Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:48 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD BIN results for sigPathway on machv2


To the developers/maintainers of the sigPathway package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/sigPathway.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1793/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sigPathway 1.62.0  (landing page)
Weil Lai
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/sigPathway
git_branch: RELEASE_3_14
git_last_commit: cd1f56e
git_last_commit_date: 2021-10-26 11:49:55 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: sigPathway
Version: 1.62.0
Command: rm -rf sigPathway.buildbin-libdir && mkdir sigPathway.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh sigPathway_1.62.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R sigPathway.buildbin-libdir
StartedAt: 2022-04-12 21:30:35 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 21:30:43 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 8.5 seconds
RetCode: 0
Status:   OK  
PackageFile: sigPathway_1.62.0.tgz
PackageFileSize: 695.1 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf sigPathway.buildbin-libdir && mkdir sigPathway.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh sigPathway_1.62.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R sigPathway.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=sigPathway.buildbin-libdir sigPathway_1.62.0.tar.gz'
>>>>>>> 

* installing *source* package ‘sigPathway’ ...
** 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 calc_gene_set_internal.c -o calc_gene_set_internal.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c calc_gene_set_stat.c -o calc_gene_set_stat.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c calc_probe_stat.c -o calc_probe_stat.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c calc_weights.c -o calc_weights.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix_fn.c -o matrix_fn.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c permute.c -o permute.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c shuffle.c -o shuffle.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c sigPathway.c -o sigPathway.o
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 sigPathway.so calc_gene_set_internal.o calc_gene_set_stat.o calc_probe_stat.o calc_weights.o matrix_fn.o permute.o shuffle.o sigPathway.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.14-bioc/meat/sigPathway.buildbin-libdir/00LOCK-sigPathway/00new/sigPathway/libs
** R
** data
** 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 (sigPathway)


>>>>>>> 
>>>>>>> FIXING LINKS FOR sigPathway.buildbin-libdir/sigPathway/libs/sigPathway.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" "sigPathway.buildbin-libdir/sigPathway/libs/sigPathway.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "sigPathway.buildbin-libdir/sigPathway/libs/sigPathway.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "sigPathway.buildbin-libdir/sigPathway/libs/sigPathway.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "sigPathway.buildbin-libdir/sigPathway/libs/sigPathway.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "sigPathway.buildbin-libdir/sigPathway/libs/sigPathway.so"