BioC 2.12: CHECK report for Biobase on petty

Package: Biobase

Version: 2.20.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.20.1.tar.gz

StartedAt: 2013-10-08 21:41:58 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:45:26 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 207.6 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Biobase.Rcheck'
* using R version 3.0.1 (2013-05-16)
* 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 '2.20.1'
* 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 ... [12s/13s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [22s/26s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
subListExtract 11.01  0.263  11.371
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test-all.R' [48s/48s]
  Running 'test-rowMedians.R' [36s/36s]
 [84s/85s] 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 -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
** testing if installed package can be loaded
* DONE (Biobase)

name	user	system	elapsed
Aggregate	0.121	0.001	0.122
ScalarObject-class	0.046	0.002	0.050
addVig2Menu	0.010	0.000	0.012
anyMissing	0.008	0.001	0.009
cache	0.021	0.003	0.026
channel	0.297	0.005	0.322
channelNames	0.085	0.001	0.086
class.AnnotatedDataFrame	0.107	0.002	0.108
class.ExpressionSet	0.724	0.014	0.744
class.MIAxE	0.064	0.001	0.065
class.MultiSet	0.086	0.003	0.089
class.NChannelSet	0.449	0.003	0.452
class.Versioned	0.218	0.003	0.220
class.VersionedBiobase	0.103	0.002	0.105
class.Versions	0.055	0.002	0.058
class.VersionsNull	0.017	0.001	0.018
class.container	0.018	0.000	0.019
class.eSet	0.412	0.008	0.421
classVersion	0.036	0.001	0.037
contents	0.009	0.001	0.010
copyEnv	0.011	0.000	0.012
copySubstitute	0.059	0.009	0.069
createPackage	0.026	0.004	0.030
data.aaMap	0.011	0.001	0.011
data.geneData	0.094	0.005	0.099
data.reporter	0.009	0.001	0.010
data.sample.ExpressionSet	0.030	0.010	0.041
data.sample.MultiSet	0.016	0.010	0.026
dumpPackTxt	0.011	0.002	0.021
esApply	3.176	0.038	3.231
getPkgVigs	0.071	0.013	0.907
isCurrent	0.105	0.001	0.106
isUnique	0.007	0.001	0.012
isVersioned	0.053	0.001	0.053
lcSuffix	0.024	0.001	0.026
listLen	0.089	0.001	0.090
makeDataPackage	0.141	0.014	0.317
matchpt	0.023	0.001	0.023
multiassign	0.017	0.000	0.017
note	0.012	0.000	0.012
openPDF	0.006	0.000	0.006
openVignette	0.007	0.000	0.007
package.version	0.011	0.000	0.014
read.AnnotatedDataFrame	0.034	0.003	0.037
read.MIAME	0.012	0.000	0.013
readExpressionSet	0.168	0.008	0.176
reverseSplit	0.015	0.001	0.015
rowMedians	0.106	0.006	0.112
rowQ	0.035	0.013	0.048
selectChannels	0.135	0.002	0.137
selectSome	0.007	0.001	0.007
strbreak	0.012	0.001	0.012
subListExtract	11.010	0.263	11.371
testBioCConnection	0.005	0.007	0.431
updateOldESet	0.002	0.003	0.006
validMsg	0.006	0.005	0.011