Back to Mac ARM64 build report for BioC 3.20 |
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This page was generated on 2024-05-20 11:32:08 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
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 105/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ATACCoGAPS 1.7.0 (landing page) Rossin Erbe
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | |||||||
To the developers/maintainers of the ATACCoGAPS package: - 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: /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_1.7.0.tar.gz |
StartedAt: 2024-05-19 05:27:18 -0400 (Sun, 19 May 2024) |
EndedAt: 2024-05-19 05:40:34 -0400 (Sun, 19 May 2024) |
EllapsedTime: 795.5 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_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/ATACCoGAPS.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-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 Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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 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 114.282 39.366 237.159 simpleMotifTFMatch 62.995 16.119 79.506 pathwayMatch 34.286 1.250 35.644 genePatternMatch 30.536 1.151 31.713 motifPatternMatch 21.118 1.530 22.833 * 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-3.20-bioc-mac-arm64/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-arm64/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 | 114.282 | 39.366 | 237.159 | |
cgapsPlot | 0.429 | 0.019 | 0.449 | |
dataSubsetBySparsity | 1.959 | 0.073 | 2.032 | |
foldAccessibility | 4.365 | 0.168 | 4.536 | |
geneAccessibility | 4.062 | 0.175 | 4.255 | |
genePatternMatch | 30.536 | 1.151 | 31.713 | |
heatmapGeneAccessibility | 4.320 | 0.199 | 4.520 | |
heatmapPatternMarkers | 2.639 | 0.141 | 2.780 | |
heatmapPatternMatrix | 1.016 | 0.026 | 1.042 | |
motifPatternMatch | 21.118 | 1.530 | 22.833 | |
motifSummarization | 0.000 | 0.000 | 0.001 | |
pathwayMatch | 34.286 | 1.250 | 35.644 | |
patternMarkerCellClassifier | 0.343 | 0.017 | 0.361 | |
peaksToGRanges | 0.303 | 0.004 | 0.308 | |
simpleMotifTFMatch | 62.995 | 16.119 | 79.506 | |