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BioC 3.0: BUILD BIN report for MANOR on oaxaca

This page was generated on 2015-04-10 10:01:51 -0700 (Fri, 10 Apr 2015).

Package 504/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MANOR 1.38.0
Pierre Neuvial
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/MANOR
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK [ OK ]

Summary

Package: MANOR
Version: 1.38.0
Command: rm -rf MANOR.buildbin-libdir && mkdir MANOR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh MANOR_1.38.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R MANOR.buildbin-libdir
StartedAt: 2015-04-10 04:43:03 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:43:07 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 3.8 seconds
RetCode: 0
Status:  OK 
PackageFile: MANOR_1.38.0.tgz
PackageFileSize: 949.2 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf MANOR.buildbin-libdir && mkdir MANOR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh MANOR_1.38.0.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_1.38.0.tar.gz'
>>>>>>> 

* installing *source* package ‘MANOR’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Rnem_arg.c -o Rnem_arg.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Rnem_exe.c -o Rnem_exe.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c exememo.c -o exememo.o
exememo.c:43:13: warning: variable 'msg' is uninitialized when used here [-Wuninitialized]
      error(msg);
            ^˜˜
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 -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c nem_alg.c -o nem_alg.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c nem_hlp.c -o nem_hlp.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c nem_mod.c -o nem_mod.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c nem_nei.c -o nem_nei.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c nem_rnd.c -o nem_rnd.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -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-3.0-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/3.1/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/3.1/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/3.1/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/3.1/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/3.1/Resources/lib/libquadmath.0.dylib" "MANOR.buildbin-libdir/MANOR/libs//MANOR.so"