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BioC 3.4: BUILD BIN report for openCyto on morelia

This page was generated on 2017-04-15 16:25:02 -0400 (Sat, 15 Apr 2017).

Package 870/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
openCyto 1.12.1
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/openCyto
Last Changed Rev: 122726 / Revision: 128728
Last Changed Date: 2016-10-17 17:08:48 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  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: openCyto
Version: 1.12.1
Command: rm -rf openCyto.buildbin-libdir && mkdir openCyto.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh openCyto_1.12.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R openCyto.buildbin-libdir
StartedAt: 2017-04-15 10:41:30 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 10:42:03 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 33.6 seconds
RetCode: 0
Status:  OK 
PackageFile: openCyto_1.12.1.tgz
PackageFileSize: 2.228 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf openCyto.buildbin-libdir && mkdir openCyto.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh openCyto_1.12.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R openCyto.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=openCyto.buildbin-libdir openCyto_1.12.1.tar.gz'
>>>>>>> 

* installing *source* package ‘openCyto’ ...
** 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"   -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"   -fPIC  -Wall -mtune=core2 -g -O2  -c misc.cpp -o misc.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"   -fPIC  -Wall -mtune=core2 -g -O2  -c unlockNamespace.c -o unlockNamespace.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 openCyto.so RcppExports.o misc.o unlockNamespace.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/openCyto.buildbin-libdir/openCyto/libs
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (openCyto)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgcc_s.1.dylib" "openCyto.buildbin-libdir/openCyto/libs//openCyto.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgfortran.3.dylib" "openCyto.buildbin-libdir/openCyto/libs//openCyto.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.5.2.dylib" "openCyto.buildbin-libdir/openCyto/libs//openCyto.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.dylib" "openCyto.buildbin-libdir/openCyto/libs//openCyto.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libquadmath.0.dylib" "openCyto.buildbin-libdir/openCyto/libs//openCyto.so"