Samuel Zimmerman
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/pathVar |
| Branch: RELEASE_3_8 |
| Last Commit: 368f103 |
| Last Changed Date: 2018-10-30 11:41:59 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:59:01 -0400 (Tue, 16 Apr 2019).
| Package 1126/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pathVar 1.12.0 Samuel Zimmerman
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: pathVar |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pathVar.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathVar_1.12.0.tar.gz |
| StartedAt: 2019-04-16 01:47:52 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:52:20 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 268.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pathVar.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pathVar.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathVar_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/pathVar.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.12.0’
* 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 ‘pathVar’ can be installed ... 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 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’
diagnosticsVarPlotsTwoSample: no visible binding for global variable
‘avg’
diagnosticsVarPlotsTwoSample: no visible binding for global variable
‘standDev’
diagnosticsVarPlotsTwoSample: no visible binding for global variable
‘medAbsDev’
diagnosticsVarPlotsTwoSample: 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’
plotAllTwoSampleDistributionCounts: no visible binding for global
variable ‘Cluster’
plotAllTwoSampleDistributionCounts: no visible binding for global
variable ‘Number_of_genes’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sigPway 89.562 3.291 93.912
diagnosticsVarPlots 48.717 0.440 50.021
diagnosticsVarPlotsTwoSample 30.387 0.257 30.944
plotAllTwoSampleDistributionCounts 10.102 1.790 10.237
pathVar-package 5.690 1.772 4.963
saveAsPDF 7.085 0.310 7.019
plotPway 5.884 1.190 5.576
pathVarTwoSamplesCont 5.337 1.001 5.055
getGenes 5.444 0.094 5.593
pathVarTwoSamplesDisc 4.108 0.952 3.742
* 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
‘/Users/biocbuild/bbs-3.8-bioc/meat/pathVar.Rcheck/00check.log’
for details.
pathVar.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pathVar ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘pathVar’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare 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 | 0.020 | 0.002 | 0.023 | |
| diagnosticsVarPlots | 48.717 | 0.440 | 50.021 | |
| diagnosticsVarPlotsTwoSample | 30.387 | 0.257 | 30.944 | |
| geneDistributionSet-class | 0.006 | 0.000 | 0.006 | |
| geneDistributionSet2-class | 0.002 | 0.001 | 0.003 | |
| geneDistributionSet3-class | 0.004 | 0.001 | 0.004 | |
| geneSet-class | 0.001 | 0.000 | 0.002 | |
| getGenes | 5.444 | 0.094 | 5.593 | |
| makeDBList | 0.001 | 0.002 | 0.001 | |
| pathVar-package | 5.690 | 1.772 | 4.963 | |
| pathVarOneSample | 3.417 | 0.053 | 3.487 | |
| pathVarTwoSamplesCont | 5.337 | 1.001 | 5.055 | |
| pathVarTwoSamplesDisc | 4.108 | 0.952 | 3.742 | |
| plotAllTwoSampleDistributionCounts | 10.102 | 1.790 | 10.237 | |
| plotPway | 5.884 | 1.190 | 5.576 | |
| pways.kegg | 0.002 | 0.002 | 0.003 | |
| pways.reactome | 0.001 | 0.000 | 0.002 | |
| saveAsPDF | 7.085 | 0.310 | 7.019 | |
| sigPway | 89.562 | 3.291 | 93.912 | |
| significantPathway-class | 0.004 | 0.005 | 0.001 | |
| significantPathway2-class | 0.003 | 0.004 | 0.001 | |
| significantPathway3-class | 0.006 | 0.006 | 0.002 | |