Benilton Carvalho
| Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025) |
| git_url: https://git.bioconductor.org/packages/oligo |
| git_branch: devel |
| git_last_commit: 50bd1ff |
| git_last_commit_date: 2025-04-15 09:36:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-06-19 12:06 -0400 (Thu, 19 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4810 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4548 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4528 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4493 |
| 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 1454/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| oligo 1.73.0 (landing page) Benilton Carvalho
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: oligo |
| Version: 1.73.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL oligo |
| StartedAt: 2025-06-16 20:26:12 -0000 (Mon, 16 Jun 2025) |
| EndedAt: 2025-06-16 20:27:00 -0000 (Mon, 16 Jun 2025) |
| EllapsedTime: 47.6 seconds |
| RetCode: 0 |
| Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL oligo ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘oligo’ ... ** this is package ‘oligo’ version ‘1.73.0’ ** using staged installation creating cache ./config.cache checking how to run the C preprocessor... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/R/R-4.5.0/site-library/preprocessCore/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -fPIC -g -O2 -Wall -Werror=format-security -c DABG.c -o DABG.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/R/R-4.5.0/site-library/preprocessCore/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -fPIC -g -O2 -Wall -Werror=format-security -c ParserGzXYS.c -o ParserGzXYS.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/R/R-4.5.0/site-library/preprocessCore/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -fPIC -g -O2 -Wall -Werror=format-security -c ParserXYS.c -o ParserXYS.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/R/R-4.5.0/site-library/preprocessCore/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -fPIC -g -O2 -Wall -Werror=format-security -c baseProfile.c -o baseProfile.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/R/R-4.5.0/site-library/preprocessCore/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -fPIC -g -O2 -Wall -Werror=format-security -c basecontent.c -o basecontent.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/R/R-4.5.0/site-library/preprocessCore/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -fPIC -g -O2 -Wall -Werror=format-security -c chipbackground.c -o chipbackground.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/R/R-4.5.0/site-library/preprocessCore/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -fPIC -g -O2 -Wall -Werror=format-security -c mas5calls.c -o mas5calls.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/R/R-4.5.0/site-library/preprocessCore/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -fPIC -g -O2 -Wall -Werror=format-security -c rma2.c -o rma2.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/R/R-4.5.0/site-library/preprocessCore/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -fPIC -g -O2 -Wall -Werror=format-security -c rma_common.c -o rma_common.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/R/R-4.5.0/site-library/preprocessCore/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -fPIC -g -O2 -Wall -Werror=format-security -c trimmed.c -o trimmed.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/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 -L/home/biocbuild/R/R-4.5.0/lib -lR installing to /home/biocbuild/R/R-4.5.0/site-library/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)