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BUILD BIN report for snapCGH on celaya2

This page was generated on 2019-10-16 12:45:47 -0400 (Wed, 16 Oct 2019).

Package 1547/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
snapCGH 1.54.0
John Marioni
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/snapCGH
Branch: RELEASE_3_9
Last Commit: 41a38a1
Last Changed Date: 2019-05-02 11:53:05 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: snapCGH
Version: 1.54.0
Command: rm -rf snapCGH.buildbin-libdir && mkdir snapCGH.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh snapCGH_1.54.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R snapCGH.buildbin-libdir
StartedAt: 2019-10-16 09:27:21 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 09:27:50 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 29.3 seconds
RetCode: 0
Status:  OK 
PackageFile: snapCGH_1.54.0.tgz
PackageFileSize: 1.14 MiB

Command output

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###
### Running command:
###
###   rm -rf snapCGH.buildbin-libdir && mkdir snapCGH.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh snapCGH_1.54.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R snapCGH.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=snapCGH.buildbin-libdir snapCGH_1.54.0.tar.gz'
>>>>>>> 

* installing *source* package ‘snapCGH’ ...
** 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 optimizer.c -o optimizer.o
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
  double denom, temp, temp2, temp3;
         ^
optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                             ^
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                      ^
optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable]
  double denom, temp, temp2, temp3;
         ^
optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                             ^
optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                      ^
optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable]
  double gammaA[3][3], gammaB[3][3], gammaC[3][3], alpha[3][nrow1], alphahat[3][nrow1], emis_prob[3][nrow1];
                                                                    ^
optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable]
  double denom, temp, temp2, temp3;
         ^
optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                             ^
optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                      ^
optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable]
  double gammaA[4][4], gammaB[4][4], gammaC[4][4], alpha[4][nrow1], alphahat[4][nrow1], emis_prob[4][nrow1];
                                                                    ^
optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable]
  double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1];
                                                                    ^
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                             ^
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                      ^
optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable]
  double denom, temp, temp2, temp3;
         ^
15 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 snapCGH.so optimizer.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/snapCGH.buildbin-libdir/00LOCK-snapCGH/00new/snapCGH/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: more than one default provided in switch() call 
** 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 (snapCGH)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "snapCGH.buildbin-libdir/snapCGH/libs//snapCGH.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "snapCGH.buildbin-libdir/snapCGH/libs//snapCGH.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "snapCGH.buildbin-libdir/snapCGH/libs//snapCGH.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "snapCGH.buildbin-libdir/snapCGH/libs//snapCGH.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "snapCGH.buildbin-libdir/snapCGH/libs//snapCGH.so"