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Package 17/389HostnameOS / ArchBUILDCHECKBUILD BIN
affyPLM 1.24.1
Ben Bolstad
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/affyPLM
Last Changed Rev: 48479 / Revision: 49923
Last Changed Date: 2010-07-27 18:56:47 -0700 (Tue, 27 Jul 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: affyPLM
Version: 1.24.1
Command: D:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings affyPLM_1.24.1.tar.gz
StartedAt: 2010-10-04 15:30:09 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 15:34:30 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 261.2 seconds
RetCode: 0
Status:  OK  
CheckDir: affyPLM.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'D:/biocbld/bbs-2.6-bioc/meat/affyPLM.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyPLM/DESCRIPTION' ... OK
* this is package 'affyPLM' version '1.24.1'
* 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 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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:171-172: 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... 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

affyPLM.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'affyPLM' ...
** libs
  making DLL ...
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c LESN.c -o LESN.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c PLM_avg_log.c -o PLM_avg_log.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c PLM_biweight.c -o PLM_biweight.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c PLM_log_avg.c -o PLM_log_avg.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c PLM_medianPM.c -o PLM_medianPM.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c PLM_median_logPM.c -o PLM_median_logPM.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c PLM_medianpolish.c -o PLM_medianpolish.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c SCAB.c -o SCAB.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c chipbackground.c -o chipbackground.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c common_types.c -o common_types.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c do_PLMrlm.c -o do_PLMrlm.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c do_PLMrma.c -o do_PLMrma.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c do_PLMthreestep.c -o do_PLMthreestep.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c idealmismatch.c -o idealmismatch.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c lm_threestep.c -o lm_threestep.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c matrix_functions.c -o matrix_functions.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c nthLargestPM.c -o nthLargestPM.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c preprocess.c -o preprocess.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c psi_fns.c -o psi_fns.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c qnorm_probeset.c -o qnorm_probeset.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c read_rmaexpress.c -o read_rmaexpress.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c rlm_PLM.c -o rlm_PLM.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c rlm_threestep.c -o rlm_threestep.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c rma_PLM.c -o rma_PLM.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c rma_common.c -o rma_common.o
rma_common.c: In function 'median':
rma_common.c:60: warning: unused variable 'i'
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c scaling.c -o scaling.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c threestep.c -o threestep.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c threestep_PLM.c -o threestep_PLM.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c threestep_common.c -o threestep_common.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c threestep_summary.c -o threestep_summary.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c threestep_summary_methods.c -o threestep_summary_methods.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -DHAVE_ZLIB  -I"D:/biocbld/bbs-2.6-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -c transfns.c -o transfns.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o affyPLM.dll tmp.def 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 -LD:/biocbld/bbs-2.6-bioc/R/bin -lRlapack -LD:/biocbld/bbs-2.6-bioc/R/bin -lRblas -lRzlib -LD:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to D:/biocbld/bbs-2.6-bioc/meat/affyPLM.Rcheck/affyPLM/libs/x64
  ... done
** 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 ...
** testing if installed package can be loaded

* DONE (affyPLM)

affyPLM.Rcheck/affyPLM-Ex.timings:

nameusersystemelapsed
PLMset2exprSet13.67 0.1713.84
bg.correct.LESN6.890.137.02
fitPLM17.62 0.6118.25
normalize.exprSet2.750.042.79
normalize.scaling4.890.165.06
preprocess6.500.176.68
rmaPLM0.560.050.61
threestep35.58 0.2835.92
threestepPLM0.580.000.58