Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-08-13 17:41 -0400 (Tue, 13 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
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 105/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ATACCoGAPS 1.6.0 (landing page) Rossin Erbe
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | 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 ATACCoGAPS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ATACCoGAPS.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: ATACCoGAPS |
Version: 1.6.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ATACCoGAPS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ATACCoGAPS_1.6.0.tar.gz |
StartedAt: 2024-08-12 00:26:46 -0400 (Mon, 12 Aug 2024) |
EndedAt: 2024-08-12 00:48:54 -0400 (Mon, 12 Aug 2024) |
EllapsedTime: 1328.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ATACCoGAPS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ATACCoGAPS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ATACCoGAPS_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ATACCoGAPS.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ATACCoGAPS/DESCRIPTION’ ... OK * this is package ‘ATACCoGAPS’ version ‘1.6.0’ * 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 ‘ATACCoGAPS’ 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 ... NOTE Package in Depends field not imported from: ‘CoGAPS’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE cgapsPlot: no visible global function definition for ‘rainbow’ cgapsPlot: no visible global function definition for ‘par’ cgapsPlot: no visible global function definition for ‘legend’ findOverlap: no visible global function definition for ‘queryHits’ geneAccessibility: no visible global function definition for ‘subjectHits’ heatmapGeneAccessibility: no visible global function definition for ‘rainbow’ heatmapPatternMarkers: no visible global function definition for ‘rainbow’ heatmapPatternMatrix: no visible global function definition for ‘rainbow’ paths: no visible global function definition for ‘p.adjust’ Undefined global functions or variables: legend p.adjust par queryHits rainbow subjectHits Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "legend", "par") importFrom("stats", "p.adjust") to your NAMESPACE file. * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed applyGREAT 148.925 29.733 269.613 simpleMotifTFMatch 114.084 10.381 151.070 pathwayMatch 58.119 1.410 71.521 genePatternMatch 53.321 1.219 63.633 motifPatternMatch 38.298 2.360 47.763 foldAccessibility 8.739 0.287 10.468 heatmapGeneAccessibility 8.470 0.225 10.245 geneAccessibility 6.961 0.225 8.434 heatmapPatternMarkers 6.634 0.193 7.883 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/ATACCoGAPS.Rcheck/00check.log’ for details.
ATACCoGAPS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ATACCoGAPS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘ATACCoGAPS’ ... ** using staged installation ** R ** data ** 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 (ATACCoGAPS)
ATACCoGAPS.Rcheck/ATACCoGAPS-Ex.timings
name | user | system | elapsed | |
RNAseqTFValidation | 0 | 0 | 0 | |
applyGREAT | 148.925 | 29.733 | 269.613 | |
cgapsPlot | 0.481 | 0.040 | 0.602 | |
dataSubsetBySparsity | 1.057 | 0.082 | 1.332 | |
foldAccessibility | 8.739 | 0.287 | 10.468 | |
geneAccessibility | 6.961 | 0.225 | 8.434 | |
genePatternMatch | 53.321 | 1.219 | 63.633 | |
heatmapGeneAccessibility | 8.470 | 0.225 | 10.245 | |
heatmapPatternMarkers | 6.634 | 0.193 | 7.883 | |
heatmapPatternMatrix | 2.162 | 0.035 | 2.596 | |
motifPatternMatch | 38.298 | 2.360 | 47.763 | |
motifSummarization | 0.000 | 0.001 | 0.000 | |
pathwayMatch | 58.119 | 1.410 | 71.521 | |
patternMarkerCellClassifier | 0.455 | 0.034 | 0.593 | |
peaksToGRanges | 0.828 | 0.012 | 1.052 | |
simpleMotifTFMatch | 114.084 | 10.381 | 151.070 | |