Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-22 11:35:25 -0400 (Wed, 22 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 3444 |
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 | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ATACCoGAPS.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ATACCoGAPS_1.6.0.tar.gz |
StartedAt: 2024-05-21 23:06:57 -0400 (Tue, 21 May 2024) |
EndedAt: 2024-05-21 23:19:42 -0400 (Tue, 21 May 2024) |
EllapsedTime: 765.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ATACCoGAPS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ATACCoGAPS.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ATACCoGAPS_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/ATACCoGAPS.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * 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 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 110.40 25.66 197.73 simpleMotifTFMatch 76.01 0.87 90.19 pathwayMatch 37.77 1.36 39.13 genePatternMatch 31.58 1.20 32.75 motifPatternMatch 21.45 2.41 23.86 * 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 'F:/biocbuild/bbs-3.19-bioc/meat/ATACCoGAPS.Rcheck/00check.log' for details.
ATACCoGAPS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL ATACCoGAPS ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 | 110.40 | 25.66 | 197.73 | |
cgapsPlot | 0.28 | 0.03 | 0.32 | |
dataSubsetBySparsity | 1.66 | 0.05 | 1.71 | |
foldAccessibility | 3.80 | 0.26 | 4.06 | |
geneAccessibility | 3.81 | 0.19 | 4.00 | |
genePatternMatch | 31.58 | 1.20 | 32.75 | |
heatmapGeneAccessibility | 4.52 | 0.27 | 4.78 | |
heatmapPatternMarkers | 3.58 | 0.14 | 3.72 | |
heatmapPatternMatrix | 1.50 | 0.03 | 1.53 | |
motifPatternMatch | 21.45 | 2.41 | 23.86 | |
motifSummarization | 0 | 0 | 0 | |
pathwayMatch | 37.77 | 1.36 | 39.13 | |
patternMarkerCellClassifier | 0.28 | 0.01 | 0.30 | |
peaksToGRanges | 0.56 | 0.10 | 0.81 | |
simpleMotifTFMatch | 76.01 | 0.87 | 90.19 | |