Package: affy

Version: 1.29.2

Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings affy_1.29.2.tar.gz

StartedAt: 2011-02-24 16:34:02 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 16:38:03 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 241.2 seconds

RetCode: 0

Status:  OK

CheckDir: affy.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/affy.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affy/DESCRIPTION' ... OK
* this is package 'affy' version '1.29.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affy' 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 whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 ... NOTE
cleancdfname: no visible binding for global variable 'mapCdfName'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' call not declared from: widgetTools
* checking data for non-ASCII characters ... 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
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'affy' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/BBS-2˜1.8-B/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c chipbackground.c -o chipbackground.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/BBS-2˜1.8-B/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c getall_locations.c -o getall_locations.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/BBS-2˜1.8-B/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c mas5calls.c -o mas5calls.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/BBS-2˜1.8-B/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c rma2.c -o rma2.o
gcc -I"E:/biocbld/BBS-2˜1.8-B/R/include" -DHAVE_ZLIB   -I"E:/biocbld/BBS-2˜1.8-B/R/library/preprocessCore/include"      -O3 -Wall  -std=gnu99 -c rma_common.c -o rma_common.o
gcc -shared -s -static-libgcc -o affy.dll tmp.def chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lRzlib -LE:/biocbld/BBS-2˜1.8-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/affy.Rcheck/affy/libs/i386
** R
** data
** demo
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Creating a new generic function for "open" in "affy"
Creating a new generic function for "close" in "affy"
Creating a new generic function for "colnames" in "affy"
Creating a new generic function for "barplot" in "affy"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (affy)

name	user	system	elapsed
AffyBatch-class	2.94	0.13	3.24
AffyRNAdeg	5.72	0.01	5.73
MAplot	27.70	0.41	28.30
ProbeSet-class	1.12	0.06	1.20
ProgressBarText-class	0.75	0.00	16.47
affy-options	0	0	0
barplot.ProbeSet	1.14	0.02	1.15
bgc	7.36	0.06	7.64
cleancdfname	0.02	0.00	0.02
expresso	26.45	0.25	27.05
expressoWidget	0	0	0
fit.li.wong	0.02	0.00	0.02
generateExprSet-methods	1.15	0.00	1.17
generateExprVal-methods	1.17	0.02	1.18
generateExprVal.method.avgdiff	0.61	0.00	0.61
list.celfiles	0	0	0
maffy.normalise	3.61	0.02	3.63
maffy.subset	0.02	0.01	0.03
mas5	54.87	0.13	55.47
mas5calls	2.89	0.03	2.94
mva.pairs	0.15	0.00	0.16
normalize-methods	0.78	0.00	0.79
normalize.loess	0.04	0.00	0.04
plot.ProbeSet	0	0	0
plot.density	1.49	0.04	1.53
plotLocation	4.86	0.18	5.14
pmcorrect	1.03	0.07	1.11
ppsetApply	0	0	0
read.affybatch	4.61	0.10	5.50
rma	4.70	0.03	4.77
setAffyOptions	0	0	0
xy2indices	4.84	0.16	5.67