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This page was generated on 2023-10-12 14:51:35 -0400 (Thu, 12 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
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

Package 221/421HostnameOS / ArchINSTALLBUILDCHECK
marinerData 1.0.0  (landing page)
Eric Davis
Snapshot Date: 2023-10-12 07:30:02 -0400 (Thu, 12 Oct 2023)
git_url: https://git.bioconductor.org/packages/marinerData
git_branch: RELEASE_3_17
git_last_commit: 39efea9
git_last_commit_date: 2023-04-25 10:52:20 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 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: 1.0.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:marinerData.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings marinerData_1.0.0.tar.gz
StartedAt: 2023-10-12 11:36:41 -0400 (Thu, 12 Oct 2023)
EndedAt: 2023-10-12 11:40:22 -0400 (Thu, 12 Oct 2023)
EllapsedTime: 220.4 seconds
RetCode: 0
Status:   OK  
CheckDir: marinerData.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:marinerData.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings marinerData_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-data-experiment/meat/marinerData.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘marinerData/DESCRIPTION’ ... OK
* this is package ‘marinerData’ version ‘1.0.0’
* 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 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 loading without being on the library search path ... OK
* checking 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘marinerData.Rmd’ using ‘UTF-8’... OK
 NONE
* 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-3.17-bioc/R/bin/R CMD INSTALL marinerData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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 version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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.

> # 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 
 14.635   1.556  31.733 

Example timings

marinerData.Rcheck/marinerData-Ex.timings

nameusersystemelapsed
FS_5kbLoops.txt0.8520.1122.582
LEUK_HEK_PJA27_inter_30.hic0.7240.1721.829
LEUK_HEK_PJA30_inter_30.hic0.7020.0511.816
LIMA_0000.bedpe0.6720.0802.124
LIMA_0030.bedpe0.6720.0832.132
LIMA_0060.bedpe0.6700.0842.131
LIMA_0090.bedpe0.6460.0841.693
LIMA_0120.bedpe0.6720.0682.499
LIMA_0240.bedpe0.6820.0641.855
LIMA_0360.bedpe0.6320.0682.269
LIMA_1440.bedpe0.6540.0831.711
WT_5kbLoops.txt0.7020.0692.203