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Package 24/479HostnameOS / ArchBUILDCHECKBUILD BIN
affyPLM 1.29.2
Ben Bolstad
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affyPLM
Last Changed Rev: 56151 / Revision: 56603
Last Changed Date: 2011-06-13 15:14:15 -0700 (Mon, 13 Jun 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  ERROR  skipped  skipped 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: affyPLM
Version: 1.29.2
Command: mkdir affyPLM.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affyPLM.buildbin-libdir affyPLM_1.29.2.tar.gz >affyPLM-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=affyPLM.buildbin-libdir --install="check:affyPLM-install.out" --force-multiarch --no-vignettes --timings affyPLM_1.29.2.tar.gz && mv affyPLM.buildbin-libdir/* affyPLM.Rcheck/ && rmdir affyPLM.buildbin-libdir
StartedAt: 2011-07-07 04:00:48 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 04:08:17 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 448.7 seconds
RetCode: 0
Status:  OK  
CheckDir: affyPLM.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/affyPLM.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyPLM/DESCRIPTION' ... OK
* this is package 'affyPLM' version '1.29.2'
* 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 installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for unstated dependencies in examples ... 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) and $(LAPACK_LIBS) ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: 'MASS'
* checking tests ...
** running tests for arch 'i386'
  Running 'C_code_tests.R'
  Running 'PLM_tests.R'
  Running 'preprocess_tests.R'
  Running 'threestepPLM_tests.R'
 OK
** running tests for arch 'x64'
  Running 'C_code_tests.R'
  Running 'PLM_tests.R'
  Running 'preprocess_tests.R'
  Running 'threestepPLM_tests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

affyPLM.Rcheck/00install.out:


install for i386

* installing *source* package 'affyPLM' ...
** libs
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c LESN.c -o LESN.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c PLM_avg_log.c -o PLM_avg_log.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c PLM_biweight.c -o PLM_biweight.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c PLM_log_avg.c -o PLM_log_avg.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c PLM_medianPM.c -o PLM_medianPM.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c SCAB.c -o SCAB.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c common_types.c -o common_types.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c do_PLMrlm.c -o do_PLMrlm.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c do_PLMrma.c -o do_PLMrma.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c idealmismatch.c -o idealmismatch.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c lm_threestep.c -o lm_threestep.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c matrix_functions.c -o matrix_functions.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c nthLargestPM.c -o nthLargestPM.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c preprocess.c -o preprocess.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c psi_fns.c -o psi_fns.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c qnorm_probeset.c -o qnorm_probeset.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c read_rmaexpress.c -o read_rmaexpress.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c rlm_PLM.c -o rlm_PLM.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c rlm_threestep.c -o rlm_threestep.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c rma_PLM.c -o rma_PLM.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o
rma_common.c: In function 'median':
rma_common.c:60:7: warning: unused variable 'i'
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c scaling.c -o scaling.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c threestep.c -o threestep.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c threestep_PLM.c -o threestep_PLM.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c threestep_common.c -o threestep_common.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c threestep_summary.c -o threestep_summary.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c transfns.c -o transfns.o
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 -LD:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -lgfortran -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lRlapack -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lRblas -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/affyPLM.buildbin-libdir/affyPLM/libs/i386
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

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

Creating a generic function for "summary" from package "base" in package "affyPLM"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'AffyExtensions.Rnw' 
   'MAplots.Rnw' 
   'QualityAssess.Rnw' 
   'ThreeStep.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'affyPLM' ...
** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c LESN.c -o LESN.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c PLM_avg_log.c -o PLM_avg_log.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c PLM_biweight.c -o PLM_biweight.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c PLM_log_avg.c -o PLM_log_avg.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c PLM_medianPM.c -o PLM_medianPM.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c PLM_median_logPM.c -o PLM_median_logPM.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c PLM_medianpolish.c -o PLM_medianpolish.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c SCAB.c -o SCAB.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c common_types.c -o common_types.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c do_PLMrlm.c -o do_PLMrlm.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c do_PLMrma.c -o do_PLMrma.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c do_PLMthreestep.c -o do_PLMthreestep.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c idealmismatch.c -o idealmismatch.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c lm_threestep.c -o lm_threestep.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c matrix_functions.c -o matrix_functions.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c nthLargestPM.c -o nthLargestPM.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c preprocess.c -o preprocess.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c psi_fns.c -o psi_fns.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c qnorm_probeset.c -o qnorm_probeset.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c read_rmaexpress.c -o read_rmaexpress.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c rlm_PLM.c -o rlm_PLM.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c rlm_threestep.c -o rlm_threestep.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c rma_PLM.c -o rma_PLM.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o
rma_common.c: In function 'median':
rma_common.c:60:7: warning: unused variable 'i'
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c scaling.c -o scaling.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c threestep.c -o threestep.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c threestep_PLM.c -o threestep_PLM.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c threestep_common.c -o threestep_common.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c threestep_summary.c -o threestep_summary.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c threestep_summary_methods.c -o threestep_summary_methods.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include" -DHAVE_ZLIB   -I"D:/biocbld/bbs-2.9-bioc/R/library/preprocessCore/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -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 -LD:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -lgfortran -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lRlapack -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lRblas -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/affyPLM.buildbin-libdir/affyPLM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affyPLM' as affyPLM_1.29.2.zip

* DONE (affyPLM)

affyPLM.Rcheck/affyPLM-Ex.timings:

nameusersystemelapsed
PLMset2exprSet10.49 0.1010.57
bg.correct.LESN4.540.114.65
fitPLM14.71 0.2214.93
normalize.exprSet1.840.011.86
normalize.scaling3.510.173.68
preprocess4.290.084.37
rmaPLM0.540.000.53
threestep25.80 0.0525.88
threestepPLM0.530.000.53