cpp:421:17: warning: variable 'maxAlnLength' set but not used [-Wunused-but-set-variable]
  421 |             int maxAlnLength; // Get values from the Alignment object.
      |                 ^~~~~~~~~~~~
fileInput/FileReader.cpp: In member function 'void clustalw::FileReader::checkInfile(int*, std::auto_ptr<clustalw::FileParser>&)':
fileInput/FileReader.cpp:692:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
  692 |     catch(exception ex)
      |                     ^~
fileInput/FileReader.cpp: In member function 'int clustalw::FileReader::readCharacterSeqs(clustalw::Alignment*, int, std::string*, ClustalWInput*)':
fileInput/FileReader.cpp:357:54: warning: 'this' pointer is null [-Wnonnull]
  357 |             seqRangeVector = fileParser->getSeqRangeR(1, noSeqs, offendingSeq, input);
      |                              ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from fileInput/FileReader.h:16,
                 from fileInput/FileReader.cpp:29:
fileInput/FileParser.h:44:26: note: in a call to non-static member function 'std::vector<clustalw::Sequence> clustalw::FileParser::getSeqRangeR(int, int, std::string*, ClustalWInput*)'
   44 |         vector<Sequence> getSeqRangeR(int firstSeq, int num, string *offendingSeq, ClustalWInput *input);
      |                          ^~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fileInput/PIRFileParser.cpp -o fileInput/PIRFileParser.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fileInput/RSFFileParser.cpp -o fileInput/RSFFileParser.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fileInput/GDEFileParser.cpp -o fileInput/GDEFileParser.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fileInput/InFileStream.cpp -o fileInput/InFileStream.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fileInput/ClustalFileParser.cpp -o fileInput/ClustalFileParser.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fileInput/PearsonFileParser.cpp -o fileInput/PearsonFileParser.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fileInput/FileParser.cpp -o fileInput/FileParser.o
fileInput/FileParser.cpp: In member function 'std::vector<clustalw::Sequence> clustalw::FileParser::getSeqRangeR(int, int, std::string*, ClustalWInput*)':
fileInput/FileParser.cpp:38:21: warning: unused variable 'n' [-Wunused-variable]
   38 |                 int n = (*input).inputSeqs.size();
      |                     ^
fileInput/FileParser.cpp: In member function 'void clustalw::FileParser::fillCharTab()':
fileInput/FileParser.cpp:56:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
   56 |     register int i;
      |                  ^
fileInput/FileParser.cpp:57:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
   57 |     register char c;
      |                   ^
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fileInput/EMBLFileParser.cpp -o fileInput/EMBLFileParser.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tree/UPGMA/RootedClusterTree.cpp -o tree/UPGMA/RootedClusterTree.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tree/UPGMA/UPGMAAlgorithm.cpp -o tree/UPGMA/UPGMAAlgorithm.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tree/UPGMA/Node.cpp -o tree/UPGMA/Node.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tree/UPGMA/RootedGuideTree.cpp -o tree/UPGMA/RootedGuideTree.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tree/UPGMA/RootedTreeOutput.cpp -o tree/UPGMA/RootedTreeOutput.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tree/Tree.cpp -o tree/Tree.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tree/ClusterTree.cpp -o tree/ClusterTree.o
tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)':
tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable]
  580 |     int rs = 0, rl = 0;
      |         ^~
tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable]
  580 |     int rs = 0, rl = 0;
      |                 ^~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tree/TreeInterface.cpp -o tree/TreeInterface.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tree/UnRootedClusterTree.cpp -o tree/UnRootedClusterTree.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tree/ClusterTreeOutput.cpp -o tree/ClusterTreeOutput.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tree/RandomGenerator.cpp -o tree/RandomGenerator.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tree/NJTree.cpp -o tree/NJTree.o
tree/NJTree.cpp: In member function 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)':
tree/NJTree.cpp:164:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  164 |     register int i;
      |                  ^
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c tree/AlignmentSteps.cpp -o tree/AlignmentSteps.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c interface/CommandLineParser.cpp -o interface/CommandLineParser.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c substitutionMatrix/SubMatrix.cpp -o substitutionMatrix/SubMatrix.o
substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeriesFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)':
substitutionMatrix/SubMatrix.cpp:1305:10: warning: unused variable 'inline1' [-Wunused-variable]
 1305 |     char inline1[1024];
      |          ^~~~~~~
substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable 'nmat' [-Wunused-variable]
 1307 |     int nmat;
      |         ^~~~
substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable 'n' [-Wunused-variable]
 1308 |     int n, llimit, ulimit;
      |         ^
substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable 'llimit' [-Wunused-variable]
 1308 |     int n, llimit, ulimit;
      |            ^~~~~~
substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable 'ulimit' [-Wunused-variable]
 1308 |     int n, llimit, ulimit;
      |                    ^~~~~~
substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readUserMatrixFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)':
