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Package 16/319HostnameOS / ArchBUILDCHECKBUILD BIN
affyPLM 1.20.0
Ben Bolstad
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/affyPLM
Last Changed Rev: 39013 / Revision: 42512
Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK [ OK ]
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: affyPLM
Version: 1.20.0
Command: E:\biocbld\bbs-2.4-bioc\R\bin\R.exe CMD INSTALL --build --library=affyPLM.buildbin-libdir affyPLM_1.20.0.tar.gz
StartedAt: 2009-10-20 18:49:04 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 18:49:30 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 25.7 seconds
RetCode: 0
Status: OK
PackageFile: affyPLM_1.20.0.zip
PackageFileSize: 5.03 MiB

Command output

* Installing *source* package 'affyPLM' ...

  Using auto-selected zip options ''

** libs
  making DLL ...
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c LESN.c -o LESN.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c PLM_avg_log.c -o PLM_avg_log.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c PLM_biweight.c -o PLM_biweight.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c PLM_log_avg.c -o PLM_log_avg.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c PLM_medianPM.c -o PLM_medianPM.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c SCAB.c -o SCAB.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c chipbackground.c -o chipbackground.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c common_types.c -o common_types.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c do_PLMrlm.c -o do_PLMrlm.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c do_PLMrma.c -o do_PLMrma.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c idealmismatch.c -o idealmismatch.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c lm_threestep.c -o lm_threestep.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c matrix_functions.c -o matrix_functions.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c nthLargestPM.c -o nthLargestPM.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c preprocess.c -o preprocess.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c psi_fns.c -o psi_fns.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c qnorm_probeset.c -o qnorm_probeset.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c read_rmaexpress.c -o read_rmaexpress.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c rlm_PLM.c -o rlm_PLM.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c rlm_threestep.c -o rlm_threestep.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c rma_PLM.c -o rma_PLM.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -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'
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c scaling.c -o scaling.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c threestep.c -o threestep.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c threestep_PLM.c -o threestep_PLM.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c threestep_common.c -o threestep_common.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c threestep_summary.c -o threestep_summary.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -I"E:/biocbld/bbs-2.4-bioc/R/include" -DHAVE_ZLIB  -I"E:/biocbld/bbs-2.4-bioc/R/library/preprocessCore/include"     -O3 -Wall  -std=gnu99 -c transfns.c -o transfns.o
gcc -shared -s -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 -LE:/biocbld/bbs-2.4-bioc/R/bin -lRlapack -LE:/biocbld/bbs-2.4-bioc/R/bin -lRblas -lRzlib -LE:/biocbld/bbs-2.4-bioc/R/bin -lR
  ... 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)'.

Loading required package: Biostrings
Loading required package: IRanges

Attaching package: 'IRanges'


	The following object(s) are masked from package:base :

	 cbind,
	 duplicated,
	 order,
	 pmax,
	 pmax.int,
	 pmin,
	 pmin.int,
	 rank,
	 rbind,
	 rep.int,
	 sapply,
	 sort,
	 table,
	 unique 

** help
*** installing help indices
 >>> Building/Updating help pages for package 'affyPLM'
     Formats: text html latex example chm 
Note: removing empty section \usage in file 'MAplot.Rd'
Note: removing empty section \usage in file 'MAplot.Rd'
  MAplot                            text    html    latex           chm
Note: removing empty section \examples in file 'PLMset-class.Rd'
Note: removing empty section \examples in file 'PLMset-class.Rd'
  PLMset-class                      text    html    latex           chm
  PLMset2exprSet                    text    html    latex   example chm
  ReadRMAExpress                    text    html    latex           chm
  affyPLM-internal                  text    html    latex           chm
  bg.correct.LESN                   text    html    latex   example chm
  fitPLM                            text    html    latex   example chm
  normalize.exprSet                 text    html    latex   example chm
  normalize.quantiles.probeset      text    html    latex           chm
  normalize.scaling                 text    html    latex   example chm
  preprocess                        text    html    latex   example chm
Note: removing empty section \examples in file 'pseudo.Rd'
Note: removing empty section \examples in file 'pseudo.Rd'
  pseudo                            text    html    latex           chm
  rmaPLM                            text    html    latex   example chm
  threestep                         text    html    latex   example chm
  threestepPLM                      text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702



Compiling e:\biocbld\bbs-2.4-bioc\tmpdir\Rtmp4ciw11\R.INSTALL678418be\affyPLM\chm\affyPLM.chm





Compile time: 0 minutes, 2 seconds

16	Topics

120	Local links

3	Internet links

1	Graphic





Created e:\biocbld\bbs-2.4-bioc\tmpdir\Rtmp4ciw11\R.INSTALL678418be\affyPLM\chm\affyPLM.chm, 38,932 bytes

Compression decreased file by 52,338 bytes.

** building package indices ...
** MD5 sums
packaged installation of 'affyPLM' as affyPLM_1.20.0.zip
* DONE (affyPLM)