Package: VariantToolsData

Version: 1.8.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:VariantToolsData.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings VariantToolsData_1.8.0.tar.gz

StartedAt: 2019-10-17 13:54:51 -0400 (Thu, 17 Oct 2019)

EndedAt: 2019-10-17 13:58:06 -0400 (Thu, 17 Oct 2019)

EllapsedTime: 195.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: VariantToolsData.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:VariantToolsData.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings VariantToolsData_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-data-experiment/meat/VariantToolsData.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.8.0’
* 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
  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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-data-experiment/meat/VariantToolsData.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL VariantToolsData
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* installing to library ‘/home/biocbuild/bbs-3.9-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)

name	user	system	elapsed
TP53Region	0.094	0.004	0.099
geno	0.011	0.004	0.014
repeats	0.004	0.000	0.005
sumDepths	0.962	0.020	0.982
tallies	0.874	0.000	0.907