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BioC 3.5: BUILD BIN report for ncdfFlow on veracruz2

This page was generated on 2017-10-18 14:30:10 -0400 (Wed, 18 Oct 2017).

Package 886/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ncdfFlow 2.22.2
Mike Jiang
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/ncdfFlow
Branch: RELEASE_3_5
Last Commit: e959176
Last Changed Date: 2017-09-12 14:28:30 -0400 (Tue, 12 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: ncdfFlow
Version: 2.22.2
Command: rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ncdfFlow_2.22.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ncdfFlow.buildbin-libdir
StartedAt: 2017-10-18 11:14:40 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 11:15:13 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 33.5 seconds
RetCode: 0
Status:  OK 
PackageFile: ncdfFlow_2.22.2.tgz
PackageFileSize: 1.346 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ncdfFlow_2.22.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ncdfFlow.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ncdfFlow.buildbin-libdir ncdfFlow_2.22.2.tar.gz'
>>>>>>> 

* installing *source* package ‘ncdfFlow’ ...
configure: No directory was specified for --with-hdf5. Trying to find hdf5 using pkg-config.
checking for pkg-config... /usr/local/bin/pkg-config
Package hdf5 was not found in the pkg-config search path.
Perhaps you should add the directory containing `hdf5.pc'
to the PKG_CONFIG_PATH environment variable
No package 'hdf5' found
configure: pkg-config was not able to find the hdf5 library.
configure: Trying some common locations."
configure: search for hdf5 library in: /usr/local/lib
configure: search for hdf5 library in: /usr/local/lib64
configure: search for hdf5 library in: /usr/local/lib/x86_64-linux-gnu
configure: search for hdf5 library in: /usr/local/lib64/x86_64-linux-gnu
checking for h5cc... /usr/local/bin/h5cc
configure: PKG_CPPFLAGS =  
configure: PKG_LIBS = -lhdf5
configure: creating ./config.status
config.status: creating src/Makevars
** 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/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.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/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c bitOps.cpp -o bitOps.o
bitOps.cpp:23:11: warning: unused variable 'nByte' [-Wunused-variable]
        unsigned nByte = bytes.size();
                 ^
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/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c hdfFlow.c -o hdfFlow.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/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.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/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c readFrame.cpp -o readFrame.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 ncdfFlow.so RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o -lhdf5 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ncdfFlow)


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