1.11.10Ben 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 | skipped | skipped |
| Windows Server 2003 | NA | ERROR | skipped | skipped |
| Mac OS X (10.4.6) | i686 | ERROR | skipped | |
* 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