BioC 3.3: CHECK report for Biobase on morelia

Package: Biobase

Version: 2.31.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biobase_2.31.3.tar.gz

StartedAt: 2016-04-20 23:36:32 -0700 (Wed, 20 Apr 2016)

EndedAt: 2016-04-20 23:37:54 -0700 (Wed, 20 Apr 2016)

EllapsedTime: 82.1 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_2.31.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/Biobase.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘2.31.3’
* 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 ... [5s/5s] 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 ... [5s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [18s/18s]
  Running ‘test-rowMedians.R’ [15s/15s]
 [34s/34s] 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	0.009	0.000	0.010
ScalarObject-class	0.01	0.00	0.01
addVig2Menu	0.001	0.000	0.001
anyMissing	0.002	0.000	0.001
cache	0.003	0.001	0.003
channel	0.116	0.001	0.118
channelNames	0.05	0.00	0.05
class.AnnotatedDataFrame	0.025	0.000	0.026
class.ExpressionSet	0.286	0.011	0.297
class.MIAxE	0.018	0.001	0.018
class.MultiSet	0.032	0.000	0.033
class.NChannelSet	0.164	0.001	0.165
class.Versioned	0.051	0.000	0.052
class.VersionedBiobase	0.031	0.001	0.031
class.Versions	0.020	0.001	0.020
class.VersionsNull	0.002	0.000	0.002
class.container	0.004	0.000	0.004
class.eSet	0.071	0.000	0.072
classVersion	0.006	0.000	0.006
contents	0.001	0.000	0.001
copyEnv	0.001	0.000	0.001
copySubstitute	0.009	0.004	0.012
createPackage	0.006	0.002	0.007
data.aaMap	0.003	0.001	0.003
data.geneData	0.044	0.002	0.047
data.reporter	0.001	0.001	0.002
data.sample.ExpressionSet	0.049	0.005	0.054
data.sample.MultiSet	0.006	0.006	0.011
dumpPackTxt	0.003	0.001	0.018
esApply	1.342	0.012	1.355
getPkgVigs	0.008	0.001	0.061
isCurrent	0.039	0.001	0.040
isUnique	0.001	0.000	0.001
isVersioned	0.017	0.000	0.017
lcSuffix	0.002	0.000	0.002
listLen	0.001	0.000	0.002
makeDataPackage	0.072	0.009	0.081
matchpt	0.007	0.001	0.006
multiassign	0.002	0.000	0.002
note	0.001	0.000	0.001
openPDF	0.001	0.000	0.001
openVignette	0.001	0.000	0.001
package.version	0.001	0.000	0.001
read.AnnotatedDataFrame	0.021	0.001	0.021
read.MIAME	0.003	0.001	0.003
readExpressionSet	0.087	0.002	0.089
reverseSplit	0.001	0.001	0.000
rowMedians	0.048	0.002	0.051
rowQ	0.020	0.009	0.029
selectChannels	0.039	0.001	0.040
selectSome	0.000	0.000	0.001
strbreak	0.001	0.000	0.001
subListExtract	0.890	0.022	0.912
testBioCConnection	0.002	0.001	0.640
updateOldESet	0.000	0.000	0.001
validMsg	0.000	0.001	0.001