Gabriel Odom
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/pathwayPCA |
| Branch: RELEASE_3_9 |
| Last Commit: a6715d9 |
| Last Changed Date: 2019-06-10 10:50:59 -0400 (Mon, 10 Jun 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:17:44 -0400 (Wed, 16 Oct 2019).
| Package 1180/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pathwayPCA 1.0.0 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 | |
| Package: pathwayPCA |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings pathwayPCA_1.0.0.tar.gz |
| StartedAt: 2019-10-16 03:48:11 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:50:58 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 166.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pathwayPCA.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings pathwayPCA_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/pathwayPCA.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.0.0’
* 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 9.074 0.329 9.403
LoadOntoPCs 0.186 0.148 6.080
getPathPCLs 0.191 0.130 9.994
getPathpVals 0.169 0.106 9.132
AESPCA_pVals 0.172 0.101 6.396
SuperPCA_pVals 0.130 0.106 8.087
* 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: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL pathwayPCA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘pathwayPCA’ ... ** using staged installation ** 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 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 (pathwayPCA)
pathwayPCA.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: 29 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
15.760 1.135 47.500
pathwayPCA.Rcheck/pathwayPCA-Ex.timings
| name | user | system | elapsed | |
| AESPCA_pVals | 0.172 | 0.101 | 6.396 | |
| CheckAssay | 0.000 | 0.000 | 0.001 | |
| CheckPwyColl | 0 | 0 | 0 | |
| CheckSampleIDs | 0 | 0 | 0 | |
| ControlFDR | 0 | 0 | 0 | |
| CreateOmics | 0.253 | 0.020 | 0.273 | |
| CreateOmicsPathway | 0.002 | 0.000 | 0.002 | |
| CreatePathwayCollection | 0.004 | 0.004 | 0.008 | |
| ExtractAESPCs | 0.185 | 0.062 | 4.073 | |
| GumbelMixpValues | 0.000 | 0.001 | 0.000 | |
| IntersectOmicsPwyCollct | 0.001 | 0.000 | 0.000 | |
| JoinPhenoAssay | 0 | 0 | 0 | |
| LoadOntoPCs | 0.186 | 0.148 | 6.080 | |
| OptimGumbelMixParams | 0 | 0 | 0 | |
| PathwaytValues | 0 | 0 | 0 | |
| PermTestCateg | 0.000 | 0.000 | 0.001 | |
| PermTestReg | 0.000 | 0.001 | 0.001 | |
| PermTestSurv | 0.000 | 0.001 | 0.000 | |
| SE2Tidy | 9.074 | 0.329 | 9.403 | |
| SubsetPathwayCollection | 0.002 | 0.000 | 0.002 | |
| SubsetPathwayData | 0.332 | 0.019 | 0.352 | |
| SuperPCA_pVals | 0.130 | 0.106 | 8.087 | |
| TabulatepValues | 0 | 0 | 0 | |
| TransposeAssay | 0.076 | 0.040 | 0.117 | |
| aespca | 0 | 0 | 0 | |
| coxTrain_fun | 0 | 0 | 0 | |
| getPathPCLs | 0.191 | 0.130 | 9.994 | |
| getPathpVals | 0.169 | 0.106 | 9.132 | |
| get_set_OmicsPathway | 1.124 | 0.240 | 1.364 | |
| get_set_OmicsRegCateg | 0.158 | 0.016 | 0.175 | |
| get_set_OmicsSurv | 0.173 | 0.000 | 0.172 | |
| glmTrain_fun | 0.000 | 0.000 | 0.001 | |
| lars.lsa | 0.000 | 0.000 | 0.001 | |
| mysvd | 0 | 0 | 0 | |
| normalize | 0 | 0 | 0 | |
| olsTrain_fun | 0 | 0 | 0 | |
| pathway_tControl | 0.001 | 0.000 | 0.000 | |
| pathway_tScores | 0.001 | 0.000 | 0.000 | |
| permuteSamps | 0.001 | 0.000 | 0.000 | |
| print.pathwayCollection | 0.005 | 0.000 | 0.004 | |
| read_gmt | 0.193 | 0.008 | 0.214 | |
| show-OmicsPathway-method | 0.167 | 0.000 | 0.167 | |
| superpc.st | 0.000 | 0.000 | 0.001 | |
| superpc.train | 0.000 | 0.000 | 0.001 | |
| write_gmt | 0.003 | 0.000 | 0.004 | |