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Package 16/353HostnameOS / ArchBUILDCHECKBUILD BIN
affyPLM 1.22.0
Ben Bolstad
Snapshot Date: 2009-12-13 23:30:35 -0800 (Sun, 13 Dec 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/affyPLM
Last Changed Rev: 42684 / Revision: 43539
Last Changed Date: 2009-10-27 16:33:29 -0700 (Tue, 27 Oct 2009)
wilson2 Linux (openSUSE 11.1) / x86_64  OK [ WARNINGS ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 
Package: affyPLM
Version: 1.22.0
Command: /home/biocbuild/bbs-2.5-bioc/R/bin/R CMD check --no-vignettes affyPLM_1.22.0.tar.gz
StartedAt: 2009-12-14 03:02:33 -0800 (Mon, 14 Dec 2009)
EndedAt: 2009-12-14 03:08:22 -0800 (Mon, 14 Dec 2009)
EllapsedTime: 349.2 seconds
RetCode: 0
Status: WARNINGS
CheckDir: affyPLM.Rcheck
Warnings: 1

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.5-bioc/meat/affyPLM.Rcheck'
* using R version 2.10.0 (2009-10-26)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'affyPLM/DESCRIPTION' ... OK
* this is package 'affyPLM' version '1.22.0'
* checking package name space information ... OK
* 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 whether the name space 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 ... NOTE
prepare_Rd: MAplot.Rd:11-13: Dropping empty section \usage
prepare_Rd: PLMset-class.Rd:163-164: Dropping empty section \examples
prepare_Rd: pseudo.Rd:37-39: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'PLMset-class':
Slots for class 'PLMset'
  Code: annotation cdfName chip.coefs const.coefs experimentData
        model.call model.description narrays ncol normVec nrow
        phenoData probe.coefs residuals residualSE se.chip.coefs
        se.const.coefs se.probe.coefs varcov weights
  Docs: annotation cdfName chip.coefs description model.description
        ncol notes nrow phenoData probe.coefs residuals residualSE
        se.chip.coefs se.probe.coefs varcov weights

* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking tests ...
  Running ‘C_code_tests.R’
  Running ‘PLM_tests.R’
  Running ‘preprocess_tests.R’
  Running ‘threestepPLM_tests.R’
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  /loc/home/biocbuild/bbs-2.5-bioc/meat/affyPLM.Rcheck/00check.log
for details

affyPLM.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package ‘affyPLM’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c LESN.c -o LESN.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c PLM_avg_log.c -o PLM_avg_log.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c PLM_log_avg.c -o PLM_log_avg.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c SCAB.c -o SCAB.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c common_types.c -o common_types.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c idealmismatch.c -o idealmismatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c preprocess.c -o preprocess.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rlm_PLM.c -o rlm_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/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’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c scaling.c -o scaling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c threestep.c -o threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c threestep_common.c -o threestep_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.5-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c transfns.c -o transfns.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o affyPLM.so LESN.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_medianPM.o PLM_median_logPM.o PLM_medianpolish.o PLM_modelmatrix.o SCAB.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o matrix_functions.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o -lgfortran -lm -L/home/biocbuild/bbs-2.5-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.5-bioc/R/lib -lRblas -lz -L/home/biocbuild/bbs-2.5-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Creating a new generic function for "summary" in "affyPLM"
** help
*** installing help indices
** building package indices ...
* DONE (affyPLM)