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This page was generated on 2023-10-20 09:38:06 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1283/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifcounter 1.24.0  (landing page)
Wolfgang Kopp
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/motifcounter
git_branch: RELEASE_3_17
git_last_commit: c986ff6
git_last_commit_date: 2023-04-25 10:53:08 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

BUILD BIN results for motifcounter on kjohnson2


To the developers/maintainers of the motifcounter 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: motifcounter
Version: 1.24.0
Command: rm -rf motifcounter.buildbin-libdir && mkdir motifcounter.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh motifcounter_1.24.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R motifcounter.buildbin-libdir
StartedAt: 2023-10-19 15:06:05 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 15:06:42 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 36.7 seconds
RetCode: 0
Status:   OK  
PackageFile: motifcounter_1.24.0.tgz
PackageFileSize: 675.7 KiB

Command output

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###
### Running command:
###
###   rm -rf motifcounter.buildbin-libdir && mkdir motifcounter.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh motifcounter_1.24.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R motifcounter.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=motifcounter.buildbin-libdir motifcounter_1.24.0.tar.gz'
>>>>>>> 

* installing *source* package ‘motifcounter’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rbackground.c -o Rbackground.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rcombinatorial.c -o Rcombinatorial.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rcompoundpoisson.c -o Rcompoundpoisson.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rminmaxscore.c -o Rminmaxscore.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Roption.c -o Roption.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Roverlap.c -o Roverlap.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rscore1d.c -o Rscore1d.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rsequence.c -o Rsequence.o
Rsequence.c:143:21: warning: unused variable 'noscores' [-Wunused-variable]
    int mins, maxs, noscores;
                    ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c Rsimulate.c -o Rsimulate.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c background.c -o background.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c combinatorial.c -o combinatorial.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c compoundpoisson.c -o compoundpoisson.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c markovchain.c -o markovchain.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c markovchain_single.c -o markovchain_single.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c matrix.c -o matrix.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c mdist_register.c -o mdist_register.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c minmaxscore.c -o minmaxscore.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c overlap.c -o overlap.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c score1d.c -o score1d.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c score2d.c -o score2d.o
score2d.c:597:15: warning: variable 'p0' set but not used [-Wunused-but-set-variable]
    double p, p0 = 0.0, p1 = 0.0, ptmp;
              ^
score2d.c:597:25: warning: variable 'p1' set but not used [-Wunused-but-set-variable]
    double p, p0 = 0.0, p1 = 0.0, ptmp;
                        ^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c scorefunctions.c -o scorefunctions.o
scorefunctions.c:84:22: warning: unused variable 'cindex' [-Wunused-variable]
    int j, i, index, cindex, ds;
                     ^
scorefunctions.c:119:17: warning: unused variable 'cindex' [-Wunused-variable]
  int s, index, cindex;
                ^
scorefunctions.c:159:19: warning: unused variable 'cindex' [-Wunused-variable]
    int s, index, cindex;
                  ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c sequence.c -o sequence.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -DIN_R -fPIC  -falign-functions=64 -Wall -g -O2  -c simulate.c -o simulate.o
clang -arch arm64 -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 motifcounter.so Rbackground.o Rcombinatorial.o Rcompoundpoisson.o Rminmaxscore.o Roption.o Roverlap.o Rscore1d.o Rsequence.o Rsimulate.o background.o combinatorial.o compoundpoisson.o markovchain.o markovchain_single.o matrix.o mdist_register.o minmaxscore.o overlap.o score1d.o score2d.o scorefunctions.o sequence.o simulate.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/motifcounter.buildbin-libdir/00LOCK-motifcounter/00new/motifcounter/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 (motifcounter)


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

>>>>>>> Paths before fix:
motifcounter.buildbin-libdir/motifcounter/libs/motifcounter.so:
	motifcounter.so (compatibility version 0.0.0, current version 0.0.0)
	/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/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" "motifcounter.buildbin-libdir/motifcounter/libs/motifcounter.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "motifcounter.buildbin-libdir/motifcounter/libs/motifcounter.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "motifcounter.buildbin-libdir/motifcounter/libs/motifcounter.so"

>>>>>>> Paths after fix:

motifcounter.buildbin-libdir/motifcounter/libs/motifcounter.so:
	motifcounter.so (compatibility version 0.0.0, current version 0.0.0)
	/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/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)