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CHECK report for VariantToolsData on malbec2

This page was generated on 2021-01-11 15:59:28 -0500 (Mon, 11 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE VariantToolsData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 374/385HostnameOS / ArchINSTALLBUILDCHECK
VariantToolsData 1.15.0
Michael Lawrence
Snapshot Date: 2021-01-11 09:00:09 -0500 (Mon, 11 Jan 2021)
URL: https://git.bioconductor.org/packages/VariantToolsData
Branch: master
Last Commit: b62c1ca
Last Changed Date: 2020-10-27 10:22:22 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  WARNINGS 

Summary

Package: VariantToolsData
Version: 1.15.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:VariantToolsData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings VariantToolsData_1.15.0.tar.gz
StartedAt: 2021-01-11 12:55:18 -0500 (Mon, 11 Jan 2021)
EndedAt: 2021-01-11 12:59:10 -0500 (Mon, 11 Jan 2021)
EllapsedTime: 232.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: VariantToolsData.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:VariantToolsData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings VariantToolsData_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/VariantToolsData.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VariantToolsData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VariantToolsData’ version ‘1.15.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘VariantToolsData’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 201.6Mb
  sub-directories of 1Mb or more:
    data       2.2Mb
    extdata  199.2Mb
* 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
TP53Region: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  geno.rda        24Kb     14Kb       xz
  tallies.rda    2.2Mb    1.3Mb       xz
* checking files in ‘vignettes’ ... OK
* checking examples ... 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 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/VariantToolsData.Rcheck/00check.log’
for details.



Installation output

VariantToolsData.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL VariantToolsData
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘VariantToolsData’ ...
** 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 (VariantToolsData)

Tests output


Example timings

VariantToolsData.Rcheck/VariantToolsData-Ex.timings

nameusersystemelapsed
TP53Region0.110.000.11
geno0.0140.0000.013
repeats0.0050.0000.005
sumDepths1.0700.0081.078
tallies0.9860.0001.372