Samuel Zimmerman
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/pathVar |
| Branch: RELEASE_3_10 |
| Last Commit: f3a638c |
| Last Changed Date: 2019-10-29 13:09:28 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:25:35 -0400 (Wed, 15 Apr 2020).
| Package 1228/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pathVar 1.16.0 Samuel Zimmerman
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: pathVar |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathVar.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings pathVar_1.16.0.tar.gz |
| StartedAt: 2020-04-15 05:21:43 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:27:29 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 346.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pathVar.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pathVar.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings pathVar_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/pathVar.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.16.0'
* 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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sigPway 75.46 0.00 76.48
diagnosticsVarPlotsTwoSample 19.57 2.84 22.50
diagnosticsVarPlots 9.82 0.49 10.31
pathVarTwoSamplesCont 3.61 0.02 5.57
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sigPway 61.62 0.06 61.67
diagnosticsVarPlots 33.20 3.58 36.80
diagnosticsVarPlotsTwoSample 18.76 2.52 21.32
* 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:/Users/biocbuild/bbs-3.10-bioc/meat/pathVar.Rcheck/00check.log'
for details.
pathVar.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/pathVar_1.16.0.tar.gz && rm -rf pathVar.buildbin-libdir && mkdir pathVar.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pathVar.buildbin-libdir pathVar_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL pathVar_1.16.0.zip && rm pathVar_1.16.0.tar.gz pathVar_1.16.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 902k 100 902k 0 0 19.2M 0 --:--:-- --:--:-- --:--:-- 20.9M
install for i386
* installing *source* package 'pathVar' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'pathVar'
finding HTML links ... done
bock html
diagnosticsVarPlots html
diagnosticsVarPlotsTwoSample html
geneDistributionSet-class html
geneDistributionSet2-class html
geneDistributionSet3-class html
geneSet-class html
getGenes html
makeDBList html
pathVar-package html
pathVarOneSample html
pathVarTwoSamplesCont html
pathVarTwoSamplesDisc html
plotAllTwoSampleDistributionCounts html
plotPway html
pways.kegg html
pways.reactome html
saveAsPDF html
sigPway html
significantPathway-class html
significantPathway2-class html
significantPathway3-class html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'pathVar' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pathVar' as pathVar_1.16.0.zip
* DONE (pathVar)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'pathVar' successfully unpacked and MD5 sums checked
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pathVar.Rcheck/examples_i386/pathVar-Ex.timings
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pathVar.Rcheck/examples_x64/pathVar-Ex.timings
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