Back to the "Multiple platform build/check report"
| Package 11/172 | OS | Arch | BUILD | CHECK | BUILD BIN |
affyPLM1.8.0Ben Bolstad | Linux (SUSE 9.2) | x86_64 | OK | OK | |
| Linux (SUSE 9.2) | i686 | OK | OK | ||
| Solaris 2.9 | sparc | OK | OK | ||
| Linux (SUSE 10.0) | x86_64 | OK | [ OK ] | ||
| Windows Server 2003 | x86_64 | ERROR | skipped | skipped |
| Package: affyPLM |
| Version: 1.8.0 |
| Command: /home/biocbuild/1.8d/R/bin/R CMD check affyPLM_1.8.0.tar.gz |
| RetCode: 0 |
| Time: 333.3 seconds |
| Status: OK |
| CheckDir: affyPLM.Rcheck |
| Warnings: 0 |
* checking for working latex ... OK * using log directory '/home/biocbuild/1.8d/Rpacks/affyPLM.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'affyPLM/DESCRIPTION' ... OK * this is package 'affyPLM' version '1.8.0' * 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 syntax errors ... OK * checking R files for library.dynam ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking Rd files ... 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 * creating affyPLM-Ex.R ... OK * checking examples ... OK * checking tests ... make[1]: Entering directory `/home/biocbuild/1.8d/Rpacks/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/1.8d/Rpacks/affyPLM.Rcheck/tests' OK * checking package vignettes in 'inst/doc' ... OK * creating affyPLM-manual.tex ... OK * checking affyPLM-manual.tex ... OK
affyPLM.Rcheck/00install.out:
* Installing *source* package 'affyPLM' ...
** libs
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c avg_log.c -o avg_log.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c biweight.c -o biweight.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c chipbackground.c -o chipbackground.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c common_types.c -o common_types.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c do_PLMrma.c -o do_PLMrma.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c idealmismatch.c -o idealmismatch.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c LESN.c -o LESN.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c lm.c -o lm.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c lm_threestep.c -o lm_threestep.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c log_avg.c -o log_avg.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c matrix_functions.c -o matrix_functions.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c median_logPM.c -o median_logPM.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c medianPM.c -o medianPM.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c medianpolish.c -o medianpolish.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c preprocess.c -o preprocess.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c psi_fns.c -o psi_fns.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c qnorm.c -o qnorm.o
qnorm.c:83: warning: 'min' defined but not used
qnorm.c:190: warning: 'qnorm_c_old' defined but not used
qnorm.c:263: warning: 'qnorm_robust_c_old' defined but not used
qnorm.c: In function 'qnorm_robust_c':
qnorm.c:493: warning: 'datvec' may be used uninitialized in this function
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
read_rmaexpress.c: In function 'fread_char':
read_rmaexpress.c:112: warning: unused variable 'i'
read_rmaexpress.c: In function 'read_rmaexpress_header':
read_rmaexpress.c:246: warning: unused variable 'dimnames'
read_rmaexpress.c: At top level:
read_rmaexpress.c:59: warning: 'swap_float_8' defined but not used
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c rlm_anova.c -o rlm_anova.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c rlm.c -o rlm.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c rlm_PLM.c -o rlm_PLM.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c rlm_se.c -o rlm_se.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c rma_background2.c -o rma_background2.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c rma_common.c -o rma_common.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c rma_PLM.c -o rma_PLM.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c SCAB.c -o SCAB.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c scaling.c -o scaling.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c threestep.c -o threestep.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c threestep_common.c -o threestep_common.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c threestep_summary.c -o threestep_summary.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c transfns.c -o transfns.o
gcc -I/home/biocbuild/1.8d/R/include -I/home/biocbuild/1.8d/R/include -I/usr/local/include -fpic -g -O2 -std=gnu99 -Wall -c weightedkerneldensity.c -o weightedkerneldensity.o
gcc -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 SCAB.o scaling.o threestep.o threestep_common.o threestep_PLM.o threestep_summary.o threestep_summary_methods.o transfns.o weightedkerneldensity.o -L/home/biocbuild/1.8d/R/lib -lRlapack
** 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: Biobase
Loading required package: gcrma
Loading required package: matchprobes
[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"
** 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.probeset text html latex
normalize.scaling 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)