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BioC 3.5: BUILD BIN report for MANOR on veracruz2

This page was generated on 2017-10-18 14:27:50 -0400 (Wed, 18 Oct 2017).

Package 746/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MANOR 1.48.0
Pierre Neuvial
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/MANOR
Branch: RELEASE_3_5
Last Commit: 811a7d4
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: MANOR
Version: 1.48.0
Command: rm -rf MANOR.buildbin-libdir && mkdir MANOR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh MANOR_1.48.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R MANOR.buildbin-libdir
StartedAt: 2017-10-18 11:07:36 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 11:07:42 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 5.3 seconds
RetCode: 0
Status:  OK 
PackageFile: MANOR_1.48.0.tgz
PackageFileSize: 954.1 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MANOR.buildbin-libdir && mkdir MANOR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh MANOR_1.48.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R MANOR.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=MANOR.buildbin-libdir MANOR_1.48.0.tar.gz'
>>>>>>> 

* installing *source* package ‘MANOR’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rnem_arg.c -o Rnem_arg.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rnem_exe.c -o Rnem_exe.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c exememo.c -o exememo.o
exememo.c:40:13: warning: variable 'msg' is uninitialized when used here [-Wuninitialized]
    sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n",
            ^˜˜
/usr/include/secure/_stdio.h:47:28: note: expanded from macro 'sprintf'
  __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
                           ^˜˜
exememo.c:39:14: note: initialize the variable 'msg' to silence this warning
    char* msg;
             ^
              = NULL
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c nem_alg.c -o nem_alg.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c nem_hlp.c -o nem_hlp.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c nem_mod.c -o nem_mod.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c nem_nei.c -o nem_nei.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c nem_rnd.c -o nem_rnd.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c nem_ver.c -o nem_ver.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 MANOR.so Rnem_arg.o Rnem_exe.o exememo.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/MANOR.buildbin-libdir/MANOR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MANOR)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "MANOR.buildbin-libdir/MANOR/libs//MANOR.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "MANOR.buildbin-libdir/MANOR/libs//MANOR.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "MANOR.buildbin-libdir/MANOR/libs//MANOR.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "MANOR.buildbin-libdir/MANOR/libs//MANOR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "MANOR.buildbin-libdir/MANOR/libs//MANOR.so"