Package: Biobase

Version: 2.13.7

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.13.7.tar.gz

StartedAt: 2011-07-07 01:51:07 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 01:53:13 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 126.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Biobase.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/Biobase.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Biobase/DESCRIPTION' ... OK
* this is package 'Biobase' version '2.13.7'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Biobase' 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
cache: no visible binding for global variable 'cache_old'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'estimateDispersions' 'estimateSizeFactors'
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
                           old_size new_size compress
  SW.rda                      338Kb    261Kb       xz
  sample.ExpressionSet.rda    271Kb     72Kb       xz
  sample.MultiSet.rda          25Kb     19Kb       xz
  seD.rda                      28Kb     18Kb    bzip2
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: '.readRDS' is deprecated.
  Warning: '.readRDS' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-rowMedians.R'
 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

WARNING: There were 2 warnings, see
  '/Users/biocbuild/bbs-2.9-bioc/meat/Biobase.Rcheck/00check.log'
for details

* installing *source* package 'Biobase' ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c Rinit.c -o Rinit.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c anyMissing.c -o anyMissing.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c envir.c -o envir.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c matchpt.c -o matchpt.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c rowMedians.c -o rowMedians.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c sublist_extract.c -o sublist_extract.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 Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/Biobase.Rcheck/Biobase/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'BiobaseDevelopment.Rnw' 
   'Bioconductor.Rnw' 
   'ExpressionSetIntroduction.Rnw' 
   'HowTo.Rnw' 
   'Qviews.Rnw' 
   'esApply.Rnw' 
** testing if installed package can be loaded

* DONE (Biobase)

name	user	system	elapsed
Aggregate	0.017	0.001	0.018
ScalarObject-class	0.055	0.000	0.055
addVig2Menu	0	0	0
anyMissing	0.002	0.000	0.002
biocReposList	0.007	0.002	0.015
cache	0.003	0.001	0.005
channel	0.305	0.001	0.318
channelNames	0.111	0.000	0.112
class.AnnotatedDataFrame	0.071	0.003	0.075
class.ExpressionSet	0.590	0.009	0.623
class.MIAxE	0.039	0.000	0.044
class.MultiSet	0.089	0.001	0.095
class.NChannelSet	0.475	0.006	0.489
class.Versioned	0.163	0.002	0.173
class.VersionedBiobase	0.079	0.001	0.080
class.Versions	0.029	0.001	0.030
class.VersionsNull	0.001	0.000	0.001
class.container	0.006	0.001	0.006
class.eSet	0.272	0.003	0.286
classVersion	0.017	0.001	0.022
combine	0.117	0.003	0.121
contents	0.001	0.001	0.002
copyEnv	0.001	0.000	0.000
copySubstitute	0.013	0.008	0.021
createPackage	0.009	0.004	0.014
data.aaMap	0.004	0.001	0.004
data.geneData	0.041	0.003	0.044
data.reporter	0.003	0.001	0.003
data.sample.ExpressionSet	0.040	0.003	0.050
data.sample.MultiSet	0.007	0.001	0.009
dumpPackTxt	0.002	0.002	0.038
esApply	3.946	0.026	4.481
getPkgVigs	0.056	0.009	0.083
isCurrent	0.098	0.001	0.099
isUnique	0.000	0.001	0.001
isVersioned	0.042	0.000	0.042
lcSuffix	0.003	0.000	0.003
listLen	0.001	0.001	0.000
makeDataPackage	0.170	0.008	0.180
matchpt	0.008	0.001	0.009
multiassign	0.001	0.000	0.001
note	0.000	0.000	0.001
openPDF	0	0	0
openVignette	0	0	0
package.version	0.001	0.000	0.002
read.AnnotatedDataFrame	0.021	0.002	0.024
read.MIAME	0.006	0.000	0.007
readExpressionSet	0.141	0.006	0.148
reverseSplit	0.003	0.000	0.004
rowMedians	0.089	0.005	0.096
rowQ	0.050	0.008	0.058
selectChannels	0.146	0.002	0.158
selectSome	0.000	0.000	0.001
strbreak	0.000	0.000	0.001
subListExtract	2.431	0.063	2.535
testBioCConnection	0.002	0.001	0.012
updateObject	0.350	0.005	0.357
updateOldESet	0	0	0
validMsg	0.000	0.001	0.000