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This page was generated on 2023-12-04 11:35:38 -0500 (Mon, 04 Dec 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4686
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4421
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4440
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: 2023-12-03 14:05:05 -0500 (Sun, 03 Dec 2023)
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 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for ATACCoGAPS on nebbiolo2


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.

raw results


Summary

Package: ATACCoGAPS
Version: 1.4.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ATACCoGAPS.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ATACCoGAPS_1.4.0.tar.gz
StartedAt: 2023-12-03 20:14:03 -0500 (Sun, 03 Dec 2023)
EndedAt: 2023-12-03 20:28:47 -0500 (Sun, 03 Dec 2023)
EllapsedTime: 884.8 seconds
RetCode: 0
Status:   OK  
CheckDir: ATACCoGAPS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ATACCoGAPS.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ATACCoGAPS_1.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ATACCoGAPS.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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         93.795  5.652 197.886
simpleMotifTFMatch 93.304  0.761  94.098
motifPatternMatch  36.836  1.303  38.140
pathwayMatch       31.403  0.636  32.040
genePatternMatch   26.232  0.624  26.856
foldAccessibility   4.921  0.584   5.505
geneAccessibility   4.786  0.292   5.077
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ATACCoGAPS.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/ATACCoGAPS.Rcheck/00check.log’
for details.



Installation output

ATACCoGAPS.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL ATACCoGAPS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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
applyGREAT 93.795 5.652197.886
cgapsPlot0.3160.0080.324
dataSubsetBySparsity0.4990.0520.551
foldAccessibility4.9210.5845.505
geneAccessibility4.7860.2925.077
genePatternMatch26.232 0.62426.856
heatmapGeneAccessibility3.6380.0283.667
heatmapPatternMarkers3.0980.1803.278
heatmapPatternMatrix0.6470.0160.663
motifPatternMatch36.836 1.30338.140
motifSummarization000
pathwayMatch31.403 0.63632.040
patternMarkerCellClassifier0.1620.0000.163
peaksToGRanges0.2470.0000.247
simpleMotifTFMatch93.304 0.76194.098