Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:37:20 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 105/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ATACCoGAPS 1.5.0 (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 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.5.0 |
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_1.5.0.tar.gz |
StartedAt: 2024-03-27 23:21:40 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 23:35:15 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 814.7 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_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/ATACCoGAPS.Rcheck' * using R Under development (unstable) (2024-03-16 r86144 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 '1.5.0' * 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 114.44 28.00 210.99 simpleMotifTFMatch 83.13 2.11 99.59 motifPatternMatch 47.73 7.45 55.21 pathwayMatch 36.33 1.41 37.72 genePatternMatch 31.23 1.03 32.26 heatmapGeneAccessibility 4.89 0.19 5.08 * 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 | 114.44 | 28.00 | 210.99 | |
cgapsPlot | 0.33 | 0.02 | 0.36 | |
dataSubsetBySparsity | 1.66 | 0.07 | 1.72 | |
foldAccessibility | 3.92 | 0.25 | 4.17 | |
geneAccessibility | 3.86 | 0.26 | 4.13 | |
genePatternMatch | 31.23 | 1.03 | 32.26 | |
heatmapGeneAccessibility | 4.89 | 0.19 | 5.08 | |
heatmapPatternMarkers | 2.54 | 0.09 | 2.63 | |
heatmapPatternMatrix | 1.06 | 0.02 | 1.07 | |
motifPatternMatch | 47.73 | 7.45 | 55.21 | |
motifSummarization | 0 | 0 | 0 | |
pathwayMatch | 36.33 | 1.41 | 37.72 | |
patternMarkerCellClassifier | 0.16 | 0.02 | 0.17 | |
peaksToGRanges | 0.40 | 0.10 | 0.61 | |
simpleMotifTFMatch | 83.13 | 2.11 | 99.59 | |