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BUILD BIN report for groHMM on merida1

This page was generated on 2021-05-06 12:35:11 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the groHMM package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 788/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
groHMM 1.24.0  (landing page)
Anusha Nagari , Tulip Nandu , W. Lee Kraus
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/groHMM
Branch: RELEASE_3_12
Last Commit: 40688b8
Last Changed Date: 2020-10-27 11:00:20 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: groHMM
Version: 1.24.0
Command: rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh groHMM_1.24.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R groHMM.buildbin-libdir
StartedAt: 2021-05-06 08:50:35 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 08:51:26 -0400 (Thu, 06 May 2021)
EllapsedTime: 50.8 seconds
RetCode: 0
Status:   OK  
PackageFile: groHMM_1.24.0.tgz
PackageFileSize: 4.26 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_1.24.0.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_1.24.0.tar.gz'
>>>>>>> 

* installing *source* package ‘groHMM’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c AnnotateProbes.c -o AnnotateProbes.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c DecayAlgorithm.c -o DecayAlgorithm.o
clang -mmacosx-version-min=10.13 -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c RegisterRRoutines.c -o RegisterRRoutines.o
clang -mmacosx-version-min=10.13 -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 -mmacosx-version-min=10.13 -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 -mmacosx-version-min=10.13 -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 -mmacosx-version-min=10.13 -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 -mmacosx-version-min=10.13 -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 -mmacosx-version-min=10.13 -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-3.12-bioc/meat/groHMM.buildbin-libdir/00LOCK-groHMM/00new/groHMM/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* 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/4.0/Resources/lib/libgcc_s.1.dylib" "groHMM.buildbin-libdir/groHMM/libs/groHMM.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "groHMM.buildbin-libdir/groHMM/libs/groHMM.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "groHMM.buildbin-libdir/groHMM/libs/groHMM.so"