Samuel Zimmerman
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/pathVar |
| git_branch: master |
| git_last_commit: 983473c |
| git_last_commit_date: 2021-10-26 12:23:07 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:15 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the pathVar package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pathVar.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1387/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pathVar 1.25.0 (landing page) Samuel Zimmerman
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: pathVar |
| Version: 1.25.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:pathVar.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings pathVar_1.25.0.tar.gz |
| StartedAt: 2022-03-17 19:49:21 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:52:33 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 192.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pathVar.Rcheck |
| Warnings: 0 |
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### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:pathVar.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings pathVar_1.25.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/pathVar.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.25.0'
* 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
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
sigPway 40.97 0.05 41.98
diagnosticsVarPlots 22.59 1.47 24.94
diagnosticsVarPlotsTwoSample 13.90 0.37 14.35
plotAllTwoSampleDistributionCounts 3.57 1.80 5.55
plotPway 3.61 0.05 12.08
pathVarTwoSamplesCont 2.81 0.06 8.30
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/pathVar.Rcheck/00check.log'
for details.
pathVar.Rcheck/00install.out
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL pathVar
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (pathVar)
Making 'packages.html' ... done
pathVar.Rcheck/pathVar-Ex.timings
| name | user | system | elapsed | |
| bock | 0.00 | 0.02 | 0.01 | |
| diagnosticsVarPlots | 22.59 | 1.47 | 24.94 | |
| diagnosticsVarPlotsTwoSample | 13.90 | 0.37 | 14.35 | |
| geneDistributionSet-class | 0 | 0 | 0 | |
| geneDistributionSet2-class | 0.02 | 0.00 | 0.01 | |
| geneDistributionSet3-class | 0 | 0 | 0 | |
| geneSet-class | 0 | 0 | 0 | |
| getGenes | 1.80 | 0.02 | 1.82 | |
| makeDBList | 0 | 0 | 0 | |
| pathVar-package | 3.81 | 0.39 | 4.65 | |
| pathVarOneSample | 3.36 | 0.09 | 3.55 | |
| pathVarTwoSamplesCont | 2.81 | 0.06 | 8.30 | |
| pathVarTwoSamplesDisc | 0.98 | 0.00 | 0.98 | |
| plotAllTwoSampleDistributionCounts | 3.57 | 1.80 | 5.55 | |
| plotPway | 3.61 | 0.05 | 12.08 | |
| pways.kegg | 0.00 | 0.01 | 0.01 | |
| pways.reactome | 0 | 0 | 0 | |
| saveAsPDF | 2.50 | 0.00 | 2.52 | |
| sigPway | 40.97 | 0.05 | 41.98 | |
| significantPathway-class | 0 | 0 | 0 | |
| significantPathway2-class | 0 | 0 | 0 | |
| significantPathway3-class | 0.00 | 0.00 | 0.07 | |