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This page was generated on 2021-10-15 15:05:48 -0400 (Fri, 15 Oct 2021).

CHECK results for pathwayPCA on nebbiolo1

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.

raw results

Package 1354/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathwayPCA 1.8.0  (landing page)
Gabriel Odom
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/pathwayPCA
git_branch: RELEASE_3_13
git_last_commit: 4ab8ed1
git_last_commit_date: 2021-05-19 12:42:02 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: pathwayPCA
Version: 1.8.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings pathwayPCA_1.8.0.tar.gz
StartedAt: 2021-10-14 10:57:24 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:00:42 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 198.1 seconds
RetCode: 0
Status:   OK  
CheckDir: pathwayPCA.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings pathwayPCA_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/pathwayPCA.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.8.0’
* 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 ... 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 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        8.769  0.372   9.146
AESPCA_pVals   0.326  0.102  12.885
LoadOntoPCs    0.268  0.076   6.116
getPathpVals   0.181  0.011   8.016
getPathPCLs    0.162  0.028   7.353
SuperPCA_pVals 0.087  0.020   6.048
* 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


Installation output

pathwayPCA.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL pathwayPCA
###
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* installing to library ‘/home/biocbuild/bbs-3.13-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)

Tests output

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-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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 47 ]
> 
> proc.time()
   user  system elapsed 
 11.891   0.826  34.737 

Example timings

pathwayPCA.Rcheck/pathwayPCA-Ex.timings

nameusersystemelapsed
AESPCA_pVals 0.326 0.10212.885
CheckAssay000
CheckPwyColl0.0010.0000.000
CheckSampleIDs0.0000.0000.001
Contains0.0010.0000.001
ControlFDR0.0010.0000.001
CreateOmics0.2680.0080.276
CreateOmicsPathway0.0000.0040.004
CreatePathwayCollection0.010.000.01
ExtractAESPCs0.2310.0694.456
GumbelMixpValues0.0010.0000.001
IntersectOmicsPwyCollct0.0000.0000.001
JoinPhenoAssay0.0000.0000.001
LoadOntoPCs0.2680.0766.116
OptimGumbelMixParams0.0010.0000.001
PathwaytValues0.0000.0000.001
PermTestCateg0.0000.0000.001
PermTestReg0.0000.0010.000
PermTestSurv000
SE2Tidy8.7690.3729.146
SubsetPathwayCollection0.0000.0030.003
SubsetPathwayData0.1620.1280.291
SuperPCA_pVals0.0870.0206.048
TabulatepValues0.0000.0010.001
TransposeAssay0.0350.0510.086
WhichPathways0.0060.0000.006
aespca0.0010.0000.000
coxTrain_fun000
getPathPCLs0.1620.0287.353
getPathpVals0.1810.0118.016
get_set_OmicsPathway0.5440.7371.281
get_set_OmicsRegCateg0.1030.0100.114
get_set_OmicsSurv0.0440.0040.049
glmTrain_fun0.0000.0000.001
lars.lsa0.0000.0000.001
mysvd0.0000.0000.001
normalize0.0000.0000.001
olsTrain_fun0.0000.0000.001
pathway_tControl0.0000.0000.001
pathway_tScores0.0000.0000.001
permuteSamps0.0000.0000.001
print.pathwayCollection0.0000.0040.003
read_gmt0.1800.0040.186
show-OmicsPathway-method0.0510.0000.051
superpc.st0.0010.0000.000
superpc.train0.0000.0010.001
write_gmt0.0000.0020.002