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Package 13/233HostnameOS / ArchBUILDCHECKBUILD BIN
affyPLM 1.14.0
Ben Bolstad
Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/affyPLM
Last Changed Rev: 27709 / Revision: 30966
Last Changed Date: 2007-10-02 17:41:09 -0700 (Tue, 02 Oct 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 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
Package: affyPLM
Version: 1.14.0
Command: D:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check affyPLM_1.14.0.tar.gz
StartedAt: 2008-04-09 18:03:59 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 18:18:11 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 851.6 seconds
RetCode: 0
Status: OK
CheckDir: affyPLM.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/affyPLM.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'affyPLM/DESCRIPTION' ... OK
* this is package 'affyPLM' version '1.14.0'
* 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 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 `/cygdrive/d/biocbld/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 `/cygdrive/d/biocbld/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

affyPLM.Rcheck/00install.out:

installing R.css in D:/biocbld/bbs-2.1-bioc/meat/affyPLM.Rcheck


---------- Making package affyPLM ------------
  adding build stamp to DESCRIPTION
  making DLL ...
making LESN.d from LESN.c
making PLM_avg_log.d from PLM_avg_log.c
making PLM_biweight.d from PLM_biweight.c
making PLM_log_avg.d from PLM_log_avg.c
making PLM_medianPM.d from PLM_medianPM.c
making PLM_median_logPM.d from PLM_median_logPM.c
making PLM_medianpolish.d from PLM_medianpolish.c
making PLM_modelmatrix.d from PLM_modelmatrix.c
making SCAB.d from SCAB.c
making chipbackground.d from chipbackground.c
making common_types.d from common_types.c
making do_PLMrlm.d from do_PLMrlm.c
making do_PLMrma.d from do_PLMrma.c
making do_PLMthreestep.d from do_PLMthreestep.c
making idealmismatch.d from idealmismatch.c
making lm_threestep.d from lm_threestep.c
making matrix_functions.d from matrix_functions.c
making nthLargestPM.d from nthLargestPM.c
making preprocess.d from preprocess.c
making psi_fns.d from psi_fns.c
making qnorm_probeset.d from qnorm_probeset.c
making read_rmaexpress.d from read_rmaexpress.c
making rlm_PLM.d from rlm_PLM.c
making rlm_threestep.d from rlm_threestep.c
making rmaPLM_pseudo.d from rmaPLM_pseudo.c
making rma_PLM.d from rma_PLM.c
making rma_background2.d from rma_background2.c
making rma_common.d from rma_common.c
making scaling.d from scaling.c
making threestep.d from threestep.c
making threestep_PLM.d from threestep_PLM.c
making threestep_common.d from threestep_common.c
making threestep_summary.d from threestep_summary.c
making threestep_summary_methods.d from threestep_summary_methods.c
making transfns.d from transfns.c
making weightedkerneldensity.d from weightedkerneldensity.c
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c LESN.c -o LESN.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c PLM_avg_log.c -o PLM_avg_log.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c PLM_biweight.c -o PLM_biweight.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c PLM_log_avg.c -o PLM_log_avg.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c PLM_medianPM.c -o PLM_medianPM.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c PLM_median_logPM.c -o PLM_median_logPM.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c PLM_medianpolish.c -o PLM_medianpolish.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c SCAB.c -o SCAB.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c chipbackground.c -o chipbackground.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c common_types.c -o common_types.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c do_PLMrlm.c -o do_PLMrlm.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c do_PLMrma.c -o do_PLMrma.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c idealmismatch.c -o idealmismatch.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c lm_threestep.c -o lm_threestep.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c matrix_functions.c -o matrix_functions.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c nthLargestPM.c -o nthLargestPM.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c preprocess.c -o preprocess.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c psi_fns.c -o psi_fns.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c qnorm_probeset.c -o qnorm_probeset.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c read_rmaexpress.c -o read_rmaexpress.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c rlm_PLM.c -o rlm_PLM.o
rlm_PLM.c:99: warning: 'rlmPLM_alloc_space' defined but not used
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c rlm_threestep.c -o rlm_threestep.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c rma_PLM.c -o rma_PLM.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c rma_background2.c -o rma_background2.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c rma_common.c -o rma_common.o
rma_common.c: In function 'median':
rma_common.c:60: warning: unused variable 'i'
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c scaling.c -o scaling.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c threestep.c -o threestep.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c threestep_PLM.c -o threestep_PLM.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c threestep_common.c -o threestep_common.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c threestep_summary.c -o threestep_summary.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c transfns.c -o transfns.o
gcc-sjlj  -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -I"d:/biocbld/bbs-2.1-bioc/R/library/preprocessCore/include"    -O3 -Wall  -c weightedkerneldensity.c -o weightedkerneldensity.o
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I d:/biocbld/bbs-2.1-bioc/R/include  -i affyPLM_res.rc -o affyPLM_res.o
gcc-sjlj  -std=gnu99  -shared -s  -o affyPLM.dll affyPLM.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_background2.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o weightedkerneldensity.o affyPLM_res.o  -Ld:/biocbld/bbs-2.1-bioc/R/bin -lgfortran -Ld:/biocbld/bbs-2.1-bioc/R/bin -lRlapack -Ld:/biocbld/bbs-2.1-bioc/R/bin -lRblas  -Ld:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -lz   -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  preparing package affyPLM 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"
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'affyPLM'
     Formats: text html latex example chm 
  MAplot                            text    html    latex           chm
  PLMset-class                      text    html    latex   example 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
  pseudo                            text    html    latex   example chm
  rmaPLM                            text    html    latex   example chm
  threestep                         text    html    latex   example chm
  threestepPLM                      text    html    latex   example chm
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "rogram Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-2.1-bioc\meat\affyPLM.Rcheck\00_pkg_src\affyPLM\chm\affyPLM.chm

HHC4016: Warning: Cannot open "rogram Files\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".


The following files were not compiled:
  adding MD5 sums

* DONE (affyPLM)