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This page was generated on 2023-11-02 11:41:01 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 1437/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oligo 1.66.0  (landing page)
Benilton Carvalho
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/oligo
git_branch: RELEASE_3_18
git_last_commit: e6e7283
git_last_commit_date: 2023-10-24 09:35:20 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 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 12.6.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

INSTALL results for oligo on kunpeng2


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.

raw results


Summary

Package: oligo
Version: 1.66.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL oligo
StartedAt: 2023-11-01 20:17:39 -0000 (Wed, 01 Nov 2023)
EndedAt: 2023-11-01 20:18:25 -0000 (Wed, 01 Nov 2023)
EllapsedTime: 46.4 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL oligo
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘oligo’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/preprocessCore/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c DABG.c -o DABG.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/preprocessCore/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c ParserXYS.c -o ParserXYS.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/preprocessCore/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c baseProfile.c -o baseProfile.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/preprocessCore/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c basecontent.c -o basecontent.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/preprocessCore/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/preprocessCore/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/site-library/preprocessCore/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.1/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-4.3.1/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 -llapack -lblas -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/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)