BioC 2.1: CHECK report for affyPLM on lamb1

Package: affyPLM

Version: 1.13.0

Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check affyPLM_1.13.0.tar.gz

RetCode: 0

Time: 317.1 seconds

Status: OK

CheckDir: affyPLM.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/affyPLM.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-04-17 r41210)
* checking for file 'affyPLM/DESCRIPTION' ... OK
* this is package 'affyPLM' version '1.13.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affyPLM' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating affyPLM-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/home/biocbuild/bbs-2.1-bioc/meat/affyPLM.Rcheck/tests'
  Running 'C_code_tests.R'
  Running 'PLM_tests.R'
  Running 'preprocess_tests.R'
  Running 'threestepPLM_tests.R'
make[1]: Leaving directory `/home/biocbuild/bbs-2.1-bioc/meat/affyPLM.Rcheck/tests'
 OK
* checking package vignettes in 'inst/doc' ... OK
* creating affyPLM-manual.tex ... OK
* checking affyPLM-manual.tex ... OK

* Installing *source* package 'affyPLM' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c avg_log.c -o avg_log.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c biweight.c -o biweight.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c common_types.c -o common_types.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c idealmismatch.c -o idealmismatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c LESN.c -o LESN.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c lm.c -o lm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c log_avg.c -o log_avg.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c median_logPM.c -o median_logPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c medianPM.c -o medianPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c medianpolish.c -o medianpolish.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-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: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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rlm_anova.c -o rlm_anova.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rlm.c -o rlm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rlm_se.c -o rlm_se.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rma_background2.c -o rma_background2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c SCAB.c -o SCAB.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c scaling.c -o scaling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c threestep.c -o threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-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/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c transfns.c -o transfns.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c weightedkerneldensity.c -o weightedkerneldensity.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -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 -lgfortran -lm -L/home/biocbuild/bbs-2.1-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.1-bioc/R/lib -lRblas  -L/home/biocbuild/bbs-2.1-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)

Package 12/234	Hostname	OS	Arch	BUILD	CHECK	BUILD BIN
affyPLM 1.13.0 Ben Bolstad Last Changed Date: 2007-04-24 11:31:42 -0700 Last Changed Rev: 24217	lamb1	Linux (SUSE 10.1)	x86_64	OK	[ OK ]
	wellington	Linux (SUSE 9.2)	i686	OK	OK
	churchill	Solaris 2.9	sparc	OK	OK
	lemming	Windows Server 2003 (32-bit)	x64	OK	OK	OK

affyPLM

1.13.0

Command output