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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings wppi_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘wppi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:03:26] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] Contains 1 files.
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:03:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:03:26] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:03:40] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] Contains 1 files.
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:03:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:03:40] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
wppi                           27.643  0.159  27.804
score_candidate_genes_from_PPI 14.343  0.111  14.455
prioritization_genes           14.074  0.180  14.256
random_walk                    13.403  0.145  13.547
count_genes                    10.334  0.712  10.253
weighted_adj                   10.402  0.093  10.495
common_neighbors                6.829  0.682  40.470
wppi_data                       6.837  0.052   6.890
filter_annot_with_network       6.627  0.129   6.756
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘wppi_workflow.Rmd’ using rmarkdown
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:06:49] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] Contains 6 files.
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:06:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-06-27 05:06:49] [INFO]    [wppi] Executing WPPI workflow.
[2024-06-27 05:06:49] [INFO]    [wppi] Collecting database knowledge.
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2024-06-27 05:06:49] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:06:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 05:06:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:06:50] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2024-06-27 05:06:50] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2024-06-27 05:06:50] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2024-06-27 05:06:50] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2024-06-27 05:06:53] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2024-06-27 05:06:53] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2024-06-27 05:06:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 05:06:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:06:53] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2024-06-27 05:06:53] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 310614 records
[2024-06-27 05:06:53] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2024-06-27 05:06:53] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2024-06-27 05:06:53] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2024-06-27 05:06:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 05:06:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:06:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 05:06:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:06:53] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2024-06-27 05:06:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2024-06-27 05:06:53] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2024-06-27 05:06:53] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2024-06-27 05:07:02] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2024-06-27 05:07:02] [INFO]    [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1]
[2024-06-27 05:07:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 05:07:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:07:02] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`.
[2024-06-27 05:07:03] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 707170 records
[2024-06-27 05:07:03] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-27 05:07:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 05:07:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:07:03] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-27 05:07:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 05:07:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:07:03] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-06-27 05:07:03] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-06-27 05:07:03] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-27 05:07:03] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-27 05:07:10] [TRACE]   [OmnipathR] HTTP 200
[2024-06-27 05:07:10] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-06-27 05:07:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 05:07:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:07:10] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-06-27 05:07:10] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-06-27 05:07:10] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-06-27 05:07:10] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-06-27 05:07:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 05:07:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:07:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-27 05:07:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-27 05:07:10] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-06-27 05:07:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-06-27 05:07:10] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-06-27 05:07:10] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-06-27 05:07:20] [WARN]    [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 1/3); error: Timeout was reached: [omabrowser.org] SSL connection timeout
[2024-06-27 05:07:25] [TRACE]   [OmnipathR] Attempt 2/3: `https://omabrowser.org/All/oma-species.txt`
[2024-06-27 05:07:35] [WARN]    [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 2/3); error: Timeout was reached: [omabrowser.org] SSL connection timeout
[2024-06-27 05:07:40] [TRACE]   [OmnipathR] Attempt 3/3: `https://omabrowser.org/All/oma-species.txt`
[2024-06-27 05:07:50] [ERROR]   [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 3/3); error: Timeout was reached: [omabrowser.org] SSL connection timeout

Quitting from lines 80-102 [workflow] (wppi_workflow.Rmd)
Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `open.connection()`:
! Timeout was reached: [omabrowser.org] SSL connection timeout
--- failed re-building ‘wppi_workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck/00check.log’
for details.