Gabriel Odom
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/pathwayPCA |
| Branch: master |
| Last Commit: c9a2e46 |
| Last Changed Date: 2019-03-29 14:11:31 -0400 (Fri, 29 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:39:32 -0400 (Tue, 09 Apr 2019).
| Package 1156/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pathwayPCA 0.99.5 Gabriel Odom
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: pathwayPCA |
| Version: 0.99.5 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathwayPCA_0.99.5.tar.gz |
| StartedAt: 2019-04-09 02:45:20 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:48:57 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 216.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pathwayPCA.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:pathwayPCA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pathwayPCA_0.99.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/pathwayPCA.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pathwayPCA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathwayPCA’ version ‘0.99.5’
* package encoding: UTF-8
* 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 ‘pathwayPCA’ 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 ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SE2Tidy 12.147 0.494 12.781
LoadOntoPCs 0.348 0.174 9.007
ExtractAESPCs 0.315 0.133 6.725
AESPCA_pVals 0.273 0.147 8.718
getPathpVals 0.255 0.018 11.652
getPathPCLs 0.238 0.025 11.782
SuperPCA_pVals 0.164 0.021 9.406
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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: OK
pathwayPCA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pathwayPCA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘pathwayPCA’ ... ** 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 (pathwayPCA)
pathwayPCA.Rcheck/tests/testthat.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(pathwayPCA)
>
> test_check("pathwayPCA")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 28 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
4.325 0.748 76.901
pathwayPCA.Rcheck/pathwayPCA-Ex.timings
| name | user | system | elapsed | |
| AESPCA_pVals | 0.273 | 0.147 | 8.718 | |
| CheckAssay | 0.000 | 0.001 | 0.001 | |
| CheckPwyColl | 0.000 | 0.000 | 0.001 | |
| CheckSampleIDs | 0 | 0 | 0 | |
| ControlFDR | 0.001 | 0.000 | 0.000 | |
| CreateOmics | 0.433 | 0.035 | 0.474 | |
| CreateOmicsPathway | 0.002 | 0.001 | 0.004 | |
| CreatePathwayCollection | 0.006 | 0.001 | 0.008 | |
| ExtractAESPCs | 0.315 | 0.133 | 6.725 | |
| GumbelMixpValues | 0.001 | 0.000 | 0.001 | |
| IntersectOmicsPwyCollct | 0 | 0 | 0 | |
| JoinPhenoAssay | 0.000 | 0.000 | 0.001 | |
| LoadOntoPCs | 0.348 | 0.174 | 9.007 | |
| OptimGumbelMixParams | 0.000 | 0.001 | 0.001 | |
| PathwaytValues | 0.001 | 0.000 | 0.001 | |
| PermTestCateg | 0.001 | 0.000 | 0.001 | |
| PermTestReg | 0.000 | 0.001 | 0.001 | |
| PermTestSurv | 0.001 | 0.000 | 0.001 | |
| SE2Tidy | 12.147 | 0.494 | 12.781 | |
| SubsetPathwayCollection | 0.003 | 0.002 | 0.004 | |
| SubsetPathwayData | 0.450 | 0.099 | 0.559 | |
| SuperPCA_pVals | 0.164 | 0.021 | 9.406 | |
| TabulatepValues | 0.000 | 0.000 | 0.001 | |
| TransposeAssay | 0.132 | 0.024 | 0.159 | |
| aespca | 0.001 | 0.000 | 0.000 | |
| coxTrain_fun | 0.000 | 0.000 | 0.001 | |
| getPathPCLs | 0.238 | 0.025 | 11.782 | |
| getPathpVals | 0.255 | 0.018 | 11.652 | |
| get_set_OmicsPathway | 2.003 | 0.495 | 2.510 | |
| get_set_OmicsRegCateg | 0.230 | 0.011 | 0.241 | |
| get_set_OmicsSurv | 0.238 | 0.009 | 0.247 | |
| glmTrain_fun | 0.001 | 0.000 | 0.001 | |
| lars.lsa | 0.000 | 0.000 | 0.001 | |
| mysvd | 0.000 | 0.000 | 0.001 | |
| normalize | 0.000 | 0.001 | 0.000 | |
| olsTrain_fun | 0.001 | 0.000 | 0.001 | |
| pathway_tControl | 0.000 | 0.001 | 0.001 | |
| pathway_tScores | 0 | 0 | 0 | |
| permuteSamps | 0.000 | 0.001 | 0.001 | |
| print.pathwayCollection | 0.005 | 0.001 | 0.006 | |
| read_gmt | 0.212 | 0.003 | 0.216 | |
| show-OmicsPathway-method | 0.197 | 0.002 | 0.206 | |
| superpc.st | 0.000 | 0.000 | 0.001 | |
| superpc.train | 0.001 | 0.000 | 0.001 | |
| write_gmt | 0.003 | 0.000 | 0.003 | |