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BioC 3.5: CHECK report for RiboProfiling on oaxaca

This page was generated on 2017-03-04 16:50:52 -0500 (Sat, 04 Mar 2017).

Package 1076/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RiboProfiling 1.5.2
A. Popa
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RiboProfiling
Last Changed Rev: 125928 / Revision: 127142
Last Changed Date: 2017-01-13 05:27:56 -0500 (Fri, 13 Jan 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK 

Summary

Package: RiboProfiling
Version: 1.5.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RiboProfiling_1.5.2.tar.gz
StartedAt: 2017-03-04 08:13:41 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 08:25:49 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 727.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: RiboProfiling.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RiboProfiling_1.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RiboProfiling.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RiboProfiling/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RiboProfiling’ version ‘1.5.2’
* 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 ‘RiboProfiling’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboProfiling’
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/RiboProfiling.Rcheck/00install.out’ for details.
* 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
applyShiftFeature: no visible global function definition for 'is'
aroundPromoter: no visible global function definition for 'is'
codonInfo: no visible global function definition for 'is'
countShiftReads: no visible global function definition for 'is'
histMatchLength: no visible global function definition for 'is'
orfRelativePos: no visible global function definition for 'is'
plotSummarizedCov: no visible global function definition for 'is'
readStartCov: no visible global function definition for 'is'
readsToStartOrEnd: no visible global function definition for 'is'
riboSeqFromBAM: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under ‘inst/doc’ ... 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
countsPlot        76.899  5.444  82.153
riboSeqFromBAM    57.672  3.782  61.270
countShiftReads   39.259  2.786  52.176
orfRelativePos    34.532  2.552  37.005
codonInfo         31.219  0.828  32.203
aroundPromoter     7.644  0.292   8.225
plotSummarizedCov  6.468  0.423   6.852
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/RiboProfiling.Rcheck/00check.log’
for details.


RiboProfiling.Rcheck/00install.out:

* installing *source* package ‘RiboProfiling’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboProfiling’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboProfiling’
* DONE (RiboProfiling)

RiboProfiling.Rcheck/RiboProfiling-Ex.timings:

nameusersystemelapsed
aroundPromoter7.6440.2928.225
codonInfo31.219 0.82832.203
codonPCA3.7970.3174.985
countShiftReads39.259 2.78652.176
countsPlot76.899 5.44482.153
histMatchLength0.3420.0190.409
orfRelativePos34.532 2.55237.005
plotSummarizedCov6.4680.4236.852
printPCA2.4780.1802.652
readStartCov4.1490.2484.379
readsToStartOrEnd0.0980.0070.104
riboSeqFromBAM57.672 3.78261.270