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This page was generated on 2023-05-26 06:18:07 -0000 (Fri, 26 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4254
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BUILD results for decoupleR on kunpeng2


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 502/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decoupleR 2.7.0  (landing page)
Pau Badia-i-Mompel
Snapshot Date: 2023-05-25 13:29:39 -0000 (Thu, 25 May 2023)
git_url: https://git.bioconductor.org/packages/decoupleR
git_branch: devel
git_last_commit: 3f12716
git_last_commit_date: 2023-04-25 15:30:09 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped

Summary

Package: decoupleR
Version: 2.7.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data decoupleR
StartedAt: 2023-05-25 21:45:53 -0000 (Thu, 25 May 2023)
EndedAt: 2023-05-25 22:07:54 -0000 (Thu, 25 May 2023)
EllapsedTime: 1321.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R 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
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-25 21:46:25] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] Contains 1 files.
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-25 21:46:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-25 21:46:25] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-05-25 21:46:27] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-25 21:46:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-25 21:46:29] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-25 21:46:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-25 21:46:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-05-25 21:46:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-05-25 21:46:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-05-25 21:47:41] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 1/3); error: OpenSSL SSL_read: Connection reset by peer, errno 104
[2023-05-25 21:47:46] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-05-25 21:56:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-25 21:56:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-25 21:56:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-25 21:56:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-25 21:56:08] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2023-05-25 21:56:08] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-05-25 21:56:10] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-05-25 21:56:10] [INFO]    [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2023-05-25 21:56:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-25 21:56:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-25 21:56:10] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2023-05-25 21:56:10] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
Warning in for (i in seq_len(n)) { :
  closing unused connection 4 (https://omnipathdb.org/annotations?resources=PROGENy&license=academic)
Warning: ggrepel: 65 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘pw_bk.Rmd’

--- re-building ‘pw_sc.Rmd’ using rmarkdown
[2023-05-25 21:56:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-25 21:56:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-25 21:56:34] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-25 21:56:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-25 21:56:37] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-05-25 21:56:37] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-05-25 21:56:37] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.

  |                                                                                                                    
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  |==============================================================================================================| 100%
--- finished re-building ‘pw_sc.Rmd’

--- re-building ‘tf_bk.Rmd’ using rmarkdown
[2023-05-25 21:56:48] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-05-25 21:56:48] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-05-25 21:56:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-05-25 21:57:13] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 1/3); error: OpenSSL SSL_read: Connection reset by peer, errno 104
[2023-05-25 21:57:18] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-05-25 21:57:47] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 2/3); error: OpenSSL SSL_read: Connection reset by peer, errno 104
[2023-05-25 21:57:52] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-05-25 21:59:24] [ERROR]   [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 3/3); error: OpenSSL SSL_read: Connection reset by peer, errno 104

Quitting from lines 109-111 [collectri] (tf_bk.Rmd)
Error: processing vignette 'tf_bk.Rmd' failed with diagnostics:
OpenSSL SSL_read: Connection reset by peer, errno 104
--- failed re-building ‘tf_bk.Rmd’

--- re-building ‘tf_sc.Rmd’ using rmarkdown
Warning in for (i in idx) if (identical(res[[i]], alist(, )[[1]])) res[[i]] = NULL :
  closing unused connection 5 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic)
[2023-05-25 21:59:26] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-05-25 21:59:26] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-05-25 21:59:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-05-25 22:02:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-25 22:02:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-25 22:02:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-25 22:02:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
Warning: closing unused connection 4 (https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic)
[2023-05-25 22:02:47] [INFO]    [OmnipathR] Cache item `099e7af92f71a88d7560d65cea14c1970f66c0b6` version 1: status changed from `unknown` to `started`.
[2023-05-25 22:02:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/099e7af92f71a88d7560d65cea14c1970f66c0b6-1.rds`.
[2023-05-25 22:02:48] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/099e7af92f71a88d7560d65cea14c1970f66c0b6-1.rds`.
[2023-05-25 22:02:48] [INFO]    [OmnipathR] Download ready [key=099e7af92f71a88d7560d65cea14c1970f66c0b6, version=1]
[2023-05-25 22:02:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-25 22:02:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-25 22:02:48] [INFO]    [OmnipathR] Cache item `099e7af92f71a88d7560d65cea14c1970f66c0b6` version 1: status changed from `started` to `ready`.
[2023-05-25 22:02:48] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2023-05-25 22:02:55] [TRACE]   [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any
[2023-05-25 22:03:02] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any
[2023-05-25 22:05:49] [SUCCESS] [OmnipathR] Downloaded 64495 interactions.

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  |==============================================================================================================| 100%
--- finished re-building ‘tf_sc.Rmd’

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

Error: Vignette re-building failed.
Execution halted