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CHECK report for SISPA on merida2

This page was generated on 2018-10-17 08:55:29 -0400 (Wed, 17 Oct 2018).

Package 1384/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SISPA 1.10.0
Bhakti Dwivedi
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/SISPA
Branch: RELEASE_3_7
Last Commit: 7fd5b26
Last Changed Date: 2018-04-30 10:35:38 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SISPA
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SISPA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SISPA_1.10.0.tar.gz
StartedAt: 2018-10-17 00:07:48 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:10:26 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 158.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: SISPA.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SISPA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SISPA_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/SISPA.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SISPA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SISPA’ version ‘1.10.0’
* 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 ‘SISPA’ can be installed ... OK
* checking installed package size ... OK
* checking package 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
cptSamples : cptsPlot: no visible global function definition for
  ‘abline’
cptSamples : cptsPlot: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline text
Consider adding
  importFrom("graphics", "abline", "text")
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 ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘SISPA.Rmd’, ‘SISPA.md’, ‘SISPA_data.Rda’,
    ‘SISPA_files/figure-html/unnamed-chunk-2-1.png’,
    ‘SISPA_files/figure-html/unnamed-chunk-3-1.png’,
    ‘SISPA_files/figure-html/unnamed-chunk-4-1.png’,
    ‘SISPA_files/figure-html/unnamed-chunk-5-1.png’,
    ‘SISPA_files/figure-html/unnamed-chunk-6-1.png’,
    ‘SISPA_files/figure-html/unnamed-chunk-7-1.png’,
    ‘sispa_overview.png’
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/SISPA.Rmd’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/SISPA.Rcheck/00check.log’
for details.



Installation output

SISPA.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SISPA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘SISPA’ ...
** R
** data
*** moving datasets to lazyload DB
** 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 (SISPA)

Tests output


Example timings

SISPA.Rcheck/SISPA-Ex.timings

nameusersystemelapsed
SISPA0.0500.0110.065
callGSVA0.0670.0140.080
callZSCORE0.0060.0010.008
cptSamples0.3770.0620.442
filterVars0.0010.0000.001
freqplot0.5740.0300.612
sortData0.0030.0000.003
waterfallplot0.2490.0010.253