substitutionMatrix/SubMatrix.cpp:1361:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 1361 |                 for (j = 0; j < curline.length(); j++) {
      |                             ~~^~~~~~~~~~~~~~~~~~
substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForHistogram(int (*)[32])':
substitutionMatrix/SubMatrix.cpp:1845:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
 1845 |     int maxRes;
      |         ^~~~~~
substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::getQTMatrixForLowScoreSeg(int (*)[32])':
substitutionMatrix/SubMatrix.cpp:1905:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
 1905 |     int maxRes;
      |         ^~~~~~
substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)':
substitutionMatrix/SubMatrix.cpp:1128:19: warning: 'n' may be used uninitialized [-Wmaybe-uninitialized]
 1128 |     return (maxRes);
      |                   ^
substitutionMatrix/SubMatrix.cpp:1023:9: note: 'n' was declared here
 1023 |     int n, llimit, ulimit;
      |         ^
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c multipleAlign/Iteration.cpp -o multipleAlign/Iteration.o
multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
multipleAlign/Iteration.cpp:170:9: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  170 |     int count;
      |         ^~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c multipleAlign/MSA.cpp -o multipleAlign/MSA.o
multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int>*, clustalw::AlignmentSteps*, int)':
multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable]
  340 |       int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18
      |           ^~~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c multipleAlign/MyersMillerProfileAlign.cpp -o multipleAlign/MyersMillerProfileAlign.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c multipleAlign/ProfileStandard.cpp -o multipleAlign/ProfileStandard.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c multipleAlign/ProfileWithSub.cpp -o multipleAlign/ProfileWithSub.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c multipleAlign/ProfileBase.cpp -o multipleAlign/ProfileBase.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c multipleAlign/LowScoreSegProfile.cpp -o multipleAlign/LowScoreSegProfile.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c general/OutputFile.cpp -o general/OutputFile.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c general/UserParameters.cpp -o general/UserParameters.o
general/UserParameters.cpp: In member function 'int clustalw::UserParameters::resIndex(std::string, char)':
general/UserParameters.cpp:475:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  475 |     register int i;
      |                  ^
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c general/Utility.cpp -o general/Utility.o
general/Utility.cpp: In member function 'char* clustalw::Utility::rTrim(char*)':
general/Utility.cpp:53:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
   53 |     register int p;
      |                  ^
general/Utility.cpp: In member function 'bool clustalw::Utility::lineType(char*, const char*)':
general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  251 |    int n;
      |        ^
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c general/InvalidCombination.cpp -o general/InvalidCombination.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c general/DebugLog.cpp -o general/DebugLog.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c general/ClustalWResources.cpp -o general/ClustalWResources.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c general/VectorOutOfRange.cpp -o general/VectorOutOfRange.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c general/SymMatrix.cpp -o general/SymMatrix.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c general/Stats.cpp -o general/Stats.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Help.cpp -o Help.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c alignment/Alignment.cpp -o alignment/Alignment.o
alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile1()':
alignment/Alignment.cpp:47:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
   47 |     register int sl;                /* which have  code = gap_pos2  */
      |                  ^~
alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile2()':
alignment/Alignment.cpp:122:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  122 |     register int sl;                /* which have  code = gap_pos2  */
      |                  ^~
alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetAlign()':
alignment/Alignment.cpp:617:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
  617 |     register int sl;
      |                  ^~
alignment/Alignment.cpp: In member function 'bool clustalw::Alignment::keepPortionOfSeqArray(int, int)':
alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable]
 1715 |     SeqArray::iterator posToAddTo = sectionToRealign.begin();
      |                        ^~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c alignment/AlignmentOutput.cpp -o alignment/AlignmentOutput.o
alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::fastaOut(clustalw::Alignment*, clustalw::outputRegion, ClustalWOutput*)':
alignment/AlignmentOutput.cpp:683:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
  683 |     catch(VectorOutOfRange e)
      |                            ^
alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::gcgOut(clustalw::Alignment*, clustalw::outputRegion)':
alignment/AlignmentOutput.cpp:878:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
  878 |     catch(VectorOutOfRange e)
      |                            ^
alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::phylipOut(clustalw::Alignment*, clustalw::outputRegion)':
alignment/AlignmentOutput.cpp:1037:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
 1037 |     catch(VectorOutOfRange e)
      |                            ^
alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nexusOut(clustalw::Alignment*, clustalw::outputRegion)':
