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Package 247/671HostnameOS / ArchBUILDCHECKBUILD BIN
gcrma 2.32.0
Z. Wu
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/gcrma
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ]

Summary

Package: gcrma
Version: 2.32.0
Command: rm -rf gcrma.buildbin-libdir && mkdir gcrma.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gcrma_2.32.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R gcrma.buildbin-libdir
StartedAt: 2013-05-01 12:24:50 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 12:25:05 -0700 (Wed, 01 May 2013)
EllapsedTime: 15.2 seconds
RetCode: 0
Status:  OK 
PackageFile: gcrma_2.32.0.tgz
PackageFileSize: 234.6 KiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=gcrma.buildbin-libdir gcrma_2.32.0.tar.gz'
>>>>>>> 

* installing *source* package 'gcrma' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c baseProfile.c -o baseProfile.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c computeAffinities.c -o computeAffinities.o
computeAffinities.c:17:48: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    PROTECT(outMatrix = allocMatrix(INTSXP, 4, strlen(pseq)));
                        ˜˜˜˜˜˜˜˜˜˜˜            ^˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s)      Rf_protect(s)
                                   ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c postmean.c -o postmean.o
postmean.c:25:49: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  K0 = max(0, floor(log(lower_bound)/log(base)) + 1.0);
     ˜        ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
postmean.c:9:41: note: expanded from macro 'max'
#define max(x1,x2) ((x1) > (x2))? (x1):(x2)
                                        ^
postmean.c:26:7: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
  K = floor(log(p)/log(base));
    ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
postmean.c:28:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  pnorms = (double *) R_alloc(K+1, sizeof(double));
                      ˜˜˜˜˜˜˜ ˜^˜
3 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o gcrma.so baseProfile.o computeAffinities.o postmean.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/gcrma.buildbin-libdir/gcrma/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 (gcrma)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "gcrma.buildbin-libdir/gcrma/libs//gcrma.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "gcrma.buildbin-libdir/gcrma/libs//gcrma.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "gcrma.buildbin-libdir/gcrma/libs//gcrma.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "gcrma.buildbin-libdir/gcrma/libs//gcrma.so"