Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2023-01-28 11:08:01 -0500 (Sat, 28 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4510
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4288
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4317
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

CHECK results for CoverageView on lconway


To the developers/maintainers of the CoverageView package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CoverageView.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 428/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoverageView 1.36.0  (landing page)
Ernesto Lowy
Snapshot Date: 2023-01-27 14:00:04 -0500 (Fri, 27 Jan 2023)
git_url: https://git.bioconductor.org/packages/CoverageView
git_branch: RELEASE_3_16
git_last_commit: 76c28ab
git_last_commit_date: 2022-11-01 11:09:32 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CoverageView
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CoverageView.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CoverageView_1.36.0.tar.gz
StartedAt: 2023-01-27 19:47:11 -0500 (Fri, 27 Jan 2023)
EndedAt: 2023-01-27 19:50:18 -0500 (Fri, 27 Jan 2023)
EllapsedTime: 187.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CoverageView.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CoverageView.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CoverageView_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/CoverageView.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoverageView/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CoverageView’ version ‘1.36.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CoverageView’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  ‘BiocFile’
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
cov.matrix 6.05  4.244   6.064
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/CoverageView.Rcheck/00check.log’
for details.



Installation output

CoverageView.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CoverageView
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘CoverageView’ ...
** using staged installation
** R
** data
** inst
** 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 (CoverageView)

Tests output


Example timings

CoverageView.Rcheck/CoverageView-Ex.timings

nameusersystemelapsed
CoverageBamFile-class0.0340.0020.036
CoverageBigWigFile-class0.0080.0010.011
cov.interval0.6000.0650.670
cov.matrix6.0504.2446.064
draw.heatmap2.1890.4532.382
draw.profile0.1290.0180.150
export.wig0.1440.0040.149
genome.covplot.cumdepth0.3070.0120.321
genome.covplot.depth0.2940.0180.314
write.profile0.320.220.54