alignment/AlignmentOutput.cpp:1166:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
 1166 |     catch(VectorOutOfRange e)
      |                            ^
alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::gdeOut(clustalw::Alignment*, clustalw::outputRegion)':
alignment/AlignmentOutput.cpp:1455:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
 1455 |     catch(VectorOutOfRange e)
      |                            ^
alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nbrfOut(clustalw::Alignment*, clustalw::outputRegion)':
alignment/AlignmentOutput.cpp:1570:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
 1570 |     catch(VectorOutOfRange e)
      |                            ^
alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::clustalOut(clustalw::Alignment*, clustalw::outputRegion, ClustalWOutput*)':
alignment/AlignmentOutput.cpp:2153:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
 2153 |     catch(VectorOutOfRange e)
      |                            ^
alignment/AlignmentOutput.cpp:2160:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
 2160 |     catch(exception e)
      |                     ^
alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::findRangeValues(clustalw::Alignment*, clustalw::rangeNum*, int, int, int)':
alignment/AlignmentOutput.cpp:2410:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
 2410 |     catch(VectorOutOfRange e)
      |                            ^
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c alignment/ObjectiveScore.cpp -o alignment/ObjectiveScore.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c alignment/Sequence.cpp -o alignment/Sequence.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Clustal.cpp -o Clustal.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RClustalWMain.cpp -o RClustalWMain.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DHAVE_CONFIG_H -I.  -Wno-deprecated -Wno-unused-result   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RClustalW.cpp -o RClustalW.o
g++ -std=gnu++17 -shared -s -static-libgcc -o ClustalW.dll tmp.def pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
make[2]: Leaving directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/ClustalW/src'
make[1]: Leaving directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/ClustalW'
----------------------------------------
--------------- ClustalW ---------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile.win --directory=ClustalOmega AR="ar"
make[1]: Entering directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/ClustalOmega'
cp windows/src/config.h src/; \
cp windows/src/clustal-omega-config.h src/; \
export PKG_LIBS=" -L"../../gc-8.2.2" -lgccpp82 -lgc82"; \
export PKG_CXXFLAGS=" -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include"; \
export PKG_CFLAGS=" -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82"; \
cd src; \
F:/biocbuild/bbs-3.18-bioc/R/bin/x64/R.exe CMD SHLIB -o ClustalOmega.dll exceptions4c/e4c_lite.c argtable2/argtable2.c argtable2/arg_end.c argtable2/arg_rem.c argtable2/arg_lit.c argtable2/arg_int.c argtable2/arg_dbl.c argtable2/arg_str.c argtable2/arg_file.c kmpp/KMeans.cpp kmpp/KmTree.cpp kmpp/KmUtils.cpp clustal/hhalign_wrapper.c clustal/ktuple_pair.c clustal/list.c clustal/log.c clustal/muscle_upgma.c clustal/muscle_tree.c clustal/mbed.c clustal/pair_dist.c clustal/progress.c clustal/seq.c clustal/symmatrix.c clustal/tree.c clustal/util.c clustal/weights.c squid/a2m.c squid/aligneval.c squid/alignio.c squid/clustal.c squid/cluster.c squid/dayhoff.c squid/eps.c squid/file.c squid/getopt.c squid/gki.c squid/gsi.c squid/gsi64.c squid/hsregex.c squid/iupac.c squid/msa.c squid/msf.c squid/phylip.c squid/revcomp.c squid/rk.c squid/selex.c squid/seqencode.c squid/shuffle.c squid/sqerror.c squid/sqio.c squid/squidcore.c squid/sre_ctype.c squid/sre_math.c squid/sre_random.c squid/sre_string.c squid/ssi.c squid/stack.c squid/stockholm.c squid/stopwatch.c squid/translate.c squid/types.c squid/vectorops.c squid/weight.c hhalign/hhalign.cpp RClustalOmega.cpp mymain.c clustal-omega.c && \
ar rcs libClustalOmega.a exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o && \
cp libClustalOmega.a ../../
using C compiler: 'gcc.exe (GCC) 12.3.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
make[2]: Entering directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/ClustalOmega/src'
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c exceptions4c/e4c_lite.c -o exceptions4c/e4c_lite.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c argtable2/argtable2.c -o argtable2/argtable2.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c argtable2/arg_end.c -o argtable2/arg_end.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c argtable2/arg_rem.c -o argtable2/arg_rem.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c argtable2/arg_lit.c -o argtable2/arg_lit.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c argtable2/arg_int.c -o argtable2/arg_int.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c argtable2/arg_dbl.c -o argtable2/arg_dbl.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c argtable2/arg_str.c -o argtable2/arg_str.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c argtable2/arg_file.c -o argtable2/arg_file.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kmpp/KMeans.cpp -o kmpp/KMeans.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kmpp/KmTree.cpp -o kmpp/KmTree.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kmpp/KmUtils.cpp -o kmpp/KmUtils.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c clustal/hhalign_wrapper.c -o clustal/hhalign_wrapper.o
In file included from clustal/hhalign_wrapper.c:22:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
clustal/hhalign_wrapper.c: In function 'SanitiseUnknown':
clustal/hhalign_wrapper.c:85:9: warning: unused variable 'iLen' [-Wunused-variable]
   85 |     int iLen; /* length of sequence */
      |         ^~~~
