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BUILD BIN report for SANTA on merida1

This page was generated on 2019-12-20 12:30:47 -0500 (Fri, 20 Dec 2019).

Package 1514/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SANTA 2.24.0
Alex J. Cornish
Snapshot Date: 2019-12-19 16:46:06 -0500 (Thu, 19 Dec 2019)
URL: https://git.bioconductor.org/packages/SANTA
Branch: RELEASE_3_10
Last Commit: 24ff5f6
Last Changed Date: 2019-10-29 13:08:37 -0500 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  ERROR  ERROR  skipped  skipped 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: SANTA
Version: 2.24.0
Command: rm -rf SANTA.buildbin-libdir && mkdir SANTA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SANTA_2.24.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SANTA.buildbin-libdir
StartedAt: 2019-12-20 08:46:40 -0500 (Fri, 20 Dec 2019)
EndedAt: 2019-12-20 08:47:30 -0500 (Fri, 20 Dec 2019)
EllapsedTime: 49.8 seconds
RetCode: 0
Status:  OK 
PackageFile: SANTA_2.24.0.tgz
PackageFileSize: 3.698 MiB

Command output

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###
### Running command:
###
###   rm -rf SANTA.buildbin-libdir && mkdir SANTA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SANTA_2.24.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SANTA.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SANTA.buildbin-libdir SANTA_2.24.0.tar.gz'
>>>>>>> 

* installing *source* package ‘SANTA’ ...
** 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 computenetK_fewzeros.c -o computenetK_fewzeros.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 computenetK_manyzeros.c -o computenetK_manyzeros.o
computenetK_manyzeros.c:29:24: warning: incompatible pointer types assigning to 'int *' from 'char *' [-Wincompatible-pointer-types]
    p_which_vw_nonzero = R_alloc(n_nonzero_vertices, sizeof(int));
                       ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 warning generated.
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 computenodeAUK.c -o computenodeAUK.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 computeweights.c -o computeweights.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 SANTA.so computenetK_fewzeros.o computenetK_manyzeros.o computenodeAUK.o computeweights.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.10-bioc/meat/SANTA.buildbin-libdir/00LOCK-SANTA/00new/SANTA/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 (SANTA)


>>>>>>> 
>>>>>>> FIXING LINKS FOR SANTA.buildbin-libdir/SANTA/libs//SANTA.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" "SANTA.buildbin-libdir/SANTA/libs//SANTA.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "SANTA.buildbin-libdir/SANTA/libs//SANTA.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" "SANTA.buildbin-libdir/SANTA/libs//SANTA.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "SANTA.buildbin-libdir/SANTA/libs//SANTA.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "SANTA.buildbin-libdir/SANTA/libs//SANTA.so"