preprocessCore 1.0.0
Benjamin Milo 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/preprocessCore | | 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 |
* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/preprocessCore.Rcheck'
* using R version 2.6.2 (2008-02-08)
* 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 D:/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 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c R_colSummarize.c -o R_colSummarize.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -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 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c R_subColSummarize.c -o R_subColSummarize.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c avg.c -o avg.o
avg.c: In function 'colaverage_no_copy':
avg.c:90: warning: unused variable 'i'
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c avg_log.c -o avg_log.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c biweight.c -o biweight.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c init_package.c -o init_package.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c lm.c -o lm.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c log_avg.c -o log_avg.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -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 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c matrix_functions.c -o matrix_functions.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c median.c -o median.o
median.c: In function 'colmedian_no_copy':
median.c:146: warning: unused variable 'i'
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c median_log.c -o median_log.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c medianpolish.c -o medianpolish.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c psi_fns.c -o psi_fns.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c qnorm.c -o qnorm.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c rlm.c -o rlm.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c rlm_anova.c -o rlm_anova.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c rlm_se.c -o rlm_se.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c rma_common.c -o rma_common.o
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I d:/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 -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 -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
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "aEdit;c:\Program Files\Intel\DMIX;c:\Program Files\Windows Resource Kits\Tools\;c:\Program 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".
Microsoft HTML Help Compiler 4.74.8702
Compiling d:\biocbld\bbs-2.1-bioc\meat\preprocessCore.Rcheck\00_pkg_src\preprocessCore\chm\preprocessCore.chm
HHC4016: Warning: Cannot open "aEdit;c:\Program Files\Intel\DMIX;c:\Program Files\Windows Resource Kits\Tools\;c:\Program 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".
The following files were not compiled:
adding MD5 sums
* DONE (preprocessCore)