BioC 3.0: CHECK report for BicARE on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings BicARE_1.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/BicARE.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BicARE/DESCRIPTION’ ... OK
* this is package ‘BicARE’ version ‘1.24.0’
* 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 ‘BicARE’ can be installed ... [12s/12s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘GSEABase’ ‘multtest’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
FLOC: no visible global function definition for ‘exprs’
bicluster: no visible global function definition for ‘exprs’
bicluster: no visible global function definition for ‘featureNames’
bicluster: no visible global function definition for ‘sampleNames’
makeReport: no visible global function definition for ‘annotation’
makeReport: no visible global function definition for ‘getSYMBOL’
makeReport: no visible global function definition for ‘setName’
residue: no visible global function definition for ‘exprs’
testAnnot: no visible global function definition for ‘pData’
testAnnot: no visible global function definition for ‘phenoData’
testAnnot: no visible global function definition for ‘mt.rawp2adjp’
testSet: no visible global function definition for ‘exprs’
testSet: no visible global function definition for ‘GeneSet’
testSet: no visible global function definition for ‘geneIdType’
testSet: no visible global function definition for ‘geneIds’
testSet: no visible global function definition for ‘mapIdentifiers’
testSet: no visible global function definition for ‘mt.rawp2adjp’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [509s/513s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
testSet 472.897  0.240 477.642
FLOC     26.525  0.004  26.653
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/BicARE.Rcheck/00check.log’
for details.

* installing *source* package ‘BicARE’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c BicARE.c -o BicARE.o
BicARE.c: In function ‘floc’:
BicARE.c:439:12: warning: unused variable ‘invk’ [-Wunused-variable]
BicARE.c: In function ‘action’:
BicARE.c:391:29: warning: ‘j’ may be used uninitialized in this function [-Wuninitialized]
BicARE.c:380:29: warning: ‘i’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.0-bioc/R/lib -L/usr/local/lib -o BicARE.so BicARE.o -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-bioc/meat/BicARE.Rcheck/BicARE/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 (BicARE)

BioC 3.0: CHECK report for BicARE on zin1

Summary

Command output

name	user	system	elapsed
FLOC	26.525	0.004	26.653
bicluster	0.277	0.004	0.281
makeReport	3.304	0.036	3.347
residue	0.000	0.004	0.004
testAnnot	0.020	0.000	0.018
testSet	472.897	0.240	477.642