BioC 2.12: CHECK report for Biobase on pelham

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Biobase.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Biobase/DESCRIPTION' ... OK
* this is package 'Biobase' version '2.19.3'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'Biobase' can be installed ... [11s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
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 ... 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [22s/22s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
subListExtract 12.459  0.336  12.866
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [37s/37s]
  Running 'test-rowMedians.R' [32s/32s]
 [69s/70s] 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-2.12-bioc/meat/Biobase.Rcheck/00check.log'
for details.

* installing *source* package 'Biobase' ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c Rinit.c -o Rinit.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c anyMissing.c -o anyMissing.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c envir.c -o envir.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c matchpt.c -o matchpt.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c rowMedians.c -o rowMedians.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c sublist_extract.c -o sublist_extract.o
llvm-gcc-4.2 -arch x86_64 -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-2.12-bioc/meat/Biobase.Rcheck/Biobase/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   '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	0.022	0.003	0.024
ScalarObject-class	0.031	0.003	0.034
addVig2Menu	0.009	0.002	0.010
anyMissing	0.011	0.002	0.012
cache	0.016	0.003	0.019
channel	0.212	0.007	0.219
channelNames	0.063	0.001	0.063
class.AnnotatedDataFrame	0.085	0.003	0.088
class.ExpressionSet	0.505	0.018	0.523
class.MIAxE	0.047	0.002	0.049
class.MultiSet	0.111	0.002	0.113
class.NChannelSet	0.429	0.008	0.438
class.Versioned	0.153	0.003	0.156
class.VersionedBiobase	0.093	0.003	0.095
class.Versions	0.042	0.002	0.043
class.VersionsNull	0.011	0.001	0.013
class.container	0.019	0.001	0.019
class.eSet	0.245	0.006	0.287
classVersion	0.035	0.001	0.041
contents	0.012	0.001	0.013
copyEnv	0.007	0.002	0.009
copySubstitute	0.057	0.012	0.079
createPackage	0.026	0.006	0.032
data.aaMap	0.011	0.001	0.012
data.geneData	0.077	0.007	0.090
data.reporter	0.022	0.002	0.029
data.sample.ExpressionSet	0.029	0.008	0.040
data.sample.MultiSet	0.017	0.006	0.028
dumpPackTxt	0.013	0.001	0.035
esApply	2.858	0.043	2.950
getPkgVigs	0.061	0.012	0.120
isCurrent	0.108	0.004	0.112
isUnique	0.008	0.001	0.008
isVersioned	0.049	0.001	0.051
lcSuffix	0.025	0.001	0.026
listLen	0.010	0.001	0.010
makeDataPackage	0.124	0.013	0.137
matchpt	0.020	0.001	0.021
multiassign	0.016	0.001	0.019
note	0.007	0.001	0.008
openPDF	0.009	0.001	0.009
openVignette	0.008	0.001	0.010
package.version	0.010	0.001	0.012
read.AnnotatedDataFrame	0.037	0.004	0.042
read.MIAME	0.015	0.001	0.015
readExpressionSet	0.149	0.006	0.154
reverseSplit	0.009	0.002	0.011
rowMedians	0.088	0.008	0.102
rowQ	0.037	0.016	0.054
selectChannels	0.118	0.003	0.157
selectSome	0.006	0.001	0.009
strbreak	0.012	0.001	0.012
subListExtract	12.459	0.336	12.866
testBioCConnection	0.005	0.006	0.182
updateOldESet	0.002	0.003	0.006
validMsg	0.005	0.006	0.012

Summary

Command output