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CHECK report for NGScopy on merida2

This page was generated on 2019-04-08 12:26:31 -0400 (Mon, 08 Apr 2019).

Package 1083/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NGScopy 1.17.1
Xiaobei Zhao
Snapshot Date: 2019-04-07 17:01:41 -0400 (Sun, 07 Apr 2019)
URL: https://git.bioconductor.org/packages/NGScopy
Branch: master
Last Commit: ae7ebdd
Last Changed Date: 2019-01-04 13:41:49 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  ERROR  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  ERROR  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  ERROR  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: NGScopy
Version: 1.17.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NGScopy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NGScopy_1.17.1.tar.gz
StartedAt: 2019-04-08 02:36:43 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 02:38:02 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 78.3 seconds
RetCode: 0
Status:  OK 
CheckDir: NGScopy.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:NGScopy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NGScopy_1.17.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/NGScopy.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NGScopy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NGScopy’ version ‘1.17.1’
* 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 ‘NGScopy’ 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
.count_starts: no visible global function definition for ‘median’
.count_starts: no visible global function definition for ‘sd’
.help_segmtype: no visible global function definition for ‘help’
.make_windows : .unit: no visible global function definition for
  ‘median’
.make_windows : .unit: no visible global function definition for ‘sd’
.plot_out: no visible global function definition for ‘pdf’
.plot_out: no visible global function definition for ‘dev.off’
.unit_plot_out: no visible global function definition for ‘par’
read_regions: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  dev.off help median par pdf read.table sd
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "median", "sd")
  importFrom("utils", "help", "read.table")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
  ‘ngscopy-case1b-cmdline.out’
Please remove them from your package.
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/NGScopy.Rcheck/00check.log’
for details.



Installation output

NGScopy.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL NGScopy
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘NGScopy’ ...
** 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
* DONE (NGScopy)

Tests output


Example timings

NGScopy.Rcheck/NGScopy-Ex.timings

nameusersystemelapsed
NGScopy-class0.8580.0230.891
df.to.gr0.0010.0000.000
help_segmtype000
ngscopy_cmdline_example0.0140.0010.016
ngscopy_unittest000
parse_segmtype000
read_regions0.0050.0010.007