Package: affyPLM

Version: 1.12.0

Command: /loc/biocbuild/bbs-2.0-bioc/R/bin/R CMD build affyPLM

RetCode: 0

Time: 548.5 seconds

Status: OK

PackageFile: affyPLM_1.12.0.tar.gz

* 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/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c avg_log.c -o avg_log.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c biweight.c -o biweight.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c common_types.c -o common_types.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c idealmismatch.c -o idealmismatch.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c LESN.c -o LESN.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c lm.c -o lm.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c log_avg.c -o log_avg.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c median_logPM.c -o median_logPM.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c medianPM.c -o medianPM.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c medianpolish.c -o medianpolish.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/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/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/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:1489: warning: unused variable `ind'
qnorm.c:1490: warning: unused variable `dimat'
qnorm.c:1494: warning: unused variable `ranks'
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/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/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/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rlm_anova.c -o rlm_anova.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rlm.c -o rlm.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/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/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rlm_se.c -o rlm_se.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rma_background2.c -o rma_background2.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/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/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c R_rlm_interfaces.c -o R_rlm_interfaces.o
R_rlm_interfaces.c: In function `R_wrlm_rma_default_model':
R_rlm_interfaces.c:197: warning: implicit declaration of function `rlm_wfit_anova'
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c SCAB.c -o SCAB.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c scaling.c -o scaling.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c threestep.c -o threestep.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/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/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/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/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c transfns.c -o transfns.o
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.0-bioc/R/include -I/loc/biocbuild/bbs-2.0-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c weightedkerneldensity.c -o weightedkerneldensity.o
gcc -std=gnu99 -shared -L/usr/local/lib -o affyPLM.so avg_log.o biweight.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o LESN.o lm.o lm_threestep.o log_avg.o matrix_functions.o median_logPM.o medianPM.o medianpolish.o nthLargestPM.o PLM_modelmatrix.o preprocess.o psi_fns.o qnorm.o qnorm_probeset.o read_rmaexpress.o rlm_anova.o rlm.o rlm_PLM.o rlm_se.o rlm_threestep.o rma_background2.o rma_common.o rma_PLM.o rmaPLM_pseudo.o R_rlm_interfaces.o SCAB.o scaling.o threestep.o threestep_common.o threestep_PLM.o threestep_summary.o threestep_summary_methods.o transfns.o weightedkerneldensity.o -lg2c -lm -lgcc_s -L/loc/biocbuild/bbs-2.0-bioc/R/lib -lRlapack -L/loc/biocbuild/bbs-2.0-bioc/R/lib -lRblas  -L/loc/biocbuild/bbs-2.0-bioc/R/lib -lR
** 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()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: affyio
Loading required package: affydata
Loading required package: gcrma
Loading required package: matchprobes
Loading required package: splines
[1] "PLMset"
[1] "cdfName"
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"
[1] "phenoData"
[1] "phenoData<-"
[1] "pData"
[1] "pData<-"
[1] "description"
[1] "annotation"
** 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 ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building 'affyPLM_1.12.0.tar.gz'