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Package 13/251HostnameOS / ArchBUILDCHECKBUILD BIN
affyPLM 1.15.4
Ben Bolstad
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affyPLM
Last Changed Rev: 28987 / Revision: 29143
Last Changed Date: 2007-12-01 11:30:04 -0800 (Sat, 01 Dec 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  OK 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  OK 
wellington Linux (openSUSE 10.3) / i686  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
lemming Windows Server 2003 (32-bit) / x64  OK  OK  OK 
Package: affyPLM
Version: 1.15.4
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check affyPLM_1.15.4.tar.gz
StartedAt: 2007-12-11 04:43:36 -0800 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 05:04:43 -0800 (Tue, 11 Dec 2007)
EllapsedTime: 1266.5 seconds
RetCode: 0
Status: OK
CheckDir: affyPLM.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/affyPLM.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-09 r43632)
* checking for file 'affyPLM/DESCRIPTION' ... OK
* this is package 'affyPLM' version '1.15.4'
* 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 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 `/loc/home/biocbuild/bbs-2.2-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 `/loc/home/biocbuild/bbs-2.2-bioc/meat/affyPLM.Rcheck/tests'
 OK
* checking package vignettes in 'inst/doc' ... NOTE
--- running texi2dvi on vignettes
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './AffyExtensions.tex' ...
Package natbib Warning: Citation `Huber:1981' on page 16 undefined on input lin
Package natbib Warning: Citation `Huber:1981' on page 16 undefined on input lin
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './AffyExtensions.tex' ...
Package natbib Warning: Citation `Huber:1981' on page 17 undefined on input lin
Package natbib Warning: Citation `Huber:1981' on page 17 undefined on input lin
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './AffyExtensions.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './MAplots.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './MAplots.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './MAplots.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './QualityAssess.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './QualityAssess.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './QualityAssess.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './ThreeStep.tex' ...
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './ThreeStep.tex' ...
* creating affyPLM-manual.tex ... OK
* checking affyPLM-manual.tex ... OK

affyPLM.Rcheck/00install.out:

/loc/home/biocbuild/bbs-2.2-bioc/meat/affyPLM.Rcheck
* Installing *source* package 'affyPLM' ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c common_types.c -o common_types.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c do_PLMrlm.c -o do_PLMrlm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c do_PLMrma.c -o do_PLMrma.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c idealmismatch.c -o idealmismatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c LESN.c -o LESN.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c lm_threestep.c -o lm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c matrix_functions.c -o matrix_functions.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c nthLargestPM.c -o nthLargestPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-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-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c PLM_biweight.c -o PLM_biweight.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-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-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-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-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c PLM_medianPM.c -o PLM_medianPM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c preprocess.c -o preprocess.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c psi_fns.c -o psi_fns.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c qnorm_probeset.c -o qnorm_probeset.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c read_rmaexpress.c -o read_rmaexpress.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rlm_PLM.c -o rlm_PLM.o
rlm_PLM.c:100: warning: ‘rlmPLM_alloc_space’ defined but not used
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rlm_threestep.c -o rlm_threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rma_background2.c -o rma_background2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-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-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rma_PLM.c -o rma_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c SCAB.c -o SCAB.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c scaling.c -o scaling.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c threestep.c -o threestep.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c threestep_common.c -o threestep_common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c threestep_PLM.c -o threestep_PLM.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c threestep_summary.c -o threestep_summary.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-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-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c transfns.c -o transfns.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.2-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -Wall -c weightedkerneldensity.c -o weightedkerneldensity.o
gcc -std=gnu99 -shared -L/usr/local/lib -o affyPLM.so chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o LESN.o lm_threestep.o matrix_functions.o nthLargestPM.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_median_logPM.o PLM_medianPM.o PLM_medianpolish.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-2.2-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.2-bioc/R/lib -lRblas  -L/home/biocbuild/bbs-2.2-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
Note: removing empty section \usage
Note: removing empty section \examples
Note: removing empty section \examples
 >>> Building/Updating help pages for package 'affyPLM'
     Formats: text html latex example 
  MAplot                            text    html    latex
  PLMset-class                      text    html    latex
  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
  rmaPLM                            text    html    latex   example
  threestep                         text    html    latex   example
  threestepPLM                      text    html    latex   example
** building package indices ...
* DONE (affyPLM)