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This page was generated on 2023-10-20 09:37:58 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 105/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ATACCoGAPS 1.2.0  (landing page)
Rossin Erbe
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/ATACCoGAPS
git_branch: RELEASE_3_17
git_last_commit: 508affb
git_last_commit_date: 2023-04-25 11:39:02 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for ATACCoGAPS on kjohnson2


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.

raw results


Summary

Package: ATACCoGAPS
Version: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2023-10-17 03:05:13 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 03:25:17 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 1203.8 seconds
RetCode: 0
Status:   OK  
CheckDir: ATACCoGAPS.Rcheck
Warnings: 0

Command output

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### 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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ATACCoGAPS.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ATACCoGAPS/DESCRIPTION’ ... OK
* this is package ‘ATACCoGAPS’ version ‘1.2.0’
* 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 R 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               151.671  8.860 334.546
simpleMotifTFMatch        68.900  4.896 113.312
motifPatternMatch         49.953  4.887  84.708
pathwayMatch              36.778  0.808  55.635
genePatternMatch          32.851  0.752  51.455
foldAccessibility          6.168  0.162   9.698
geneAccessibility          5.454  0.154   8.597
heatmapGeneAccessibility   5.083  0.115   7.990
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.17-bioc-mac-arm64/meat/ATACCoGAPS.Rcheck/00check.log’
for details.



Installation output

ATACCoGAPS.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ATACCoGAPS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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)

Tests output


Example timings

ATACCoGAPS.Rcheck/ATACCoGAPS-Ex.timings

nameusersystemelapsed
RNAseqTFValidation000
applyGREAT151.671 8.860334.546
cgapsPlot0.3300.0290.553
dataSubsetBySparsity0.8800.0361.405
foldAccessibility6.1680.1629.698
geneAccessibility5.4540.1548.597
genePatternMatch32.851 0.75251.455
heatmapGeneAccessibility5.0830.1157.990
heatmapPatternMarkers2.6460.1224.258
heatmapPatternMatrix1.0020.0231.582
motifPatternMatch49.953 4.88784.708
motifSummarization000
pathwayMatch36.778 0.80855.635
patternMarkerCellClassifier0.1730.0090.294
peaksToGRanges0.3470.0120.557
simpleMotifTFMatch 68.900 4.896113.312