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INSTALL report for affyPLM on malbec1

This page was generated on 2020-09-19 10:13:52 -0400 (Sat, 19 Sep 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE affyPLM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 33/1912HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyPLM 1.65.0
Ben Bolstad
Snapshot Date: 2020-09-18 14:43:25 -0400 (Fri, 18 Sep 2020)
URL: https://git.bioconductor.org/packages/affyPLM
Branch: master
Last Commit: 6b1f227
Last Changed Date: 2020-04-27 14:08:49 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: affyPLM
Version: 1.65.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL affyPLM
StartedAt: 2020-09-18 16:21:06 -0400 (Fri, 18 Sep 2020)
EndedAt: 2020-09-18 16:21:31 -0400 (Fri, 18 Sep 2020)
EllapsedTime: 25.3 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL affyPLM
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘affyPLM’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c LESN.c -o LESN.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PLM_avg_log.c -o PLM_avg_log.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PLM_log_avg.c -o PLM_log_avg.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c SCAB.c -o SCAB.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c common_types.c -o common_types.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/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]
   int first_ind;
       ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/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]
   int first_ind;
       ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/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]
   int first_ind;
       ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/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]
   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]
   int first_ind;
       ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c lm_threestep.c -o lm_threestep.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c matrix_functions.c -o matrix_functions.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/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]
   int which_lesn;
       ^~~~~~~~~~
preprocess.c: In function ‘pp_bothstages’:
preprocess.c:677:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable]
   int rows,cols;
            ^~~~
preprocess.c:677:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable]
   int rows,cols;
       ^~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c psi_fns.c -o psi_fns.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/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]
   int first_ind;
       ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/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]
   int rows,cols;
            ^~~~
rlm_PLM.c:1481:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable]
   int rows,cols;
       ^~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rma_PLM.c -o rma_PLM.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/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]
   int i;
       ^
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c scaling.c -o scaling.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/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]
   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]
   int rows,cols;
            ^~~~
threestep.c:193:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable]
   int rows,cols;
       ^~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c threestep_common.c -o threestep_common.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/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]
   int first_ind;
       ^~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c transfns.c -o transfns.o
gcc -shared -L/home/biocbuild/bbs-3.12-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 -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.12-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -lz -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/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)