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BioC 3.5: BUILD BIN report for TitanCNA on oaxaca

This page was generated on 2017-03-04 16:47:21 -0500 (Sat, 04 Mar 2017).

Package 1279/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TitanCNA 1.13.1
Gavin Ha , Sohrab P Shah
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TitanCNA
Last Changed Rev: 126021 / Revision: 127142
Last Changed Date: 2017-01-19 09:28:52 -0500 (Thu, 19 Jan 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK [ OK ]

Summary

Package: TitanCNA
Version: 1.13.1
Command: rm -rf TitanCNA.buildbin-libdir && mkdir TitanCNA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh TitanCNA_1.13.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R TitanCNA.buildbin-libdir
StartedAt: 2017-03-04 12:31:38 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 12:32:09 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 30.9 seconds
RetCode: 0
Status:  OK 
PackageFile: TitanCNA_1.13.1.tgz
PackageFileSize: 3.906 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf TitanCNA.buildbin-libdir && mkdir TitanCNA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh TitanCNA_1.13.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R TitanCNA.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=TitanCNA.buildbin-libdir TitanCNA_1.13.1.tar.gz'
>>>>>>> 

* installing *source* package ‘TitanCNA’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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 -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c getPositionOverlapC.c -o getPositionOverlapC.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c register.c -o register.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -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-3.5-bioc/meat/TitanCNA.buildbin-libdir/TitanCNA/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* 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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/Resources/lib/libquadmath.0.dylib" "TitanCNA.buildbin-libdir/TitanCNA/libs//TitanCNA.so"