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This page was generated on 2024-03-26 14:51:26 -0400 (Tue, 26 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
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Package 221/425HostnameOS / ArchINSTALLBUILDCHECK
marinerData 1.3.0  (landing page)
Eric Davis
Snapshot Date: 2024-03-26 07:30:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/marinerData
git_branch: devel
git_last_commit: bef5714
git_last_commit_date: 2023-10-24 09:24:23 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

CHECK results for marinerData on nebbiolo1


To the developers/maintainers of the marinerData package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: marinerData
Version: 1.3.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:marinerData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings marinerData_1.3.0.tar.gz
StartedAt: 2024-03-26 11:52:31 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 11:55:47 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 195.7 seconds
RetCode: 0
Status:   OK  
CheckDir: marinerData.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:marinerData.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings marinerData_1.3.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/marinerData.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘marinerData/DESCRIPTION’ ... OK
* this is package ‘marinerData’ version ‘1.3.0’
* 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 ‘marinerData’ 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

marinerData.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL marinerData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘marinerData’ ...
** 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 (marinerData)

Tests output

marinerData.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(marinerData)
> 
> test_check("marinerData")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 14.504   0.914  24.660 

Example timings

marinerData.Rcheck/marinerData-Ex.timings

nameusersystemelapsed
FS_5kbLoops.txt0.7890.0951.925
LEUK_HEK_PJA27_inter_30.hic0.7190.0481.372
LEUK_HEK_PJA30_inter_30.hic0.6930.0211.423
LIMA_0000.bedpe0.6430.0481.410
LIMA_0030.bedpe0.6630.0442.103
LIMA_0060.bedpe0.7140.0551.822
LIMA_0090.bedpe0.6860.0161.346
LIMA_0120.bedpe0.6470.0311.196
LIMA_0240.bedpe0.6580.0291.307
LIMA_0360.bedpe0.6470.0481.242
LIMA_1440.bedpe0.6810.0441.340
WT_5kbLoops.txt0.6860.0161.298