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This page was generated on 2022-04-13 12:06:33 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

INSTALL results for FLAMES on tokay2


To the developers/maintainers of the FLAMES package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FLAMES.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 648/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FLAMES 1.0.2  (landing page)
Voogd Oliver
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/FLAMES
git_branch: RELEASE_3_14
git_last_commit: e96c59c
git_last_commit_date: 2021-11-03 18:27:48 -0400 (Wed, 03 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FLAMES
Version: 1.0.2
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/FLAMES_1.0.2.tar.gz && rm -rf FLAMES.buildbin-libdir && mkdir FLAMES.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FLAMES.buildbin-libdir FLAMES_1.0.2.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL FLAMES_1.0.2.zip && rm FLAMES_1.0.2.tar.gz FLAMES_1.0.2.zip
StartedAt: 2022-04-12 06:06:10 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 06:08:26 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 135.8 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/FLAMES_1.0.2.tar.gz && rm -rf FLAMES.buildbin-libdir && mkdir FLAMES.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FLAMES.buildbin-libdir FLAMES_1.0.2.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL FLAMES_1.0.2.zip && rm FLAMES_1.0.2.tar.gz FLAMES_1.0.2.zip
###
##############################################################################
##############################################################################


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 71  641k   71  459k    0     0   683k      0 --:--:-- --:--:-- --:--:--  683k
100  641k  100  641k    0     0   780k      0 --:--:-- --:--:-- --:--:--  780k

install for i386

* installing *source* package 'FLAMES' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
sh: C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin.R: No such file or directory
"C:/rtools40/mingw32/bin/"gcc   -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bam.c -o bam.o
bam.c: In function 'bam_remove_B':
bam.c:163:2: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  for (k = 0; k < b->core.n_cigar; ++k)
  ^~~
bam.c:165:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
   if (k == b->core.n_cigar) return 0; // no 'B'
   ^~
bam.c:226:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
   for (k = 1; k < l; ++k)
   ^~~
bam.c:230:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
    for (k = i = 0; k < l; ++k)
    ^~~
bam.c:230:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
bam.c:233:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
     l = i;
     ^
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c edit_dist.cpp -o edit_dist.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fastq_utils.cpp -o fastq_utils.o
In file included from fastq_utils.h:4,
                 from fastq_utils.cpp:1:
fastq_utils.h: In function 'int ks_getuntil(kstream_t*, int, kstring_t*, int*)':
kseq.h:118:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if (str->m - str->l < i - ks->begin + 1) {     \
        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
kseq.h:143:2: note: in expansion of macro '__KS_GETUNTIL'
  __KS_GETUNTIL(__read, __bufsize)
  ^~~~~~~~~~~~~
kseq.h:218:2: note: in expansion of macro 'KSTREAM_INIT'
  KSTREAM_INIT(type_t, __read, 4096)   \
  ^~~~~~~~~~~~
fastq_utils.h:13:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^~~~~~~~~
fastq_utils.h: At global scope:
kseq.h:171:13: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
  static int kseq_read(kseq_t *seq)         \
             ^~~~~~~~~
kseq.h:171:13: note: in definition of macro '__KSEQ_READ'
  static int kseq_read(kseq_t *seq)         \
             ^~~~~~~~~
fastq_utils.h:13:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_cell_barcode.cpp -o match_cell_barcode.o
In file included from fastq_utils.h:4,
                 from match_cell_barcode.cpp:13:
fastq_utils.h: In function 'int ks_getuntil(kstream_t*, int, kstring_t*, int*)':
kseq.h:118:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if (str->m - str->l < i - ks->begin + 1) {     \
        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
kseq.h:143:2: note: in expansion of macro '__KS_GETUNTIL'
  __KS_GETUNTIL(__read, __bufsize)
  ^~~~~~~~~~~~~
kseq.h:218:2: note: in expansion of macro 'KSTREAM_INIT'
  KSTREAM_INIT(type_t, __read, 4096)   \
  ^~~~~~~~~~~~
fastq_utils.h:13:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c merge_bulk.cpp -o merge_bulk.o
In file included from fastq_utils.h:4,
                 from merge_bulk.cpp:1:
fastq_utils.h: In function 'int ks_getuntil(kstream_t*, int, kstring_t*, int*)':
kseq.h:118:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
    if (str->m - str->l < i - ks->begin + 1) {     \
        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
kseq.h:143:2: note: in expansion of macro '__KS_GETUNTIL'
  __KS_GETUNTIL(__read, __bufsize)
  ^~~~~~~~~~~~~
kseq.h:218:2: note: in expansion of macro 'KSTREAM_INIT'
  KSTREAM_INIT(type_t, __read, 4096)   \
  ^~~~~~~~~~~~
fastq_utils.h:13:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^~~~~~~~~
sh: C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin.R: No such file or directory
"C:/rtools40/mingw32/bin/"gcc   -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ssw.c -o ssw.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ssw_cpp.cpp -o ssw_cpp.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o FLAMES.dll tmp.def RcppExports.o bam.o edit_dist.o fastq_utils.o match_cell_barcode.o merge_bulk.o ssw.o ssw_cpp.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/FLAMES.buildbin-libdir/00LOCK-FLAMES/00new/FLAMES/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'FLAMES'
    finding HTML links ... done
    bulk_long_pipeline                      html  
    finding level-2 HTML links ... done

