BioC 3.5: CHECK report for SISPA on malbec2

Package: SISPA

Version: 1.6.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SISPA_1.6.0.tar.gz

StartedAt: 2017-10-18 02:33:41 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:35:36 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 114.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SISPA.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SISPA_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/SISPA.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.6.0’
* 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’
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/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	0.048	0.012	0.068
callGSVA	0.172	0.036	0.214
callZSCORE	0.004	0.000	0.004
cptSamples	0.588	0.028	0.621
filterVars	0	0	0
freqplot	1.164	0.060	1.224
sortData	0.004	0.000	0.002
waterfallplot	0.672	0.000	0.674