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| Package: affyPLM |
| Version: 1.8.0 |
| Command: D:\biocbld\R-2.3.0\bin\R.exe CMD build affyPLM |
| RetCode: 0 |
| Time: 300.9 seconds |
| Status: OK |
| PackageFile: affyPLM_1.8.0.tar.gz |
* checking for file 'affyPLM/DESCRIPTION' ... OK
* preparing 'affyPLM':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking whether 'INDEX' is up-to-date ... NO
* use '--force' to overwrite the existing 'INDEX'
* installing the package to re-build vignettes
installing R.css in D:/biocbld/work-area/1.8d/tmpdir/Rinst726093963
---------- 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 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/R-2.3.0/include -Wall -O2 -c LESN.c -o LESN.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c SCAB.c -o SCAB.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c avg_log.c -o avg_log.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c biweight.c -o biweight.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c chipbackground.c -o chipbackground.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c common_types.c -o common_types.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c do_PLMrlm.c -o do_PLMrlm.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c do_PLMrma.c -o do_PLMrma.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c idealmismatch.c -o idealmismatch.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c lm.c -o lm.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c lm_threestep.c -o lm_threestep.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c log_avg.c -o log_avg.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c matrix_functions.c -o matrix_functions.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c medianPM.c -o medianPM.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c median_logPM.c -o median_logPM.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c medianpolish.c -o medianpolish.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c nthLargestPM.c -o nthLargestPM.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c preprocess.c -o preprocess.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c psi_fns.c -o psi_fns.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c qnorm.c -o qnorm.o
qnorm.c: In function `qnorm_robust_c':
qnorm.c:493: warning: 'datvec' might be used uninitialized in this function
qnorm.c: At top level:
qnorm.c:83: warning: 'min' defined but not used
qnorm.c:190: warning: 'qnorm_c_old' defined but not used
qnorm.c:263: warning: 'qnorm_robust_c_old' defined but not used
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c qnorm_probeset.c -o qnorm_probeset.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c read_rmaexpress.c -o read_rmaexpress.o
read_rmaexpress.c: In function `fread_char':
read_rmaexpress.c:112: warning: unused variable `i'
read_rmaexpress.c: In function `read_rmaexpress_header':
read_rmaexpress.c:246: warning: unused variable `dimnames'
read_rmaexpress.c: At top level:
read_rmaexpress.c:59: warning: 'swap_float_8' defined but not used
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c rlm.c -o rlm.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c rlm_PLM.c -o rlm_PLM.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c rlm_anova.c -o rlm_anova.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c rlm_se.c -o rlm_se.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c rlm_threestep.c -o rlm_threestep.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c rma_PLM.c -o rma_PLM.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c rma_background2.c -o rma_background2.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c rma_common.c -o rma_common.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c scaling.c -o scaling.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c threestep.c -o threestep.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c threestep_PLM.c -o threestep_PLM.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c threestep_common.c -o threestep_common.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c threestep_summary.c -o threestep_summary.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c transfns.c -o transfns.o
gcc -Id:/biocbld/R-2.3.0/include -Wall -O2 -c weightedkerneldensity.c -o weightedkerneldensity.o
windres --include-dir d:/biocbld/R-2.3.0/include -i affyPLM_res.rc -o affyPLM_res.o
gcc -shared -s -o affyPLM.dll affyPLM.def LESN.o PLM_modelmatrix.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/R-2.3.0/bin -Ld:/biocbld/R-2.3.0/bin -lRlapack -Ld:/biocbld/R-2.3.0/bin -lRblas -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()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: affyio
Loading required package: affydata
Loading required package: Biobase
Loading required package: gcrma
Loading required package: matchprobes
[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"
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.probeset text html latex chm
normalize.scaling 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\work-area\1.8d\madman\Rpacks\affyPLM\chm\affyPLM.chm
Compile time: 0 minutes, 0 seconds
15 Topics
102 Local links
3 Internet links
1 Graphic
Created d:\biocbld\work-area\1.8d\madman\Rpacks\affyPLM\chm\affyPLM.chm, 37,135 bytes
Compression decreased file by 46,606 bytes.
adding MD5 sums
* DONE (affyPLM)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building 'affyPLM_1.8.0.tar.gz'