BioC 3.3: CHECK report for pathVar on linux2.bioconductor.org
This page was generated on 2015-10-27 12:13:50 -0400 (Tue, 27 Oct 2015).
pathVar 1.1.0 Samuel Zimmerman
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pathVar | Last Changed Rev: 109592 / Revision: 109948 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
Summary
Package: pathVar |
Version: 1.1.0 |
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings pathVar_1.1.0.tar.gz |
StartedAt: 2015-10-27 06:36:08 -0400 (Tue, 27 Oct 2015) |
EndedAt: 2015-10-27 06:38:29 -0400 (Tue, 27 Oct 2015) |
EllapsedTime: 141.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pathVar.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings pathVar_1.1.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/pathVar.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pathVar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathVar’ version ‘1.1.0’
* 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 ‘pathVar’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
diagnosticsVarPlots: no visible binding for global variable ‘avg’
diagnosticsVarPlots: no visible binding for global variable ‘standDev’
diagnosticsVarPlots: no visible binding for global variable ‘medAbsDev’
diagnosticsVarPlots: no visible binding for global variable ‘cv’
pathVarOneSample: no visible binding for global variable ‘APval’
pathVarOneSample: no visible binding for global variable
‘PercOfGenesInPway’
pathVarTwoSamplesCont: no visible binding for global variable ‘APval’
pathVarTwoSamplesCont: no visible binding for global variable
‘PercOfGenesInPway’
pathVarTwoSamplesDisc: no visible binding for global variable ‘APval’
pathVarTwoSamplesDisc: no visible binding for global variable
‘PercOfGenesInPway’
plotOneSample: no visible binding for global variable ‘Cluster’
plotOneSample: no visible binding for global variable ‘Number_of_genes’
plotTwoSamplesCont: no visible binding for global variable ‘PwayName’
plotTwoSamplesCont: no visible binding for global variable
‘NumOfGenesFromDataSetInPathway’
plotTwoSamplesCont: no visible binding for global variable ‘value’
plotTwoSamplesCont: no visible binding for global variable
‘..density..’
plotTwoSamplesCont: no visible binding for global variable ‘group’
plotTwoSamplesDisc: no visible binding for global variable ‘Cluster’
plotTwoSamplesDisc: no visible binding for global variable
‘Number_of_genes’
sigOneSample: no visible binding for global variable ‘APval’
sigOneSample: no visible binding for global variable ‘PwayName’
sigTwoSamplesCont: no visible binding for global variable ‘APval’
sigTwoSamplesCont: no visible binding for global variable ‘PwayName’
sigTwoSamplesDisc: no visible binding for global variable ‘APval’
sigTwoSamplesDisc: no visible binding for global variable ‘PwayName’
Undefined global functions or variables:
..density.. APval Cluster NumOfGenesFromDataSetInPathway
Number_of_genes PercOfGenesInPway PwayName avg cv group medAbsDev
standDev value
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [114s/114s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
sigPway 74.755 0.040 74.840
diagnosticsVarPlots 13.279 1.366 14.658
pathVar-package 5.219 0.008 5.231
* 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
‘/home/biocbuild/bbs-3.3-bioc/meat/pathVar.Rcheck/00check.log’
for details.
pathVar.Rcheck/00install.out:
* installing *source* package ‘pathVar’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pathVar)
pathVar.Rcheck/pathVar-Ex.timings:
name | user | system | elapsed
|
bock | 0.003 | 0.000 | 0.003 |
|
diagnosticsVarPlots | 13.279 | 1.366 | 14.658 |
|
geneDistributionSet-class | 0.006 | 0.001 | 0.006 |
|
geneDistributionSet2-class | 0.003 | 0.000 | 0.003 |
|
geneDistributionSet3-class | 0.003 | 0.000 | 0.003 |
|
geneSet-class | 0.002 | 0.000 | 0.002 |
|
getGenes | 3.020 | 0.000 | 3.022 |
|
makeDBList | 0.001 | 0.000 | 0.001 |
|
pathVar-package | 5.219 | 0.008 | 5.231 |
|
pathVarOneSample | 4.472 | 0.000 | 4.477 |
|
pathVarTwoSamplesCont | 2.833 | 0.000 | 2.840 |
|
pathVarTwoSamplesDisc | 1.378 | 0.000 | 1.381 |
|
plotPway | 3.929 | 0.000 | 3.931 |
|
pways.kegg | 0.002 | 0.000 | 0.002 |
|
pways.reactome | 0.001 | 0.003 | 0.002 |
|
saveAsPDF | 3.137 | 0.005 | 3.144 |
|
sigPway | 74.755 | 0.040 | 74.840 |
|
significantPathway-class | 0.001 | 0.000 | 0.001 |
|
significantPathway2-class | 0.001 | 0.000 | 0.001 |
|
significantPathway3-class | 0.002 | 0.000 | 0.002 |
|