BUILD BIN results for genoCN on kjohnson1
To the developers/maintainers of the genoCN package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genoCN.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
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raw results
Summary
Command output
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### Running command:
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### rm -rf genoCN.buildbin-libdir && mkdir genoCN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh genoCN_1.58.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R genoCN.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=genoCN.buildbin-libdir genoCN_1.58.0.tar.gz'
>>>>>>>
* installing *source* package ‘genoCN’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tnorm_mle.c -o tnorm_mle.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utility.c -o utility.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c xCNV.c -o xCNV.o
xCNV.c:317:16: warning: unused variable 'K' [-Wunused-variable]
int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
^
xCNV.c:317:25: warning: unused variable 'k' [-Wunused-variable]
int L, N, M, K, i, z, k, nGtp, contam=*contamR, CNA=*CNAR;
^
xCNV.c:762:10: warning: variable 'LL' set but not used [-Wunused-but-set-variable]
int L, LL, N, NN, M, MM, S, LS, CNA = *RCNA,
^
xCNV.c:787:10: warning: unused variable 'mu_b_tmp' [-Wunused-variable]
double mu_b_tmp, sd_b_tmp;
^
xCNV.c:787:20: warning: unused variable 'sd_b_tmp' [-Wunused-variable]
double mu_b_tmp, sd_b_tmp;
^
5 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o genoCN.so tnorm_mle.o utility.o xCNV.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/genoCN.buildbin-libdir/00LOCK-genoCN/00new/genoCN/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 (genoCN)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR genoCN.buildbin-libdir/genoCN/libs/genoCN.so
>>>>>>>
>>>>>>> Paths before fix:
genoCN.buildbin-libdir/genoCN/libs/genoCN.so:
genoCN.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
/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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "genoCN.buildbin-libdir/genoCN/libs/genoCN.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "genoCN.buildbin-libdir/genoCN/libs/genoCN.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "genoCN.buildbin-libdir/genoCN/libs/genoCN.so"
>>>>>>> Paths after fix:
genoCN.buildbin-libdir/genoCN/libs/genoCN.so:
genoCN.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
/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)
