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BioC 3.1: CHECK report for inSilicoMerging on zin2

This page was generated on 2015-10-09 09:24:55 -0700 (Fri, 09 Oct 2015).

Package 497/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
inSilicoMerging 1.12.0
InSilico DB
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/inSilicoMerging
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: inSilicoMerging
Version: 1.12.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings inSilicoMerging_1.12.0.tar.gz
StartedAt: 2015-10-09 02:44:51 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:46:45 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 113.9 seconds
RetCode: 0
Status:  OK 
CheckDir: inSilicoMerging.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings inSilicoMerging_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-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 ‘1.12.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/61s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plotMDS             7.069  0.024  16.760
plotRLE             3.546  0.013  11.859
merge               3.169  0.160  21.415
plotGeneWiseBoxPlot 2.570  0.005  10.031
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘inSilicoMerging_unit_tests.R’ [2s/26s]
 [2s/27s] 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-3.1-bioc/meat/inSilicoMerging.Rcheck/00check.log’
for details.


inSilicoMerging.Rcheck/00install.out:

* 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)

inSilicoMerging.Rcheck/inSilicoMerging-Ex.timings:

nameusersystemelapsed
merge 3.169 0.16021.415
plotGeneWiseBoxPlot 2.570 0.00510.031
plotMDS 7.069 0.02416.760
plotRLE 3.546 0.01311.859