Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:02:59 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 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 873/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gINTomics 1.0.0 (landing page) Angelo Velle
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
To the developers/maintainers of the gINTomics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gINTomics.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: gINTomics |
Version: 1.0.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data gINTomics |
StartedAt: 2024-05-30 22:20:16 -0400 (Thu, 30 May 2024) |
EndedAt: 2024-05-30 22:22:13 -0400 (Thu, 30 May 2024) |
EllapsedTime: 117.3 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data gINTomics ### ############################################################################## ############################################################################## * checking for file ‘gINTomics/DESCRIPTION’ ... OK * preparing ‘gINTomics’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘gINTomics.Rmd’ using rmarkdown [2024-05-30 22:21:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-30 22:21:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 22:21:40] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-05-30 22:21:40] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-30 22:21:40] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-05-30 22:21:40] [TRACE] [OmnipathR] Contains 1 files. [2024-05-30 22:21:40] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-30 22:21:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-30 22:21:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 22:21:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-05-30 22:21:40] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-30 22:21:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-30 22:21:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 22:21:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-30 22:21:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 22:21:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-30 22:21:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 22:21:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-30 22:21:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 22:21:40] [TRACE] [OmnipathR] Cache locked: FALSE [2024-05-30 22:22:01] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-05-30 22:22:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-30 22:22:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 22:22:01] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-05-30 22:22:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-30 22:22:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 22:22:01] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-05-30 22:22:01] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-05-30 22:22:01] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-05-30 22:22:01] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-05-30 22:22:02] [WARN] [OmnipathR] HTTP 403 [2024-05-30 22:22:02] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403 [2024-05-30 22:22:07] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-05-30 22:22:07] [WARN] [OmnipathR] HTTP 403 [2024-05-30 22:22:07] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403 [2024-05-30 22:22:12] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-05-30 22:22:12] [WARN] [OmnipathR] HTTP 403 [2024-05-30 22:22:12] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403 Quitting from lines 139-142 [unnamed-chunk-9] (gINTomics.Rmd) Error: processing vignette 'gINTomics.Rmd' failed with diagnostics: ℹ In index: 1. ℹ With name: hsa. Caused by error in `map_int()`: ℹ In index: 1. Caused by error: ! HTTP 403 --- failed re-building ‘gINTomics.Rmd’ SUMMARY: processing the following file failed: ‘gINTomics.Rmd’ Error: Vignette re-building failed. Execution halted