BioC 3.2: CHECK report for inSilicoMerging on linux1.bioconductor.org

Package: inSilicoMerging

Version: 1.14.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings inSilicoMerging_1.14.0.tar.gz

StartedAt: 2015-10-27 04:51:55 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:53:12 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 76.9 seconds

RetCode: 0

Status:  OK

CheckDir: inSilicoMerging.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings inSilicoMerging_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/inSilicoMerging.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘inSilicoMerging/DESCRIPTION’ ... OK
* this is package ‘inSilicoMerging’ version ‘1.14.0’
* 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 ‘inSilicoMerging’ can be installed ... [2s/2s] 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
Package in Depends field not imported from: ‘Biobase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
commonGenes : <anonymous>: no visible global function definition for
  ‘exprs’
geneBMCESet: no visible global function definition for ‘exprs<-’
geneBMCESet: no visible global function definition for ‘exprs’
geneNormESet: no visible global function definition for ‘exprs<-’
geneNormESet: no visible global function definition for ‘exprs’
identify_common_genes: no visible global function definition for
  ‘exprs’
makeColorMap: no visible global function definition for ‘pData’
makeColorVec: no visible global function definition for ‘pData’
matchExprsPheno: no visible global function definition for ‘exprs’
matchExprsPheno: no visible global function definition for ‘pData<-’
matchExprsPheno: no visible global function definition for ‘pData’
mergeCOMBAT: no visible global function definition for ‘pData’
mergeCOMBAT: no visible global function definition for ‘exprs’
mergeCOMBAT: no visible global function definition for ‘exprs<-’
mergeNONE: no visible global function definition for ‘annotation’
mergeNONE: no visible global function definition for ‘exprs’
mergeNONE: no visible global function definition for ‘exprs<-’
mergeNONE: no visible global function definition for ‘pData<-’
mergeNONE: no visible global function definition for ‘fData<-’
mergeNONE: no visible global function definition for ‘annotation<-’
plotGeneWiseBoxPlot: no visible global function definition for ‘exprs’
plotGeneWiseBoxPlot: no visible global function definition for ‘pData’
plotMDS: no visible global function definition for ‘exprs’
plotMDS: no visible global function definition for ‘pData’
plotRLE: no visible global function definition for ‘exprs’
plotRLE: no visible global function definition for ‘rowMedians’
xpn: no visible global function definition for ‘exprs’
xpn: no visible global function definition for ‘exprs<-’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [20s/44s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plotMDS             7.943  0.065  12.029
plotRLE             4.623  0.027   8.560
merge               3.767  0.110  16.135
plotGeneWiseBoxPlot 2.334  0.004   6.605
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘inSilicoMerging_unit_tests.R’ [3s/15s]
 [3s/15s] 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/inSilicoMerging.Rcheck/00check.log’
for details.

* installing *source* package ‘inSilicoMerging’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (inSilicoMerging)

name	user	system	elapsed
merge	3.767	0.110	16.135
plotGeneWiseBoxPlot	2.334	0.004	6.605
plotMDS	7.943	0.065	12.029
plotRLE	4.623	0.027	8.560