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CHECK report for packFinder on malbec2

This page was generated on 2020-10-17 11:55:20 -0400 (Sat, 17 Oct 2020).

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 1256/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
packFinder 1.0.0
Jack Gisby
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/packFinder
Branch: RELEASE_3_11
Last Commit: d9d3786
Last Changed Date: 2020-04-27 15:33:20 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: packFinder
Version: 1.0.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:packFinder.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings packFinder_1.0.0.tar.gz
StartedAt: 2020-10-17 03:53:42 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:54:34 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 51.9 seconds
RetCode: 0
Status:  OK 
CheckDir: packFinder.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:packFinder.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings packFinder_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/packFinder.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.0.0’
* 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 6.401  0.185   6.593
* 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-3.11-bioc/R/bin/R CMD INSTALL packFinder
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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"
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 31 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  8.803   0.256   9.045 

Example timings

packFinder.Rcheck/packFinder-Ex.timings

nameusersystemelapsed
arabidopsisThalianaRefseq6.4010.1856.593
blastAnalysis000
blastAnnotate0.0020.0030.006
collapseSeqs0.5520.0010.551
filterWildcards0.0850.0040.088
getPackSeqs1.2740.0041.277
getPacksFromCsv0.0040.0000.004
getPacksFromFasta0.0720.0000.071
getPacksFromGRanges0.0530.0000.053
getTsds0.0840.0040.089
identifyPotentialPackElements0.8960.0040.899
identifyTirMatches0.0790.0040.082
makeBlastDb000
packAlign0.0750.0000.075
packBlast0.0000.0000.001
packClust0.0690.0110.082
packMatches1.2190.0081.227
packSearch1.2120.0001.211
packsToCsv0.0040.0000.013
packsToFasta0.0810.0030.085
packsToGRanges0.0210.0000.021
readBlast0.0040.0000.005
readUc0.0040.0000.004
tirClust0.4930.0000.510