Gabriel Odom
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/pathwayPCA |
| Branch: RELEASE_3_10 |
| Last Commit: 3ee316f |
| Last Changed Date: 2019-10-29 13:11:33 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:15:24 -0400 (Wed, 15 Apr 2020).
| Package 1230/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pathwayPCA 1.2.0 Gabriel Odom
| 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: pathwayPCA |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings pathwayPCA_1.2.0.tar.gz |
| StartedAt: 2020-04-15 06:22:50 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 06:25:46 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 176.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pathwayPCA.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings pathwayPCA_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/pathwayPCA.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.2.0’
* 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 11.636 0.348 12.083
LoadOntoPCs 0.200 0.136 8.255
getPathPCLs 0.212 0.116 10.837
AESPCA_pVals 0.224 0.080 8.236
ExtractAESPCs 0.184 0.068 5.402
getPathpVals 0.152 0.100 10.845
SuperPCA_pVals 0.124 0.108 8.469
* 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-3.10-bioc/R/bin/R CMD INSTALL pathwayPCA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 47 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
16.444 0.992 49.170
pathwayPCA.Rcheck/pathwayPCA-Ex.timings
| name | user | system | elapsed | |
| AESPCA_pVals | 0.224 | 0.080 | 8.236 | |
| CheckAssay | 0 | 0 | 0 | |
| CheckPwyColl | 0.000 | 0.000 | 0.001 | |
| CheckSampleIDs | 0.000 | 0.000 | 0.001 | |
| Contains | 0.000 | 0.000 | 0.003 | |
| ControlFDR | 0.000 | 0.000 | 0.001 | |
| CreateOmics | 0.232 | 0.036 | 0.288 | |
| CreateOmicsPathway | 0.004 | 0.000 | 0.002 | |
| CreatePathwayCollection | 0.008 | 0.000 | 0.008 | |
| ExtractAESPCs | 0.184 | 0.068 | 5.402 | |
| GumbelMixpValues | 0.000 | 0.000 | 0.001 | |
| IntersectOmicsPwyCollct | 0 | 0 | 0 | |
| JoinPhenoAssay | 0 | 0 | 0 | |
| LoadOntoPCs | 0.200 | 0.136 | 8.255 | |
| OptimGumbelMixParams | 0.000 | 0.000 | 0.001 | |
| PathwaytValues | 0 | 0 | 0 | |
| PermTestCateg | 0 | 0 | 0 | |
| PermTestReg | 0.000 | 0.000 | 0.001 | |
| PermTestSurv | 0.000 | 0.000 | 0.001 | |
| SE2Tidy | 11.636 | 0.348 | 12.083 | |
| SubsetPathwayCollection | 0.000 | 0.004 | 0.003 | |
| SubsetPathwayData | 0.344 | 0.036 | 0.382 | |
| SuperPCA_pVals | 0.124 | 0.108 | 8.469 | |
| TabulatepValues | 0.000 | 0.000 | 0.001 | |
| TransposeAssay | 0.092 | 0.024 | 0.115 | |
| WhichPathways | 0.012 | 0.000 | 0.009 | |
| aespca | 0 | 0 | 0 | |
| coxTrain_fun | 0 | 0 | 0 | |
| getPathPCLs | 0.212 | 0.116 | 10.837 | |
| getPathpVals | 0.152 | 0.100 | 10.845 | |
| get_set_OmicsPathway | 1.060 | 0.256 | 1.324 | |
| get_set_OmicsRegCateg | 0.172 | 0.000 | 0.175 | |
| get_set_OmicsSurv | 0.144 | 0.008 | 0.152 | |
| glmTrain_fun | 0 | 0 | 0 | |
| lars.lsa | 0 | 0 | 0 | |
| mysvd | 0 | 0 | 0 | |
| normalize | 0.004 | 0.000 | 0.000 | |
| olsTrain_fun | 0.000 | 0.000 | 0.001 | |
| pathway_tControl | 0.000 | 0.000 | 0.001 | |
| pathway_tScores | 0 | 0 | 0 | |
| permuteSamps | 0 | 0 | 0 | |
| print.pathwayCollection | 0.000 | 0.004 | 0.004 | |
| read_gmt | 0.188 | 0.004 | 0.206 | |
| show-OmicsPathway-method | 0.196 | 0.000 | 0.196 | |
| superpc.st | 0.000 | 0.000 | 0.001 | |
| superpc.train | 0.000 | 0.000 | 0.001 | |
| write_gmt | 0.004 | 0.000 | 0.003 | |