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This page was generated on 2024-12-04 09:55 -0500 (Wed, 04 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-11-14 r87333) -- "Unsuffered Consequences" 861
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Package 4/216HostnameOS / ArchINSTALLBUILDCHECK
affyPLM 1.83.0  (landing page)
Ben Bolstad
Snapshot Date: 2024-12-04 06:00 -0500 (Wed, 04 Dec 2024)
git_url: https://git.bioconductor.org/packages/affyPLM
git_branch: devel
git_last_commit: 1ddbcf0
git_last_commit_date: 2024-10-29 09:22:04 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  

INSTALL results for affyPLM on teran2

To the developers/maintainers of the affyPLM package:
- 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: 1.83.0
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL affyPLM
StartedAt: 2024-12-04 06:29:43 -0500 (Wed, 04 Dec 2024)
EndedAt: 2024-12-04 06:30:05 -0500 (Wed, 04 Dec 2024)
EllapsedTime: 22.2 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL affyPLM
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘affyPLM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c LESN.c -o LESN.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c PLM_avg_log.c -o PLM_avg_log.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c PLM_log_avg.c -o PLM_log_avg.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c SCAB.c -o SCAB.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c common_types.c -o common_types.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c do_PLMrlm.c -o do_PLMrlm.o
do_PLMrlm.c: In function ‘do_PLM_rlm’:
do_PLMrlm.c:620:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
  620 |   int first_ind;
      |       ^~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c do_PLMrma.c -o do_PLMrma.o
do_PLMrma.c: In function ‘do_PLMrma’:
do_PLMrma.c:209:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
  209 |   int first_ind;
      |       ^~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
do_PLMthreestep.c: In function ‘do_PLMthreestep’:
do_PLMthreestep.c:118:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
  118 |   int first_ind;
      |       ^~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c idealmismatch.c -o idealmismatch.o
idealmismatch.c: In function ‘IdealMM_correct_single’:
idealmismatch.c:71:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
   71 |   int first_ind;
      |       ^~~~~~~~~
idealmismatch.c: In function ‘SpecificBiweightCorrect_single’:
idealmismatch.c:183:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
  183 |   int first_ind;
      |       ^~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c lm_threestep.c -o lm_threestep.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c matrix_functions.c -o matrix_functions.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c preprocess.c -o preprocess.o
preprocess.c: In function ‘pp_background’:
preprocess.c:158:7: warning: variable ‘which_lesn’ set but not used [-Wunused-but-set-variable]
  158 |   int which_lesn;
      |       ^~~~~~~~~~
preprocess.c: In function ‘pp_bothstages’:
preprocess.c:677:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable]
  677 |   int rows,cols;
      |            ^~~~
preprocess.c:677:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable]
  677 |   int rows,cols;
      |       ^~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c psi_fns.c -o psi_fns.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c qnorm_probeset.c -o qnorm_probeset.o
qnorm_probeset.c: In function ‘qnorm_probeset_c’:
qnorm_probeset.c:110:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
  110 |   int first_ind;
      |       ^~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c rlm_PLM.c -o rlm_PLM.o
rlm_PLM.c: In function ‘R_rlm_PLMset_c’:
rlm_PLM.c:1481:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable]
 1481 |   int rows,cols;
      |            ^~~~
rlm_PLM.c:1481:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable]
 1481 |   int rows,cols;
      |       ^~~~
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/rapidbuild/bbs-3.21-bioc-rapid/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/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c rma_PLM.c -o rma_PLM.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c rma_common.c -o rma_common.o
rma_common.c: In function ‘median’:
rma_common.c:60:7: warning: unused variable ‘i’ [-Wunused-variable]
   60 |   int i;
      |       ^
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c scaling.c -o scaling.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c threestep.c -o threestep.o
threestep.c: In function ‘threestep_summary’:
threestep.c:82:15: warning: variable ‘MM’ set but not used [-Wunused-but-set-variable]
   82 |   double *PM,*MM;
      |               ^~
threestep.c: In function ‘R_threestep_c’:
threestep.c:193:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable]
  193 |   int rows,cols;
      |            ^~~~
threestep.c:193:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable]
  193 |   int rows,cols;
      |       ^~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c threestep_common.c -o threestep_common.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c threestep_summary.c -o threestep_summary.o
threestep_summary.c: In function ‘do_3summary’:
threestep_summary.c:73:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable]
   73 |   int first_ind;
      |       ^~~~~~~~~
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/preprocessCore/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c transfns.c -o transfns.o
gcc -shared -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/rapidbuild/bbs-3.21-bioc-rapid/R/lib -lRblas -lgfortran -lm -lquadmath -lz
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/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)