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This page was generated on 2024-12-10 15:01 -0500 (Tue, 10 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4749
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 101/430HostnameOS / ArchINSTALLBUILDCHECK
dorothea 1.19.0  (landing page)
Pau Badia-i-Mompel
Snapshot Date: 2024-12-10 07:30 -0500 (Tue, 10 Dec 2024)
git_url: https://git.bioconductor.org/packages/dorothea
git_branch: devel
git_last_commit: 93c8143
git_last_commit_date: 2024-10-29 09:50:54 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  

CHECK results for dorothea on nebbiolo1

To the developers/maintainers of the dorothea 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: dorothea
Version: 1.19.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:dorothea.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings dorothea_1.19.0.tar.gz
StartedAt: 2024-12-10 12:13:39 -0500 (Tue, 10 Dec 2024)
EndedAt: 2024-12-10 12:27:59 -0500 (Tue, 10 Dec 2024)
EllapsedTime: 860.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: dorothea.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:dorothea.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings dorothea_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/dorothea.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘dorothea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dorothea’ version ‘1.19.0’
* package encoding: UTF-8
* 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 ‘dorothea’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 32.7Mb
  sub-directories of 1Mb or more:
    data       5.0Mb
    extdata   16.6Mb
    help       1.4Mb
    testdata   9.5Mb
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
run_viper 15.628  0.486  16.117
* 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 ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘dorothea.Rmd’ using rmarkdown
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-10 12:16:28] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] Contains 6 files.
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-10 12:16:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-12-10 12:16:28] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-10 12:16:28] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-10 12:16:28] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-12-10 12:16:28] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-12-10 12:16:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-12-10 12:19:18] [WARN]    [OmnipathR] HTTP 504
[2024-12-10 12:19:18] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504
[2024-12-10 12:19:23] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-12-10 12:20:54] [WARN]    [OmnipathR] HTTP 504
[2024-12-10 12:20:54] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504
[2024-12-10 12:20:59] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-12-10 12:22:29] [WARN]    [OmnipathR] HTTP 504
[2024-12-10 12:22:29] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504
[2024-12-10 12:22:29] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2024-12-10 12:22:29] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-12-10 12:22:30] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-12-10 12:22:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-10 12:22:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-10 12:22:30] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2024-12-10 12:22:30] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2024-12-10 12:22:30] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-12-10 12:22:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-12-10 12:24:00] [WARN]    [OmnipathR] HTTP 504
[2024-12-10 12:24:00] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504
[2024-12-10 12:24:05] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-12-10 12:25:35] [WARN]    [OmnipathR] HTTP 504
[2024-12-10 12:25:35] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504
[2024-12-10 12:25:40] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-12-10 12:27:11] [WARN]    [OmnipathR] HTTP 504
[2024-12-10 12:27:11] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504
[2024-12-10 12:27:11] [WARN]    [OmnipathR] Accessing `dorothea` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
[2024-12-10 12:27:11] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-12-10 12:27:11] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-12-10 12:27:11] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-12-10 12:27:11] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-12-10 12:27:11] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-12-10 12:27:20] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz`
[2024-12-10 12:27:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-10 12:27:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-10 12:27:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-10 12:27:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-10 12:27:20] [INFO]    [OmnipathR] Cache item `fd6905e4319c257381102863e2b4443ca0969f15` version 1: status changed from `unknown` to `started`.
[2024-12-10 12:27:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/fd6905e4319c257381102863e2b4443ca0969f15-1.rds`.
[2024-12-10 12:27:22] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/fd6905e4319c257381102863e2b4443ca0969f15-1.rds`.
[2024-12-10 12:27:22] [INFO]    [OmnipathR] Download ready [key=fd6905e4319c257381102863e2b4443ca0969f15, version=1]
[2024-12-10 12:27:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-10 12:27:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-10 12:27:22] [INFO]    [OmnipathR] Cache item `fd6905e4319c257381102863e2b4443ca0969f15` version 1: status changed from `started` to `ready`.
[2024-12-10 12:27:22] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-12-10 12:27:37] [TRACE]   [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any

Quitting from lines 67-69 [model] (dorothea.Rmd)
Error: processing vignette 'dorothea.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘dorothea.Rmd’

SUMMARY: processing the following file failed:
  ‘dorothea.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.21-data-experiment/meat/dorothea.Rcheck/00check.log’
for details.

Installation output

dorothea.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL dorothea
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘dorothea’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (dorothea)

Tests output

dorothea.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-10-21 r87258) -- "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.

> library(testthat)
> library(dorothea)
> 
> test_check("dorothea")
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 19 ]

[ FAIL 0 | WARN 11 | SKIP 0 | PASS 19 ]
> 
> proc.time()
   user  system elapsed 
 26.866   1.264  28.123

Example timings

dorothea.Rcheck/dorothea-Ex.timings

nameusersystemelapsed
df2regulon0.4330.0560.489
pipe0.0000.0000.001
run_viper15.628 0.48616.117