Benilton Carvalho
| Snapshot Date: 2025-10-19 13:45 -0400 (Sun, 19 Oct 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 2025-10-20 12:06 -0400 (Mon, 20 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
| 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 1482/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| oligo 1.73.0 (landing page) Benilton Carvalho
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 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. |
| Package: oligo |
| Version: 1.73.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL oligo |
| StartedAt: 2025-10-19 15:13:09 -0400 (Sun, 19 Oct 2025) |
| EndedAt: 2025-10-19 15:13:23 -0400 (Sun, 19 Oct 2025) |
| EllapsedTime: 14.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL oligo
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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... clang -arch arm64 -std=gnu2x -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 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c DABG.c -o DABG.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c ParserGzXYS.c -o ParserGzXYS.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c ParserXYS.c -o ParserXYS.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c baseProfile.c -o baseProfile.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c basecontent.c -o basecontent.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c chipbackground.c -o chipbackground.o
chipbackground.c:120:58: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand]
if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1==0)){
^ ~~~~~~
chipbackground.c:120:58: note: use '&' for a bitwise operation
if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1==0)){
^~
&
chipbackground.c:120:58: note: remove constant to silence this warning
if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1==0)){
~^~~~~~~~~
chipbackground.c:243:58: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand]
if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1 ==0)){
^ ~~~~~~~
chipbackground.c:243:58: note: use '&' for a bitwise operation
if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1 ==0)){
^~
&
chipbackground.c:243:58: note: remove constant to silence this warning
if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1 ==0)){
~^~~~~~~~~~
2 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c mas5calls.c -o mas5calls.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c rma2.c -o rma2.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c rma_common.c -o rma_common.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include -falign-functions=64 -Wall -g -O2 -fPIC -falign-functions=64 -Wall -g -O2 -c trimmed.c -o trimmed.o
trimmed.c:49:13: warning: variable 'n1' set but not used [-Wunused-but-set-variable]
int i, j, n1, n2, n3;
^
trimmed.c:49:17: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
int i, j, n1, n2, n3;
^
trimmed.c:49:21: warning: variable 'n3' set but not used [-Wunused-but-set-variable]
int i, j, n1, n2, n3;
^
3 warnings generated.
clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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)