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CHECK report for SISPA on malbec1

This page was generated on 2021-05-06 12:29:12 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the SISPA package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1728/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SISPA 1.20.0  (landing page)
Bhakti Dwivedi
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/SISPA
Branch: RELEASE_3_12
Last Commit: aa0aff3
Last Changed Date: 2020-10-27 11:08:51 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: SISPA
Version: 1.20.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:SISPA.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings SISPA_1.20.0.tar.gz
StartedAt: 2021-05-06 06:08:06 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:11:38 -0400 (Thu, 06 May 2021)
EllapsedTime: 212.1 seconds
RetCode: 0
Status:   OK  
CheckDir: SISPA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:SISPA.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings SISPA_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/SISPA.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘1.20.0’
* 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 ‘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
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
cptSamples 2.268  3.976   2.916
SISPA      1.816  3.492   2.291
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/SISPA.Rcheck/00check.log’
for details.



Installation output

SISPA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL SISPA
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘SISPA’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘SISPA.Rmd’ using ‘UTF-8’ 
** 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
SISPA1.8163.4922.291
callGSVA1.0961.9281.385
callZSCORE0.0040.0000.005
cptSamples2.2683.9762.916
filterVars0.0000.0000.001
freqplot0.2880.0240.311
sortData0.0040.0000.003
waterfallplot0.2200.0080.230