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BioC 3.1: BUILD BIN report for groHMM on morelia

This page was generated on 2015-10-09 09:42:23 -0700 (Fri, 09 Oct 2015).

Package 441/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
groHMM 1.3.1
Anusha Nagari, W. Lee Kraus
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/groHMM
Last Changed Rev: 106614 / Revision: 109384
Last Changed Date: 2015-07-21 07:39:34 -0700 (Tue, 21 Jul 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: groHMM
Version: 1.3.1
Command: rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh groHMM_1.3.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R groHMM.buildbin-libdir
StartedAt: 2015-10-09 07:49:24 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 07:49:40 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 16.0 seconds
RetCode: 0
Status:  OK 
PackageFile: groHMM_1.3.1.tgz
PackageFileSize: 4.14 MiB

Command output

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###
### Running command:
###
###   rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh groHMM_1.3.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R groHMM.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=groHMM.buildbin-libdir groHMM_1.3.1.tar.gz'
>>>>>>> 

* installing *source* package ‘groHMM’ ...
It is recommended to use ‘given’ instead of ‘middle’.
It is recommended to use ‘given’ instead of ‘middle’.
** 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 AnnotateProbes.c -o AnnotateProbes.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 DecayAlgorithm.c -o DecayAlgorithm.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 MLEfit.c -o MLEfit.o
In file included from MLEfit.c:44:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static  double MargainalizeSumLogProbOver(int state, int position, 
               ^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static  double expSum(double *logValues, int length) {
               ^
2 warnings 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 RegisterRRoutines.c -o RegisterRRoutines.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 Windowing.c -o Windowing.o
Windowing.c:147:6: warning: unused variable 'II' [-Wunused-variable]
        int II = 0;
            ^
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 hmmEM.c -o hmmEM.o
In file included from hmmEM.c:51:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static  double MargainalizeSumLogProbOver(int state, int position, 
               ^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static  double expSum(double *logValues, int length) {
               ^
2 warnings 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 hmmFwBw.c -o hmmFwBw.o
In file included from hmmFwBw.c:46:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static  double MargainalizeSumLogProbOver(int state, int position, 
               ^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static  double expSum(double *logValues, int length) {
               ^
2 warnings 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 hmmMiscFunctions.c -o hmmMiscFunctions.o
hmmMiscFunctions.c:385:10: warning: unused variable 'wi' [-Wunused-variable]
  double wi, *newEx;
         ^
hmmMiscFunctions.c:418:10: warning: unused variable 'epsilon' [-Wunused-variable]
  double epsilon=0.00001;
         ^
2 warnings 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 hmmViterbi.c -o hmmViterbi.o
In file included from hmmViterbi.c:49:
./hmmHeader.h:281:16: warning: unused function 'MargainalizeSumLogProbOver' [-Wunused-function]
static  double MargainalizeSumLogProbOver(int state, int position, 
               ^
./hmmHeader.h:301:16: warning: unused function 'expSum' [-Wunused-function]
static  double expSum(double *logValues, int length) {
               ^
2 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 groHMM.so AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/groHMM.buildbin-libdir/groHMM/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (groHMM)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgcc_s.1.dylib" "groHMM.buildbin-libdir/groHMM/libs//groHMM.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.3.dylib" "groHMM.buildbin-libdir/groHMM/libs//groHMM.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.5.2.dylib" "groHMM.buildbin-libdir/groHMM/libs//groHMM.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "groHMM.buildbin-libdir/groHMM/libs//groHMM.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libquadmath.0.dylib" "groHMM.buildbin-libdir/groHMM/libs//groHMM.so"