Back to Mac ARM64 build report for BioC 3.20 |
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This page was generated on 2024-05-20 11:32:23 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 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 2215/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
wppi 1.13.0 (landing page) Ana Galhoz
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | ||||||||
To the developers/maintainers of the wppi 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. |
Package: wppi |
Version: 1.13.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data wppi |
StartedAt: 2024-05-19 04:25:37 -0400 (Sun, 19 May 2024) |
EndedAt: 2024-05-19 04:26:18 -0400 (Sun, 19 May 2024) |
EllapsedTime: 40.8 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data wppi ### ############################################################################## ############################################################################## * checking for file ‘wppi/DESCRIPTION’ ... OK * preparing ‘wppi’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘wppi_workflow.Rmd’ using rmarkdown [2024-05-19 04:25:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-19 04:25:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-19 04:25:51] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-19 04:25:51] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-19 04:25:51] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-19 04:25:51] [TRACE] [OmnipathR] Contains 1 files. [2024-05-19 04:25:51] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-19 04:25:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-19 04:25:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-19 04:25:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-19 04:25:51] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2024-05-19 04:25:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-19 04:25:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-19 04:25:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-19 04:25:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-19 04:25:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-19 04:25:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-19 04:25:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-19 04:25:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-19 04:25:52] [TRACE] [OmnipathR] Cache locked: FALSE [2024-05-19 04:25:52] [INFO] [wppi] Executing WPPI workflow. [2024-05-19 04:25:52] [INFO] [wppi] Collecting database knowledge. [2024-05-19 04:25:52] [TRACE] [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`. [2024-05-19 04:25:52] [INFO] [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2024-05-19 04:25:52] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`. [2024-05-19 04:25:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-19 04:25:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-19 04:25:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-19 04:25:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-19 04:25:52] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`. [2024-05-19 04:25:52] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`. [2024-05-19 04:25:52] [INFO] [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2024-05-19 04:25:52] [TRACE] [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` [2024-05-19 04:25:55] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`. [2024-05-19 04:25:55] [INFO] [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1] [2024-05-19 04:25:55] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-19 04:25:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-19 04:25:55] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`. [2024-05-19 04:25:55] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 308924 records [2024-05-19 04:25:55] [TRACE] [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`. [2024-05-19 04:25:55] [INFO] [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2024-05-19 04:25:55] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`. [2024-05-19 04:25:55] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-19 04:25:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-19 04:25:55] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-19 04:25:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-19 04:25:55] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`. [2024-05-19 04:25:55] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`. [2024-05-19 04:25:55] [INFO] [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2024-05-19 04:25:55] [TRACE] [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz` [2024-05-19 04:26:05] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`. [2024-05-19 04:26:05] [INFO] [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1] [2024-05-19 04:26:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-19 04:26:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-19 04:26:05] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`. [2024-05-19 04:26:06] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 642871 records [2024-05-19 04:26:06] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-05-19 04:26:06] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-19 04:26:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-19 04:26:06] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-05-19 04:26:06] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-19 04:26:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-19 04:26:06] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-05-19 04:26:06] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-05-19 04:26:06] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-05-19 04:26:06] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-05-19 04:26:06] [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 [2024-05-19 04:26:11] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-05-19 04:26:12] [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 [2024-05-19 04:26:17] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-05-19 04:26:17] [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 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 `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 ‘wppi_workflow.Rmd’ SUMMARY: processing the following file failed: ‘wppi_workflow.Rmd’ Error: Vignette re-building failed. Execution halted