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CHECK report for GeneMeta on malbec1

This page was generated on 2020-04-15 12:04:28 -0400 (Wed, 15 Apr 2020).

Package 656/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneMeta 1.58.0
Bioconductor Package Maintainer
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/GeneMeta
Branch: RELEASE_3_10
Last Commit: e7e32ae
Last Changed Date: 2019-10-29 13:07:34 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  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: GeneMeta
Version: 1.58.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GeneMeta.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GeneMeta_1.58.0.tar.gz
StartedAt: 2020-04-15 00:15:39 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:17:06 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 86.6 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneMeta.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GeneMeta.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GeneMeta_1.58.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/GeneMeta.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneMeta/DESCRIPTION’ ... OK
* this is package ‘GeneMeta’ version ‘1.58.0’
* 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 ‘GeneMeta’ 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.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘Biobase’
A package should be listed in only one of these fields.
* 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 ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘genefilter’
  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
File ‘GeneMeta/R/meta1.R’:
  .onLoad calls:
    require("methods")

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

CountPlot: no visible global function definition for ‘plot’
CountPlot: no visible global function definition for ‘points’
IDRplot: no visible global function definition for ‘plot’
IDRplot: no visible global function definition for ‘lines’
getdF_matrix: no visible global function definition for ‘rowttests’
zScores: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  lines pchisq plot points rowttests
Consider adding
  importFrom("graphics", "lines", "plot", "points")
  importFrom("stats", "pchisq")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: CountPlot.Rd:39: Dropping empty section \keyword
prepare_Rd: CountPlot.Rd:30: Dropping empty section \value
prepare_Rd: CountPlot.Rd:38: Dropping empty section \examples
prepare_Rd: tau.Rd:25: Dropping empty section \details
prepare_Rd: tau.Rd:26: Dropping empty section \value
* 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
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/GeneMeta.Rcheck/00check.log’
for details.



Installation output

GeneMeta.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL GeneMeta
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘GeneMeta’ ...
** 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 (GeneMeta)

Tests output


Example timings

GeneMeta.Rcheck/GeneMeta-Ex.timings

nameusersystemelapsed
Nevins0.2560.0040.258
dstar0.0040.0000.006
f.Q000
tau000
zscore0.4040.0040.408