Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-24 11:38 -0400 (Mon, 24 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4690 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4404 |
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 1488/2242 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PCAN 1.33.0 (landing page) Matthew Page
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the PCAN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PCAN.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: PCAN |
Version: 1.33.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PCAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PCAN_1.33.0.tar.gz |
StartedAt: 2024-06-23 22:05:40 -0400 (Sun, 23 Jun 2024) |
EndedAt: 2024-06-23 22:09:57 -0400 (Sun, 23 Jun 2024) |
EllapsedTime: 257.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PCAN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PCAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PCAN_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PCAN.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * 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 ‘PCAN/DESCRIPTION’ ... OK * this is package ‘PCAN’ version ‘1.33.0’ * 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 ‘PCAN’ 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 code 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 ... NOTE checkRd: (-1) hpGeneHeatmap.Rd:33: Lost braces 33 | \item{...}{parameters for the code{\link{heatmap}} function} | ^ * 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 hpGeneListComp 55.612 6.469 62.606 hpGeneHeatmap 55.300 6.582 62.784 compareHPSets 53.398 6.197 60.213 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/PCAN.Rcheck/00check.log’ for details.
PCAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PCAN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘PCAN’ ... ** 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 (PCAN)
PCAN.Rcheck/PCAN-Ex.timings
name | user | system | elapsed | |
calcHpSim | 1.937 | 0.299 | 2.248 | |
compareHPSets | 53.398 | 6.197 | 60.213 | |
computeHpIC | 1.748 | 0.248 | 2.008 | |
geneByHp | 1.724 | 0.290 | 2.029 | |
geneByTrait | 0.042 | 0.003 | 0.045 | |
geneDef | 2.483 | 0.388 | 2.891 | |
hpByTrait | 2.545 | 0.372 | 2.935 | |
hpDef | 1.925 | 0.268 | 2.211 | |
hpGeneHeatmap | 55.300 | 6.582 | 62.784 | |
hpGeneListComp | 55.612 | 6.469 | 62.606 | |
hpSetCompBestMatch | 2.453 | 0.417 | 2.893 | |
hpSetCompSummary | 2.510 | 0.382 | 2.915 | |
hp_ancestors | 1.839 | 0.311 | 2.165 | |
hp_class | 0.051 | 0.002 | 0.053 | |
hp_descendants | 1.723 | 0.332 | 2.074 | |
hqStrNw | 0 | 0 | 0 | |
hsEntrezByRPath | 0 | 0 | 0 | |
rPath | 0 | 0 | 0 | |
traitDef | 2.643 | 0.388 | 3.069 | |