Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-15 12:33 -0400 (Sat, 15 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" | 4685 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4400 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4349 |
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 105/2242 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ATACCoGAPS 1.7.0 (landing page) Rossin Erbe
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 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: 1.7.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ATACCoGAPS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ATACCoGAPS_1.7.0.tar.gz |
StartedAt: 2024-06-14 20:31:57 -0400 (Fri, 14 Jun 2024) |
EndedAt: 2024-06-14 20:44:59 -0400 (Fri, 14 Jun 2024) |
EllapsedTime: 781.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ATACCoGAPS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ATACCoGAPS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ATACCoGAPS_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ATACCoGAPS.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘ATACCoGAPS/DESCRIPTION’ ... OK * this is package ‘ATACCoGAPS’ version ‘1.7.0’ * 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 loading without being on the library search path ... 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 81.668 5.078 174.363 simpleMotifTFMatch 74.230 0.437 74.703 pathwayMatch 27.044 0.456 27.501 genePatternMatch 24.171 0.632 24.804 motifPatternMatch 15.901 0.552 16.453 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/ATACCoGAPS.Rcheck/00check.log’ for details.
ATACCoGAPS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ATACCoGAPS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 | 81.668 | 5.078 | 174.363 | |
cgapsPlot | 0.308 | 0.008 | 0.316 | |
dataSubsetBySparsity | 0.439 | 0.059 | 0.499 | |
foldAccessibility | 4.398 | 0.472 | 4.870 | |
geneAccessibility | 4.009 | 0.304 | 4.313 | |
genePatternMatch | 24.171 | 0.632 | 24.804 | |
heatmapGeneAccessibility | 3.365 | 0.036 | 3.402 | |
heatmapPatternMarkers | 3.095 | 0.180 | 3.276 | |
heatmapPatternMatrix | 0.645 | 0.016 | 0.662 | |
motifPatternMatch | 15.901 | 0.552 | 16.453 | |
motifSummarization | 0 | 0 | 0 | |
pathwayMatch | 27.044 | 0.456 | 27.501 | |
patternMarkerCellClassifier | 0.240 | 0.008 | 0.248 | |
peaksToGRanges | 0.241 | 0.000 | 0.240 | |
simpleMotifTFMatch | 74.230 | 0.437 | 74.703 | |