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This page was generated on 2023-04-12 11:06:07 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

BUILD BIN results for FLAMES on lconway


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 682/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FLAMES 1.4.3  (landing page)
Oliver Voogd
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/FLAMES
git_branch: RELEASE_3_16
git_last_commit: 8e3c42d
git_last_commit_date: 2023-03-06 01:05:53 -0400 (Mon, 06 Mar 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: FLAMES
Version: 1.4.3
Command: rm -rf FLAMES.buildbin-libdir && mkdir FLAMES.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh FLAMES_1.4.3.tar.gz /Library/Frameworks/R.framework/Resources/bin/R FLAMES.buildbin-libdir
StartedAt: 2023-04-10 23:43:37 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 23:45:25 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 107.7 seconds
RetCode: 0
Status:   OK  
PackageFile: FLAMES_1.4.3.tgz
PackageFileSize: 2.635 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf FLAMES.buildbin-libdir && mkdir FLAMES.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh FLAMES_1.4.3.tar.gz /Library/Frameworks/R.framework/Resources/bin/R FLAMES.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=FLAMES.buildbin-libdir FLAMES_1.4.3.tar.gz'
>>>>>>> 

* installing *source* package ‘FLAMES’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppFunctions.cpp -o RcppFunctions.o
In file included from RcppFunctions.cpp:7:
In file included from ./main-functions/match_cell_barcode.h:13:
./main-functions/../utility/fastq_utils.h:12:1: warning: unused function 'kseq_init' [-Wunused-function]
KSEQ_INIT(gzFile, gzread)
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:240:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:237:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_BASIC(SCOPE, type_t)                                     \
        ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:165:16: note: expanded from macro '__KSEQ_BASIC'
        SCOPE kseq_t *kseq_init(type_t fd)                                                                      \
                      ^
In file included from RcppFunctions.cpp:7:
In file included from ./main-functions/match_cell_barcode.h:13:
./main-functions/../utility/fastq_utils.h:12:1: warning: unused function 'kseq_destroy' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:240:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:237:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_BASIC(SCOPE, type_t)                                     \
        ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:171:13: note: expanded from macro '__KSEQ_BASIC'
        SCOPE void kseq_destroy(kseq_t *ks)                                                                     \
                   ^
In file included from RcppFunctions.cpp:7:
In file included from ./main-functions/match_cell_barcode.h:13:
./main-functions/../utility/fastq_utils.h:12:1: warning: unused function 'kseq_read' [-Wunused-function]
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:240:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                  ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:238:2: note: expanded from macro 'KSEQ_INIT2'
        __KSEQ_READ(SCOPE)
        ^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include/htslib/kseq.h:185:12: note: expanded from macro '__KSEQ_READ'
        SCOPE int kseq_read(kseq_t *seq) \
                  ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c main-functions/match_cell_barcode.cpp -o main-functions/match_cell_barcode.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c utility/edit_dist.cpp -o utility/edit_dist.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c utility/fastq_utils.cpp -o utility/fastq_utils.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c utility/ssw/ssw_cpp.cpp -o utility/ssw/ssw_cpp.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam.c -o bam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c utility/ssw/ssw.c -o utility/ssw/ssw.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o FLAMES.so RcppExports.o RcppFunctions.o main-functions/match_cell_barcode.o utility/edit_dist.o utility/fastq_utils.o utility/ssw/ssw_cpp.o bam.o utility/ssw/ssw.o /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.16-bioc/meat/FLAMES.buildbin-libdir/00LOCK-FLAMES/00new/FLAMES/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FLAMES)


>>>>>>> 
>>>>>>> FIXING LINKS FOR FLAMES.buildbin-libdir/FLAMES/libs/FLAMES.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "FLAMES.buildbin-libdir/FLAMES/libs/FLAMES.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "FLAMES.buildbin-libdir/FLAMES/libs/FLAMES.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "FLAMES.buildbin-libdir/FLAMES/libs/FLAMES.so"