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This page was generated on 2024-03-04 11:37:06 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 23/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affy 1.80.0  (landing page)
Robert D. Shear
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/affy
git_branch: RELEASE_3_18
git_last_commit: a0d64df
git_last_commit_date: 2023-10-24 09:31:50 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

BUILD BIN results for affy on lconway


To the developers/maintainers of the affy package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/affy.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: affy
Version: 1.80.0
Command: rm -rf affy.buildbin-libdir && mkdir affy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affy_1.80.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R affy.buildbin-libdir
StartedAt: 2024-03-04 00:28:08 -0500 (Mon, 04 Mar 2024)
EndedAt: 2024-03-04 00:28:38 -0500 (Mon, 04 Mar 2024)
EllapsedTime: 29.3 seconds
RetCode: 0
Status:   OK  
PackageFile: affy_1.80.0.tgz
PackageFileSize: 1.984 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf affy.buildbin-libdir && mkdir affy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affy_1.80.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R affy.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=affy.buildbin-libdir affy_1.80.0.tar.gz'
>>>>>>> 

* installing *source* package ‘affy’ ...
** using staged installation
creating cache ./config.cache
checking how to run the C preprocessor... clang -arch x86_64 -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/preprocessCore/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c chipbackground.c -o chipbackground.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/preprocessCore/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c getall_locations.c -o getall_locations.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/preprocessCore/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c mas5calls.c -o mas5calls.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/preprocessCore/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c rma2.c -o rma2.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/preprocessCore/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c rma_common.c -o rma_common.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.18-bioc/meat/affy.buildbin-libdir/00LOCK-affy/00new/affy/libs
** R
** data
** demo
** 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 (affy)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR affy.buildbin-libdir/affy/libs/affy.so
>>>>>>> 

>>>>>>> Paths before fix:
affy.buildbin-libdir/affy/libs/affy.so:
	affy.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.2)
	/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/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "affy.buildbin-libdir/affy/libs/affy.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "affy.buildbin-libdir/affy/libs/affy.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "affy.buildbin-libdir/affy/libs/affy.so"

>>>>>>> Paths after fix:
affy.buildbin-libdir/affy/libs/affy.so:
	affy.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.2)
	/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)