Package: affy

Version: 1.31.2

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affy_1.31.2.tar.gz

StartedAt: 2011-06-22 01:02:38 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 01:07:31 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 293.2 seconds

RetCode: 0

Status:  OK

CheckDir: affy.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/affy.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affy/DESCRIPTION’ ... OK
* this is package ‘affy’ version ‘1.31.2’
* 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 installed package size ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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) and $(LAPACK_LIBS) ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... 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
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic -c chipbackground.c -o chipbackground.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic -c getall_locations.c -o getall_locations.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic -c mas5calls.c -o mas5calls.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic -c rma2.c -o rma2.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic -c rma_common.c -o rma_common.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-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 generic function for "open" from package "base" in package “affy”
Creating a generic function for "close" from package "base" in package “affy”
Creating a generic function for "colnames" from package "base" in package “affy”
Creating a generic function for "barplot" from package "graphics" in package “affy”
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘affy.Rnw’ 
   ‘builtinMethods.Rnw’ 
   ‘customMethods.Rnw’ 
   ‘vim.Rnw’ 
** testing if installed package can be loaded

* DONE (affy)

name	user	system	elapsed
AffyBatch-class	3.572	0.144	3.842
AffyRNAdeg	6.899	0.224	7.256
MAplot	23.084	1.677	25.700
ProbeSet-class	1.453	0.064	1.575
ProgressBarText-class	1.056	0.028	16.570
affy-options	0.001	0.001	0.002
barplot.ProbeSet	1.457	0.054	1.532
bgc	6.426	0.588	7.204
cleancdfname	0.010	0.003	0.013
expresso	34.561	1.374	36.963
expressoWidget	0.000	0.000	0.001
fit.li.wong	0.036	0.002	0.038
generateExprSet-methods	1.368	0.047	1.436
generateExprVal-methods	1.510	0.052	1.570
generateExprVal.method.avgdiff	0.951	0.028	0.986
list.celfiles	0.000	0.000	0.001
maffy.normalise	4.751	0.123	5.039
maffy.subset	0.061	0.007	0.068
mas5	76.066	0.727	78.155
mas5calls	4.146	0.225	4.407
mva.pairs	0.167	0.009	0.178
normalize-methods	1.001	0.036	1.047
normalize.loess	0.052	0.004	0.057
plot.ProbeSet	0.007	0.001	0.009
plot.density	1.820	0.273	2.114
plotLocation	4.122	0.441	4.737
pmcorrect	1.409	0.051	1.475
ppsetApply	0.003	0.000	0.003
read.affybatch	3.389	0.581	4.204
rma	4.935	0.190	5.164
setAffyOptions	0.000	0.000	0.001
xy2indices	4.621	0.425	5.162