BioC 3.5: CHECK report for NGScopy on malbec2

Package: NGScopy

Version: 1.10.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings NGScopy_1.10.0.tar.gz

StartedAt: 2017-08-16 00:59:07 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:00:12 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 64.9 seconds

RetCode: 0

Status:  OK

CheckDir: NGScopy.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings NGScopy_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/NGScopy.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NGScopy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NGScopy’ version ‘1.10.0’
* 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 ‘NGScopy’ 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 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
.count_starts: no visible global function definition for ‘median’
.count_starts: no visible global function definition for ‘sd’
.help_segmtype: no visible global function definition for ‘help’
.make_windows : .unit: no visible global function definition for
  ‘median’
.make_windows : .unit: no visible global function definition for ‘sd’
.plot_out: no visible global function definition for ‘pdf’
.plot_out: no visible global function definition for ‘dev.off’
.unit_plot_out: no visible global function definition for ‘par’
read_regions: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  dev.off help median par pdf read.table sd
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "median", "sd")
  importFrom("utils", "help", "read.table")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
  ‘ngscopy-case1b-cmdline.out’
Please remove them from your package.
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/NGScopy.Rcheck/00check.log’
for details.

* installing *source* package ‘NGScopy’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (NGScopy)

name	user	system	elapsed
NGScopy-class	0.784	0.024	0.856
df.to.gr	0.004	0.000	0.000
help_segmtype	0	0	0
ngscopy_cmdline_example	0.012	0.000	0.013
ngscopy_unittest	0.000	0.000	0.001
parse_segmtype	0.000	0.000	0.001
read_regions	0.008	0.000	0.006