clustal/hhalign_wrapper.c:84:9: warning: unused variable 'iR' [-Wunused-variable]
   84 |     int iR; /* iterator for residue */
      |         ^~
clustal/hhalign_wrapper.c: In function 'ReAttachLeadingGaps':
clustal/hhalign_wrapper.c:239:9: warning: variable 'iSize2' set but not used [-Wunused-but-set-variable]
  239 |     int iSize2 = 0; /* #seqs in 2nd profile */
      |         ^~~~~~
clustal/hhalign_wrapper.c:238:9: warning: variable 'iSize1' set but not used [-Wunused-but-set-variable]
  238 |     int iSize1 = 0; /* #seqs in 1st profile */
      |         ^~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c clustal/ktuple_pair.c -o clustal/ktuple_pair.o
In file included from clustal/ktuple_pair.c:29:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
clustal/ktuple_pair.c: In function 'KTuplePairDist':
clustal/ktuple_pair.c:758: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas]
  758 |         #pragma omp critical(ktuple)
      | 
clustal/ktuple_pair.c:801: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas]
  801 |             #pragma omp critical(ktuple)
      | 
clustal/ktuple_pair.c:822: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas]
  822 |     #pragma omp critical(ktuple)
      | 
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c clustal/list.c -o clustal/list.o
In file included from clustal/list.c:32:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c clustal/log.c -o clustal/log.o
In file included from clustal/log.c:22:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c clustal/muscle_upgma.c -o clustal/muscle_upgma.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c clustal/muscle_tree.c -o clustal/muscle_tree.o
clustal/muscle_tree.c:519:1: warning: 'IsEdge' defined but not used [-Wunused-function]
  519 | IsEdge(unsigned uNodeIndex1, unsigned uNodeIndex2, tree_t *tree)
      | ^~~~~~
clustal/muscle_tree.c:42:21: warning: 'VERY_NEGATIVE_DOUBLE' defined but not used [-Wunused-const-variable=]
   42 | static const double VERY_NEGATIVE_DOUBLE = -9e29;
      |                     ^~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c clustal/mbed.c -o clustal/mbed.o
In file included from clustal/mbed.c:28:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
clustal/mbed.c: In function 'BisectingKmeans':
clustal/mbed.c:786:16: warning: variable 'dCost' set but not used [-Wunused-but-set-variable]
  786 |         double dCost = -1.0;
      |                ^~~~~
clustal/mbed.c: At top level:
clustal/mbed.c:69:18: warning: 'MAX_ALLOWED_SEQ_PER_PRECLUSTER' defined but not used [-Wunused-const-variable=]
   69 | static const int MAX_ALLOWED_SEQ_PER_PRECLUSTER = 100;
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c clustal/pair_dist.c -o clustal/pair_dist.o
In file included from clustal/pair_dist.c:22:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
clustal/pair_dist.c: In function 'SquidIdPairDist':
clustal/pair_dist.c:206: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas]
  206 |         #pragma omp critical(squidid)
      | 
clustal/pair_dist.c:218: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
  218 |         #pragma omp atomic
      | 
clustal/pair_dist.c:228: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas]
  228 |             #pragma omp critical(squidid)
      | 
clustal/pair_dist.c:177:10: warning: unused variable 'bPrintCR' [-Wunused-variable]
  177 |     bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE;
      |          ^~~~~~~~
clustal/pair_dist.c: In function 'PairDistances':
clustal/pair_dist.c:336: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  336 |             #pragma omp parallel for private(iChunk) schedule(dynamic)
      | 
clustal/pair_dist.c:359: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  359 |             #pragma omp parallel for private(iChunk) schedule(dynamic)
      | 
clustal/pair_dist.c:376: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  376 |             #pragma omp parallel for private(iChunk) schedule(dynamic)
      | 
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c clustal/progress.c -o clustal/progress.o
In file included from clustal/progress.c:22:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c clustal/seq.c -o clustal/seq.o
In file included from clustal/seq.c:30:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
clustal/seq.c: In function 'AliStat':
clustal/seq.c:68:9: warning: unused variable 'iAux' [-Wunused-variable]
   68 |     int iAux;
      |         ^~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c clustal/symmatrix.c -o clustal/symmatrix.o
In file included from clustal/symmatrix.c:30:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c clustal/tree.c -o clustal/tree.o
In file included from clustal/tree.c:22:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c clustal/util.c -o clustal/util.o
In file included from clustal/util.c:22:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c clustal/weights.c -o clustal/weights.o
In file included from clustal/weights.c:72:
./config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/a2m.c -o squid/a2m.o
In file included from squid/squid.h:32,
                 from squid/a2m.c:20:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/aligneval.c -o squid/aligneval.o
In file included from squid/squid.h:32,
                 from squid/aligneval.c:59:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/alignio.c -o squid/alignio.o
In file included from squid/squid.h:32,
                 from squid/alignio.c:21:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/clustal.c -o squid/clustal.o
In file included from squid/squid.h:32,
                 from squid/clustal.c:24:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
squid/clustal.c: In function 'WriteClustal':
squid/clustal.c:214:7: warning: unused variable 'cons' [-Wunused-variable]
  214 |   int cons;
      |       ^~~~
squid/clustal.c: In function 'WriteClustalForR':
squid/clustal.c:438:13: warning: unused variable 'cons' [-Wunused-variable]
