BioC 2.8: CHECK report for Biobase on lamb1

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/Biobase.Rcheck’
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biobase/DESCRIPTION’ ... OK
* this is package ‘Biobase’ version ‘2.12.2’
* checking package namespace 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 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 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 was 1 warning, see
  ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/Biobase.Rcheck/00check.log’
for details

* installing *source* package ‘Biobase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c envir.c -o envir.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c sublist_extract.c -o sublist_extract.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/Biobase.Rcheck/Biobase/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (Biobase)

name	user	system	elapsed
Aggregate	0.012	0.000	0.014
ScalarObject-class	0.024	0.000	0.023
addVig2Menu	0	0	0
anyMissing	0.000	0.000	0.001
biocReposList	0	0	0
cache	0.004	0.000	0.002
channel	0.272	0.000	0.270
channelNames	0.060	0.000	0.062
class.AnnotatedDataFrame	0.100	0.000	0.102
class.ExpressionSet	0.408	0.004	0.420
class.MIAxE	0.028	0.000	0.028
class.MultiSet	0.064	0.000	0.063
class.NChannelSet	0.388	0.000	0.388
class.Versioned	0.12	0.00	0.12
class.VersionedBiobase	0.056	0.000	0.056
class.Versions	0.024	0.000	0.020
class.VersionsNull	0.000	0.000	0.001
class.container	0.004	0.000	0.004
class.eSet	0.188	0.004	0.190
classVersion	0.012	0.000	0.012
combine	0.084	0.000	0.085
contents	0.004	0.000	0.001
copyEnv	0.000	0.000	0.001
copySubstitute	0.000	0.012	0.011
createPackage	0.004	0.008	0.010
data.aaMap	0.000	0.000	0.003
data.geneData	0.024	0.000	0.030
data.reporter	0.004	0.000	0.002
data.sample.ExpressionSet	0.016	0.000	0.017
data.sample.MultiSet	0.004	0.000	0.005
dumpPackTxt	0.000	0.004	0.021
esApply	3.092	0.000	3.139
getPkgVigs	0.032	0.008	0.056
isCurrent	0.084	0.000	0.084
isUnique	0	0	0
isVersioned	0.096	0.000	0.097
lcSuffix	0.004	0.000	0.002
listLen	0.000	0.000	0.001
makeDataPackage	0.084	0.000	0.148
matchpt	0.008	0.000	0.006
multiassign	0	0	0
note	0	0	0
openPDF	0	0	0
openVignette	0	0	0
package.version	0.000	0.000	0.001
read.AnnotatedDataFrame	0.012	0.000	0.048
read.MIAME	0.004	0.000	0.006
readExpressionSet	0.104	0.004	0.111
reverseSplit	0.000	0.000	0.001
rowMedians	0.060	0.004	0.070
rowQ	0.028	0.000	0.028
selectChannels	0.112	0.000	0.204
selectSome	0.000	0.000	0.001
strbreak	0.000	0.000	0.001
subListExtract	1.916	0.068	2.129
testBioCConnection	0.004	0.000	0.006
updateObject	0.232	0.000	0.235
updateOldESet	0	0	0
validMsg	0	0	0

Summary

Command output