Anusha Nagari
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/groHMM |
| Branch: RELEASE_3_6 |
| Last Commit: d79ee3c |
| Last Changed Date: 2018-03-14 16:19:20 -0400 (Wed, 14 Mar 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:39:44 -0400 (Thu, 12 Apr 2018).
| Package 620/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| groHMM 1.12.0 Anusha Nagari
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | [ OK ] | |
| Package: groHMM |
| Version: 1.12.0 |
| Command: rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh groHMM_1.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R groHMM.buildbin-libdir |
| StartedAt: 2018-04-12 11:36:18 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 11:36:45 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 26.8 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: groHMM_1.12.0.tgz |
| PackageFileSize: 4.129 MiB |
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### Running command:
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### rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh groHMM_1.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R groHMM.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=groHMM.buildbin-libdir groHMM_1.12.0.tar.gz'
>>>>>>>
* installing *source* package ‘groHMM’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c AnnotateProbes.c -o AnnotateProbes.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c DecayAlgorithm.c -o DecayAlgorithm.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -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 -fPIC -Wall -g -O2 -c RegisterRRoutines.c -o RegisterRRoutines.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -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 -fPIC -Wall -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 -fPIC -Wall -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 -fPIC -Wall -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 -fPIC -Wall -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-3.6-bioc/meat/groHMM.buildbin-libdir/groHMM/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* 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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/Resources/lib/libquadmath.0.dylib" "groHMM.buildbin-libdir/groHMM/libs//groHMM.so"