| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:40:36 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 518/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.8.0 (landing page) Pau Badia-i-Mompel
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the decoupleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decoupleR.git to reflect on this report. See Troubleshooting Build Report for more information. - 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: decoupleR |
| Version: 2.8.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings decoupleR_2.8.0.tar.gz |
| StartedAt: 2023-11-02 09:50:21 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 09:56:49 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 387.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: decoupleR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings decoupleR_2.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/decoupleR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.8.0’
* 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 ‘decoupleR’ 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 dependencies in R code ... NOTE
[2023-11-02 09:51:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-02 09:51:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:51:01] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-11-02 09:51:01] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-11-02 09:51:01] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-11-02 09:51:01] [TRACE] [OmnipathR] Contains 8 files.
[2023-11-02 09:51:01] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-11-02 09:51:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-02 09:51:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:51:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-11-02 09:51:01] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2023-11-02 09:51:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-11-02 09:51:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:51:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-11-02 09:51:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:51:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-11-02 09:51:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:51:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-11-02 09:51:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:51:01] [TRACE] [OmnipathR] Cache locked: FALSE
* 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 ‘decoupleR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_dorothea
> ### Title: DoRothEA gene regulatory network.
> ### Aliases: get_dorothea
>
> ### ** Examples
>
> dorothea <- get_dorothea(organism='human', levels=c('A', 'B', 'C'))
[2023-11-02 09:54:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2023-11-02 09:54:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2023-11-02 09:54:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2023-11-02 09:54:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2023-11-02 09:54:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2023-11-02 09:54:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2023-11-02 09:54:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2023-11-02 09:54:25] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2023-11-02 09:54:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-02 09:54:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:54:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-02 09:54:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:54:25] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`.
[2023-11-02 09:54:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2023-11-02 09:54:28] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2023-11-02 09:54:28] [INFO] [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1]
[2023-11-02 09:54:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-02 09:54:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:54:28] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`.
[2023-11-02 09:54:28] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 906959 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
[2023-11-02 09:56:30] [TRACE] [OmnipathR] Cache locked: FALSE
[2023-11-02 09:56:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-11-02 09:56:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:56:32] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-11-02 09:56:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:56:32] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2023-11-02 09:56:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-02 09:56:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:56:32] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2023-11-02 09:56:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-02 09:56:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:56:32] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2023-11-02 09:56:32] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2023-11-02 09:56:32] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2023-11-02 09:56:32] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/decoupleR.Rcheck/00check.log’
for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘decoupleR’ ... ** using staged installation ** R ** 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 (decoupleR)
decoupleR.Rcheck/tests/testthat.Rout.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
> library(testthat)
> library(decoupleR)
>
> test_check("decoupleR")
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
[2023-11-02 09:56:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-02 09:56:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:56:30] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-11-02 09:56:30] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-11-02 09:56:30] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-11-02 09:56:30] [TRACE] [OmnipathR] Contains 5 files.
[2023-11-02 09:56:30] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-11-02 09:56:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-02 09:56:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:56:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-11-02 09:56:30] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2023-11-02 09:56:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-11-02 09:56:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:56:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-11-02 09:56:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:56:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-11-02 09:56:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:56:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-11-02 09:56:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:56:30] [TRACE] [OmnipathR] Cache locked: FALSE
[2023-11-02 09:56:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-11-02 09:56:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:56:32] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-11-02 09:56:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:56:32] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2023-11-02 09:56:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-02 09:56:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:56:32] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2023-11-02 09:56:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-11-02 09:56:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-11-02 09:56:32] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2023-11-02 09:56:32] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2023-11-02 09:56:32] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2023-11-02 09:56:32] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.125 | 0.000 | 0.130 | |
| convert_f_defaults | 0.090 | 0.004 | 0.099 | |
| decouple | 0.001 | 0.000 | 0.001 | |
| dot-fit_preprocessing | 0.032 | 0.000 | 0.033 | |
| extract_sets | 0.036 | 0.000 | 0.036 | |
| filt_minsize | 0.072 | 0.000 | 0.072 | |
| get_collectri | 133.942 | 7.984 | 158.894 | |