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This page was generated on 2024-05-20 11:32:12 -0400 (Mon, 20 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4381
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 844/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gINTomics 1.1.0  (landing page)
Angelo Velle
Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 2024)
git_url: https://git.bioconductor.org/packages/gINTomics
git_branch: devel
git_last_commit: c1c358f
git_last_commit_date: 2024-04-30 11:56:24 -0400 (Tue, 30 Apr 2024)
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for gINTomics on kjohnson1


To the developers/maintainers of the gINTomics 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: gINTomics
Version: 1.1.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data gINTomics
StartedAt: 2024-05-18 18:49:18 -0400 (Sat, 18 May 2024)
EndedAt: 2024-05-18 18:51:32 -0400 (Sat, 18 May 2024)
EllapsedTime: 133.8 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/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
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 18:50:58] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 18:50:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 18:50:58] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-05-18 18:51:20] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-18 18:51:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 18:51:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 18:51:20] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-18 18:51:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 18:51:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 18:51:20] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-05-18 18:51:20] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-05-18 18:51:20] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-18 18:51:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-18 18:51:21] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: SSL peer certificate or SSH remote key was not OK: [useast.ensembl.org] SSL certificate problem: certificate has expired
[2024-05-18 18:51:26] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-18 18:51:26] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: SSL peer certificate or SSH remote key was not OK: [useast.ensembl.org] SSL certificate problem: certificate has expired
[2024-05-18 18:51:31] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-18 18:51:31] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: SSL peer certificate or SSH remote key was not OK: [useast.ensembl.org] SSL certificate problem: certificate has expired

Quitting from lines  at 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 in `curl::curl_fetch_disk()`:
! SSL peer certificate or SSH remote key was not OK: [useast.ensembl.org] SSL certificate problem: certificate has expired
--- failed re-building ‘gINTomics.Rmd’

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

Error: Vignette re-building failed.
Execution halted