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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 31/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyPLM 1.82.0  (landing page)
Ben Bolstad
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/affyPLM
git_branch: RELEASE_3_20
git_last_commit: 16d7387
git_last_commit_date: 2024-10-29 09:22:04 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

BUILD BIN results for affyPLM on kjohnson1

To the developers/maintainers of the affyPLM package:
- 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 Troubleshooting Build Report for more information.
- 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: affyPLM
Version: 1.82.0
Command: rm -rf affyPLM.buildbin-libdir && mkdir affyPLM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affyPLM_1.82.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R affyPLM.buildbin-libdir
StartedAt: 2024-12-21 13:47:27 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 13:47:54 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 27.2 seconds
RetCode: 0
Status:   OK  
PackageFile: affyPLM_1.82.0.tgz
PackageFileSize: 4.48 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf affyPLM.buildbin-libdir && mkdir affyPLM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affyPLM_1.82.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R affyPLM.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=affyPLM.buildbin-libdir affyPLM_1.82.0.tar.gz'
>>>>>>> 

* installing *source* package ‘affyPLM’ ...
** 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'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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:677:7: warning: variable 'rows' set but not used [-Wunused-but-set-variable]
  int rows,cols;
      ^
preprocess.c:677:12: 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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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 -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
installing to /Users/biocbuild/bbs-3.20-bioc/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/4.4-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.2)
	/Library/Frameworks/R.framework/Versions/4.4-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/4.4-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" "affyPLM.buildbin-libdir/affyPLM/libs/affyPLM.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-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/4.4-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/4.4-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/4.4-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/4.4-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.2)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-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/4.4-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)