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CHECK report for RmiR on malbec2

This page was generated on 2019-04-09 11:27:57 -0400 (Tue, 09 Apr 2019).

Package 1364/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RmiR 1.39.0
Francesco Favero
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/RmiR
Branch: master
Last Commit: 8d8dd4a
Last Changed Date: 2018-10-30 11:54:28 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: RmiR
Version: 1.39.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RmiR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RmiR_1.39.0.tar.gz
StartedAt: 2019-04-09 03:16:36 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:18:11 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 95.4 seconds
RetCode: 0
Status:  OK 
CheckDir: RmiR.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RmiR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RmiR_1.39.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/RmiR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RmiR/DESCRIPTION’ ... OK
* this is package ‘RmiR’ version ‘1.39.0’
* 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 ‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
RmiR       16.538  0.340  18.711
RmiRtc      8.005  0.028   8.034
plotRmiRtc  7.172  0.024   7.198
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/RmiR.Rcheck/00check.log’
for details.



Installation output

RmiR.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL RmiR
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘RmiR’ ...
** using staged installation
** R
** data
** 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 (RmiR)

Tests output


Example timings

RmiR.Rcheck/RmiR-Ex.timings

nameusersystemelapsed
RmiR16.538 0.34018.711
RmiRtc8.0050.0288.034
data0.030.000.03
plotRmiRtc7.1720.0247.198