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BioC 3.4: INSTALL report for ncdfFlow on morelia

This page was generated on 2017-04-15 16:23:55 -0400 (Sat, 15 Apr 2017).

Package 831/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ncdfFlow 2.20.2
Mike Jiang
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/ncdfFlow
Last Changed Rev: 127538 / Revision: 128728
Last Changed Date: 2017-03-20 19:02:34 -0400 (Mon, 20 Mar 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: ncdfFlow
Version: 2.20.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ncdfFlow
StartedAt: 2017-04-14 15:19:50 -0700 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 15:20:12 -0700 (Fri, 14 Apr 2017)
EllapsedTime: 22.2 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ncdfFlow
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
* 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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c hdfFlow.c -o hdfFlow.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c init.c -o init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -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 /Library/Frameworks/R.framework/Versions/3.3/Resources/library/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)