Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1517/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PCAN 1.34.0 (landing page) Matthew Page
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | 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: 1.34.0 |
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_1.34.0.tar.gz |
StartedAt: 2024-12-20 07:28:22 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 07:35:16 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 413.6 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_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PCAN.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PCAN/DESCRIPTION’ ... OK * this is package ‘PCAN’ version ‘1.34.0’ * 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 91.292 8.241 102.982 hpGeneHeatmap 89.708 7.448 98.987 compareHPSets 88.485 7.471 99.034 hpSetCompSummary 4.514 0.512 6.099 hpSetCompBestMatch 4.444 0.490 5.077 traitDef 4.324 0.508 5.130 * 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 | 3.058 | 0.508 | 3.588 | |
compareHPSets | 88.485 | 7.471 | 99.034 | |
computeHpIC | 2.962 | 0.324 | 3.369 | |
geneByHp | 3.215 | 0.357 | 4.262 | |
geneByTrait | 0.069 | 0.004 | 0.073 | |
geneDef | 4.310 | 0.515 | 4.942 | |
hpByTrait | 4.384 | 0.461 | 4.928 | |
hpDef | 3.144 | 0.346 | 3.541 | |
hpGeneHeatmap | 89.708 | 7.448 | 98.987 | |
hpGeneListComp | 91.292 | 8.241 | 102.982 | |
hpSetCompBestMatch | 4.444 | 0.490 | 5.077 | |
hpSetCompSummary | 4.514 | 0.512 | 6.099 | |
hp_ancestors | 3.176 | 0.307 | 4.109 | |
hp_class | 0.083 | 0.003 | 0.090 | |
hp_descendants | 3.005 | 0.332 | 3.483 | |
hqStrNw | 0.000 | 0.000 | 0.001 | |
hsEntrezByRPath | 0 | 0 | 0 | |
rPath | 0 | 0 | 0 | |
traitDef | 4.324 | 0.508 | 5.130 | |