Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:40 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 1496/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
pathwayPCA 1.19.0 (landing page) Gabriel Odom
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: pathwayPCA |
Version: 1.19.0 |
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_1.19.0.tar.gz |
StartedAt: 2024-03-02 08:16:26 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 08:21:52 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 325.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pathwayPCA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/pathwayPCA.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pathwayPCA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pathwayPCA’ version ‘1.19.0’ * 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 (user + system) or elapsed time > 5s user system elapsed SE2Tidy 18.852 0.694 21.896 SuperPCA_pVals 1.078 0.047 12.214 LoadOntoPCs 0.687 0.287 12.684 AESPCA_pVals 0.675 0.247 12.983 ExtractAESPCs 0.570 0.252 9.282 getPathPCLs 0.440 0.049 14.864 getPathpVals 0.432 0.041 15.007 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pathwayPCA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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)
pathwayPCA.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 27.253 1.883 91.661
pathwayPCA.Rcheck/pathwayPCA-Ex.timings
name | user | system | elapsed | |
AESPCA_pVals | 0.675 | 0.247 | 12.983 | |
CheckAssay | 0.000 | 0.001 | 0.001 | |
CheckPwyColl | 0.000 | 0.001 | 0.000 | |
CheckSampleIDs | 0.000 | 0.001 | 0.001 | |
Contains | 0.001 | 0.001 | 0.002 | |
ControlFDR | 0.000 | 0.001 | 0.001 | |
CreateOmics | 0.613 | 0.059 | 0.757 | |
CreateOmicsPathway | 0.280 | 0.019 | 0.350 | |
CreatePathwayCollection | 0.011 | 0.004 | 0.018 | |
ExtractAESPCs | 0.570 | 0.252 | 9.282 | |
GumbelMixpValues | 0.000 | 0.001 | 0.002 | |
IntersectOmicsPwyCollct | 0.000 | 0.001 | 0.001 | |
JoinPhenoAssay | 0.000 | 0.001 | 0.001 | |
LoadOntoPCs | 0.687 | 0.287 | 12.684 | |
OptimGumbelMixParams | 0.000 | 0.001 | 0.001 | |
PathwaytValues | 0.000 | 0.001 | 0.002 | |
PermTestCateg | 0.001 | 0.001 | 0.002 | |
PermTestReg | 0.001 | 0.001 | 0.002 | |
PermTestSurv | 0.000 | 0.001 | 0.001 | |
SE2Tidy | 18.852 | 0.694 | 21.896 | |
SubsetPathwayCollection | 0.004 | 0.005 | 0.011 | |
SubsetPathwayData | 0.505 | 0.213 | 0.805 | |
SuperPCA_pVals | 1.078 | 0.047 | 12.214 | |
TabulatepValues | 0.000 | 0.002 | 0.002 | |
TransposeAssay | 0.119 | 0.117 | 0.244 | |
WhichPathways | 0.011 | 0.005 | 0.016 | |
aespca | 0 | 0 | 0 | |
coxTrain_fun | 0.001 | 0.001 | 0.002 | |
getPathPCLs | 0.440 | 0.049 | 14.864 | |
getPathpVals | 0.432 | 0.041 | 15.007 | |
get_set_OmicsPathway | 1.521 | 1.588 | 3.795 | |
get_set_OmicsRegCateg | 0.366 | 0.026 | 0.450 | |
get_set_OmicsSurv | 0.380 | 0.024 | 0.472 | |
glmTrain_fun | 0.000 | 0.001 | 0.001 | |
lars.lsa | 0.000 | 0.001 | 0.001 | |
mysvd | 0.000 | 0.001 | 0.001 | |
normalize | 0.001 | 0.001 | 0.002 | |
olsTrain_fun | 0.000 | 0.001 | 0.001 | |
pathway_tControl | 0.000 | 0.001 | 0.001 | |
pathway_tScores | 0.001 | 0.001 | 0.001 | |
permuteSamps | 0.000 | 0.001 | 0.001 | |
print.pathwayCollection | 0.007 | 0.004 | 0.015 | |
read_gmt | 0.193 | 0.006 | 0.224 | |
show-OmicsPathway-method | 0.441 | 0.021 | 0.497 | |
superpc.st | 0.000 | 0.001 | 0.002 | |
superpc.train | 0.000 | 0.001 | 0.002 | |
write_gmt | 0.005 | 0.001 | 0.005 | |