BioC 3.3: CHECK report for pathVar on windows2.bioconductor.org
This page was generated on 2015-10-27 12:16:15 -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
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| Command: rm -rf pathVar.buildbin-libdir pathVar.Rcheck && mkdir pathVar.buildbin-libdir pathVar.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pathVar.buildbin-libdir pathVar_1.1.0.tar.gz >pathVar.Rcheck\00install.out 2>&1 && cp pathVar.Rcheck\00install.out pathVar-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=pathVar.buildbin-libdir --install="check:pathVar-install.out" --force-multiarch --no-vignettes --timings pathVar_1.1.0.tar.gz
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| StartedAt: 2015-10-27 04:51:33 -0400 (Tue, 27 Oct 2015)
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| EndedAt: 2015-10-27 04:56:41 -0400 (Tue, 27 Oct 2015)
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| EllapsedTime: 307.5 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: pathVar.Rcheck
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| Warnings: 0
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Command output
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### Running command:
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### rm -rf pathVar.buildbin-libdir pathVar.Rcheck && mkdir pathVar.buildbin-libdir pathVar.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pathVar.buildbin-libdir pathVar_1.1.0.tar.gz >pathVar.Rcheck\00install.out 2>&1 && cp pathVar.Rcheck\00install.out pathVar-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=pathVar.buildbin-libdir --install="check:pathVar-install.out" --force-multiarch --no-vignettes --timings pathVar_1.1.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/pathVar.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [105s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
sigPway 68.41 0.03 68.47
diagnosticsVarPlots 10.26 0.36 11.13
pathVar-package 5.66 0.03 5.69
** running examples for arch 'x64' ... [157s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
sigPway 79.34 0.06 79.44
diagnosticsVarPlots 51.05 2.37 53.44
* 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
'c:/biocbld/bbs-3.3-bioc/meat/pathVar.Rcheck/00check.log'
for details.
pathVar.Rcheck/00install.out:
install for i386
* 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
install for x64
* installing *source* package 'pathVar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pathVar' as pathVar_1.1.0.zip
* DONE (pathVar)
pathVar.Rcheck/examples_i386/pathVar-Ex.timings:
| name | user | system | elapsed
|
| bock | 0 | 0 | 0 |
|
| diagnosticsVarPlots | 10.26 | 0.36 | 11.13 |
|
| geneDistributionSet-class | 0 | 0 | 0 |
|
| geneDistributionSet2-class | 0 | 0 | 0 |
|
| geneDistributionSet3-class | 0 | 0 | 0 |
|
| geneSet-class | 0 | 0 | 0 |
|
| getGenes | 3.70 | 0.02 | 4.47 |
|
| makeDBList | 0 | 0 | 0 |
|
| pathVar-package | 5.66 | 0.03 | 5.69 |
|
| pathVarOneSample | 4.22 | 0.00 | 4.22 |
|
| pathVarTwoSamplesCont | 2.86 | 0.01 | 2.87 |
|
| pathVarTwoSamplesDisc | 1.37 | 0.00 | 1.38 |
|
| plotPway | 2.83 | 0.00 | 2.83 |
|
| pways.kegg | 0 | 0 | 0 |
|
| pways.reactome | 0 | 0 | 0 |
|
| saveAsPDF | 3.46 | 0.00 | 3.47 |
|
| sigPway | 68.41 | 0.03 | 68.47 |
|
| significantPathway-class | 0 | 0 | 0 |
|
| significantPathway2-class | 0 | 0 | 0 |
|
| significantPathway3-class | 0 | 0 | 0 |
|
pathVar.Rcheck/examples_x64/pathVar-Ex.timings:
| name | user | system | elapsed
|
| bock | 0 | 0 | 0 |
|
| diagnosticsVarPlots | 51.05 | 2.37 | 53.44 |
|
| geneDistributionSet-class | 0 | 0 | 0 |
|
| geneDistributionSet2-class | 0.00 | 0.02 | 0.01 |
|
| geneDistributionSet3-class | 0 | 0 | 0 |
|
| geneSet-class | 0 | 0 | 0 |
|
| getGenes | 3.09 | 0.01 | 3.11 |
|
| makeDBList | 0 | 0 | 0 |
|
| pathVar-package | 4.56 | 0.02 | 4.59 |
|
| pathVarOneSample | 3.94 | 0.00 | 3.94 |
|
| pathVarTwoSamplesCont | 3.17 | 0.00 | 3.17 |
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| pathVarTwoSamplesDisc | 1.27 | 0.00 | 1.27 |
|
| plotPway | 3.33 | 0.00 | 3.33 |
|
| pways.kegg | 0 | 0 | 0 |
|
| pways.reactome | 0 | 0 | 0 |
|
| saveAsPDF | 3.44 | 0.00 | 3.44 |
|
| sigPway | 79.34 | 0.06 | 79.44 |
|
| significantPathway-class | 0 | 0 | 0 |
|
| significantPathway2-class | 0 | 0 | 0 |
|
| significantPathway3-class | 0 | 0 | 0 |
|