Back to Build/check report for BioC 3.20 experimental data
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This page was generated on 2024-08-22 14:51 -0400 (Thu, 22 Aug 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4703
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 107/425HostnameOS / ArchINSTALLBUILDCHECK
easierData 1.11.0  (landing page)
Oscar Lapuente-Santana
Snapshot Date: 2024-08-22 07:30 -0400 (Thu, 22 Aug 2024)
git_url: https://git.bioconductor.org/packages/easierData
git_branch: devel
git_last_commit: 768730d
git_last_commit_date: 2024-04-30 11:10:02 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  


CHECK results for easierData on nebbiolo2

To the developers/maintainers of the easierData 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: easierData
Version: 1.11.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:easierData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings easierData_1.11.0.tar.gz
StartedAt: 2024-08-22 11:27:31 -0400 (Thu, 22 Aug 2024)
EndedAt: 2024-08-22 11:41:15 -0400 (Thu, 22 Aug 2024)
EllapsedTime: 823.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: easierData.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:easierData.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings easierData_1.11.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/easierData.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘easierData/DESCRIPTION’ ... OK
* this is package ‘easierData’ version ‘1.11.0’
* 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 ‘easierData’ 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘easierData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: list_easierData
> ### Title: List the datasets
> ### Aliases: list_easierData
> 
> ### ** Examples
> 
> df <- list_easierData()
Error in value[[3L]](cond) : failed to connect
  reason: Timeout was reached: [bioconductor.org] SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Calls: list_easierData ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
* 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: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.20-data-experiment/meat/easierData.Rcheck/00check.log’
for details.


Installation output

easierData.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL easierData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘easierData’ ...
** 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 (easierData)

Tests output

easierData.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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.

> library(testthat)
> library(easierData)
> 
> test_check("easierData")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
 26.770   1.357  32.278 

Example timings

easierData.Rcheck/easierData-Ex.timings

nameusersystemelapsed
get_HGNC_annotation0.0000.0000.001
get_Mariathasan2018_PDL1_treatment000
get_TCGA_mean_pancancer000
get_TCGA_sd_pancancer0.0010.0000.000
get_cor_scores_genes000
get_group_lrpairs000
get_intercell_networks000
get_lr_frequency_TCGA000
get_opt_models0.0010.0000.000
get_opt_xtrain_stats000
get_scores_signature_genes000