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BioC 3.4: INSTALL report for affyPLM on zin1

This page was generated on 2016-09-21 03:35:42 -0700 (Wed, 21 Sep 2016).

Package 27/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyPLM 1.49.1
Ben Bolstad
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affyPLM
Last Changed Rev: 120596 / Revision: 121152
Last Changed Date: 2016-08-30 14:45:52 -0700 (Tue, 30 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: affyPLM
Version: 1.49.1
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD INSTALL affyPLM
StartedAt: 2016-09-19 20:09:35 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 20:09:47 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 11.9 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD INSTALL affyPLM
###
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* installing to library ‘/home/biocbuild/bbs-3.4-bioc/R/library’
* installing *source* package ‘affyPLM’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c LESN.c -o LESN.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c PLM_avg_log.c -o PLM_avg_log.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c PLM_log_avg.c -o PLM_log_avg.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c SCAB.c -o SCAB.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c common_types.c -o common_types.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c lm_threestep.c -o lm_threestep.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c matrix_functions.c -o matrix_functions.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c psi_fns.c -o psi_fns.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c read_rmaexpress.c -o read_rmaexpress.o
read_rmaexpress.c: In function ‘gzfread_int32’:
read_rmaexpress.c:375:19: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
   result = gzread(instream,destination,sizeof(int)*n);
                   ^
In file included from read_rmaexpress.c:31:0:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
                     ^
read_rmaexpress.c: In function ‘gzfread_float64’:
read_rmaexpress.c:395:19: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
   result = gzread(instream,destination,sizeof(double)*n);
                   ^
In file included from read_rmaexpress.c:31:0:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
                     ^
read_rmaexpress.c: In function ‘gzfread_char’:
read_rmaexpress.c:412:20: warning: passing argument 1 of ‘gzread’ from incompatible pointer type [-Wincompatible-pointer-types]
   result =  gzread(instream,destination,sizeof(char)*n);
                    ^
In file included from read_rmaexpress.c:31:0:
/usr/include/zlib.h:1313:21: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
                     ^
read_rmaexpress.c: In function ‘gz_read_rmaexpress_header’:
read_rmaexpress.c:456:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   currentFile = gzopen(filename,mode);
               ^
read_rmaexpress.c: In function ‘gz_read_rmaexpress’:
read_rmaexpress.c:575:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   currentFile = gzopen(filename,mode);
               ^
read_rmaexpress.c: In function ‘isCompressedRMAExpress’:
read_rmaexpress.c:719:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   currentFile = gzopen(filename,mode);
               ^
read_rmaexpress.c:731:11: warning: passing argument 1 of ‘gzclose’ from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(currentFile);
           ^
In file included from read_rmaexpress.c:31:0:
/usr/include/zlib.h:1511:24: note: expected ‘gzFile {aka struct gzFile_s *}’ but argument is of type ‘struct gzFile_s **’
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c rma_PLM.c -o rma_PLM.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c scaling.c -o scaling.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c threestep_common.c -o threestep_common.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/preprocessCore/include"   -fpic  -g -O2  -Wall -c transfns.c -o transfns.o
gcc -shared -L/home/biocbuild/bbs-3.4-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 -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.4-bioc/R/lib -lRblas -lz -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/R/library/affyPLM/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘affyPLM’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (affyPLM)