BioC 3.4: CHECK report for RmiR on moscato1

Package: RmiR

Version: 1.29.0

Command: D:\biocbld\bbs-3.4-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings RmiR_1.29.0.tar.gz

StartedAt: 2016-09-20 15:35:30 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 15:37:37 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 126.8 seconds

RetCode: 0

Status:  OK

CheckDir: RmiR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbld\bbs-3.4-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings RmiR_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/RmiR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RmiR/DESCRIPTION' ... OK
* this is package 'RmiR' version '1.29.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'RmiR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' call to 'RSVGTipsDevice' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'RSVGTipsDevice' 'RmiR.Hs.miRNA'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotRmiRtc: no visible global function definition for 'devSVGTips'
plotRmiRtc: no visible global function definition for 'plot'
plotRmiRtc: no visible global function definition for
  'setSVGShapeToolTip'
plotRmiRtc: no visible global function definition for 'setSVGShapeURL'
plotRmiRtc: no visible global function definition for 'points'
plotRmiRtc: no visible global function definition for 'lines'
plotRmiRtc: no visible global function definition for 'legend'
plotRmiRtc: no visible global function definition for 'dev.off'
readRmiRtc: no visible global function definition for 'write.table'
Undefined global functions or variables:
  dev.off devSVGTips legend lines plot points setSVGShapeToolTip
  setSVGShapeURL write.table
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("utils", "write.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 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 or elapsed time > 5s
            user system elapsed
RmiR       13.64   0.31   50.24
RmiRtc      5.43   0.08    5.50
plotRmiRtc  5.16   0.03    5.70
* 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: 4 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/RmiR.Rcheck/00check.log'
for details.

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

name	user	system	elapsed
RmiR	13.64	0.31	50.24
RmiRtc	5.43	0.08	5.50
data	0.03	0.00	0.04
plotRmiRtc	5.16	0.03	5.70