Package: affy

Version: 1.34.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affy_1.34.0.tar.gz

StartedAt: 2012-09-23 23:06:04 -0700 (Sun, 23 Sep 2012)

EndedAt: 2012-09-23 23:10:05 -0700 (Sun, 23 Sep 2012)

EllapsedTime: 240.2 seconds

RetCode: 0

Status:  OK

CheckDir: affy.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/affy.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'affy/DESCRIPTION' ... OK
* this is package 'affy' version '1.34.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 ... OK
* 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 compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from '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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/affy.Rcheck/00check.log'
for details.

* 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 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c chipbackground.c -o chipbackground.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c getall_locations.c -o getall_locations.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c mas5calls.c -o mas5calls.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c rma2.c -o rma2.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c rma_common.c -o rma_common.o
gcc -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-2.10-bioc/meat/affy.Rcheck/affy/libs/i386
** R
** data
** demo
** inst
** preparing package for lazy loading
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 'barplot' from package 'graphics' in package 'affy'
** help
*** installing help indices
** building package indices
** installing vignettes
   'affy.Rnw' 
   'builtinMethods.Rnw' 
   'customMethods.Rnw' 
   'vim.Rnw' 
** testing if installed package can be loaded

* DONE (affy)

name	user	system	elapsed
AffyBatch-class	8.060	0.236	8.302
AffyRNAdeg	5.648	0.158	5.810
MAplot	24.292	1.409	25.913
ProbeSet-class	0.948	0.074	1.029
ProgressBarText-class	1.314	0.020	16.815
affy-options	0.000	0.000	0.001
barplot.ProbeSet	0.961	0.068	1.034
bgc	6.769	0.597	7.426
cleancdfname	0.007	0.005	0.012
expresso	25.365	0.893	26.269
expressoWidget	0.001	0.000	0.000
fit.li.wong	0.613	0.049	0.662
generateExprSet-methods	0.831	0.052	0.884
generateExprVal-methods	0.971	0.061	1.034
generateExprVal.method.avgdiff	1.002	0.062	1.071
list.celfiles	0.000	0.001	0.001
maffy.normalise	3.728	0.107	3.838
maffy.subset	0.028	0.004	0.032
mas5	47.035	0.409	47.451
mas5calls	3.161	0.168	3.332
mva.pairs	0.136	0.009	0.145
normalize-methods	0.461	0.028	0.493
normalize.loess	0.029	0.005	0.035
plot.ProbeSet	0.020	0.003	0.023
plot.density	1.129	0.164	1.298
plotLocation	2.801	0.332	3.210
pmcorrect	0.567	0.045	0.613
ppsetApply	0.000	0.000	0.001
read.affybatch	2.961	0.424	3.429
rma	3.672	0.166	3.856
setAffyOptions	0.001	0.001	0.001
xy2indices	3.986	0.397	4.444