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CHECK report for methylGSA on malbec1

This page was generated on 2020-04-15 12:14:28 -0400 (Wed, 15 Apr 2020).

Package 1022/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylGSA 1.4.9
Xu Ren
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/methylGSA
Branch: RELEASE_3_10
Last Commit: 15f84c4
Last Changed Date: 2020-02-23 17:45:04 -0400 (Sun, 23 Feb 2020)
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: methylGSA
Version: 1.4.9
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:methylGSA.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings methylGSA_1.4.9.tar.gz
StartedAt: 2020-04-15 05:52:00 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:58:25 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 385.0 seconds
RetCode: 0
Status:  OK 
CheckDir: methylGSA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:methylGSA.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings methylGSA_1.4.9.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/methylGSA.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 ‘methylGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylGSA’ version ‘1.4.9’
* package encoding: UTF-8
* 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 ‘methylGSA’ 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 ... NOTE
getAnnot: no visible global function definition for ‘getAnnotation’
getAnnot: no visible binding for global variable
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
getAnnot: no visible binding for global variable
  ‘IlluminaHumanMethylationEPICanno.ilm10b4.hg19’
Undefined global functions or variables:
  IlluminaHumanMethylation450kanno.ilmn12.hg19
  IlluminaHumanMethylationEPICanno.ilm10b4.hg19 getAnnotation
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
methylglm 6.672  0.048   6.757
methylRRA 5.892  0.180   6.086
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/methylGSA.Rcheck/00check.log’
for details.



Installation output

methylGSA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL methylGSA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘methylGSA’ ...
** using staged installation
** 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 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 (methylGSA)

Tests output

methylGSA.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(methylGSA)

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)


Attaching package: 'methylGSA'

The following object is masked from 'package:graphics':

    barplot

> 
> test_check("methylGSA")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 33 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 43.356   1.228  44.233 

Example timings

methylGSA.Rcheck/methylGSA-Ex.timings

nameusersystemelapsed
barplot0.2400.0080.247
getDescription0.4160.0240.440
getGS0.3760.0120.422
methylRRA5.8920.1806.086
methylglm6.6720.0486.757
methylgometh000
prepareAnnot0.9720.0040.984
runExample000