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This page was generated on 2025-02-13 11:39 -0500 (Thu, 13 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4719
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4481
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4492
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4445
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 31/2295HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyPLM 1.83.3  (landing page)
Ben Bolstad
Snapshot Date: 2025-02-12 13:40 -0500 (Wed, 12 Feb 2025)
git_url: https://git.bioconductor.org/packages/affyPLM
git_branch: devel
git_last_commit: d5e983d
git_last_commit_date: 2025-01-29 10:23:37 -0500 (Wed, 29 Jan 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

INSTALL results for affyPLM on nebbiolo1

To the developers/maintainers of the affyPLM package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/affyPLM.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.

raw results


Summary

Package: affyPLM
Version: 1.83.3
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL affyPLM
StartedAt: 2025-02-12 15:16:56 -0500 (Wed, 12 Feb 2025)
EndedAt: 2025-02-12 15:17:15 -0500 (Wed, 12 Feb 2025)
EllapsedTime: 19.5 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL affyPLM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘affyPLM’ ...
** this is package ‘affyPLM’ version ‘1.83.3’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c LESN.c -o LESN.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c PLM_avg_log.c -o PLM_avg_log.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c PLM_biweight.c -o PLM_biweight.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c PLM_log_avg.c -o PLM_log_avg.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c PLM_medianPM.c -o PLM_medianPM.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c SCAB.c -o SCAB.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c chipbackground.c -o chipbackground.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c common_types.c -o common_types.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c do_PLMrlm.c -o do_PLMrlm.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c do_PLMrma.c -o do_PLMrma.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c idealmismatch.c -o idealmismatch.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c lm_threestep.c -o lm_threestep.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c matrix_functions.c -o matrix_functions.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c nthLargestPM.c -o nthLargestPM.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c preprocess.c -o preprocess.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c psi_fns.c -o psi_fns.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c qnorm_probeset.c -o qnorm_probeset.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c read_rmaexpress.c -o read_rmaexpress.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c rlm_PLM.c -o rlm_PLM.o
rlm_PLM.c: In function ‘rlm_PLMset_nameoutput’:
rlm_PLM.c:870:32: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=]
  870 |           snprintf(tmp_str2,9,"%d",j+1);
      |                                ^~
rlm_PLM.c:870:31: note: directive argument in the range [1, 2147483647]
  870 |           snprintf(tmp_str2,9,"%d",j+1);
      |                               ^~~~
In file included from /usr/include/stdio.h:980,
                 from /home/biocbuild/bbs-3.21-bioc/R/include/R.h:44,
                 from preprocess.h:4,
                 from rlm_PLM.c:71:
In function ‘snprintf’,
    inlined from ‘rlm_PLMset_nameoutput’ at rlm_PLM.c:870:4:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:54:10: note: ‘__builtin___snprintf_chk’ output between 2 and 11 bytes into a destination of size 9
   54 |   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   55 |                                    __glibc_objsize (__s), __fmt,
      |                                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   56 |                                    __va_arg_pack ());
      |                                    ~~~~~~~~~~~~~~~~~
rlm_PLM.c: In function ‘rlm_PLMset_nameoutput’:
rlm_PLM.c:868:32: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=]
  868 |           snprintf(tmp_str2,9,"%d",j+2);
      |                                ^~
rlm_PLM.c:868:31: note: directive argument in the range [2, 2147483647]
  868 |           snprintf(tmp_str2,9,"%d",j+2);
      |                               ^~~~
In function ‘snprintf’,
    inlined from ‘rlm_PLMset_nameoutput’ at rlm_PLM.c:868:4:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:54:10: note: ‘__builtin___snprintf_chk’ output between 2 and 11 bytes into a destination of size 9
   54 |   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   55 |                                    __glibc_objsize (__s), __fmt,
      |                                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   56 |                                    __va_arg_pack ());
      |                                    ~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c rlm_threestep.c -o rlm_threestep.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c rma_PLM.c -o rma_PLM.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c rma_common.c -o rma_common.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c scaling.c -o scaling.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c threestep.c -o threestep.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c threestep_PLM.c -o threestep_PLM.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c threestep_common.c -o threestep_common.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c threestep_summary.c -o threestep_summary.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -c transfns.c -o transfns.o
gcc -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o affyPLM.so LESN.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_medianPM.o PLM_median_logPM.o PLM_medianpolish.o PLM_modelmatrix.o SCAB.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o matrix_functions.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o -llapack -L/home/biocbuild/bbs-3.21-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -lz -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-affyPLM/00new/affyPLM/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (affyPLM)