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This page was generated on 2021-10-15 15:06:38 -0400 (Fri, 15 Oct 2021).

BUILD BIN results for groHMM on machv2

To the developers/maintainers of the groHMM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/groHMM.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 813/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
groHMM 1.26.0  (landing page)
Anusha Nagari , Tulip Nandu , W. Lee Kraus
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/groHMM
git_branch: RELEASE_3_13
git_last_commit: 6be33d3
git_last_commit_date: 2021-05-19 12:09:04 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: groHMM
Version: 1.26.0
Command: rm -rf groHMM.buildbin-libdir && mkdir groHMM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh groHMM_1.26.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R groHMM.buildbin-libdir
StartedAt: 2021-10-15 02:39:26 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 02:40:24 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 57.9 seconds
RetCode: 0
Status:   OK  
PackageFile: groHMM_1.26.0.tgz
PackageFileSize: 4.262 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_1.26.0.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_1.26.0.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-3.13-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/4.1/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/4.1/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/4.1/Resources/lib/libquadmath.0.dylib" "groHMM.buildbin-libdir/groHMM/libs/groHMM.so"