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CHECK report for Qtlizer on machv2

This page was generated on 2020-10-17 11:59:19 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Qtlizer PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1396/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Qtlizer 1.2.0
Matthias Munz
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/Qtlizer
Branch: RELEASE_3_11
Last Commit: b1126f9
Last Changed Date: 2020-06-08 15:15:27 -0400 (Mon, 08 Jun 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: Qtlizer
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Qtlizer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Qtlizer_1.2.0.tar.gz
StartedAt: 2020-10-17 04:17:15 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:17:50 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 35.0 seconds
RetCode: 0
Status:  OK 
CheckDir: Qtlizer.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Qtlizer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Qtlizer_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Qtlizer.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Qtlizer/DESCRIPTION’ ... OK
* this is package ‘Qtlizer’ 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 ‘Qtlizer’ 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 ... NOTE
File ‘Qtlizer/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("\n  ---------\n  \n  For example usage please run: vignette('Qtlizer')\n  \n  Web-based GUI: http://genehopper.de/qtlizer\n  Documentation: http://genehopper.de/help#qtlizer_docu\n  Github Repo: https://github.com/matmu/Qtlizer\n  \n  Citation appreciated:\n  Munz M, Wohlers I, Simon E, Busch H, Schaefer A* and Erdmann J* (2018) Qtlizer: comprehensive QTL annotation of GWAS results. bioRxiv DOI: https://doi.org/10.1101/495903\n  \n  ---------",     domain = NULL, appendLF = TRUE)

See section ‘Good practice’ in '?.onAttach'.
* 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
get_qtls 4.787  0.341   6.623
* 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-3.11-bioc/meat/Qtlizer.Rcheck/00check.log’
for details.



Installation output

Qtlizer.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Qtlizer
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘Qtlizer’ ...
** 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 (Qtlizer)

Tests output


Example timings

Qtlizer.Rcheck/Qtlizer-Ex.timings

nameusersystemelapsed
get_qtls4.7870.3416.623