Back to Build/check report for BioC 3.11 experimental data

CHECK report for VariantToolsData on malbec2

This page was generated on 2020-10-15 20:46:02 -0400 (Thu, 15 Oct 2020).

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 378/391HostnameOS / ArchINSTALLBUILDCHECK
VariantToolsData 1.12.0
Michael Lawrence
Snapshot Date: 2020-10-15 07:30:17 -0400 (Thu, 15 Oct 2020)
URL: https://git.bioconductor.org/packages/VariantToolsData
Branch: RELEASE_3_11
Last Commit: f6341fd
Last Changed Date: 2020-04-27 16:20:19 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository

Summary

Package: VariantToolsData
Version: 1.12.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:VariantToolsData.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings VariantToolsData_1.12.0.tar.gz
StartedAt: 2020-10-15 14:19:34 -0400 (Thu, 15 Oct 2020)
EndedAt: 2020-10-15 14:25:14 -0400 (Thu, 15 Oct 2020)
EllapsedTime: 339.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: VariantToolsData.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:VariantToolsData.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings VariantToolsData_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-data-experiment/meat/VariantToolsData.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 ‘VariantToolsData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VariantToolsData’ version ‘1.12.0’
* 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 ... OK
* 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
  repeats.rda     10Kb      9Kb    bzip2
  tallies.rda    2.2Mb    1.4Mb       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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-data-experiment/meat/VariantToolsData.Rcheck/00check.log’
for details.



Installation output

VariantToolsData.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL VariantToolsData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-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
TP53Region0.1190.0000.119
geno0.0150.0000.016
repeats0.0050.0000.005
sumDepths1.6980.0121.710
tallies0.3930.0000.489