Back to Build/check report for BioC 3.20 annotations
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This page was generated on 2024-12-18 08:30 -0500 (Wed, 18 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4743
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 17/47HostnameOS / ArchINSTALLBUILDCHECK
ENCODExplorerData 0.99.5  (landing page)
Eric Fournier
Snapshot Date: 2024-12-18 06:00 -0500 (Wed, 18 Dec 2024)
git_url: https://git.bioconductor.org/packages/ENCODExplorerData
git_branch: RELEASE_3_20
git_last_commit: c69d7b9
git_last_commit_date: 2019-12-04 22:43:28 -0500 (Wed, 04 Dec 2019)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published


CHECK results for ENCODExplorerData on nebbiolo2

To the developers/maintainers of the ENCODExplorerData 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: ENCODExplorerData
Version: 0.99.5
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ENCODExplorerData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ENCODExplorerData_0.99.5.tar.gz
StartedAt: 2024-12-18 06:33:25 -0500 (Wed, 18 Dec 2024)
EndedAt: 2024-12-18 06:43:08 -0500 (Wed, 18 Dec 2024)
EllapsedTime: 582.9 seconds
RetCode: 0
Status:   OK  
CheckDir: ENCODExplorerData.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ENCODExplorerData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ENCODExplorerData_0.99.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-data-annotation/meat/ENCODExplorerData.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘ENCODExplorerData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ENCODExplorerData’ version ‘0.99.5’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘ENCODExplorerData’ 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 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
encode_df_full                    47.076  2.036  49.407
encode_df_lite                    18.388  0.920  19.564
get_schemas                        7.653  0.420  26.223
clean_table                        0.166  0.004 122.091
fetch_and_clean_raw_ENCODE_tables  0.091  0.018 121.132
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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

ENCODExplorerData.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ENCODExplorerData
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘ENCODExplorerData’ ...
** 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 (ENCODExplorerData)

Tests output

ENCODExplorerData.Rcheck/tests/runTests.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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.

> #Run all tests in the ENCODExplorer package
> BiocGenerics:::testPackage("ENCODExplorerData")


RUNIT TEST PROTOCOL -- Wed Dec 18 06:43:03 2024 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ENCODExplorerData RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  0.534   0.064   0.586 

Example timings

ENCODExplorerData.Rcheck/ENCODExplorerData-Ex.timings

nameusersystemelapsed
build_file_db_from_raw_tables000
clean_table 0.166 0.004122.091
encode_df_full47.076 2.03649.407
encode_df_lite18.388 0.92019.564
fetch_and_clean_raw_ENCODE_tables 0.091 0.018121.132
generate_encode_df_full0.0010.0000.000
generate_encode_df_lite000
get_encode_types0.0970.0170.445
get_schema_urls0.0970.0060.265
get_schemas 7.653 0.42026.223