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affyPLM

1.11.10

Ben Bolstad
Linux (SUSE 9.2) x86_64 ERROR skipped
Linux (SUSE 10.1) x86_64 ERROR skipped
Linux (SUSE 9.2) i686 ERROR skipped
Solaris 2.9 sparc[ ERROR ]skipped
Windows Server 2003 x86_64 ERROR skippedskipped
Windows Server 2003 NA ERROR skippedskipped
Mac OS X (10.4.6) i686 ERROR skipped
Package: affyPLM
Version: 1.11.10
Command: /loc/biocbuild/2.0d/R/bin/R CMD build affyPLM
RetCode: 1
Time: 233.2 seconds
Status: ERROR
PackageFile: None

Command output

* checking for file 'affyPLM/DESCRIPTION' ... OK
* preparing 'affyPLM':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking whether 'INDEX' is up-to-date ... NO
* use '--force' to overwrite the existing 'INDEX'
* installing the package to re-build vignettes
* Installing *source* package 'affyPLM' ...
** libs
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c LESN.c -o LESN.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c R_rlm_interfaces.c -o R_rlm_interfaces.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c SCAB.c -o SCAB.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c avg_log.c -o avg_log.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c biweight.c -o biweight.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c common_types.c -o common_types.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c idealmismatch.c -o idealmismatch.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c lm.c -o lm.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c log_avg.c -o log_avg.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c medianPM.c -o medianPM.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c median_logPM.c -o median_logPM.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c medianpolish.c -o medianpolish.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c preprocess.c -o preprocess.o
preprocess.c: In function 'pp_bothstages':
preprocess.c:667: warning: unused variable 'exprs'
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c qnorm.c -o qnorm.o
qnorm.c: In function 'qnorm_c_determine_target':
qnorm.c:1494: warning: unused variable 'ranks'
qnorm.c:1490: warning: unused variable 'dimat'
qnorm.c:1489: warning: unused variable 'ind'
qnorm.c: In function 'R_qnorm_using_target':
qnorm.c:1572: warning: unused variable 'dim2'
qnorm.c: In function 'qnorm_c_determine_target':
qnorm.c:1564: warning: control reaches end of non-void function
qnorm.c: At top level:
qnorm.c:118: warning: 'min' defined but not used
qnorm.c:357: warning: 'qnorm_c_old' defined but not used
qnorm.c:431: warning: 'qnorm_robust_c_old' defined but not used
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
read_rmaexpress.c: In function 'read_rmaexpress_header':
read_rmaexpress.c:249: warning: unused variable 'dimnames'
read_rmaexpress.c: In function 'gz_read_rmaexpress_header':
read_rmaexpress.c:431: warning: unused variable 'dimnames'
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c rlm.c -o rlm.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c rlm_PLM.c -o rlm_PLM.o
rlm_PLM.c:99: warning: 'rlmPLM_alloc_space' defined but not used
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c rlm_anova.c -o rlm_anova.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c rlm_se.c -o rlm_se.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c rma_background2.c -o rma_background2.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/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: warning: unused variable 'i'
rma_common.c: In function 'median_nocopy':
rma_common.c:103: warning: unused variable 'i'
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c scaling.c -o scaling.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c threestep.c -o threestep.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c threestep_common.c -o threestep_common.o
threestep_common.c: In function 'median_low':
threestep_common.c:45: warning: unused variable 'i'
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c transfns.c -o transfns.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fPIC  -g -O2 -Wall -c weightedkerneldensity.c -o weightedkerneldensity.o
