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This page was generated on 2022-01-18 11:05:59 -0500 (Tue, 18 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for methylGSA on nebbiolo1


To the developers/maintainers of the methylGSA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylGSA.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 1117/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylGSA 1.13.0  (landing page)
Xu Ren
Snapshot Date: 2022-01-17 13:55:17 -0500 (Mon, 17 Jan 2022)
git_url: https://git.bioconductor.org/packages/methylGSA
git_branch: master
git_last_commit: 1c17b01
git_last_commit_date: 2021-10-26 12:45:38 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'clusterProfiler' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'clusterProfiler' which is not available

Summary

Package: methylGSA
Version: 1.13.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:methylGSA.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings methylGSA_1.13.0.tar.gz
StartedAt: 2022-01-17 19:52:06 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 19:57:34 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 328.2 seconds
RetCode: 0
Status:   OK  
CheckDir: methylGSA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:methylGSA.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings methylGSA_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/methylGSA.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.13.0’
* 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 (user + system) or elapsed time > 5s
           user system elapsed
methylglm 5.056  0.104    5.16
* 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-3.15-bioc/meat/methylGSA.Rcheck/00check.log’
for details.



Installation output

methylGSA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL methylGSA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 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")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
 36.662   1.697  38.405 

Example timings

methylGSA.Rcheck/methylGSA-Ex.timings

nameusersystemelapsed
barplot0.2360.0320.268
getDescription0.1880.0160.204
getGS0.2740.0350.308
methylRRA3.9520.1294.082
methylglm5.0560.1045.160
methylgometh0.0010.0000.000
prepareAnnot0.5720.0160.588
runExample0.0010.0000.001