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This page was generated on 2021-12-03 13:04:59 -0500 (Fri, 03 Dec 2021).

CHECK results for recountmethylation on nebbiolo2

To the developers/maintainers of the recountmethylation package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/recountmethylation.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 1567/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
recountmethylation 1.4.0  (landing page)
Sean K Maden
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/recountmethylation
git_branch: RELEASE_3_14
git_last_commit: 13a580a
git_last_commit_date: 2021-10-26 13:02:20 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: recountmethylation
Version: 1.4.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:recountmethylation.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings recountmethylation_1.4.0.tar.gz
StartedAt: 2021-12-02 08:40:52 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 08:42:03 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 71.3 seconds
RetCode: 0
Status:   OK  
CheckDir: recountmethylation.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:recountmethylation.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings recountmethylation_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/recountmethylation.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recountmethylation/DESCRIPTION’ ... OK
* this is package ‘recountmethylation’ version ‘1.4.0’
* 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 ‘recountmethylation’ 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
gds_idat2rg 18.517  1.383  23.063
get_rmdl     0.238  0.030   6.428
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-servermatrix.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: OK


Installation output

recountmethylation.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL recountmethylation
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘recountmethylation’ ...
** using staged installation
** R
** 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 (recountmethylation)

Tests output

recountmethylation.Rcheck/tests/test-servermatrix.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> testthat::context("Test the server matrix properties")
> 
> testthat::test_that("Properties of server matrix returned from get_rmdl 
+     and servermatrix", {
+     sm <- recountmethylation::get_servermatrix()
+     testthat::expect_true(is(sm, "matrix"))
+     testthat::expect_equal(ncol(sm), 4)
+     testthat::expect_true(is(sm[,1], "character"))
+ })
Test passed 🥳
> 
> proc.time()
   user  system elapsed 
  1.242   0.105   6.462 

Example timings

recountmethylation.Rcheck/recountmethylation-Ex.timings

nameusersystemelapsed
data_mdpost0.0580.0050.063
gds_idat2rg18.517 1.38323.063
gds_idatquery1.8310.1894.653
get_rmdl0.2380.0306.428
get_servermatrix0.0040.0000.004
getdb000
getrg0.1640.0000.164
hread0.0050.0000.005
matchds_1to20.0010.0000.001
rgse0.1140.0050.132
servermatrix0.0210.0000.354
smfilt0.0020.0000.002