    bulk_windows_pipeline_setup             html  
    callBasilisk                            html  
    create_config                           html  
    generate_umap                           html  
    generic_long_pipeline                   html  
    get_default_config_file                 html  
    gff3_to_bed12                           html  
    match_cell_barcode                      html  
    merge_bulk_fastq                        html  
    merge_bulk_fastq_cpp                    html  
    merge_bulk_fastq_python                 html  
    minimap2_align                          html  
    minimap2_check_callable                 html  
    parse_gff_tree                          html  
    parse_json_config                       html  
    print_config                            html  
    samtools_as_bam                         html  
    samtools_sort_index                     html  
    sc_DTU_analysis                         html  
    sc_long_pipeline                        html  
    sc_mutations                            html  
    sc_windows_pipeline_setup               html  
    windows_pipeline_isoforms               html  
    windows_pipeline_quantification         html  
    write_config                            html  
** 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

install for x64

* installing *source* package 'FLAMES' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
sh: C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin.R: No such file or directory
"C:/rtools40/mingw64/bin/"gcc   -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bam.c -o bam.o
bam.c: In function 'bam_remove_B':
bam.c:163:2: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  for (k = 0; k < b->core.n_cigar; ++k)
  ^~~
bam.c:165:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
   if (k == b->core.n_cigar) return 0; // no 'B'
   ^~
bam.c:226:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
   for (k = 1; k < l; ++k)
   ^~~
bam.c:230:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
    for (k = i = 0; k < l; ++k)
    ^~~
bam.c:230:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
bam.c:233:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
     l = i;
     ^
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c edit_dist.cpp -o edit_dist.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fastq_utils.cpp -o fastq_utils.o
In file included from fastq_utils.h:4,
                 from fastq_utils.cpp:1:
fastq_utils.h: In function 'int ks_getuntil(kstream_t*, int, kstring_t*, int*)':
kseq.h:118:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if (str->m - str->l < i - ks->begin + 1) {     \
        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
kseq.h:143:2: note: in expansion of macro '__KS_GETUNTIL'
  __KS_GETUNTIL(__read, __bufsize)
  ^~~~~~~~~~~~~
kseq.h:218:2: note: in expansion of macro 'KSTREAM_INIT'
  KSTREAM_INIT(type_t, __read, 4096)   \
  ^~~~~~~~~~~~
fastq_utils.h:13:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^~~~~~~~~
fastq_utils.h: At global scope:
kseq.h:171:13: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
  static int kseq_read(kseq_t *seq)         \
             ^~~~~~~~~
kseq.h:171:13: note: in definition of macro '__KSEQ_READ'
  static int kseq_read(kseq_t *seq)         \
             ^~~~~~~~~
fastq_utils.h:13:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c match_cell_barcode.cpp -o match_cell_barcode.o
In file included from fastq_utils.h:4,
                 from match_cell_barcode.cpp:13:
fastq_utils.h: In function 'int ks_getuntil(kstream_t*, int, kstring_t*, int*)':
kseq.h:118:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if (str->m - str->l < i - ks->begin + 1) {     \
        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
kseq.h:143:2: note: in expansion of macro '__KS_GETUNTIL'
  __KS_GETUNTIL(__read, __bufsize)
  ^~~~~~~~~~~~~
kseq.h:218:2: note: in expansion of macro 'KSTREAM_INIT'
  KSTREAM_INIT(type_t, __read, 4096)   \
  ^~~~~~~~~~~~
fastq_utils.h:13:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c merge_bulk.cpp -o merge_bulk.o
In file included from fastq_utils.h:4,
                 from merge_bulk.cpp:1:
fastq_utils.h: In function 'int ks_getuntil(kstream_t*, int, kstring_t*, int*)':
kseq.h:118:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
    if (str->m - str->l < i - ks->begin + 1) {     \
        ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
kseq.h:143:2: note: in expansion of macro '__KS_GETUNTIL'
  __KS_GETUNTIL(__read, __bufsize)
  ^~~~~~~~~~~~~
kseq.h:218:2: note: in expansion of macro 'KSTREAM_INIT'
  KSTREAM_INIT(type_t, __read, 4096)   \
  ^~~~~~~~~~~~
fastq_utils.h:13:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^~~~~~~~~
sh: C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin.R: No such file or directory
"C:/rtools40/mingw64/bin/"gcc   -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c ssw.c -o ssw.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ssw_cpp.cpp -o ssw_cpp.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o FLAMES.dll tmp.def RcppExports.o bam.o edit_dist.o fastq_utils.o match_cell_barcode.o merge_bulk.o ssw.o ssw_cpp.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/FLAMES.buildbin-libdir/FLAMES/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FLAMES' as FLAMES_1.0.2.zip
* DONE (FLAMES)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'FLAMES' successfully unpacked and MD5 sums checked