This page was generated on 2023-10-20 09:38:03 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (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 |
| genoCN 1.52.0 (landing page)
Wei Sun
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/genoCN |
| git_branch: RELEASE_3_17 |
| git_last_commit: 690f281 |
| git_last_commit_date: 2023-04-25 09:50:28 -0400 (Tue, 25 Apr 2023) |
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |
BUILD BIN results for genoCN on kjohnson2
To the developers/maintainers of the genoCN 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
Command output
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### Running command:
###
### rm -rf genoCN.buildbin-libdir && mkdir genoCN.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh genoCN_1.52.0.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_1.52.0.tar.gz'
>>>>>>>
* installing *source* package ‘genoCN’ ...
** 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 -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: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;
^
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,
^
5 warnings generated.
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 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-3.17-bioc-mac-arm64/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/4.3-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" "genoCN.buildbin-libdir/genoCN/libs/genoCN.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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)