Package: affy

Version: 1.29.2

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings affy_1.29.2.tar.gz

StartedAt: 2011-02-24 17:02:37 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 17:06:05 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 207.9 seconds

RetCode: 0

Status:  OK

CheckDir: affy.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/affy.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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’ ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -c getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -DHAVE_ZLIB=1  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/preprocessCore/include"   -fpic  -g -O2 -c rma_common.c -o rma_common.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/affy.Rcheck/affy/libs
** 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	3.028	0.092	3.192
AffyRNAdeg	5.328	0.052	5.384
MAplot	20.881	0.236	21.140
ProbeSet-class	0.680	0.020	0.697
ProgressBarText-class	0.836	0.012	16.342
affy-options	0.000	0.000	0.001
barplot.ProbeSet	0.693	0.020	0.717
bgc	5.732	0.112	5.853
cleancdfname	0.000	0.004	0.008
expresso	25.473	0.096	28.180
expressoWidget	0	0	0
fit.li.wong	0.008	0.000	0.010
generateExprSet-methods	0.713	0.000	0.712
generateExprVal-methods	0.756	0.016	0.769
generateExprVal.method.avgdiff	0.672	0.000	0.676
list.celfiles	0.000	0.000	0.001
maffy.normalise	2.912	0.048	2.960
maffy.subset	0.028	0.004	0.034
mas5	55.235	0.204	56.752
mas5calls	2.932	0.008	5.493
mva.pairs	0.116	0.016	0.130
normalize-methods	0.460	0.000	0.463
normalize.loess	0.036	0.000	0.035
plot.ProbeSet	0.008	0.000	0.005
plot.density	1.349	0.020	1.367
plotLocation	2.604	0.084	2.697
pmcorrect	0.668	0.016	0.691
ppsetApply	0.000	0.000	0.001
read.affybatch	2.472	0.044	2.618
rma	3.412	0.036	3.490
setAffyOptions	0.000	0.000	0.001
xy2indices	2.644	0.076	2.727