  438 |         int cons;
      |             ^~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/cluster.c -o squid/cluster.o
In file included from squid/squid.h:32,
                 from squid/cluster.c:124:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/dayhoff.c -o squid/dayhoff.o
In file included from squid/squid.h:32,
                 from squid/dayhoff.c:28:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/eps.c -o squid/eps.o
In file included from squid/squid.h:32,
                 from squid/eps.c:23:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/file.c -o squid/file.o
In file included from squid/squid.h:32,
                 from squid/file.c:28:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/getopt.c -o squid/getopt.o
In file included from squid/squid.h:32,
                 from squid/getopt.c:17:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/gki.c -o squid/gki.o
In file included from squid/squid.h:32,
                 from squid/gki.c:82:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/gsi.c -o squid/gsi.o
In file included from squid/squid.h:32,
                 from squid/gsi.c:35:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/gsi64.c -o squid/gsi64.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/hsregex.c -o squid/hsregex.o
In file included from squid/squid.h:32,
                 from squid/hsregex.c:33:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/iupac.c -o squid/iupac.o
In file included from squid/squid.h:32,
                 from squid/iupac.c:17:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/msa.c -o squid/msa.o
In file included from squid/squid.h:32,
                 from squid/msa.c:22:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/msf.c -o squid/msf.o
In file included from squid/squid.h:32,
                 from squid/msf.c:25:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
squid/msf.c: In function 'ReadMSF':
squid/msf.c:87:11: warning: variable 'alleged_checksum' set but not used [-Wunused-but-set-variable]
   87 |   int     alleged_checksum;
      |           ^~~~~~~~~~~~~~~~
squid/msf.c:85:11: warning: variable 'alleged_alen' set but not used [-Wunused-but-set-variable]
   85 |   int     alleged_alen;
      |           ^~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/phylip.c -o squid/phylip.o
In file included from squid/squid.h:32,
                 from squid/phylip.c:23:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
squid/phylip.c: In function 'ReadPhylip':
squid/phylip.c:80:15: warning: variable 'alen' set but not used [-Wunused-but-set-variable]
   80 |   int   nseq, alen;
      |               ^~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/revcomp.c -o squid/revcomp.o
In file included from squid/squid.h:32,
                 from squid/revcomp.c:19:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/rk.c -o squid/rk.o
In file included from squid/squid.h:32,
                 from squid/rk.c:26:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/selex.c -o squid/selex.o
In file included from squid/squid.h:32,
                 from squid/selex.c:43:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/seqencode.c -o squid/seqencode.o
In file included from squid/squid.h:32,
                 from squid/seqencode.c:18:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/shuffle.c -o squid/shuffle.o
In file included from squid/squid.h:32,
                 from squid/shuffle.c:42:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/sqerror.c -o squid/sqerror.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/sqio.c -o squid/sqio.o
In file included from squid/squid.h:32,
                 from squid/sqio.c:57:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/squidcore.c -o squid/squidcore.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/sre_ctype.c -o squid/sre_ctype.o
In file included from squid/squid.h:32,
                 from squid/sre_ctype.c:19:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/sre_math.c -o squid/sre_math.o
In file included from squid/squid.h:32,
                 from squid/sre_math.c:19:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/sre_random.c -o squid/sre_random.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/sre_string.c -o squid/sre_string.o
In file included from squid/squid.h:32,
                 from squid/sre_string.c:23:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/ssi.c -o squid/ssi.o
In file included from squid/squid.h:32,
                 from squid/ssi.c:16:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/stack.c -o squid/stack.o
In file included from squid/squid.h:32,
                 from squid/stack.c:18:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/stockholm.c -o squid/stockholm.o
In file included from squid/squid.h:32,
                 from squid/stockholm.c:31:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/stopwatch.c -o squid/stopwatch.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/translate.c -o squid/translate.o
In file included from squid/squid.h:32,
                 from squid/translate.c:19:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/types.c -o squid/types.o
In file included from squid/squid.h:32,
                 from squid/types.c:20:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
In function 'Byteswap',
    inlined from 'sre_ntoh64' at squid/types.c:210:3:
squid/types.c:137:12: warning: array subscript 4 is outside array bounds of 'sqd_uint64[1]' {aka 'long unsigned int[1]'} [-Warray-bounds]
  137 |       byte = swap[nbytes - x - 1];
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~~~
squid/types.c: In function 'sre_ntoh64':
squid/types.c:205:23: note: at offset 4 into object 'net_int64' of size 4
  205 | sre_ntoh64(sqd_uint64 net_int64)
      |            ~~~~~~~~~~~^~~~~~~~~
In function 'Byteswap',
    inlined from 'sre_ntoh64' at squid/types.c:210:3:
squid/types.c:138:28: warning: array subscript 4 is outside array bounds of 'sqd_uint64[1]' {aka 'long unsigned int[1]'} [-Warray-bounds]
