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CHECK report for SISPA on celaya2

This page was generated on 2019-10-16 12:56:33 -0400 (Wed, 16 Oct 2019).

Package 1534/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SISPA 1.14.0
Bhakti Dwivedi
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/SISPA
Branch: RELEASE_3_9
Last Commit: 24437ec
Last Changed Date: 2019-05-02 11:53:57 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SISPA
Version: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2019-10-16 06:57:05 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 07:00:18 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 192.9 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_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/SISPA.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.14.0’
* 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-3.9-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/3.6/Resources/library’
* installing *source* package ‘SISPA’ ...
** using staged installation
** 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 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 (SISPA)

Tests output


Example timings

SISPA.Rcheck/SISPA-Ex.timings

nameusersystemelapsed
SISPA0.0860.0290.117
callGSVA0.0860.0280.113
callZSCORE0.0060.0020.008
cptSamples0.6500.1420.793
filterVars0.0000.0010.001
freqplot0.3720.0170.389
sortData0.0030.0010.005
waterfallplot0.2980.0030.306