Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-11-02 11:40:25 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 128/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Basic4Cseq 1.38.0  (landing page)
Carolin Walter
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/Basic4Cseq
git_branch: RELEASE_3_18
git_last_commit: edbd20b
git_last_commit_date: 2023-10-24 09:57:44 -0400 (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 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for Basic4Cseq on kunpeng2


To the developers/maintainers of the Basic4Cseq package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Basic4Cseq.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: Basic4Cseq
Version: 1.38.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:Basic4Cseq.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings Basic4Cseq_1.38.0.tar.gz
StartedAt: 2023-11-02 08:31:10 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 08:36:41 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 330.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: Basic4Cseq.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:Basic4Cseq.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings Basic4Cseq_1.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Basic4Cseq.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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
* using option ‘--no-vignettes’
* checking for file ‘Basic4Cseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Basic4Cseq’ version ‘1.38.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Basic4Cseq’ 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 ... 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Basic4Cseq-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readsToFragments
> ### Title: Determine fragment coverage of a 4C-seq fragment library
> ### Aliases: readsToFragments readsToFragments,Data4Cseq,character-method
> ### Keywords: readsToFragments
> 
> ### ** Examples
> 
>     data(liverData)
>     file <- system.file("extdata", "vfl_aagctt_catg_mm9_54_vp.csv", package="Basic4Cseq")
>     rawFragments(liverData) = readsToFragments(liverData, file)
* 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 ERROR
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/Basic4Cseq.Rcheck/00check.log’
for details.


Installation output

Basic4Cseq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL Basic4Cseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘Basic4Cseq’ ...
** 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 (Basic4Cseq)

Tests output


Example timings

Basic4Cseq.Rcheck/Basic4Cseq-Ex.timings

nameusersystemelapsed
Data4Cseq-class0.0020.0000.001
Data4Cseq0.1300.0120.145
checkRestrictionEnzymeSequence0.0000.0000.001
chooseNearCisFragments0.0090.0040.013
createVirtualFragmentLibrary0.0010.0000.001
drawDigestionFragmentHistogram0.0030.0030.007
drawHeatmap000
exportVisualizationFragmentData000
getReadDistribution0.2380.0040.243
giveEnzymeSequence0.0000.0020.003
importVisualizationFragmentData0.0050.0040.009
liverData0.0040.0000.003
liverDataRaw0.0030.0000.003
normalizeFragmentData0.0020.0040.006
plotTransInteractions000
prepare4CseqData000
printBEDFragmentLibrary0.0010.0000.000
printWigFile000
readPointsOfInterestFile0.0030.0000.003