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This page was generated on 2022-10-19 13:22:38 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 BitSeq on merida1


To the developers/maintainers of the BitSeq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BitSeq.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 205/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BitSeq 1.40.0  (landing page)
Antti Honkela , Panagiotis Papastamoulis
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/BitSeq
git_branch: RELEASE_3_15
git_last_commit: 66cfe24
git_last_commit_date: 2022-04-26 11:10:42 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: BitSeq
Version: 1.40.0
Command: rm -rf BitSeq.buildbin-libdir && mkdir BitSeq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BitSeq_1.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BitSeq.buildbin-libdir
StartedAt: 2022-10-19 09:59:58 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 10:02:25 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 147.4 seconds
RetCode: 0
Status:   OK  
PackageFile: BitSeq_1.40.0.tgz
PackageFileSize: 1.343 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BitSeq.buildbin-libdir && mkdir BitSeq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BitSeq_1.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BitSeq.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BitSeq.buildbin-libdir BitSeq_1.40.0.tar.gz'
>>>>>>> 

* installing *source* package ‘BitSeq’ ...
** using staged installation
configure: Version def: -DBS_VERSION=\"1.40.0\"
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++14 accepts -g... yes
checking for clang++ -mmacosx-version-min=10.13 -std=gnu++14 option to support OpenMP... unsupported
configure: No Open MP support.
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/Makevars.win
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c ArgumentParser.cpp -o ArgumentParser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c CollapsedSampler.cpp -o CollapsedSampler.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c FileHeader.cpp -o FileHeader.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c GibbsParameters.cpp -o GibbsParameters.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c GibbsSampler.cpp -o GibbsSampler.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c MyTimer.cpp -o MyTimer.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c PosteriorSamples.cpp -o PosteriorSamples.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c R_init_BitSeq.cpp -o R_init_BitSeq.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp:265:9: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
       (! frag->second->core.flag & BAM_FREVERSE))){
        ^                         ~
ReadDistribution.cpp:265:9: note: add parentheses after the '!' to evaluate the bitwise operator first
       (! frag->second->core.flag & BAM_FREVERSE))){
        ^
          (                                     )
ReadDistribution.cpp:265:9: note: add parentheses around left hand side expression to silence this warning
       (! frag->second->core.flag & BAM_FREVERSE))){
        ^
        (                        )
ReadDistribution.cpp:687:14: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
            (! frag->second->core.flag & BAM_FREVERSE))){
             ^                         ~
ReadDistribution.cpp:687:14: note: add parentheses after the '!' to evaluate the bitwise operator first
            (! frag->second->core.flag & BAM_FREVERSE))){
             ^
               (                                     )
ReadDistribution.cpp:687:14: note: add parentheses around left hand side expression to silence this warning
            (! frag->second->core.flag & BAM_FREVERSE))){
             ^
             (                        )
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rhtslib_bam_plbuf.c -o Rhtslib_bam_plbuf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rhtslib_sam.c -o Rhtslib_sam.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c Sampler.cpp -o Sampler.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c SimpleSparse.cpp -o SimpleSparse.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c TagAlignments.cpp -o TagAlignments.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c TranscriptExpression.cpp -o TranscriptExpression.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c TranscriptInfo.cpp -o TranscriptInfo.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c TranscriptSequence.cpp -o TranscriptSequence.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c VariationalBayes.cpp -o VariationalBayes.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c common.cpp -o common.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c estimateDE.cpp -o estimateDE.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c estimateExpression.cpp -o estimateExpression.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c estimateHyperPar.cpp -o estimateHyperPar.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c estimateVBExpression.cpp -o estimateVBExpression.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c getGeneExpression.cpp -o getGeneExpression.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c getVariance.cpp -o getVariance.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c lowess.cpp -o lowess.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c misc.cpp -o misc.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c parseAlignment.cpp -o parseAlignment.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.40.0\" -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include  -I.  -fPIC  -Wall -g -O2  -c transposeFiles.cpp -o transposeFiles.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 BitSeq.so ArgumentParser.o CollapsedSampler.o FileHeader.o GibbsParameters.o GibbsSampler.o MyTimer.o PosteriorSamples.o R_init_BitSeq.o ReadDistribution.o Rhtslib_bam_plbuf.o Rhtslib_sam.o Sampler.o SimpleSparse.o TagAlignments.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o VariationalBayes.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o estimateVBExpression.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o misc.o parseAlignment.o transposeFiles.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-3.15-bioc/meat/BitSeq.buildbin-libdir/00LOCK-BitSeq/00new/BitSeq/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 (BitSeq)


>>>>>>> 
>>>>>>> FIXING LINKS FOR BitSeq.buildbin-libdir/BitSeq/libs/BitSeq.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" "BitSeq.buildbin-libdir/BitSeq/libs/BitSeq.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "BitSeq.buildbin-libdir/BitSeq/libs/BitSeq.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "BitSeq.buildbin-libdir/BitSeq/libs/BitSeq.so"