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This page was generated on 2023-10-20 09:38:14 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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

Package 2173/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
universalmotif 1.18.1  (landing page)
Benjamin Jean-Marie Tremblay
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/universalmotif
git_branch: RELEASE_3_17
git_last_commit: 7e7936a
git_last_commit_date: 2023-06-19 07:52:45 -0400 (Mon, 19 Jun 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

BUILD BIN results for universalmotif on kjohnson2


To the developers/maintainers of the universalmotif 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: universalmotif
Version: 1.18.1
Command: rm -rf universalmotif.buildbin-libdir && mkdir universalmotif.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh universalmotif_1.18.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R universalmotif.buildbin-libdir
StartedAt: 2023-10-19 18:02:33 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 18:08:07 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 334.2 seconds
RetCode: 0
Status:   OK  
PackageFile: universalmotif_1.18.1.tgz
PackageFileSize: 5.658 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf universalmotif.buildbin-libdir && mkdir universalmotif.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh universalmotif_1.18.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R universalmotif.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=universalmotif.buildbin-libdir universalmotif_1.18.1.tar.gz'
>>>>>>> 

* installing *source* package ‘universalmotif’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
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/RcppThread/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/RcppThread/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c add_multifreq.cpp -o add_multifreq.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/RcppThread/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c calc_complexity.cpp -o calc_complexity.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/RcppThread/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c compare_motifs.cpp -o compare_motifs.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/RcppThread/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c get_bkg.cpp -o get_bkg.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/RcppThread/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c motif_finder.cpp -o motif_finder.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/RcppThread/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c motif_peaks.cpp -o motif_peaks.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/RcppThread/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c motif_pvalue.cpp -o motif_pvalue.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/RcppThread/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c scan_sequences.cpp -o scan_sequences.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/RcppThread/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c shuffle_sequences.cpp -o shuffle_sequences.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/RcppThread/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c trim_motifs.cpp -o trim_motifs.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/RcppThread/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c universalmotif-class.cpp -o universalmotif-class.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/RcppThread/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utils-exported.cpp -o utils-exported.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/RcppThread/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utils-internal.cpp -o utils-internal.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o universalmotif.so RcppExports.o add_multifreq.o calc_complexity.o compare_motifs.o get_bkg.o motif_finder.o motif_peaks.o motif_pvalue.o scan_sequences.o shuffle_sequences.o trim_motifs.o universalmotif-class.o utils-exported.o utils-internal.o -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug universalmotif.so; fi
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/universalmotif.buildbin-libdir/00LOCK-universalmotif/00new/universalmotif/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘convert_motifs’ with signature ‘motifs="MotifList"’: no definition for class “MotifList”
in method for ‘convert_motifs’ with signature ‘motifs="TFFMFirst"’: no definition for class “TFFMFirst”
in method for ‘convert_motifs’ with signature ‘motifs="PFMatrix"’: no definition for class “PFMatrix”
in method for ‘convert_motifs’ with signature ‘motifs="PWMatrix"’: no definition for class “PWMatrix”
in method for ‘convert_motifs’ with signature ‘motifs="ICMatrix"’: no definition for class “ICMatrix”
in method for ‘convert_motifs’ with signature ‘motifs="XMatrixList"’: no definition for class “XMatrixList”
in method for ‘convert_motifs’ with signature ‘motifs="pwm"’: no definition for class “pwm”
in method for ‘convert_motifs’ with signature ‘motifs="pcm"’: no definition for class “pcm”
in method for ‘convert_motifs’ with signature ‘motifs="pfm"’: no definition for class “pfm”
in method for ‘convert_motifs’ with signature ‘motifs="PWM"’: no definition for class “PWM”
in method for ‘convert_motifs’ with signature ‘motifs="Motif"’: no definition for class “Motif”
** 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 (universalmotif)


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

>>>>>>> Paths before fix:
universalmotif.buildbin-libdir/universalmotif/libs/universalmotif.so:
	universalmotif.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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)

>>>>>>> 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" "universalmotif.buildbin-libdir/universalmotif/libs/universalmotif.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "universalmotif.buildbin-libdir/universalmotif/libs/universalmotif.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "universalmotif.buildbin-libdir/universalmotif/libs/universalmotif.so"

>>>>>>> Paths after fix:

universalmotif.buildbin-libdir/universalmotif/libs/universalmotif.so:
	universalmotif.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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)