BioC 3.3: CHECK report for Biobase on oaxaca

Package: Biobase

Version: 2.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biobase_2.32.0.tar.gz

StartedAt: 2016-10-12 23:35:33 -0700 (Wed, 12 Oct 2016)

EndedAt: 2016-10-12 23:37:01 -0700 (Wed, 12 Oct 2016)

EllapsedTime: 88.1 seconds

RetCode: 0

Status:  OK

CheckDir: Biobase.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biobase_2.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/Biobase.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biobase/DESCRIPTION’ ... OK
* this is package ‘Biobase’ version ‘2.32.0’
* 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 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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
openVignette: no visible global function definition for ‘menu’
package.version: no visible global function definition for
  ‘packageDescription’
read.AnnotatedDataFrame: no visible global function definition for
  ‘read.table’
readExpressionSet: no visible binding for global variable ‘read.table’
write.AnnotatedDataFrame: no visible global function definition for
  ‘write.table’
write.exprs,ExpressionSet: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  menu packageDescription read.table write.table
Consider adding
  importFrom("utils", "menu", "packageDescription", "read.table",
             "write.table")
to your NAMESPACE file.
* 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 compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
  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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/Biobase.Rcheck/00check.log’
for details.

* installing *source* package ‘Biobase’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Rinit.c -o Rinit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c anyMissing.c -o anyMissing.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c envir.c -o envir.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c matchpt.c -o matchpt.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c rowMedians.c -o rowMedians.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c sublist_extract.c -o sublist_extract.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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-3.3-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	0.006	0.001	0.007
ScalarObject-class	0.009	0.000	0.009
addVig2Menu	0.001	0.000	0.001
anyMissing	0.002	0.000	0.001
cache	0.003	0.001	0.005
channel	0.134	0.001	0.136
channelNames	0.056	0.000	0.057
class.AnnotatedDataFrame	0.035	0.001	0.035
class.ExpressionSet	0.245	0.011	0.256
class.MIAxE	0.022	0.000	0.022
class.MultiSet	0.037	0.001	0.037
class.NChannelSet	0.211	0.001	0.214
class.Versioned	0.065	0.001	0.066
class.VersionedBiobase	0.029	0.000	0.029
class.Versions	0.017	0.001	0.017
class.VersionsNull	0.001	0.000	0.001
class.container	0.002	0.000	0.002
class.eSet	0.101	0.001	0.102
classVersion	0.006	0.000	0.006
contents	0.001	0.000	0.002
copyEnv	0.001	0.000	0.001
copySubstitute	0.011	0.003	0.014
createPackage	0.007	0.002	0.009
data.aaMap	0.002	0.000	0.002
data.geneData	0.049	0.003	0.052
data.reporter	0.002	0.001	0.003
data.sample.ExpressionSet	0.061	0.006	0.068
data.sample.MultiSet	0.006	0.007	0.013
dumpPackTxt	0.005	0.001	0.021
esApply	1.542	0.018	1.563
getPkgVigs	0.010	0.002	0.042
isCurrent	0.037	0.000	0.038
isUnique	0.001	0.000	0.001
isVersioned	0.015	0.000	0.014
lcSuffix	0.003	0.001	0.003
listLen	0.002	0.000	0.001
makeDataPackage	0.075	0.009	0.084
matchpt	0.005	0.000	0.006
multiassign	0.001	0.000	0.001
note	0	0	0
openPDF	0.000	0.000	0.001
openVignette	0.000	0.000	0.001
package.version	0.001	0.000	0.001
read.AnnotatedDataFrame	0.018	0.001	0.019
read.MIAME	0.003	0.000	0.003
readExpressionSet	0.077	0.002	0.079
reverseSplit	0.001	0.000	0.001
rowMedians	0.047	0.001	0.049
rowQ	0.017	0.009	0.026
selectChannels	0.06	0.00	0.06
selectSome	0.000	0.000	0.001
strbreak	0.002	0.000	0.002
subListExtract	0.885	0.018	0.904
testBioCConnection	0.003	0.001	0.534
updateOldESet	0.000	0.000	0.001
validMsg	0.001	0.000	0.001