Back to Build/check report for BioC 3.20 experimental data |
|
This page was generated on 2024-07-02 14:51 -0400 (Tue, 02 Jul 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" | 4693 |
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 100/425 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
dorothea 1.17.0 (landing page) Pau Badia-i-Mompel
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | ||||||||
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. |
Package: dorothea |
Version: 1.17.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data dorothea |
StartedAt: 2024-07-02 10:22:17 -0400 (Tue, 02 Jul 2024) |
EndedAt: 2024-07-02 10:33:11 -0400 (Tue, 02 Jul 2024) |
EllapsedTime: 654.8 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data dorothea ### ############################################################################## ############################################################################## * checking for file ‘dorothea/DESCRIPTION’ ... OK * preparing ‘dorothea’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘dorothea.Rmd’ using rmarkdown [2024-07-02 10:23:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-02 10:23:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-02 10:23:01] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-07-02 10:23:01] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-07-02 10:23:01] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-07-02 10:23:01] [TRACE] [OmnipathR] Contains 8 files. [2024-07-02 10:23:01] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-07-02 10:23:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-02 10:23:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-02 10:23:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-07-02 10:23:01] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-07-02 10:23:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-07-02 10:23:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-02 10:23:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-07-02 10:23:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-02 10:23:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-07-02 10:23:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-02 10:23:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-07-02 10:23:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-02 10:23:02] [TRACE] [OmnipathR] Cache locked: FALSE [2024-07-02 10:23:02] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-07-02 10:23:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-02 10:23:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-02 10:23:02] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-07-02 10:23:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-02 10:23:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-02 10:23:02] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-07-02 10:23:02] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-07-02 10:23:02] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-07-02 10:23:02] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-07-02 10:24:33] [WARN] [OmnipathR] HTTP 504 [2024-07-02 10:24:33] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 [2024-07-02 10:24:38] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-07-02 10:26:08] [WARN] [OmnipathR] HTTP 504 [2024-07-02 10:26:08] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 [2024-07-02 10:26:13] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-07-02 10:27:44] [WARN] [OmnipathR] HTTP 504 [2024-07-02 10:27:44] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 [2024-07-02 10:27:44] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-07-02 10:27:44] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-07-02 10:27:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-02 10:27:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-02 10:27:44] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2. [2024-07-02 10:27:44] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html [2024-07-02 10:27:44] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-07-02 10:27:44] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-07-02 10:29:14] [WARN] [OmnipathR] HTTP 504 [2024-07-02 10:29:14] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 [2024-07-02 10:29:19] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-07-02 10:30:50] [WARN] [OmnipathR] HTTP 504 [2024-07-02 10:30:50] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 [2024-07-02 10:30:55] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-07-02 10:32:26] [WARN] [OmnipathR] HTTP 504 [2024-07-02 10:32:26] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 [2024-07-02 10:32:26] [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. [2024-07-02 10:32:26] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz` [2024-07-02 10:32:26] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz` [2024-07-02 10:32:26] [TRACE] [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz` [2024-07-02 10:32:26] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz` [2024-07-02 10:32:27] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz` [2024-07-02 10:32:34] [INFO] [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_dorothea_9606.tsv.gz` [2024-07-02 10:32:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-02 10:32:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-02 10:32:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-02 10:32:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-02 10:32:34] [INFO] [OmnipathR] Cache item `fd6905e4319c257381102863e2b4443ca0969f15` version 1: status changed from `unknown` to `started`. [2024-07-02 10:32:34] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/fd6905e4319c257381102863e2b4443ca0969f15-1.rds`. [2024-07-02 10:32:36] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/fd6905e4319c257381102863e2b4443ca0969f15-1.rds`. [2024-07-02 10:32:36] [INFO] [OmnipathR] Download ready [key=fd6905e4319c257381102863e2b4443ca0969f15, version=1] [2024-07-02 10:32:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-02 10:32:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-02 10:32:36] [INFO] [OmnipathR] Cache item `fd6905e4319c257381102863e2b4443ca0969f15` version 1: status changed from `started` to `ready`. [2024-07-02 10:32:36] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-07-02 10:32:52] [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