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This page was generated on 2024-03-28 11:36:58 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1717/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RepViz 1.19.0  (landing page)
Thomas Faux, Asta Laiho
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/RepViz
git_branch: devel
git_last_commit: a618024
git_last_commit_date: 2023-10-24 11:13:01 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for RepViz on nebbiolo1


To the developers/maintainers of the RepViz package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RepViz.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: RepViz
Version: 1.19.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RepViz.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RepViz_1.19.0.tar.gz
StartedAt: 2024-03-28 01:59:18 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 02:01:41 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 143.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RepViz.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RepViz.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RepViz_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/RepViz.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* 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 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘RepViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RepViz’ version ‘1.19.0’
* 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 ‘RepViz’ 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    CHANGES IN VERSION 0.99.26
      RELEASE
      + Correction of a visual bug that appeared when there is low signal. This was due to the fact that the coverage was stopping at the last read instead of at the end of the window. As the result the lines of signal on the plot appeared cutted.
* 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 loading without being on the library search path ... 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 ... NOTE
unitTest: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'RepViz.Rd':
RepViz
  Code: function(region, genome = c("hg19", "hg38", "mm10"), BAM =
                 NULL, BED = NULL, avgTrack = TRUE, geneTrack = TRUE,
                 max = NULL, verbose = TRUE, cex = 1, col = NULL)
  Docs: function(region, genome = c("hg19", "hg38", "mm10"), BAM =
                 NULL, BED = NULL, avgTrack = TRUE, geneTrack = TRUE,
                 max = NULL, verbose = TRUE, cex = 1)
  Argument names in code not in docs:
    col

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'RepViz.Rd':
  ‘col’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to ‘/tmp/Rtmp8J7wcE’, resetting
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/RepViz.Rcheck/00check.log’
for details.


Installation output

RepViz.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL RepViz
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘RepViz’ ...
** using staged installation
** R
** 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 (RepViz)

Tests output


Example timings

RepViz.Rcheck/RepViz-Ex.timings

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