Ben Bolstad
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/affyPLM |
| git_branch: RELEASE_3_17 |
| git_last_commit: d20fa58 |
| git_last_commit_date: 2023-05-01 20:07:56 -0400 (Mon, 01 May 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:57 -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 | ||||
| Package 29/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| affyPLM 1.76.1 (landing page) Ben Bolstad
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the affyPLM 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. |
| Package: affyPLM |
| Version: 1.76.1 |
| Command: rm -rf affyPLM.buildbin-libdir && mkdir affyPLM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affyPLM_1.76.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R affyPLM.buildbin-libdir |
| StartedAt: 2023-10-19 11:05:19 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 11:06:15 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 56.1 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: affyPLM_1.76.1.tgz |
| PackageFileSize: 4.634 MiB |
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### Running command:
###
### rm -rf affyPLM.buildbin-libdir && mkdir affyPLM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affyPLM_1.76.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R affyPLM.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=affyPLM.buildbin-libdir affyPLM_1.76.1.tar.gz'
>>>>>>>
* installing *source* package ‘affyPLM’ ...
** 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'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LESN.c -o LESN.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PLM_avg_log.c -o PLM_avg_log.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PLM_biweight.c -o PLM_biweight.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PLM_log_avg.c -o PLM_log_avg.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PLM_medianPM.c -o PLM_medianPM.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PLM_median_logPM.c -o PLM_median_logPM.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PLM_medianpolish.c -o PLM_medianpolish.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SCAB.c -o SCAB.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c chipbackground.c -o chipbackground.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c common_types.c -o common_types.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c do_PLMrlm.c -o do_PLMrlm.o
do_PLMrlm.c:620:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
int first_ind;
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c do_PLMrma.c -o do_PLMrma.o
do_PLMrma.c:209:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
int first_ind;
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c do_PLMthreestep.c -o do_PLMthreestep.o
do_PLMthreestep.c:118:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
int first_ind;
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c idealmismatch.c -o idealmismatch.o
idealmismatch.c:71:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
int first_ind;
^
idealmismatch.c:183:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
int first_ind;
^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lm_threestep.c -o lm_threestep.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrix_functions.c -o matrix_functions.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nthLargestPM.c -o nthLargestPM.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c preprocess.c -o preprocess.o
preprocess.c:158:7: warning: variable 'which_lesn' set but not used [-Wunused-but-set-variable]
int which_lesn;
^
preprocess.c:677:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable]
int rows,cols;
^
preprocess.c:677:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
int rows,cols;
^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c psi_fns.c -o psi_fns.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c qnorm_probeset.c -o qnorm_probeset.o
qnorm_probeset.c:110:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
int first_ind;
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c read_rmaexpress.c -o read_rmaexpress.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rlm_PLM.c -o rlm_PLM.o
rlm_PLM.c:1481:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
int rows,cols;
^
rlm_PLM.c:1481:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable]
int rows,cols;
^
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rlm_threestep.c -o rlm_threestep.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rma_PLM.c -o rma_PLM.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rma_common.c -o rma_common.o
rma_common.c:60:7: warning: unused variable 'i' [-Wunused-variable]
int i;
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scaling.c -o scaling.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c threestep.c -o threestep.o
threestep.c:82:15: warning: variable 'MM' set but not used [-Wunused-but-set-variable]
double *PM,*MM;
^
threestep.c:193:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
int rows,cols;
^
threestep.c:193:12: warning: variable 'cols' set but not used [-Wunused-but-set-variable]
int rows,cols;
^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c threestep_PLM.c -o threestep_PLM.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c threestep_common.c -o threestep_common.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c threestep_summary.c -o threestep_summary.o
threestep_summary.c:73:7: warning: variable 'first_ind' set but not used [-Wunused-but-set-variable]
int first_ind;
^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c threestep_summary_methods.c -o threestep_summary_methods.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c transfns.c -o transfns.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 affyPLM.so LESN.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_medianPM.o PLM_median_logPM.o PLM_medianpolish.o PLM_modelmatrix.o SCAB.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o matrix_functions.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.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 -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/affyPLM.buildbin-libdir/00LOCK-affyPLM/00new/affyPLM/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 (affyPLM)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR affyPLM.buildbin-libdir/affyPLM/libs/affyPLM.so
>>>>>>>
>>>>>>> Paths before fix:
affyPLM.buildbin-libdir/affyPLM/libs/affyPLM.so:
affyPLM.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 4.3.1)
/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)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
/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" "affyPLM.buildbin-libdir/affyPLM/libs/affyPLM.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "affyPLM.buildbin-libdir/affyPLM/libs/affyPLM.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "affyPLM.buildbin-libdir/affyPLM/libs/affyPLM.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" "affyPLM.buildbin-libdir/affyPLM/libs/affyPLM.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" "affyPLM.buildbin-libdir/affyPLM/libs/affyPLM.so"
>>>>>>> Paths after fix:
affyPLM.buildbin-libdir/affyPLM/libs/affyPLM.so:
affyPLM.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 4.3.1)
/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)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
/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)