inSilicoMerging 1.14.0
InSilico DB
| Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/inSilicoMerging | | Last Changed Rev: 109589 / Revision: 110496 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings inSilicoMerging_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/inSilicoMerging.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [3s/3s] 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 ... [24s/57s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotMDS 6.726 0.351 12.158
plotRLE 5.355 0.512 10.903
merge 5.187 0.646 23.378
plotGeneWiseBoxPlot 3.988 0.343 9.397
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘inSilicoMerging_unit_tests.R’ [4s/21s]
[4s/22s] 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
‘/Users/biocbuild/bbs-3.2-bioc/meat/inSilicoMerging.Rcheck/00check.log’
for details.