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BUILD BIN report for genoCN on celaya2

This page was generated on 2020-01-16 13:32:29 -0500 (Thu, 16 Jan 2020).

Package 671/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoCN 1.39.0
Wei Sun
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/genoCN
Branch: master
Last Commit: 26bd17c
Last Changed Date: 2019-10-29 13:35:15 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  WARNINGS 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: genoCN
Version: 1.39.0
Command: rm -rf genoCN.buildbin-libdir && mkdir genoCN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh genoCN_1.39.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R genoCN.buildbin-libdir
StartedAt: 2020-01-16 10:59:10 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 10:59:28 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 18.0 seconds
RetCode: 0
Status:  OK 
PackageFile: genoCN_1.39.0.tgz
PackageFileSize: 959.2 KiB

Command output

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###
### Running command:
###
###   rm -rf genoCN.buildbin-libdir && mkdir genoCN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh genoCN_1.39.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R genoCN.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=genoCN.buildbin-libdir genoCN_1.39.0.tar.gz'
>>>>>>> 

* installing *source* package ‘genoCN’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c tnorm_mle.c -o tnorm_mle.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c utility.c -o utility.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c xCNV.c -o xCNV.o
xCNV.c:317:25: warning: unused variable 'k' [-Wunused-variable]
  int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
                        ^
xCNV.c:317:16: warning: unused variable 'K' [-Wunused-variable]
  int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
               ^
xCNV.c:787:20: warning: unused variable 'sd_b_tmp' [-Wunused-variable]
  double mu_b_tmp, sd_b_tmp;
                   ^
xCNV.c:787:10: warning: unused variable 'mu_b_tmp' [-Wunused-variable]
  double mu_b_tmp, sd_b_tmp;
         ^
4 warnings generated.
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 genoCN.so tnorm_mle.o utility.o xCNV.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/genoCN.buildbin-libdir/00LOCK-genoCN/00new/genoCN/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (genoCN)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "genoCN.buildbin-libdir/genoCN/libs//genoCN.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "genoCN.buildbin-libdir/genoCN/libs//genoCN.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.5.2.dylib" "genoCN.buildbin-libdir/genoCN/libs//genoCN.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.dylib" "genoCN.buildbin-libdir/genoCN/libs//genoCN.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "genoCN.buildbin-libdir/genoCN/libs//genoCN.so"