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This page was generated on 2023-05-26 06:18:05 -0000 (Fri, 26 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4254
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CHECK results for BOBaFIT on kunpeng2


To the developers/maintainers of the BOBaFIT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BOBaFIT.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 226/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BOBaFIT 1.5.0  (landing page)
Gaia Mazzocchetti
Snapshot Date: 2023-05-25 13:29:39 -0000 (Thu, 25 May 2023)
git_url: https://git.bioconductor.org/packages/BOBaFIT
git_branch: devel
git_last_commit: 518e797
git_last_commit_date: 2023-04-25 15:35:19 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

Summary

Package: BOBaFIT
Version: 1.5.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:BOBaFIT.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings BOBaFIT_1.5.0.tar.gz
StartedAt: 2023-05-26 04:24:26 -0000 (Fri, 26 May 2023)
EndedAt: 2023-05-26 04:34:48 -0000 (Fri, 26 May 2023)
EllapsedTime: 622.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: BOBaFIT.Rcheck
Warnings: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:BOBaFIT.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings BOBaFIT_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘BOBaFIT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BOBaFIT’ version ‘1.5.0’
* 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 ‘BOBaFIT’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'ggplot2::geom_segment' by 'ggbio::geom_segment' when loading 'BOBaFIT'
See ‘/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘utils’ ‘testthat’
A package should be listed in only one of these fields.
* 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'chrtab'
* 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 ... 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
DRrefit_plot   42.232  1.075  43.486
DRrefit        29.075  1.004  30.196
PlotChrCluster 22.326  0.585  23.021
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘BOBaFIT.Rmd’ using ‘UTF-8’... OK
  ‘Data-Preparation.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
Warning in readLines(tf) :
  incomplete final line found on '/tmp/RtmpAzKqAA/file1a720359cfca70'
--- re-building ‘BOBaFIT.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/computeNormalChromosome-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/chrlist plot-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/DRrefit_test-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/DRrefit_test-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/DRrefit_test-3.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/DRrefit_test-4.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/DRrefit_test-5.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/DRrefit_test-6.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/DRrefit_test-7.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/DRrefit_test-8.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/DRrefit_test-9.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/DRrefit_test-10.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/DRrefit_plot 1-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/DRrefit_plot 2-1.png" but not available.
Write Error
Write Error
Write Error
Write Error
Write Error
Write Error
Write Error
Write Error
Write Error
Write Error
Write Error
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/PlotChrCluster_test-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/PlotChrCluster_test-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/PlotChrCluster_test-3.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/PlotChrCluster_test-4.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/PlotChrCluster_test-5.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/PlotChrCluster_test-6.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/vign_test/BOBaFIT/vignettes/BOBaFIT_files/figure-html/PlotChrCluster_test-7.png" but not available.
The ma

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
* checking PDF version of manual without index ... ERROR
* DONE

Status: 2 ERRORs, 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/BOBaFIT.Rcheck/00check.log’
for details.

Installation output

BOBaFIT.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL BOBaFIT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘BOBaFIT’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'ggplot2::geom_segment' by 'ggbio::geom_segment' when loading 'BOBaFIT'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'ggplot2::geom_segment' by 'ggbio::geom_segment' when loading 'BOBaFIT'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'ggplot2::geom_segment' by 'ggbio::geom_segment' when loading 'BOBaFIT'
** testing if installed package keeps a record of temporary installation path
* DONE (BOBaFIT)

Tests output

BOBaFIT.Rcheck/tests/testthat.Rout


R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(BOBaFIT)
Warning message:
replacing previous import 'ggplot2::geom_segment' by 'ggbio::geom_segment' when loading 'BOBaFIT' 
> 
> test_check("BOBaFIT")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> 
> proc.time()
   user  system elapsed 
 21.642   1.088  22.764

Example timings

BOBaFIT.Rcheck/BOBaFIT-Ex.timings

nameusersystemelapsed
DRrefit29.075 1.00430.196
DRrefit_plot42.232 1.07543.486
PlotChrCluster22.326 0.58523.021
Popeye2.0600.0922.160
computeNormalChromosomes3.2070.1363.355