Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:46 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the pathwayPCA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pathwayPCA.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 1354/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
pathwayPCA 1.8.0 (landing page) Gabriel Odom
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: pathwayPCA |
Version: 1.8.0 |
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_1.8.0.tar.gz |
StartedAt: 2021-10-14 22:09:17 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:12:26 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 189.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pathwayPCA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running 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_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/pathwayPCA.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (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 ‘1.8.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 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 SE2Tidy 12.527 0.354 12.889 AESPCA_pVals 0.532 0.262 8.480 LoadOntoPCs 0.516 0.261 8.672 ExtractAESPCs 0.359 0.188 5.572 getPathpVals 0.251 0.022 11.189 getPathPCLs 0.206 0.027 10.468 SuperPCA_pVals 0.199 0.019 8.633 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.13-bioc/meat/pathwayPCA.Rcheck/00check.log’ for details.
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/4.1/Resources/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 47 ] > > proc.time() user system elapsed 16.921 0.984 51.158
pathwayPCA.Rcheck/pathwayPCA-Ex.timings
name | user | system | elapsed | |
AESPCA_pVals | 0.532 | 0.262 | 8.480 | |
CheckAssay | 0.000 | 0.001 | 0.001 | |
CheckPwyColl | 0 | 0 | 0 | |
CheckSampleIDs | 0 | 0 | 0 | |
Contains | 0.001 | 0.000 | 0.001 | |
ControlFDR | 0.000 | 0.001 | 0.001 | |
CreateOmics | 0.353 | 0.045 | 0.399 | |
CreateOmicsPathway | 0.002 | 0.002 | 0.005 | |
CreatePathwayCollection | 0.010 | 0.002 | 0.012 | |
ExtractAESPCs | 0.359 | 0.188 | 5.572 | |
GumbelMixpValues | 0.000 | 0.000 | 0.001 | |
IntersectOmicsPwyCollct | 0.000 | 0.001 | 0.000 | |
JoinPhenoAssay | 0.001 | 0.000 | 0.000 | |
LoadOntoPCs | 0.516 | 0.261 | 8.672 | |
OptimGumbelMixParams | 0.001 | 0.001 | 0.001 | |
PathwaytValues | 0.000 | 0.001 | 0.001 | |
PermTestCateg | 0.000 | 0.001 | 0.001 | |
PermTestReg | 0.000 | 0.001 | 0.001 | |
PermTestSurv | 0.001 | 0.000 | 0.000 | |
SE2Tidy | 12.527 | 0.354 | 12.889 | |
SubsetPathwayCollection | 0.002 | 0.001 | 0.003 | |
SubsetPathwayData | 0.206 | 0.098 | 0.305 | |
SuperPCA_pVals | 0.199 | 0.019 | 8.633 | |
TabulatepValues | 0.000 | 0.001 | 0.001 | |
TransposeAssay | 0.092 | 0.065 | 0.182 | |
WhichPathways | 0.008 | 0.002 | 0.010 | |
aespca | 0 | 0 | 0 | |
coxTrain_fun | 0.000 | 0.001 | 0.000 | |
getPathPCLs | 0.206 | 0.027 | 10.468 | |
getPathpVals | 0.251 | 0.022 | 11.189 | |
get_set_OmicsPathway | 0.978 | 0.860 | 1.879 | |
get_set_OmicsRegCateg | 0.083 | 0.006 | 0.090 | |
get_set_OmicsSurv | 0.190 | 0.014 | 0.203 | |
glmTrain_fun | 0.001 | 0.001 | 0.000 | |
lars.lsa | 0 | 0 | 0 | |
mysvd | 0.000 | 0.000 | 0.001 | |
normalize | 0.000 | 0.000 | 0.001 | |
olsTrain_fun | 0.000 | 0.000 | 0.001 | |
pathway_tControl | 0.000 | 0.001 | 0.001 | |
pathway_tScores | 0.000 | 0.000 | 0.001 | |
permuteSamps | 0.000 | 0.001 | 0.000 | |
print.pathwayCollection | 0.004 | 0.002 | 0.006 | |
read_gmt | 0.182 | 0.002 | 0.186 | |
show-OmicsPathway-method | 0.189 | 0.015 | 0.205 | |
superpc.st | 0.001 | 0.001 | 0.001 | |
superpc.train | 0.000 | 0.000 | 0.002 | |
write_gmt | 0.002 | 0.000 | 0.003 | |