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This page was generated on 2024-04-18 11:32:06 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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 104/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ATACCoGAPS 1.4.0  (landing page)
Rossin Erbe
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/ATACCoGAPS
git_branch: RELEASE_3_18
git_last_commit: 1e97480
git_last_commit_date: 2023-10-24 11:42:56 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'TFBSTools' which is only available as a source package that needs compilation

CHECK results for ATACCoGAPS on kjohnson1


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: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2024-04-17 05:57:00 -0400 (Wed, 17 Apr 2024)
EndedAt: 2024-04-17 06:11:06 -0400 (Wed, 17 Apr 2024)
EllapsedTime: 846.1 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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/ATACCoGAPS.Rcheck’
* using R version 4.3.3 (2024-02-29)
* 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 Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ATACCoGAPS/DESCRIPTION’ ... OK
* this is package ‘ATACCoGAPS’ version ‘1.4.0’
* 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         117.509 37.204 237.431
simpleMotifTFMatch  70.869 13.598  84.752
motifPatternMatch   41.950  4.224  46.668
pathwayMatch        34.332  1.279  35.671
genePatternMatch    30.393  1.107  31.509
* 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-3.18-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
RNAseqTFValidation0.0010.0000.001
applyGREAT117.509 37.204237.431
cgapsPlot0.4230.0230.448
dataSubsetBySparsity2.0840.1012.188
foldAccessibility4.4690.2104.690
geneAccessibility4.3060.2514.560
genePatternMatch30.393 1.10731.509
heatmapGeneAccessibility4.3110.1834.496
heatmapPatternMarkers2.4250.1092.536
heatmapPatternMatrix1.0120.0231.036
motifPatternMatch41.950 4.22446.668
motifSummarization000
pathwayMatch34.332 1.27935.671
patternMarkerCellClassifier0.2490.0030.253
peaksToGRanges0.2980.0050.303
simpleMotifTFMatch70.86913.59884.752