Package: preprocessCore

Version: 1.0.0

Command: E:\biocbld\bbs-2.1-bioc\R\bin\R.exe CMD check preprocessCore_1.0.0.tar.gz

RetCode: 0

Time: 44.7 seconds

Status: OK

CheckDir: preprocessCore.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory 'E:/biocbld/bbs-2.1-bioc/meat/preprocessCore.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'preprocessCore/DESCRIPTION' ... OK
* this is package 'preprocessCore' version '1.0.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'preprocessCore' 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 preprocessCore-Ex.R ... OK
* checking examples ... OK
* creating preprocessCore-manual.tex ... OK
* checking preprocessCore-manual.tex ... OK

installing R.css in E:/biocbld/bbs-2.1-bioc/meat/preprocessCore.Rcheck


---------- Making package preprocessCore ------------
  adding build stamp to DESCRIPTION
  making DLL ...
making R_colSummarize.d from R_colSummarize.c
making R_rlm_interfaces.d from R_rlm_interfaces.c
making R_subColSummarize.d from R_subColSummarize.c
making avg.d from avg.c
making avg_log.d from avg_log.c
making biweight.d from biweight.c
making init_package.d from init_package.c
making lm.d from lm.c
making log_avg.d from log_avg.c
making log_median.d from log_median.c
making matrix_functions.d from matrix_functions.c
making median.d from median.c
making median_log.d from median_log.c
making medianpolish.d from medianpolish.c
making psi_fns.d from psi_fns.c
making qnorm.d from qnorm.c
making rlm.d from rlm.c
making rlm_anova.d from rlm_anova.c
making rlm_se.d from rlm_se.c
making rma_common.d from rma_common.c
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c R_colSummarize.c -o R_colSummarize.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c R_rlm_interfaces.c -o R_rlm_interfaces.o
R_rlm_interfaces.c: In function 'R_medianpolish_rma_default_model':
R_rlm_interfaces.c:274: warning: unused variable 'se'
R_rlm_interfaces.c:273: warning: unused variable 'weights'
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c R_subColSummarize.c -o R_subColSummarize.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c avg.c -o avg.o
avg.c: In function 'colaverage_no_copy':
avg.c:90: warning: unused variable 'i'
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c avg_log.c -o avg_log.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c biweight.c -o biweight.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c init_package.c -o init_package.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c lm.c -o lm.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c log_avg.c -o log_avg.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c log_median.c -o log_median.o
log_median.c: In function 'logmedian_no_copy':
log_median.c:138: warning: unused variable 'i'
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c matrix_functions.c -o matrix_functions.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c median.c -o median.o
median.c: In function 'colmedian_no_copy':
median.c:146: warning: unused variable 'i'
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c median_log.c -o median_log.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c medianpolish.c -o medianpolish.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c psi_fns.c -o psi_fns.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c qnorm.c -o qnorm.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c rlm.c -o rlm.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c rlm_anova.c -o rlm_anova.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c rlm_se.c -o rlm_se.o
gcc-sjlj  -std=gnu99  -Ie:/biocbld/bbs-2.1-bioc/R/include    -Wall -O3  -c rma_common.c -o rma_common.o
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.1-bioc/R/include  -i preprocessCore_res.rc -o preprocessCore_res.o
gcc-sjlj  -std=gnu99  -shared -s  -o preprocessCore.dll preprocessCore.def R_colSummarize.o R_rlm_interfaces.o R_subColSummarize.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_common.o preprocessCore_res.o  -Le:/biocbld/bbs-2.1-bioc/R/bin -lgfortran -Le:/biocbld/bbs-2.1-bioc/R/bin -lRlapack -Le:/biocbld/bbs-2.1-bioc/R/bin -lRblas   -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  preparing package preprocessCore for lazy loading
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'preprocessCore'
     Formats: text html latex example chm 
  colSummarize                      text    html    latex   example chm
  normalize.quantiles               text    html    latex           chm
  normalize.quantiles.in.blocks     text    html    latex   example chm
  normalize.quantiles.robust        text    html    latex           chm
  normalize.quantiles.target        text    html    latex           chm
  rcModels                          text    html    latex   example chm
  subColSummarize                   text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.1-bioc\meat\preprocessCore.Rcheck\00_pkg_src\preprocessCore\chm\preprocessCore.chm


Compile time: 0 minutes, 0 seconds
8	Topics
39	Local links
6	Internet links
1	Graphic


Created e:\biocbld\bbs-2.1-bioc\meat\preprocessCore.Rcheck\00_pkg_src\preprocessCore\chm\preprocessCore.chm, 27,175 bytes
Compression decreased file by 14,220 bytes.
  adding MD5 sums

* DONE (preprocessCore)