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BioC 3.5: BUILD BIN report for ChemmineR on veracruz2

This page was generated on 2017-10-18 14:28:38 -0400 (Wed, 18 Oct 2017).

Package 201/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChemmineR 2.28.3
Thomas Girke
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/ChemmineR
Branch: RELEASE_3_5
Last Commit: e66f230
Last Changed Date: 2017-09-11 19:55:56 -0400 (Mon, 11 Sep 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: ChemmineR
Version: 2.28.3
Command: rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineR_2.28.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ChemmineR.buildbin-libdir
StartedAt: 2017-10-18 10:40:37 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 10:41:03 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 26.5 seconds
RetCode: 0
Status:  OK 
PackageFile: ChemmineR_2.28.3.tgz
PackageFileSize: 2.302 MiB

Command output

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##############################################################################
###
### Running command:
###
###   rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineR_2.28.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ChemmineR.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ChemmineR.buildbin-libdir ChemmineR_2.28.3.tar.gz'
>>>>>>> 

* installing *source* package ‘ChemmineR’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c DisjointSets.cpp -o DisjointSets.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c cluster.cc -o cluster.o
cluster.cc:49:13: warning: unused function 'prepare_neighbors' [-Wunused-function]
void static prepare_neighbors(const char* nbr_file, int skip, int p)
            ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c cstrsplit.cc -o cstrsplit.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c desc.cc -o desc.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c fingerprints.cc -o fingerprints.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c formats.cc -o formats.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c molecule.cc -o molecule.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c r_wrap.cc -o r_wrap.o
r_wrap.cc:1689:14: warning: explicitly assigning value of variable of type 'void *' to itself [-Wself-assign]
  clientdata = clientdata;
  ˜˜˜˜˜˜˜˜˜˜ ^ ˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c script.cc -o script.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include  -DNO_MAIN -DNO_DEBUG -fPIC  -Wall -g -O2  -c similarity.cc -o similarity.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 ChemmineR.so DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/ChemmineR.buildbin-libdir/ChemmineR/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 (ChemmineR)


>>>>>>> 
>>>>>>> FIXING LINKS FOR ChemmineR.buildbin-libdir/ChemmineR/libs//ChemmineR.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" "ChemmineR.buildbin-libdir/ChemmineR/libs//ChemmineR.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "ChemmineR.buildbin-libdir/ChemmineR/libs//ChemmineR.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" "ChemmineR.buildbin-libdir/ChemmineR/libs//ChemmineR.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "ChemmineR.buildbin-libdir/ChemmineR/libs//ChemmineR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "ChemmineR.buildbin-libdir/ChemmineR/libs//ChemmineR.so"