  138 |       swap[nbytes - x - 1] = swap[x];
      |       ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
squid/types.c: In function 'sre_ntoh64':
squid/types.c:205:23: note: at offset 4 into object 'net_int64' of size 4
  205 | sre_ntoh64(sqd_uint64 net_int64)
      |            ~~~~~~~~~~~^~~~~~~~~
squid/types.c: In function 'sre_hton64':
squid/types.c:137:12: warning: array subscript 4 is outside array bounds of 'sqd_uint64[1]' {aka 'long unsigned int[1]'} [-Warray-bounds]
  137 |       byte = swap[nbytes - x - 1];
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~~~
squid/types.c:215:1: note: at offset 4 into object 'net_int64' of size 4
  215 | sre_hton64(sqd_uint64 host_int64)
      | ^~~~~~~~~~
squid/types.c:138:28: warning: array subscript 4 is outside array bounds of 'sqd_uint64[1]' {aka 'long unsigned int[1]'} [-Warray-bounds]
  138 |       swap[nbytes - x - 1] = swap[x];
      |       ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
squid/types.c:215:1: note: at offset 4 into object 'net_int64' of size 4
  215 | sre_hton64(sqd_uint64 host_int64)
      | ^~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/vectorops.c -o squid/vectorops.o
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c squid/weight.c -o squid/weight.o
In file included from squid/squid.h:32,
                 from squid/weight.c:19:
squid/../config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hhalign/hhalign.cpp -o hhalign/hhalign.o
In file included from hhalign/hhalign.cpp:62:
hhalign/util-C.h: In function 'float fast_log2(float)':
hhalign/util-C.h:94:16: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   94 |   int a = (((*((int *)&x)) & 0x7F800000) >>23 )-0x7f;
      |               ~^~~~~~~~~~
hhalign/util-C.h:95:16: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   95 |   int b =  ((*((int *)&x)) & 0x007FE000) >>13;
      |               ~^~~~~~~~~~
hhalign/util-C.h:96:16: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   96 |   int c =  ((*((int *)&x)) & 0x00001FFF);
      |               ~^~~~~~~~~~
hhalign/util-C.h: In function 'float fpow2(float)':
hhalign/util-C.h:111:14: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  111 |   int lx = *((int*)&tx) - 0x4b400000;   // integer value of x
      |             ~^~~~~~~~~~
hhalign/util-C.h: In function 'float fast_pow2(float)':
hhalign/util-C.h:158:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  158 |           pow2[b]=(*((unsigned int *)(&f)) & 0x7FFFFF); // store the mantisse of 2^(1+b/1024)
      |                     ~^~~~~~~~~~~~~~~~~~~~~
hhalign/util-C.h:202:12: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  202 |   return *((float*)&y);
      |           ~^~~~~~~~~~~
In file included from hhalign/hhalign.cpp:76:
hhalign/hhhmm-C.h: In member function 'int HMM::ReadHMMer3(FILE*, char*)':
hhalign/hhhmm-C.h:1141:12: warning: variable 'dAlphaInv' set but not used [-Wunused-but-set-variable]
 1141 |     double dAlphaInv = 1.00 / (double)(iAlpha); /* weight of AA */
      |            ^~~~~~~~~
hhalign/hhhmm-C.h: In member function 'void HMM::WriteToFileHMMER(char*)':
hhalign/hhhmm-C.h:2206:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 2206 |   for (i=0; i<=par.argc-1; ++i) fprintf(outf,"%s ",par.argv[i]); fprintf(outf,"\n");
      |   ^~~
hhalign/hhhmm-C.h:2206:66: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 2206 |   for (i=0; i<=par.argc-1; ++i) fprintf(outf,"%s ",par.argv[i]); fprintf(outf,"\n");
      |                                                                  ^~~~~~~
In file included from hhalign/hhalign.cpp:77:
hhalign/hhalignment-C.h: In member function 'void Alignment::Read(FILE*, char*, char*)':
hhalign/hhalignment-C.h:245:32: warning: variable 'ptr2' set but not used [-Wunused-but-set-variable]
  245 |                   char *ptr1, *ptr2;
      |                                ^~~~
hhalign/hhalignment-C.h: In member function 'int Alignment::FilterWithCoreHMM(char*, float, HMM&)':
hhalign/hhalignment-C.h:1429:19: warning: variable 'score_M' set but not used [-Wunused-but-set-variable]
 1429 |             float score_M=0.0;
      |                   ^~~~~~~
hhalign/hhalignment-C.h:1430:19: warning: variable 'score_prev' set but not used [-Wunused-but-set-variable]
 1430 |             float score_prev=0.0;
      |                   ^~~~~~~~~~
hhalign/hhalignment-C.h: In member function 'void Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM&, char*)':
hhalign/hhalignment-C.h:1905:18: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
 1905 |               if (ncol<NCOLMIN)
      |                  ^
hhalign/hhalignment-C.h: In member function 'void Alignment::Transitions_from_I_state(HMM&, char*)':
hhalign/hhalignment-C.h:2137:28: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
 2137 |                         if (ncol>=NCOLMIN)
      |                            ^
hhalign/hhalignment-C.h: In member function 'void Alignment::Transitions_from_D_state(HMM&, char*)':
hhalign/hhalignment-C.h:2344:32: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
 2344 |                             if (ncol<NCOLMIN)
      |                                ^
In file included from hhalign/hhalign.cpp:81:
hhalign/hhhitlist-C.h: In member function 'void HitList::MaxLikelihoodEVD(HMM&, int)':
hhalign/hhhitlist-C.h:663:9: warning: the address of 'HMM::fam' will never be NULL [-Waddress]
  663 |   if (q.fam && q.fam[0]>='a' && q.fam[0]<='k' && q.fam[1]=='.')
      |       ~~^~~
In file included from hhalign/hhalign.cpp:70:
hhalign/hhhmm.h:53:8: note: 'HMM::fam' declared here
   53 |   char fam[NAMELEN];        // family ID (derived from name) (FAM field)
      |        ^~~
hhalign/hhhitlist-C.h: In member function 'void HitList::CalculateHHblastCorrelation(HMM&)':
hhalign/hhhitlist-C.h:840:9: warning: the address of 'HMM::fam' will never be NULL [-Waddress]
  840 |   if (q.fam && q.fam[0]>='a' && q.fam[0]<='k' && q.fam[1]=='.')