gcc -std=gnu99 -G -L/usr/local/lib -o affyPLM.so LESN.o PLM_modelmatrix.o R_rlm_interfaces.o SCAB.o avg_log.o biweight.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm.o lm_threestep.o log_avg.o matrix_functions.o medianPM.o median_logPM.o medianpolish.o nthLargestPM.o preprocess.o psi_fns.o qnorm.o qnorm_probeset.o read_rmaexpress.o rlm.o rlm_PLM.o rlm_anova.o rlm_se.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_background2.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o weightedkerneldensity.o -lgfortran -lm -lgcc_s -L/loc/biocbuild/2.0d/R/lib -lRlapack -L/loc/biocbuild/2.0d/R/lib -lRblas  
** R
** inst
** save image
Loading required package: affy
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: affyio
Loading required package: affydata
Loading required package: gcrma
Loading required package: matchprobes
Loading required package: splines
[1] "PLMset"
[1] "initialize"
[1] "cdfName"
[1] "exprs"
[1] "exprs<-"
[1] "se.exprs"
[1] "se.exprs<-"
[1] "sampleNames"
[1] "sampleNames<-"
[1] "featureNames"
[1] "featureNames<-"
Creating a new generic function for "weights" in "affyPLM"
[1] "weights"
[1] "weights<-"
[1] "weights<-"
[1] "coefs"
[1] "coefs"
[1] "coefs<-"
[1] "coefs<-"
[1] "coefs.probe"
[1] "coefs.probe"
[1] "se"
[1] "se"
[1] "se.probe"
[1] "se.probe"
[1] "se<-"
[1] "se<-"
[1] "indexProbes"
[1] "indexProbesProcessed"
[1] "indexProbesProcessed"
[1] "image"
[1] "boxplot"
[1] "show"
[1] "coefs.const"
[1] "coefs.const"
[1] "se.const"
[1] "se.const"
Creating a new generic function for "summary" in "affyPLM"
[1] "summary"
[1] "Mbox"
[1] "resid<-"
[1] "resid<-"
Creating a new generic function for "resid" in "affyPLM"
[1] "resid"
[1] "residuals<-"
[1] "residuals<-"
Creating a new generic function for "residuals" in "affyPLM"
[1] "residuals"
[1] "normvec"
[1] "normvec"
[1] "varcov"
[1] "varcov"
[1] "residSE"
[1] "residSE"
[1] "sampleNames"
[1] "sampleNames<-"
[1] "model.description"
[1] "model.description"
[1] "MAplot"
[1] "nuse"
[1] "nuse"
[1] "NUSE"
[1] "NUSE"
[1] "RLE"
[1] "RLE"
** help
 >>> Building/Updating help pages for package 'affyPLM'
     Formats: text html latex example 
  MAplot                            text    html    latex
  PLMset-class                      text    html    latex   example
  PLMset2exprSet                    text    html    latex   example
  ReadRMAExpress                    text    html    latex
  affyPLM-internal                  text    html    latex
  bg.correct.LESN                   text    html    latex   example
  fitPLM                            text    html    latex   example
  normalize.exprSet                 text    html    latex   example
  normalize.quantiles.in.blocks     text    html    latex   example
  normalize.quantiles.probeset      text    html    latex
  normalize.quantiles.target        text    html    latex
  normalize.scaling                 text    html    latex   example
  preprocess                        text    html    latex   example
  pseudo                            text    html    latex   example
  rmaPLM                            text    html    latex   example
  threestep                         text    html    latex   example
  threestepPLM                      text    html    latex   example
** building package indices ...
* DONE (affyPLM)
* creating vignettes ... ERROR
Loading required package: affy
Loading required package: Biobase

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: affyio
Loading required package: affydata
Loading required package: gcrma
Loading required package: matchprobes
Loading required package: splines

Error:  chunk 11 (label=MMcovariate) 
Error in validObject(.Object) : invalid class "PLMset" object: 1: sample numbers differ between assayData and phenoData
invalid class "PLMset" object: 2: sampleNames differ between assayData and phenoData
Error in buildVignettes(dir = ".") : Error:  chunk 11 (label=MMcovariate) 
Error in validObject(.Object) : invalid class "PLMset" object: 1: sample numbers differ between assayData and phenoData
invalid class "PLMset" object: 2: sampleNames differ between assayData and phenoData
Execution halted