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This page was generated on 2024-02-18 02:28:11 -0500 (Sun, 18 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4424
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4400
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 130/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Basic4Cseq 1.39.0  (landing page)
Carolin Walter
Snapshot Date: 2024-02-16 14:10:20 -0500 (Fri, 16 Feb 2024)
git_url: https://git.bioconductor.org/packages/Basic4Cseq
git_branch: devel
git_last_commit: 13edfac
git_last_commit_date: 2023-10-24 09:57:44 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for Basic4Cseq on merida1


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.

raw results


Summary

Package: Basic4Cseq
Version: 1.39.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Basic4Cseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Basic4Cseq_1.39.0.tar.gz
StartedAt: 2024-02-17 00:16:29 -0500 (Sat, 17 Feb 2024)
EndedAt: 2024-02-17 00:25:14 -0500 (Sat, 17 Feb 2024)
EllapsedTime: 525.2 seconds
RetCode: 0
Status:   OK  
CheckDir: Basic4Cseq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Basic4Cseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Basic4Cseq_1.39.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Basic4Cseq.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Basic4Cseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Basic4Cseq’ version ‘1.39.0’
* 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 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 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
readsToFragments 6.592  2.823   11.97
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

Basic4Cseq.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Basic4Cseq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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-class0.0030.0020.005
Data4Cseq0.1730.0110.211
checkRestrictionEnzymeSequence0.0010.0000.001
chooseNearCisFragments0.0180.0070.067
createVirtualFragmentLibrary0.0000.0010.001
drawDigestionFragmentHistogram0.0090.0020.012
drawHeatmap0.0000.0000.001
exportVisualizationFragmentData0.0000.0010.001
getReadDistribution1.2630.0231.485
giveEnzymeSequence0.0020.0010.005
importVisualizationFragmentData0.0150.0200.039
liverData0.0050.0060.011
liverDataRaw0.0050.0050.012
normalizeFragmentData0.0110.0060.018
plotTransInteractions0.0010.0010.001
prepare4CseqData0.0000.0010.001
printBEDFragmentLibrary0.0010.0000.003
printWigFile0.0000.0010.001
readPointsOfInterestFile0.0050.0020.007
readsToFragments 6.592 2.82311.970
simulateDigestion0.0040.0010.004
visualizeViewpoint0.0750.0070.101