      |       ~~^~~
hhalign/hhhmm.h:53:8: note: 'HMM::fam' declared here
   53 |   char fam[NAMELEN];        // family ID (derived from name) (FAM field)
      |        ^~~
hhalign/hhhitlist-C.h: In member function 'void HitList::TransitiveScoring()':
hhalign/hhhitlist-C.h:1259:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
 1259 |   size_t unused; /* disable fread gcc warning */
      |          ^~~~~~
hhalign/hhhitlist-C.h: In member function 'void HitList::TransitiveScoring2()':
hhalign/hhhitlist-C.h:1624:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
 1624 |   size_t unused; /* disable fread gcc warning */
      |          ^~~~~~
hhalign/hhhitlist-C.h: In member function 'void HitList::TransitiveScoring3()':
hhalign/hhhitlist-C.h:1994:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
 1994 |   size_t unused; /* disable fread gcc warning */
      |          ^~~~~~
hhalign/hhhitlist-C.h: In member function 'void HitList::TransitiveScoring4()':
hhalign/hhhitlist-C.h:2359:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable]
 2359 |   size_t unused; /* disable fread gcc warning */
      |          ^~~~~~
In file included from hhalign/hhalign.cpp:82:
hhalign/hhfunc-C.h: In function 'void AddBackgroundFrequencies(float**, float**, float**, int, hmm_light*, char**, char*, int, char*)':
hhalign/hhfunc-C.h:74:9: warning: unused variable 'iT' [-Wunused-variable]
   74 |     int iT; /* transition state iterator */
      |         ^~
hhalign/hhfunc-C.h:80:11: warning: unused variable 'fGThgiew' [-Wunused-variable]
   80 |     float fGThgiew = UNITY - fGWeight; /* weight of 'true' transitions */
      |           ^~~~~~~~
hhalign/hhfunc-C.h:85:11: warning: unused variable 'zf1SeqTrans' [-Wunused-variable]
   85 |     float zf1SeqTrans[] = {0.98, 0.01, 0.01, 0.25, 0.75, 0.25, 0.75};
      |           ^~~~~~~~~~~
hhalign/hhfunc-C.h:86:11: warning: unused variable 'zf1SeqInit' [-Wunused-variable]
   86 |     float zf1SeqInit[]  = {0.98, 0.01, 0.01, 0.99, 0.01, 0.99, 0.01};
      |           ^~~~~~~~~~
hhalign/hhfunc-C.h:87:11: warning: unused variable 'zf1SeqDel' [-Wunused-variable]
   87 |     float zf1SeqDel[]   = {0.24, 0.01, 0.75, 0.01, 0.01, 0.01, 0.01};
      |           ^~~~~~~~~
hhalign/hhfunc-C.h:88:11: warning: unused variable 'zf1SeqRevrt' [-Wunused-variable]
   88 |     float zf1SeqRevrt[] = {0.98, 0.01, 0.01, 0.01, 0.01, 0.99, 0.01};
      |           ^~~~~~~~~~~
hhalign/hhfunc-C.h: In function 'int ReadAndPrepare(int, char**, int, hmm_light*, char*, char*, double*, char*, HMM&, Alignment*)':
hhalign/hhfunc-C.h:328:17: warning: unused variable 'NEFF_SCORE' [-Wunused-variable]
  328 |       const int NEFF_SCORE = 10; /* FIXME: Magic Number */
      |                 ^~~~~~~~~~
hhalign/hhfunc-C.h:511:17: warning: unused variable 'NEFF_SCORE' [-Wunused-variable]
  511 |       const int NEFF_SCORE = 10; /* FIXME: Magic Number */
      |                 ^~~~~~~~~~
hhalign/hhalign.cpp: In function 'int hhalign(char**, int, double*, char**, int, double*, double*, hmm_light*, char*, char*, char*, char*, hhalign_para, hhalign_scores*, int, int, char*, char*)':
hhalign/hhalign.cpp:721:9: warning: variable 'Nali' set but not used [-Wunused-but-set-variable]
  721 |     int Nali;                    /* number of normally backtraced alignments
      |         ^~~~
hhalign/hhhmm-C.h: In constructor 'HMM::HMM(int, int)':
hhalign/hhhmm-C.h:69:32: warning: argument 1 range [18446744073709551615, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   69 |     Neff_I = new float[maxres]();     // Neff_I[i] = diversity of subalignment of seqs that have insert in col i
      |                                ^
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\new_allocator.h:34,
                 from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\x86_64-w64-mingw32.static.posix\bits\c++allocator.h:33,
                 from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\allocator.h:46,
                 from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\string:41,
                 from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\locale_classes.h:40,
                 from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\bits\ios_base.h:41,
                 from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\ios:42,
                 from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\ostream:38,
                 from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\iostream:39,
                 from hhalign/hhalign.cpp:34:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\new:128:26: note: in a call to allocation function 'void* operator new [](std::size_t)' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^~~~~~~~
hhalign/hhhmm-C.h:70:32: warning: argument 1 range [18446744073709551615, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   70 |     Neff_D = new float[maxres]();     // Neff_D[i] = diversity of subalignment of seqs that have delete in col i
      |                                ^
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\new:128:26: note: in a call to allocation function 'void* operator new [](std::size_t)' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^~~~~~~~
hhalign/hhhmm-C.h:77:25: warning: argument 1 range [18446744073709551615, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   77 |     l = new int[maxres]();            // l[i] = pos. of j'th match state in aligment
      |                         ^
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\new:128:26: note: in a call to allocation function 'void* operator new [](std::size_t)' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^~~~~~~~
hhalign/hhhmm-C.h:66:32: warning: argument 1 range [18446744073709551615, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   66 |     seq = new char*[maxseqdis]();     // residues of stored sequences (first at pos 1!)
