Ben Bolstad
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/affyPLM |
| git_branch: RELEASE_3_16 |
| git_last_commit: 429ed7b |
| git_last_commit_date: 2023-01-19 11:13:30 -0400 (Thu, 19 Jan 2023) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:58 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the affyPLM package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/affyPLM.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 30/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| affyPLM 1.74.2 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: affyPLM |
| Version: 1.74.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL affyPLM |
| StartedAt: 2023-04-10 15:11:10 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 15:11:40 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 30.6 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL affyPLM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘affyPLM’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c LESN.c -o LESN.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PLM_avg_log.c -o PLM_avg_log.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PLM_biweight.c -o PLM_biweight.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PLM_log_avg.c -o PLM_log_avg.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PLM_medianPM.c -o PLM_medianPM.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PLM_median_logPM.c -o PLM_median_logPM.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PLM_medianpolish.c -o PLM_medianpolish.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c SCAB.c -o SCAB.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c chipbackground.c -o chipbackground.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c common_types.c -o common_types.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c lm_threestep.c -o lm_threestep.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c matrix_functions.c -o matrix_functions.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c nthLargestPM.c -o nthLargestPM.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c psi_fns.c -o psi_fns.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c read_rmaexpress.c -o read_rmaexpress.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rlm_threestep.c -o rlm_threestep.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rma_PLM.c -o rma_PLM.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c scaling.c -o scaling.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c threestep_PLM.c -o threestep_PLM.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c threestep_common.c -o threestep_common.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c threestep_summary_methods.c -o threestep_summary_methods.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/preprocessCore/include' -I/usr/local/include -fPIC -Wall -g -O2 -c transfns.c -o transfns.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: dylib (/usr/local/gfortran/lib/libgfortran.dylib) was built for newer macOS version (10.14) than being linked (10.13)
ld: warning: dylib (/usr/local/gfortran/lib/libquadmath.dylib) was built for newer macOS version (10.14) than being linked (10.13)
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/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)