Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-02-06 11:06:40 -0500 (Mon, 06 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4483 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" | 4249 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4272 |
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 |
To the developers/maintainers of the graphite package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graphite.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 846/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
graphite 1.45.0 (landing page) Gabriele Sales
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
Package: graphite |
Version: 1.45.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graphite.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graphite_1.45.0.tar.gz |
StartedAt: 2023-02-06 02:03:34 -0500 (Mon, 06 Feb 2023) |
EndedAt: 2023-02-06 02:14:08 -0500 (Mon, 06 Feb 2023) |
EllapsedTime: 634.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: graphite.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:graphite.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings graphite_1.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/graphite.Rcheck’ * using R Under development (unstable) (2023-01-10 r83596) * using platform: x86_64-apple-darwin17.0 (64-bit) * R was compiled by Apple clang version 12.0.0 (clang-1200.0.32.29) GNU Fortran (GCC) 8.2.0 * running under: macOS Mojave 10.14.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘graphite/DESCRIPTION’ ... OK * this is package ‘graphite’ version ‘1.45.0’ * 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 ‘graphite’ 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 ... WARNING checkRd: (5) PathwayList-class.Rd:24-27: \item in \describe must have non-empty label checkRd: (5) PathwayList-class.Rd:28-31: \item in \describe must have non-empty label checkRd: (5) PathwayList-class.Rd:32-35: \item in \describe must have non-empty label checkRd: (5) PathwayList-class.Rd:36-40: \item in \describe must have non-empty label checkRd: (5) PathwayList-class.Rd:41-44: \item in \describe must have non-empty label checkRd: (5) PathwayList-class.Rd:45-48: \item in \describe must have non-empty label checkRd: (5) PathwayList-class.Rd:49-52: \item in \describe must have non-empty label checkRd: (5) PathwayList-class.Rd:53-56: \item in \describe must have non-empty label checkRd: (5) PathwayList-class.Rd:57-60: \item in \describe must have non-empty label * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed runClipper 21.592 0.662 29.771 convertIdentifiers 9.423 0.102 12.581 runSPIA 7.967 0.744 11.703 Pathway-class 7.475 0.097 13.602 pathwayGraph 6.644 0.040 8.664 pathways 6.249 0.028 8.216 runTopologyGSA 4.714 0.112 6.126 * 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 WARNING See ‘/Users/biocbuild/bbs-3.17-bioc/meat/graphite.Rcheck/00check.log’ for details.
graphite.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL graphite ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’ * installing *source* package ‘graphite’ ... ** using staged installation ** R ** 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 (graphite)
graphite.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" Copyright (C) 2023 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(graphite) > > test_check("graphite") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 95 ] > > proc.time() user system elapsed 88.378 3.126 271.449
graphite.Rcheck/graphite-Ex.timings
name | user | system | elapsed | |
Pathway-class | 7.475 | 0.097 | 13.602 | |
as.list.PathwayList | 1.504 | 0.116 | 2.224 | |
buildPathway | 0.012 | 0.001 | 0.023 | |
convertIdentifiers | 9.423 | 0.102 | 12.581 | |
cytoscapePlot | 0.000 | 0.000 | 0.001 | |
pathwayDatabases | 0.012 | 0.000 | 0.015 | |
pathwayGraph | 6.644 | 0.040 | 8.664 | |
pathways | 6.249 | 0.028 | 8.216 | |
runClipper | 21.592 | 0.662 | 29.771 | |
runSPIA | 7.967 | 0.744 | 11.703 | |
runTopologyGSA | 4.714 | 0.112 | 6.126 | |