      |                                ^
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\c++\new:128:26: note: in a call to allocation function 'void* operator new [](std::size_t)' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^~~~~~~~
hhalign/hhhmm-C.h: In member function 'int HMM::Read(FILE*, char*)':
hhalign/hhhmm-C.h:294:20: warning: 'char* strncat(char*, const char*, size_t)' output may be truncated copying between 0 and 510 bytes from a string of length 262139 [-Wstringop-truncation]
  294 |             strncat(file,ptr,NAMELEN-1-strlen(file));   // append file name read from file to path
      |             ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hhalign/hhhmm-C.h:285:27: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 254 bytes from a string of length 262140 [-Wstringop-truncation]
  285 |           if (ptr) strncpy(fam,ptr,IDLEN-1); else strcpy(fam,""); //copy family name to basename
      |                    ~~~~~~~^~~~~~~~~~~~~~~~~
hhalign/hhhmm-C.h:269:22: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation]
  269 |               strncpy(longname,ptr,DESCLEN-1); //copy full name to longname
      |               ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
hhalign/hhhmm-C.h:271:22: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 510 bytes from a string of length 262139 [-Wstringop-truncation]
  271 |               strncpy(name,ptr,NAMELEN-1);     //copy longname to name...
      |               ~~~~~~~^~~~~~~~~~~~~~~~~~~~
hhalign/hhhmm-C.h: In member function 'int HMM::ReadHMMer(FILE*, char*)':
hhalign/hhhmm-C.h:668:18: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 510 bytes from a string of length 262139 [-Wstringop-truncation]
  668 |           strncpy(name,ptr,NAMELEN-1);    // copy full name to name
      |           ~~~~~~~^~~~~~~~~~~~~~~~~~~~
hhalign/hhhmm-C.h:684:22: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation]
  684 |               strncpy(desc,ptr,DESCLEN-1);   // copy description to name...
      |               ~~~~~~~^~~~~~~~~~~~~~~~~~~~
hhalign/hhhmm-C.h:676:18: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation]
  676 |           strncpy(longname,ptr,DESCLEN-1); // copy Accession id to longname...
      |           ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
hhalign/hhhmm-C.h:1006:10: warning: 'char* strncat(char*, const char*, size_t)' output may be truncated copying between 0 and 32764 bytes from a string of length 32764 [-Wstringop-truncation]
 1006 |   strncat(longname,desc,DESCLEN-strlen(longname)-1);
      |   ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hhalign/hhhmm-C.h: In member function 'int HMM::ReadHMMer3(FILE*, char*)':
hhalign/hhhmm-C.h:1167:25: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 510 bytes from a string of length 262139 [-Wstringop-truncation]
 1167 |                  strncpy(name,ptr,NAMELEN-1);    // copy full name to name
      |                  ~~~~~~~^~~~~~~~~~~~~~~~~~~~
hhalign/hhhmm-C.h:1183:33: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation]
 1183 |                          strncpy(desc,ptr,DESCLEN-1);   // copy description to name...
      |                          ~~~~~~~^~~~~~~~~~~~~~~~~~~~
hhalign/hhhmm-C.h:1175:25: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 32764 bytes from a string of length 262139 [-Wstringop-truncation]
 1175 |                  strncpy(longname,ptr,DESCLEN-1); // copy Accession id to longname...
      |                  ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
hhalign/hhhmm-C.h:1500:9: warning: 'char* strncat(char*, const char*, size_t)' output may be truncated copying between 0 and 32764 bytes from a string of length 32764 [-Wstringop-truncation]
 1500 |  strncat(longname,desc,DESCLEN-strlen(longname)-1);
      |  ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hhalign/hhalignment-C.h: In member function 'void Alignment::Read(FILE*, char*, char*)':
hhalign/hhalignment-C.h:247:26: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 32764 bytes from a string of length 262142 [-Wstringop-truncation]
  247 |                   strncpy(longname,ptr1,DESCLEN-1); // copy whole commentary line after '# ' into longname
      |                   ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -std=c++98 -DMATH_H_CLIB -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RClustalOmega.cpp -o RClustalOmega.o
In file included from RClustalOmega.cpp:27:
config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mymain.c -o mymain.o
In file included from mymain.c:22:
config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
gcc  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"   -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -lgccpp82 -lgc82   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c clustal-omega.c -o clustal-omega.o
In file included from clustal-omega.c:22:
config.h:132: warning: "NDEBUG" redefined
  132 | #define NDEBUG /**/
      | 
<command-line>: note: this is the location of the previous definition
clustal-omega.c:134:18: warning: 'ITERATION_SCORE_IMPROVEMENT_THRESHOLD' defined but not used [-Wunused-const-variable=]
  134 | static const int ITERATION_SCORE_IMPROVEMENT_THRESHOLD = 0.01;
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o ClustalOmega.dll tmp.def exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o -L../../gc-8.2.2 -lgccpp82 -lgc82 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
make[2]: Leaving directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/ClustalOmega/src'
make[1]: Leaving directory '/f/biocbuild/bbs-3.18-bioc/tmpdir/RtmpAVo32n/R.INSTALL222bc348629b8/msa/src/ClustalOmega'
----------------------------------------
------------- ClustalOmega -------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
g++ -std=gnu++17 -shared -s -static-libgcc -o msa.dll tmp.def R_init_msa.o SplitCharVector2List.o SplitCharVector2Matrix.o -Wl,--whole-archive ./libGC.a ./libMuscle.a ./libClustalW.a ./libClustalOmega.a -Wl,--no-whole-archive -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/meat/msa.buildbin-libdir/00LOCK-msa/00new/msa/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'msa' as msa_1.34.0.zip
* DONE (msa)