Package: affyPLM

Version: 1.12.0

Command: D:\biocbld\bbs-2.0-bioc\R\bin\R.exe CMD check affyPLM_1.12.0.tar.gz

RetCode: 0

Time: 608.3 seconds

Status: OK

CheckDir: affyPLM.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.0-bioc/meat/affyPLM.Rcheck'
* using R version 2.5.1 (2007-06-27)
* checking for file 'affyPLM/DESCRIPTION' ... OK
* this is package 'affyPLM' version '1.12.0'
* 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 for CRLF line endings in C/C++/Fortran sources/headers ... 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-2.0-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-2.0-bioc/meat/affyPLM.Rcheck/tests'
 OK
* checking package vignettes in 'inst/doc' ... OK
* creating affyPLM-manual.tex ... OK
* checking affyPLM-manual.tex ... OK

installing R.css in D:/biocbld/bbs-2.0-bioc/meat/affyPLM.Rcheck


---------- Making package affyPLM ------------
  adding build stamp to DESCRIPTION
  making DLL ...
making LESN.d from LESN.c
making PLM_modelmatrix.d from PLM_modelmatrix.c
making R_rlm_interfaces.d from R_rlm_interfaces.c
making SCAB.d from SCAB.c
making avg_log.d from avg_log.c
making biweight.d from biweight.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.d from lm.c
making lm_threestep.d from lm_threestep.c
making log_avg.d from log_avg.c
making matrix_functions.d from matrix_functions.c
making medianPM.d from medianPM.c
making median_logPM.d from median_logPM.c
making medianpolish.d from medianpolish.c
making nthLargestPM.d from nthLargestPM.c
making preprocess.d from preprocess.c
making psi_fns.d from psi_fns.c
making qnorm.d from qnorm.c
making qnorm_probeset.d from qnorm_probeset.c
making read_rmaexpress.d from read_rmaexpress.c
making rlm.d from rlm.c
making rlm_PLM.d from rlm_PLM.c
making rlm_anova.d from rlm_anova.c
making rlm_se.d from rlm_se.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  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c LESN.c -o LESN.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c R_rlm_interfaces.c -o R_rlm_interfaces.o
R_rlm_interfaces.c: In function `R_wrlm_rma_default_model':
R_rlm_interfaces.c:197: warning: implicit declaration of function `rlm_wfit_anova'
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c SCAB.c -o SCAB.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c avg_log.c -o avg_log.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c biweight.c -o biweight.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c chipbackground.c -o chipbackground.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c common_types.c -o common_types.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c do_PLMrlm.c -o do_PLMrlm.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c do_PLMrma.c -o do_PLMrma.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c idealmismatch.c -o idealmismatch.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c lm.c -o lm.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c lm_threestep.c -o lm_threestep.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c log_avg.c -o log_avg.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c matrix_functions.c -o matrix_functions.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c medianPM.c -o medianPM.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c median_logPM.c -o median_logPM.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c medianpolish.c -o medianpolish.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c nthLargestPM.c -o nthLargestPM.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c preprocess.c -o preprocess.o
preprocess.c: In function `pp_bothstages':
preprocess.c:667: warning: unused variable `exprs'
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c psi_fns.c -o psi_fns.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c qnorm.c -o qnorm.o
qnorm.c: In function `qnorm_c_determine_target':
qnorm.c:1489: warning: unused variable `ind'
qnorm.c:1490: warning: unused variable `dimat'
qnorm.c:1494: warning: unused variable `ranks'
qnorm.c:1564: warning: no return statement in function returning non-void
qnorm.c: In function `R_qnorm_using_target':
qnorm.c:1572: warning: unused variable `dim2'
qnorm.c: In function `qnorm_c_determine_target':
qnorm.c:1564: warning: control reaches end of non-void function
qnorm.c: At top level:
qnorm.c:118: warning: 'min' defined but not used
qnorm.c:357: warning: 'qnorm_c_old' defined but not used
qnorm.c:431: warning: 'qnorm_robust_c_old' defined but not used
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c qnorm_probeset.c -o qnorm_probeset.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c read_rmaexpress.c -o read_rmaexpress.o
