Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:41 -0400 (Fri, 15 Oct 2021).

CHECK results for GeneMeta on nebbiolo1

To the developers/maintainers of the GeneMeta package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneMeta.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 717/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneMeta 1.64.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/GeneMeta
git_branch: RELEASE_3_13
git_last_commit: 24685d2
git_last_commit_date: 2021-05-19 11:35:57 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GeneMeta
Version: 1.64.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GeneMeta.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GeneMeta_1.64.0.tar.gz
StartedAt: 2021-10-14 09:56:42 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:58:14 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 92.5 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneMeta.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GeneMeta.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GeneMeta_1.64.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/GeneMeta.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.64.0’
* 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 ‘points’
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 points rowttests
Consider adding
  importFrom("graphics", "lines", "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-3.13-bioc/meat/GeneMeta.Rcheck/00check.log’
for details.



Installation output

GeneMeta.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL GeneMeta
###
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* installing to library ‘/home/biocbuild/bbs-3.13-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
Nevins0.2340.0010.233
dstar0.0030.0000.004
f.Q0.0000.0000.001
tau0.0000.0000.001
zscore0.2940.0150.309