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BUILD BIN report for TitanCNA on merida2

This page was generated on 2019-04-09 13:29:38 -0400 (Tue, 09 Apr 2019).

Package 1616/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TitanCNA 1.21.2
Gavin Ha
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/TitanCNA
Branch: master
Last Commit: 2bec919
Last Changed Date: 2018-12-19 19:56:37 -0400 (Wed, 19 Dec 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS [ OK ]

Summary

Package: TitanCNA
Version: 1.21.2
Command: rm -rf TitanCNA.buildbin-libdir && mkdir TitanCNA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh TitanCNA_1.21.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R TitanCNA.buildbin-libdir
StartedAt: 2019-04-09 06:40:04 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:41:21 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 76.6 seconds
RetCode: 0
Status:  OK 
PackageFile: TitanCNA_1.21.2.tgz
PackageFileSize: 4.115 MiB

Command output

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###
### Running command:
###
###   rm -rf TitanCNA.buildbin-libdir && mkdir TitanCNA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh TitanCNA_1.21.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R TitanCNA.buildbin-libdir
###
##############################################################################
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=TitanCNA.buildbin-libdir TitanCNA_1.21.2.tar.gz'
>>>>>>> 

* installing *source* package ‘TitanCNA’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fwd_backC_clonalCN.c -o fwd_backC_clonalCN.o
fwd_backC_clonalCN.c:257:21: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
            if ((iZS==jZS)){
                 ˜˜˜^˜˜˜˜
fwd_backC_clonalCN.c:257:21: note: remove extraneous parentheses around the comparison to silence this warning
            if ((iZS==jZS)){
                ˜   ^    ˜
fwd_backC_clonalCN.c:257:21: note: use '=' to turn this equality comparison into an assignment
            if ((iZS==jZS)){
                    ^˜
                    =
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c getPositionOverlapC.c -o getPositionOverlapC.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c register.c -o register.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c viterbiC_clonalCN.c -o viterbiC_clonalCN.o
clang -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 TitanCNA.so fwd_backC_clonalCN.o getPositionOverlapC.o register.o viterbiC_clonalCN.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/TitanCNA.buildbin-libdir/TitanCNA/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::slice’ by ‘dplyr::slice’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomeInfoDb::intersect’ by ‘dplyr::intersect’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::desc’ by ‘dplyr::desc’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’
Warning: replacing previous import ‘dplyr::select’ by ‘VariantAnnotation::select’ when loading ‘TitanCNA’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::collapse’ by ‘dplyr::collapse’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::union’ by ‘dplyr::union’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::slice’ by ‘dplyr::slice’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomeInfoDb::intersect’ by ‘dplyr::intersect’ when loading ‘TitanCNA’
Warning: replacing previous import ‘GenomicRanges::setdiff’ by ‘dplyr::setdiff’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘TitanCNA’
Warning: replacing previous import ‘IRanges::desc’ by ‘dplyr::desc’ when loading ‘TitanCNA’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ when loading ‘TitanCNA’
Warning: replacing previous import ‘dplyr::select’ by ‘VariantAnnotation::select’ when loading ‘TitanCNA’
* DONE (TitanCNA)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "TitanCNA.buildbin-libdir/TitanCNA/libs//TitanCNA.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "TitanCNA.buildbin-libdir/TitanCNA/libs//TitanCNA.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "TitanCNA.buildbin-libdir/TitanCNA/libs//TitanCNA.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "TitanCNA.buildbin-libdir/TitanCNA/libs//TitanCNA.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "TitanCNA.buildbin-libdir/TitanCNA/libs//TitanCNA.so"