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This page was generated on 2024-05-22 11:36:44 -0400 (Wed, 22 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4665
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4400
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4427
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 511/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decoupleR 2.11.0  (landing page)
Pau Badia-i-Mompel
Snapshot Date: 2024-05-20 14:05:07 -0400 (Mon, 20 May 2024)
git_url: https://git.bioconductor.org/packages/decoupleR
git_branch: devel
git_last_commit: aa9e0db
git_last_commit_date: 2024-04-30 11:34:47 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.4 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

BUILD results for decoupleR on palomino4


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.

raw results

Summary

Package: decoupleR
Version: 2.11.0
Command: chmod a+r decoupleR -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data decoupleR
StartedAt: 2024-05-20 17:55:02 -0400 (Mon, 20 May 2024)
EndedAt: 2024-05-20 17:58:19 -0400 (Mon, 20 May 2024)
EllapsedTime: 196.9 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r decoupleR -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data decoupleR
###
##############################################################################
##############################################################################


* checking for file 'decoupleR/DESCRIPTION' ... OK
* preparing 'decoupleR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'decoupleR.Rmd' using rmarkdown
--- finished re-building 'decoupleR.Rmd'

--- re-building 'pw_bk.Rmd' using rmarkdown
[2024-05-20 17:55:38] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-20 17:55:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:55:38] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-20 17:55:38] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:55:39] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:55:39] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:55:39] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:55:39] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-05-20 17:55:39] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:55:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:55:40] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:55:45] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:55:45] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:55:50] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:55:51] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:55:51] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-20 17:55:51] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-20 17:55:51] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-20 17:55:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:55:51] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2024-05-20 17:55:51] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2024-05-20 17:55:51] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:55:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:55:51] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:55:56] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:55:56] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:56:01] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:56:01] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:56:01] [WARN]    [OmnipathR] Accessing `PROGENy` 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.
[2024-05-20 17:56:02] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-05-20 17:56:02] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-05-20 17:56:02] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-05-20 17:56:02] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-05-20 17:56:02] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-05-20 17:56:04] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-05-20 17:56:04] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-20 17:56:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:56:04] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-20 17:56:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:56:04] [INFO]    [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `unknown` to `started`.
[2024-05-20 17:56:04] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2024-05-20 17:56:07] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2024-05-20 17:56:07] [INFO]    [OmnipathR] Download ready [key=103f85125e0134e3d65e4e63d22c339270d103e8, version=1]
[2024-05-20 17:56:07] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-20 17:56:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:56:07] [INFO]    [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `started` to `ready`.
[2024-05-20 17:56:07] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
Warning: ggrepel: 445 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building 'pw_bk.Rmd'

--- re-building 'pw_sc.Rmd' using rmarkdown
[2024-05-20 17:56:30] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-20 17:56:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:56:30] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-20 17:56:30] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-20 17:56:30] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-20 17:56:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:56:30] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 3.
[2024-05-20 17:56:30] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-3.html
[2024-05-20 17:56:30] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:56:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:56:30] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:56:35] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:56:36] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:56:41] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:56:41] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:56:41] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-20 17:56:41] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-20 17:56:41] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-20 17:56:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:56:41] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 4.
[2024-05-20 17:56:41] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-4.html
[2024-05-20 17:56:41] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:56:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:56:41] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:56:46] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:56:46] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:56:51] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:56:52] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:56:52] [WARN]    [OmnipathR] Accessing `PROGENy` 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.
[2024-05-20 17:56:52] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-05-20 17:56:54] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2024-05-20 17:56:54] [INFO]    [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2024-05-20 17:56:54] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.

  |                                                                                                                    
  |                                                                                                              |   0%
  |                                                                                                                    
  |==============================================================================================================| 100%
--- finished re-building 'pw_sc.Rmd'

--- re-building 'tf_bk.Rmd' using rmarkdown
[2024-05-20 17:57:06] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-20 17:57:06] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-20 17:57:06] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-20 17:57:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:57:06] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 5.
[2024-05-20 17:57:06] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-5.html
[2024-05-20 17:57:06] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:57:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:57:06] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:57:11] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:57:12] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:57:17] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:57:17] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:57:17] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-20 17:57:17] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-20 17:57:17] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-20 17:57:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:57:17] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 6.
[2024-05-20 17:57:17] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-6.html
[2024-05-20 17:57:17] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:57:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:57:17] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:57:22] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:57:22] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:57:27] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:57:28] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:57:28] [WARN]    [OmnipathR] Accessing `collectri` 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.
[2024-05-20 17:57:28] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-05-20 17:57:28] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-05-20 17:57:28] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-05-20 17:57:28] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-05-20 17:57:28] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-05-20 17:57:30] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-05-20 17:57:30] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-20 17:57:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:57:30] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-20 17:57:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:57:30] [INFO]    [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `unknown` to `started`.
[2024-05-20 17:57:30] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2024-05-20 17:57:31] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2024-05-20 17:57:31] [INFO]    [OmnipathR] Download ready [key=a2bbed8b281906d09d7cf983d102402e5de5da8c, version=1]
[2024-05-20 17:57:31] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-20 17:57:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:57:31] [INFO]    [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `started` to `ready`.
[2024-05-20 17:57:31] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-20 17:57:37] [TRACE]   [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any

Quitting from lines 118-120 [collectri] (tf_bk.Rmd)
Error: processing vignette 'tf_bk.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'tf_bk.Rmd'

--- re-building 'tf_sc.Rmd' using rmarkdown
[2024-05-20 17:57:43] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-20 17:57:43] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-20 17:57:43] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-20 17:57:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:57:43] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 7.
[2024-05-20 17:57:43] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-7.html
[2024-05-20 17:57:43] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:57:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:57:44] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:57:49] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:57:49] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:57:54] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:57:54] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:57:54] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-20 17:57:54] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-20 17:57:54] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-20 17:57:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-20 17:57:54] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 8.
[2024-05-20 17:57:54] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-8.html
[2024-05-20 17:57:54] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:57:54] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:57:55] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:58:00] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:58:00] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:58:05] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-20 17:58:05] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-20 17:58:05] [WARN]    [OmnipathR] Accessing `collectri` 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.
[2024-05-20 17:58:05] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-05-20 17:58:06] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2024-05-20 17:58:06] [INFO]    [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-05-20 17:58:06] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-20 17:58:12] [TRACE]   [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any

Quitting from lines 86-88 [collectri] (tf_sc.Rmd)
Error: processing vignette 'tf_sc.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'tf_sc.Rmd'

SUMMARY: processing the following files failed:
  'tf_bk.Rmd' 'tf_sc.Rmd'

Error: Vignette re-building failed.
Execution halted