Benilton Carvalho
| Snapshot Date: 2024-05-08 14:00:19 -0400 (Wed, 08 May 2024) |
| git_url: https://git.bioconductor.org/packages/oligo |
| git_branch: RELEASE_3_19 |
| git_last_commit: f9b9ea0 |
| git_last_commit_date: 2024-04-30 10:14:15 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-09 11:41:12 -0400 (Thu, 09 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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 1453/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| oligo 1.68.0 (landing page) Benilton Carvalho
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.68.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL oligo |
| StartedAt: 2024-05-08 20:17:43 -0000 (Wed, 08 May 2024) |
| EndedAt: 2024-05-08 20:18:29 -0000 (Wed, 08 May 2024) |
| EllapsedTime: 46.7 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL oligo
###
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘oligo’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c DABG.c -o DABG.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c: In function ‘gzcountLines’:
ParserGzXYS.c:18:17: warning: passing argument 1 of ‘gzeof’ from incompatible pointer type [-Wincompatible-pointer-types]
18 | while (!gzeof(file)){
| ^~~~
| |
| struct gzFile_s **
In file included from /usr/include/zlib.h:34,
from ParserGzXYS.c:4:
/usr/include/zlib.h:1594:27: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
1594 | ZEXTERN int ZEXPORT gzeof OF((gzFile file));
| ^~
ParserGzXYS.c:19:12: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types]
19 | gzgets(file, buffer, 1000);
| ^~~~
| |
| struct gzFile_s **
In file included from /usr/include/zlib.h:34,
from ParserGzXYS.c:4:
/usr/include/zlib.h:1491:31: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
1491 | ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
| ^~
ParserGzXYS.c: In function ‘gzxys_header_field’:
ParserGzXYS.c:46:6: warning: assignment to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types]
46 | fp = gzopen(currentFile, "rb");
| ^
ParserGzXYS.c:50:10: warning: passing argument 1 of ‘gzgets’ from incompatible pointer type [-Wincompatible-pointer-types]
50 | gzgets(fp, buffer, LINEMAX);
| ^~
| |
| struct gzFile_s **
In file included from /usr/include/zlib.h:34,
from ParserGzXYS.c:4:
/usr/include/zlib.h:1491:31: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
1491 | ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
| ^~
ParserGzXYS.c:51:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
51 | gzclose(fp);
| ^~
| |
| struct gzFile_s **
In file included from /usr/include/zlib.h:34,
from ParserGzXYS.c:4:
/usr/include/zlib.h:1630:32: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
1630 | ZEXTERN int ZEXPORT gzclose OF((gzFile file));
| ^~
ParserGzXYS.c: In function ‘R_read_gzxys_files’:
ParserGzXYS.c:134:6: warning: assignment to ‘struct gzFile_s **’ from incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’} [-Wincompatible-pointer-types]
134 | fp = gzopen(CHAR(STRING_ELT(filenames, 0)), "rb");
| ^
ParserGzXYS.c:138:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
138 | gzclose(fp);
| ^~
| |
| struct gzFile_s **
In file included from /usr/include/zlib.h:34,
from ParserGzXYS.c:4:
/usr/include/zlib.h:1630:32: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’} but argument is of type ‘struct gzFile_s **’
1630 | ZEXTERN int ZEXPORT gzclose OF((gzFile file));
| ^~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ParserXYS.c -o ParserXYS.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c baseProfile.c -o baseProfile.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c basecontent.c -o basecontent.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c mas5calls.c -o mas5calls.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rma2.c -o rma2.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c rma_common.c -o rma_common.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/preprocessCore/include' -I/usr/local/include -fPIC -g -O2 -Wall -c trimmed.c -o trimmed.o
gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/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 -lgfortran -lm -lopenblas -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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)