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| Package 12/188 | OS | Arch | BUILD | CHECK | BUILD BIN |
affyPLM1.10.0Ben Bolstad | Linux (SUSE 9.2) | x86_64 | OK | OK | |
| Linux (SUSE 9.2) | i686 | OK | OK | ||
| Solaris 2.9 | sparc | OK | OK | ||
| Windows Server 2003 | x86_64 | OK | [ OK ] | OK |
| Package: affyPLM |
| Version: 1.10.0 |
| Command: D:\biocbld\1.9d\R\bin\R.exe CMD check affyPLM_1.10.0.tar.gz |
| RetCode: 0 |
| Time: 610.4 seconds |
| Status: OK |
| CheckDir: affyPLM.Rcheck |
| Warnings: 0 |
* checking for working latex ... OK * using log directory 'D:/biocbld/1.9d/Rpacks/affyPLM.Rcheck' * using R version 2.4.0 (2006-10-03) * checking for file 'affyPLM/DESCRIPTION' ... OK * this is package 'affyPLM' version '1.10.0' * 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 syntax errors ... OK * checking R files for non-ASCII characters ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... 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/1.9d/Rpacks/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/1.9d/Rpacks/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/1.9d/Rpacks/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/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c LESN.c -o LESN.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c PLM_modelmatrix.c -o PLM_modelmatrix.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c R_rlm_interfaces.c -o R_rlm_interfaces.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c SCAB.c -o SCAB.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c avg_log.c -o avg_log.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c biweight.c -o biweight.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c chipbackground.c -o chipbackground.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c common_types.c -o common_types.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c do_PLMrlm.c -o do_PLMrlm.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c do_PLMrma.c -o do_PLMrma.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c do_PLMthreestep.c -o do_PLMthreestep.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c idealmismatch.c -o idealmismatch.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c lm.c -o lm.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c lm_threestep.c -o lm_threestep.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c log_avg.c -o log_avg.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c matrix_functions.c -o matrix_functions.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c medianPM.c -o medianPM.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c median_logPM.c -o median_logPM.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c medianpolish.c -o medianpolish.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c nthLargestPM.c -o nthLargestPM.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c preprocess.c -o preprocess.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c psi_fns.c -o psi_fns.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c qnorm.c -o qnorm.o
qnorm.c: In function `qnorm_c_determine_target':
qnorm.c:1521: warning: unused variable `ind'
qnorm.c:1522: warning: unused variable `dimat'
qnorm.c:1526: warning: unused variable `ranks'
qnorm.c: In function `R_qnorm_using_target':
qnorm.c:1604: warning: unused variable `dim2'
qnorm.c: In function `qnorm_c_determine_target':
qnorm.c:1596: warning: control reaches end of non-void function
qnorm.c: At top level:
qnorm.c:116: warning: 'min' defined but not used
qnorm.c:389: warning: 'qnorm_c_old' defined but not used
qnorm.c:463: warning: 'qnorm_robust_c_old' defined but not used
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c qnorm_probeset.c -o qnorm_probeset.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -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/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c rlm.c -o rlm.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c rlm_PLM.c -o rlm_PLM.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c rlm_anova.c -o rlm_anova.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c rlm_se.c -o rlm_se.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c rlm_threestep.c -o rlm_threestep.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c rma_PLM.c -o rma_PLM.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c rma_background2.c -o rma_background2.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c rma_common.c -o rma_common.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c scaling.c -o scaling.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c threestep.c -o threestep.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c threestep_PLM.c -o threestep_PLM.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c threestep_common.c -o threestep_common.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c threestep_summary.c -o threestep_summary.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c transfns.c -o transfns.o
gcc -Id:/biocbld/1.9d/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/1.9d/R/include -Wall -O2 -std=gnu99 -c weightedkerneldensity.c -o weightedkerneldensity.o
windres --include-dir d:/biocbld/1.9d/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/1.9d/R/bin -lg2c -Ld:/biocbld/1.9d/R/bin -lRlapack -Ld:/biocbld/1.9d/R/bin -lRblas -Ld:/biocbld/1.9d/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()' 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: 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"
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
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\1.9d\Rpacks\affyPLM.Rcheck\00_pkg_src\affyPLM\chm\affyPLM.chm
Compile time: 0 minutes, 0 seconds
17 Topics
107 Local links
7 Internet links
1 Graphic
Created d:\biocbld\1.9d\Rpacks\affyPLM.Rcheck\00_pkg_src\affyPLM\chm\affyPLM.chm, 40,232 bytes
Compression decreased file by 53,128 bytes.
adding MD5 sums
* DONE (affyPLM)