read_rmaexpress.c: In function `read_rmaexpress_header':
read_rmaexpress.c:249: warning: unused variable `dimnames'
read_rmaexpress.c: In function `gz_read_rmaexpress_header':
read_rmaexpress.c:431: warning: unused variable `dimnames'
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c rlm.c -o rlm.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c rlm_PLM.c -o rlm_PLM.o
rlm_PLM.c:99: warning: 'rlmPLM_alloc_space' defined but not used
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c rlm_anova.c -o rlm_anova.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c rlm_se.c -o rlm_se.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c rlm_threestep.c -o rlm_threestep.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c rma_PLM.c -o rma_PLM.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c rma_background2.c -o rma_background2.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c rma_common.c -o rma_common.o
rma_common.c: In function `median':
rma_common.c:60: warning: unused variable `i'
rma_common.c: In function `median_nocopy':
rma_common.c:103: warning: unused variable `i'
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c scaling.c -o scaling.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c threestep.c -o threestep.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c threestep_PLM.c -o threestep_PLM.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c threestep_common.c -o threestep_common.o
threestep_common.c: In function `median_low':
threestep_common.c:45: warning: unused variable `i'
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c threestep_summary.c -o threestep_summary.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c transfns.c -o transfns.o
gcc  -Id:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.0-bioc/R/include  -Wall -O3 -std=gnu99   -c weightedkerneldensity.c -o weightedkerneldensity.o
windres -I d:/biocbld/bbs-2.0-bioc/R/include  -i affyPLM_res.rc -o affyPLM_res.o
gcc  -shared -s  -o affyPLM.dll affyPLM.def LESN.o PLM_modelmatrix.o R_rlm_interfaces.o SCAB.o avg_log.o biweight.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm.o lm_threestep.o log_avg.o matrix_functions.o medianPM.o median_logPM.o medianpolish.o nthLargestPM.o preprocess.o psi_fns.o qnorm.o qnorm_probeset.o read_rmaexpress.o rlm.o rlm_PLM.o rlm_anova.o rlm_se.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-2.0-bioc/R/bin -lg2c -Ld:/biocbld/bbs-2.0-bioc/R/bin -lRlapack -Ld:/biocbld/bbs-2.0-bioc/R/bin -lRblas  -Ld:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -lz   -lR
  ... DLL made
  installing DLL
  installing R files
  save image
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: affydata
Loading required package: gcrma
Loading required package: matchprobes
Loading required package: splines
[1] "PLMset"
[1] "cdfName"
Creating a new generic function for "weights" in "affyPLM"
[1] "weights"
[1] "weights<-"
[1] "weights<-"
[1] "coefs"
[1] "coefs"
[1] "coefs<-"
[1] "coefs<-"
[1] "coefs.probe"
[1] "coefs.probe"
[1] "se"
[1] "se"
[1] "se.probe"
[1] "se.probe"
[1] "se<-"
[1] "se<-"
[1] "indexProbes"
[1] "indexProbesProcessed"
[1] "indexProbesProcessed"
[1] "image"
[1] "boxplot"
[1] "show"
[1] "coefs.const"
[1] "coefs.const"
[1] "se.const"
[1] "se.const"
Creating a new generic function for "summary" in "affyPLM"
[1] "summary"
[1] "Mbox"
[1] "resid<-"
[1] "resid<-"
Creating a new generic function for "resid" in "affyPLM"
[1] "resid"
[1] "residuals<-"
[1] "residuals<-"
Creating a new generic function for "residuals" in "affyPLM"
[1] "residuals"
[1] "normvec"
[1] "normvec"
[1] "varcov"
[1] "varcov"
[1] "residSE"
[1] "residSE"
[1] "sampleNames"
[1] "sampleNames<-"
[1] "model.description"
[1] "model.description"
[1] "MAplot"
[1] "nuse"
[1] "nuse"
[1] "NUSE"
[1] "NUSE"
[1] "RLE"
[1] "RLE"
[1] "phenoData"
[1] "phenoData<-"
[1] "pData"
[1] "pData<-"
[1] "description"
[1] "annotation"
  installing inst files
  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.in.blocks     text    html    latex   example chm
  normalize.quantiles.probeset      text    html    latex           chm
  normalize.quantiles.target        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
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-2.0-bioc\meat\affyPLM.Rcheck\00_pkg_src\affyPLM\chm\affyPLM.chm


Compile time: 0 minutes, 0 seconds
18	Topics
116	Local links
7	Internet links
1	Graphic


Created d:\biocbld\bbs-2.0-bioc\meat\affyPLM.Rcheck\00_pkg_src\affyPLM\chm\affyPLM.chm, 42,494 bytes
Compression decreased file by 60,736 bytes.
  adding MD5 sums

* DONE (affyPLM)