affyPLM

Package: affyPLM
Version: 1.48.0
Title: Methods for fitting probe-level models
Author: Ben Bolstad <bmb@bmbolstad.com>
Maintainer: Ben Bolstad <bmb@bmbolstad.com>
Depends: R (>= 2.6.0), BiocGenerics (>= 0.3.2), affy (>= 1.11.0),
Biobase (>= 2.17.8), gcrma, stats, preprocessCore (>= 1.5.1)
Imports: BiocGenerics, zlibbioc, graphics, grDevices, methods
Suggests: affydata, MASS
LinkingTo: preprocessCore
Description: A package that extends and improves the functionality of
the base affy package. Routines that make heavy use of
compiled code for speed. Central focus is on implementation of
methods for fitting probe-level models and tools using these
models. PLM based quality assessment tools.
License: GPL (>= 2)
URL: https://github.com/bmbolstad/affyPLM
biocViews: Microarray, OneChannel, Preprocessing, QualityControl
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2016-05-04 02:40:57 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'affyPLM' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c LESN.c -o LESN.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c PLM_avg_log.c -o PLM_avg_log.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c PLM_biweight.c -o PLM_biweight.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c PLM_log_avg.c -o PLM_log_avg.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c PLM_medianPM.c -o PLM_medianPM.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c SCAB.c -o SCAB.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c chipbackground.c -o chipbackground.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c common_types.c -o common_types.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c do_PLMrlm.c -o do_PLMrlm.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c do_PLMrma.c -o do_PLMrma.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c idealmismatch.c -o idealmismatch.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c lm_threestep.c -o lm_threestep.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c matrix_functions.c -o matrix_functions.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c nthLargestPM.c -o nthLargestPM.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c preprocess.c -o preprocess.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c psi_fns.c -o psi_fns.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c qnorm_probeset.c -o qnorm_probeset.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -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/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c rlm_PLM.c -o rlm_PLM.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c rlm_threestep.c -o rlm_threestep.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c rma_PLM.c -o rma_PLM.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c rma_common.c -o rma_common.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c scaling.c -o scaling.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c threestep.c -o threestep.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c threestep_PLM.c -o threestep_PLM.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c threestep_common.c -o threestep_common.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c threestep_summary.c -o threestep_summary.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c transfns.c -o transfns.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -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/ddbj/local/lib64/R/lib -lRlapack -L/home/ddbj/local/lib64/R/lib -lRblas -lz -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/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
  converting help for package 'affyPLM'
    finding HTML links ... done
    MAplot                                  html  
    PLMset-class                            html  
    PLMset2exprSet                          html  
    ReadRMAExpress                          html  
    affyPLM-internal                        html  
    bg.correct.LESN                         html  
    fitPLM                                  html  
    normalize.exprSet                       html  
    normalize.quantiles.probeset            html  
    normalize.scaling                       html  
    preprocess                              html  
    pseudo                                  html  
    rmaPLM                                  html  
    threestep                               html  
    threestepPLM                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (affyPLM)
Making 'packages.html' ... done