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CHECK report for RTopper on merida1

This page was generated on 2019-04-16 11:56:04 -0400 (Tue, 16 Apr 2019).

Package 1365/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTopper 1.28.0
Luigi Marchionni
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/RTopper
Branch: RELEASE_3_8
Last Commit: 483ee0e
Last Changed Date: 2018-10-30 11:41:48 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RTopper
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RTopper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RTopper_1.28.0.tar.gz
StartedAt: 2019-04-16 02:32:24 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:33:44 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 79.8 seconds
RetCode: 0
Status:  OK 
CheckDir: RTopper.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RTopper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RTopper_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/RTopper.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTopper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTopper’ version ‘1.28.0’
* 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 ‘RTopper’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘limma’
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
computeScore: no visible global function definition for ‘glm’
computeScore: no visible global function definition for ‘binomial’
computeScore: no visible global function definition for ‘AIC’
convertToDr: no visible binding for global variable ‘data’
myMean : medianM: no visible binding for global variable ‘median’
Undefined global functions or variables:
  AIC binomial data glm median
Consider adding
  importFrom("stats", "AIC", "binomial", "glm", "median")
  importFrom("utils", "data")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
computeDrStat 16.298  0.457  16.873
convertToDr    5.398  0.036   5.473
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/RTopper.Rcheck/00check.log’
for details.



Installation output

RTopper.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RTopper
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘RTopper’ ...
** R
** data
** 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
* DONE (RTopper)

Tests output


Example timings

RTopper.Rcheck/RTopper-Ex.timings

nameusersystemelapsed
adjustPvalGSE0.0280.0040.034
combineGSE0.0070.0010.008
computeDrStat16.298 0.45716.873
convertToDr5.3980.0365.473
dat0.0840.0080.091
fgsList0.0150.0010.016
gseResultsSep0.0180.0020.020
intScores0.0060.0010.007
pheno0.0990.0090.111
runBatchGSE0.0820.0050.089
sepScores0.0140.0020.015