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This page was generated on 2024-04-18 11:32:08 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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Package 346/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromVAR 1.24.0  (landing page)
Alicia Schep
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/chromVAR
git_branch: RELEASE_3_18
git_last_commit: e2d61b0
git_last_commit_date: 2023-10-24 11:00:14 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'TFBSTools' which is only available as a source package that needs compilation

BUILD BIN results for chromVAR on kjohnson1


To the developers/maintainers of the chromVAR package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: chromVAR
Version: 1.24.0
Command: rm -rf chromVAR.buildbin-libdir && mkdir chromVAR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh chromVAR_1.24.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R chromVAR.buildbin-libdir
StartedAt: 2024-04-18 08:39:48 -0400 (Thu, 18 Apr 2024)
EndedAt: 2024-04-18 08:41:31 -0400 (Thu, 18 Apr 2024)
EllapsedTime: 102.6 seconds
RetCode: 0
Status:   OK  
PackageFile: chromVAR_1.24.0.tgz
PackageFileSize: 1.46 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf chromVAR.buildbin-libdir && mkdir chromVAR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh chromVAR_1.24.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R chromVAR.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=chromVAR.buildbin-libdir chromVAR_1.24.0.tar.gz'
>>>>>>> 

* installing *source* package ‘chromVAR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c pwm_similarity.cpp -o pwm_similarity.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.cpp -o utils.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o chromVAR.so RcppExports.o pwm_similarity.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/chromVAR.buildbin-libdir/00LOCK-chromVAR/00new/chromVAR/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (chromVAR)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR chromVAR.buildbin-libdir/chromVAR/libs/chromVAR.so
>>>>>>> 

>>>>>>> Paths before fix:
chromVAR.buildbin-libdir/chromVAR/libs/chromVAR.so:
	chromVAR.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.3)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "chromVAR.buildbin-libdir/chromVAR/libs/chromVAR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "chromVAR.buildbin-libdir/chromVAR/libs/chromVAR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "chromVAR.buildbin-libdir/chromVAR/libs/chromVAR.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "chromVAR.buildbin-libdir/chromVAR/libs/chromVAR.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "chromVAR.buildbin-libdir/chromVAR/libs/chromVAR.so"

>>>>>>> Paths after fix:
chromVAR.buildbin-libdir/chromVAR/libs/chromVAR.so:
	chromVAR.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.3)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)