BioC 3.5: CHECK report for SISPA on veracruz2

Package: SISPA

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SISPA_1.6.0.tar.gz

StartedAt: 2017-08-16 08:21:14 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 08:23:30 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 136.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SISPA.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SISPA_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SISPA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.6.0’
* 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 loading without being on the library search path ... 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’
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/SISPA.Rcheck/00check.log’
for details.

* installing *source* package ‘SISPA’ ...
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SISPA)

name	user	system	elapsed
SISPA	0.037	0.003	0.043
callGSVA	0.191	0.006	0.204
callZSCORE	0.005	0.001	0.007
cptSamples	0.784	0.005	0.810
filterVars	0.001	0.001	0.002
freqplot	0.931	0.026	0.976
sortData	0.002	0.000	0.002
waterfallplot	0.776	0.002	0.804