Package: SISPA

Version: 1.16.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SISPA.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SISPA_1.16.0.tar.gz

StartedAt: 2020-04-15 03:23:50 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:25:57 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 126.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SISPA.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:SISPA.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings SISPA_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/SISPA.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.16.0’
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/SISPA.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL SISPA
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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)

name	user	system	elapsed
SISPA	0.052	0.036	0.093
callGSVA	0.052	0.028	0.100
callZSCORE	0.008	0.000	0.005
cptSamples	0.388	0.052	0.451
filterVars	0	0	0
freqplot	0.736	0.040	0.774
sortData	0.000	0.000	0.002
waterfallplot	0.228	0.000	0.232