Benilton Carvalho
| Snapshot Date: 2025-04-16 13:40 -0400 (Wed, 16 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/oligo |
| git_branch: RELEASE_3_21 |
| git_last_commit: bced021 |
| git_last_commit_date: 2025-04-15 09:36:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-17 11:44 -0400 (Thu, 17 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4667 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 1469/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| oligo 1.72.0 (landing page) Benilton Carvalho
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the oligo package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oligo.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. |
| Package: oligo |
| Version: 1.72.0 |
| Command: rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh oligo_1.72.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R oligo.buildbin-libdir |
| StartedAt: 2025-04-17 01:32:39 -0400 (Thu, 17 Apr 2025) |
| EndedAt: 2025-04-17 01:33:41 -0400 (Thu, 17 Apr 2025) |
| EllapsedTime: 61.4 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: oligo_1.72.0.tgz |
| PackageFileSize: 27.83 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh oligo_1.72.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R oligo.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=oligo.buildbin-libdir oligo_1.72.0.tar.gz' >>>>>>> * installing *source* package ‘oligo’ ... ** this is package ‘oligo’ version ‘1.72.0’ ** 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/4.5-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 DABG.c -o DABG.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.5-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 ParserGzXYS.c -o ParserGzXYS.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.5-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 ParserXYS.c -o ParserXYS.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.5-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 baseProfile.c -o baseProfile.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.5-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 basecontent.c -o basecontent.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-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/4.5-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/4.5-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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.5-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 trimmed.c -o trimmed.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 oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -F/Library/Frameworks/R.framework/.. -framework R installing to /Users/biocbuild/bbs-3.21-bioc/meat/oligo.buildbin-libdir/00LOCK-oligo/00new/oligo/libs ** R ** inst ** byte-compile and prepare package for lazy loading Note: in method for ‘pm<-’ with signature ‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’: expanding the signature to include omitted arguments in definition: subset = "missing", target = "missing" Note: in method for ‘mm<-’ with signature ‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’: expanding the signature to include omitted arguments in definition: subset = "missing", target = "missing" ** 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 (oligo) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR oligo.buildbin-libdir/oligo/libs/oligo.so >>>>>>> >>>>>>> Paths before fix: oligo.buildbin-libdir/oligo/libs/oligo.so: oligo.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/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /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/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "oligo.buildbin-libdir/oligo/libs/oligo.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "oligo.buildbin-libdir/oligo/libs/oligo.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "oligo.buildbin-libdir/oligo/libs/oligo.so" >>>>>>> Paths after fix: oligo.buildbin-libdir/oligo/libs/oligo.so: oligo.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/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)