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CHECK report for packFinder on malbec1

This page was generated on 2021-05-06 12:28:29 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the packFinder package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1288/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
packFinder 1.2.0  (landing page)
Jack Gisby
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/packFinder
Branch: RELEASE_3_12
Last Commit: 25949e3
Last Changed Date: 2020-10-27 11:52:38 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: packFinder
Version: 1.2.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:packFinder.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings packFinder_1.2.0.tar.gz
StartedAt: 2021-05-06 04:15:52 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:16:44 -0400 (Thu, 06 May 2021)
EllapsedTime: 51.2 seconds
RetCode: 0
Status:   OK  
CheckDir: packFinder.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:packFinder.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings packFinder_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/packFinder.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘packFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘packFinder’ version ‘1.2.0’
* 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 ‘packFinder’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
arabidopsisThalianaRefseq 5.012  0.128   5.146
* 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: OK


Installation output

packFinder.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL packFinder
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘packFinder’ ...
** 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 (packFinder)

Tests output

packFinder.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(packFinder)
> 
> test_check("packFinder")
DNAStringSet object of length 1:
      width seq                                             names               
[1] 3800001 GGTGTTAAAAGGTTCTTGAGTG...TAGTCAGGTTTCTAACAGAAAA Chr3
[1] "File successfully written to tempTestOutput/packMatches.csv"
[1] "FASTA written to tempTestOutput/packMatches.fasta"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 31 ]
> 
> proc.time()
   user  system elapsed 
  7.804   0.260   8.074 

Example timings

packFinder.Rcheck/packFinder-Ex.timings

nameusersystemelapsed
arabidopsisThalianaRefseq5.0120.1285.146
blastAnalysis000
blastAnnotate0.0040.0000.007
collapseSeqs0.7360.0040.742
filterWildcards0.1120.0040.117
getPackSeqs1.6520.0041.657
getPacksFromCsv0.0040.0000.019
getPacksFromFasta0.0640.0080.073
getPacksFromGRanges0.0560.0000.055
getTsds0.0920.0120.103
identifyPotentialPackElements0.7440.0000.747
identifyTirMatches0.1240.0080.130
makeBlastDb000
packAlign0.0640.0000.064
packBlast000
packClust0.0680.0000.066
packMatches1.6840.0041.692
packSearch1.8280.0041.836
packsToCsv0.0000.0000.003
packsToFasta0.0880.0000.088
packsToGRanges0.0160.0000.019
readBlast0.0040.0000.005
readUc0.0040.0000.004
tirClust0.5640.0040.581