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This page was generated on 2023-10-20 09:38:13 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 2028/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
strandCheckR 1.18.0  (landing page)
Thu-Hien To
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/strandCheckR
git_branch: RELEASE_3_17
git_last_commit: 21313d7
git_last_commit_date: 2023-04-25 11:03:17 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for strandCheckR on kjohnson2


To the developers/maintainers of the strandCheckR package:
- 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: strandCheckR
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:strandCheckR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings strandCheckR_1.18.0.tar.gz
StartedAt: 2023-10-19 05:01:34 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 05:10:40 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 545.5 seconds
RetCode: 0
Status:   OK  
CheckDir: strandCheckR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:strandCheckR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings strandCheckR_1.18.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/strandCheckR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘strandCheckR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘strandCheckR’ version ‘1.18.0’
* 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 ‘strandCheckR’ 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 ... NOTE
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
intersectWithFeature 3.38  0.173   5.995
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/strandCheckR.Rcheck/00check.log’
for details.



Installation output

strandCheckR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘strandCheckR’ ...
** 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 (strandCheckR)

Tests output

strandCheckR.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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(strandCheckR)
> 
> test_check("strandCheckR")
[ FAIL 0 | WARN 2 | SKIP 1 | PASS 28 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_keptProbaWin.R:1:1'

[ FAIL 0 | WARN 2 | SKIP 1 | PASS 28 ]
> 
> proc.time()
   user  system elapsed 
 19.598   0.816  33.150 

Example timings

strandCheckR.Rcheck/strandCheckR-Ex.timings

nameusersystemelapsed
checkPairedEnd0.0600.0080.116
filterDNA0.6550.0481.264
getStrandFromBamFile1.1920.0232.191
getStrandFromReadInfo0.3530.0230.664
getWinOverlapEachIRange0.1160.0070.217
getWinOverlapEachReadFragment0.2790.0220.540
getWinOverlapGRanges0.2810.0130.526
intersectWithFeature3.3800.1735.995
plotHist0.6920.0141.184
plotWin2.4860.0964.586
strandCheckR-package2.0700.0933.843