| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-06 11:37:43 -0400 (Mon, 06 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4661 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4392 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4423 |
| 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 511/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.11.0 (landing page) Pau Badia-i-Mompel
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: decoupleR |
| Version: 2.11.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.11.0.tar.gz |
| StartedAt: 2024-05-04 02:50:21 -0400 (Sat, 04 May 2024) |
| EndedAt: 2024-05-04 03:30:22 -0400 (Sat, 04 May 2024) |
| EllapsedTime: 2400.9 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: decoupleR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/decoupleR.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.11.0’
* 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 ‘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 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 dependencies in R code ... NOTE
[2024-05-04 02:51:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 02:51:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 02:51:36] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-04 02:51:36] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-05-04 02:51:36] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-04 02:51:36] [TRACE] [OmnipathR] Contains 8 files.
[2024-05-04 02:51:36] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-05-04 02:51:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 02:51:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 02:51:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-04 02:51:36] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-04 02:51:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-04 02:51:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 02:51:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-04 02:51:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 02:51:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-04 02:51:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 02:51:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-04 02:51:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 02:51:36] [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 ... WARNING
Missing link or links in Rd file 'run_gsva.Rd':
‘GSVA::gsva’ ‘GeneSetCollection’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_dorothea 1279.189 13.338 1608.236
get_collectri 313.055 3.423 403.341
run_fgsea 26.646 0.410 32.521
run_aucell 17.289 1.678 23.216
get_progeny 10.016 0.832 20.545
run_consensus 4.485 0.031 5.485
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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")
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[2024-05-04 03:29:58] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 03:29:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 03:29:58] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-04 03:29:58] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-05-04 03:29:58] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-04 03:29:58] [TRACE] [OmnipathR] Contains 8 files.
[2024-05-04 03:29:58] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-05-04 03:29:58] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 03:29:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 03:29:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-04 03:29:59] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-04 03:29:59] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-04 03:29:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 03:29:59] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-04 03:29:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 03:29:59] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-04 03:29:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 03:29:59] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-04 03:29:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 03:29:59] [TRACE] [OmnipathR] Cache locked: FALSE
[2024-05-04 03:30:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-04 03:30:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 03:30:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-04 03:30:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 03:30:00] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-04 03:30:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 03:30:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 03:30:00] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-04 03:30:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 03:30:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 03:30:01] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-05-04 03:30:01] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-05-04 03:30:01] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-04 03:30:01] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-04 03:30:19] [TRACE] [OmnipathR] HTTP 200
[2024-05-04 03:30:19] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-05-04 03:30:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 03:30:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 03:30:19] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-05-04 03:30:19] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-05-04 03:30:19] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-05-04 03:30:19] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-05-04 03:30:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 03:30:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 03:30:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 03:30:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 03:30:20] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-05-04 03:30:20] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-05-04 03:30:20] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-05-04 03:30:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-05-04 03:30:21] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-05-04 03:30:21] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-05-04 03:30:21] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 03:30:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 03:30:21] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-05-04 03:30:21] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-05-04 03:30:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-04 03:30:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-04 03:30:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-04 03:30:22] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-04 03:30:22] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-04 03:30:22] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-04 03:30:22] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-04 03:30:22] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-04 03:30:22] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.178 | 0.028 | 0.284 | |
| convert_f_defaults | 0.063 | 0.009 | 0.094 | |
| decouple | 0.002 | 0.001 | 0.003 | |
| dot-fit_preprocessing | 0.048 | 0.007 | 0.069 | |
| extract_sets | 0.047 | 0.002 | 0.062 | |
| filt_minsize | 0.101 | 0.002 | 0.128 | |
| get_collectri | 313.055 | 3.423 | 403.341 | |
| get_dorothea | 1279.189 | 13.338 | 1608.236 | |
| get_profile_of | 0.001 | 0.001 | 0.002 | |
| get_progeny | 10.016 | 0.832 | 20.545 | |
| get_resource | 0.708 | 0.044 | 2.150 | |
| get_toy_data | 0.005 | 0.001 | 0.006 | |
| intersect_regulons | 0.051 | 0.003 | 0.062 | |
| pipe | 0.000 | 0.000 | 0.001 | |
| pivot_wider_profile | 0.000 | 0.001 | 0.001 | |
| randomize_matrix | 0.001 | 0.000 | 0.001 | |
| rename_net | 0.074 | 0.001 | 0.093 | |
| run_aucell | 17.289 | 1.678 | 23.216 | |
| run_consensus | 4.485 | 0.031 | 5.485 | |
| run_fgsea | 26.646 | 0.410 | 32.521 | |
| run_gsva | 3.263 | 0.191 | 4.537 | |
| run_mdt | 0.276 | 0.026 | 0.501 | |
| run_mlm | 0.209 | 0.004 | 0.342 | |
| run_ora | 1.092 | 0.012 | 1.489 | |
| run_udt | 0.675 | 0.010 | 0.829 | |
| run_ulm | 0.166 | 0.003 | 0.203 | |
| run_viper | 1.560 | 0.129 | 1.999 | |
| run_wmean | 1.735 | 0.023 | 2.030 | |
| run_wsum | 1.597 | 0.017 | 1.942 | |
| show_methods | 0.116 | 0.010 | 0.159 | |
| show_resources | 0.133 | 0.006 | 0.615 | |
| tidyeval | 0.000 | 0.000 | 0.001 | |