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IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1
Package 13/247HostnameOSArchBUILDCHECKBUILD BIN

affyPLM

1.13.9

Ben Bolstad
Last Changed Date: 2007-08-12 11:55:18 -0700
Last Changed Rev: 26352
lamb1 Linux (SUSE 10.1) x86_64  OK [ WARNINGS ]
wellington Linux (SUSE 9.2) i686  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) x64  ERROR skippedskipped
pitt Mac OS X (10.4.10) i386  OK  WARNINGS  OK 
Package: affyPLM
Version: 1.13.9
Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check affyPLM_1.13.9.tar.gz
RetCode: 0
Time: 445.1 seconds
Status: WARNINGS
CheckDir: affyPLM.Rcheck
Warnings: 1

Command output

* 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) (2007-08-06 r42439)
* checking for file 'affyPLM/DESCRIPTION' ... OK
* this is package 'affyPLM' version '1.13.9'
* 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 ... WARNING
Undocumented S4 methods:
  generic 'indexProbes' and siglist 'PLMset,character'
  generic 'sampleNames<-' and siglist 'PLMset,character'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* 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
* 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

WARNING: There was 1 warning, see
  /home/biocbuild/bbs-2.1-bioc/meat/affyPLM.Rcheck/00check.log
for details

affyPLM.Rcheck/00install.out:

* 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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c avg_log.c -o avg_log.o
avg_log.c: In function 'AverageLog_threestep':
avg_log.c:64: warning: implicit declaration of function 'AverageLog'
avg_log.c: In function 'AverageLog_PLM':
avg_log.c:80: warning: implicit declaration of function 'averagelog_no_copy'
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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c biweight.c -o biweight.o
biweight.c: In function 'TukeyBiweight_threestep':
biweight.c:66: warning: implicit declaration of function 'TukeyBiweight'
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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c common_types.c -o common_types.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c preprocess.c -o preprocess.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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
qnorm_probeset.c: In function 'qnorm_probeset_c':
qnorm_probeset.c:154: warning: implicit declaration of function 'AverageLog_noSE'
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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/home/biocbuild/bbs-2.1-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-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c threestep_common.c -o threestep_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-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-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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 -I"/home/biocbuild/bbs-2.1-bioc/R/library/preprocessCore/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_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_probeset.o read_rmaexpress.o rlm_PLM.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 -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
** preparing package for lazy loading
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: preprocessCore
Loading required package: gcrma
Loading required package: matchprobes
Loading required package: splines
Creating a new generic function for "weights" in "affyPLM"
Creating a new generic function for "summary" in "affyPLM"
Creating a new generic function for "resid" in "affyPLM"
Creating a new generic function for "residuals" in "affyPLM"
** 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
  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)