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This page was generated on 2023-10-16 11:37:21 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1481/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pathwayPCA 1.16.1  (landing page)
Gabriel Odom
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/pathwayPCA
git_branch: RELEASE_3_17
git_last_commit: 68921ca
git_last_commit_date: 2023-06-29 10:15:15 -0400 (Thu, 29 Jun 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for pathwayPCA on merida1


To the developers/maintainers of the pathwayPCA package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: pathwayPCA
Version: 1.16.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pathwayPCA_1.16.1.tar.gz
StartedAt: 2023-10-16 05:07:56 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 05:13:45 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 349.3 seconds
RetCode: 0
Status:   OK  
CheckDir: pathwayPCA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pathwayPCA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pathwayPCA_1.16.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/pathwayPCA.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pathwayPCA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathwayPCA’ version ‘1.16.1’
* 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 (user + system) or elapsed time > 5s
                 user system elapsed
SE2Tidy        18.216  0.676  23.391
LoadOntoPCs     0.669  0.284  14.927
AESPCA_pVals    0.682  0.226  14.845
ExtractAESPCs   0.597  0.254  10.021
getPathPCLs     0.583  0.068  16.886
SuperPCA_pVals  0.544  0.043  13.677
getPathpVals    0.475  0.040  16.880
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pathwayPCA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘pathwayPCA’ ...
** using staged installation
** R
** data
** 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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 
 26.276   1.567  89.386 

Example timings

pathwayPCA.Rcheck/pathwayPCA-Ex.timings

nameusersystemelapsed
AESPCA_pVals 0.682 0.22614.845
CheckAssay0.0000.0000.001
CheckPwyColl0.0000.0010.001
CheckSampleIDs0.0000.0010.001
Contains0.0010.0000.001
ControlFDR0.0000.0010.001
CreateOmics0.6250.0550.860
CreateOmicsPathway0.3030.0170.411
CreatePathwayCollection0.0120.0030.019
ExtractAESPCs 0.597 0.25410.021
GumbelMixpValues0.0010.0010.004
IntersectOmicsPwyCollct0.0010.0010.001
JoinPhenoAssay0.0000.0000.001
LoadOntoPCs 0.669 0.28414.927
OptimGumbelMixParams0.0000.0010.004
PathwaytValues0.0010.0020.002
PermTestCateg0.0000.0000.001
PermTestReg0.0000.0010.002
PermTestSurv0.0010.0010.001
SE2Tidy18.216 0.67623.391
SubsetPathwayCollection0.0040.0050.014
SubsetPathwayData0.5250.2210.902
SuperPCA_pVals 0.544 0.04313.677
TabulatepValues0.0000.0010.001
TransposeAssay0.1190.0760.225
WhichPathways0.0110.0040.017
aespca0.0010.0010.001
coxTrain_fun0.0000.0000.001
getPathPCLs 0.583 0.06816.886
getPathpVals 0.475 0.04016.880
get_set_OmicsPathway1.6371.5283.984
get_set_OmicsRegCateg0.3940.0220.527
get_set_OmicsSurv0.5050.0350.682
glmTrain_fun0.0000.0010.001
lars.lsa0.0010.0010.002
mysvd0.0000.0010.001
normalize0.0000.0000.001
olsTrain_fun0.0000.0010.001
pathway_tControl0.0000.0010.001
pathway_tScores0.0010.0010.001
permuteSamps0.0000.0000.001
print.pathwayCollection0.0060.0030.012
read_gmt0.2060.0050.273
show-OmicsPathway-method0.4900.0220.657
superpc.st0.0000.0020.003
superpc.train0.0000.0020.002
write_gmt0.0050.0020.011