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CHECK report for RNAprobR on merida1

This page was generated on 2019-12-10 13:21:09 -0500 (Tue, 10 Dec 2019).

Package 1456/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAprobR 1.18.0
Nikos Sidiropoulos
Snapshot Date: 2019-12-09 16:45:09 -0500 (Mon, 09 Dec 2019)
URL: https://git.bioconductor.org/packages/RNAprobR
Branch: RELEASE_3_10
Last Commit: 35a155a
Last Changed Date: 2019-10-29 13:09:12 -0500 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RNAprobR
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RNAprobR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RNAprobR_1.18.0.tar.gz
StartedAt: 2019-12-10 05:23:45 -0500 (Tue, 10 Dec 2019)
EndedAt: 2019-12-10 05:28:07 -0500 (Tue, 10 Dec 2019)
EllapsedTime: 261.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: RNAprobR.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RNAprobR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RNAprobR_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/RNAprobR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAprobR/DESCRIPTION’ ... OK
* this is package ‘RNAprobR’ version ‘1.18.0’
* 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 ‘RNAprobR’ 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 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'GenomicRangesList' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/RNAprobR.Rcheck/00check.log’
for details.



Installation output

RNAprobR.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RNAprobR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘RNAprobR’ ...
** using staged installation
** R
** inst
** 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 (RNAprobR)

Tests output


Example timings

RNAprobR.Rcheck/RNAprobR-Ex.timings

nameusersystemelapsed
BED2txDb0.9370.0430.982
GR2norm_df0.4620.0120.477
bedgraph2norm3.3570.1333.505
comp0.2150.0010.217
compdata0.3480.0030.353
correct_oversaturation0.1030.0010.105
dtcr0.4760.0130.492
k2n_calc0.0110.0010.013
norm2bedgraph0.8440.0040.850
norm_df2GR0.0210.0000.023
plotRNA0.3080.0020.312
plotReads0.1570.0010.159
readsamples0.0250.0010.026
slograt0.4280.0010.434
swinsor0.2860.0020.289
swinsor_vector0.0420.0010.044
winsor0.0040.0010.004