Ana Galhoz
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: RELEASE_3_19 |
| git_last_commit: 1ad2e46 |
| git_last_commit_date: 2024-04-30 11:33:03 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:39 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 2282/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.12.0 (landing page) Ana Galhoz
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | NA | |||||||||
|
To the developers/maintainers of the wppi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/wppi.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. |
| Package: wppi |
| Version: 1.12.0 |
| 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 |
| StartedAt: 2024-10-17 06:21:12 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 06:22:59 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 106.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: wppi.Rcheck |
| Warnings: NA |
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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
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 22.04.5 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
[2024-10-17 06:21:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:21:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:21:39] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 06:21:39] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-10-17 06:21:39] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 06:21:39] [TRACE] [OmnipathR] Contains 1 files.
[2024-10-17 06:21:39] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-10-17 06:21:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:21:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:21:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 06:21:39] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-17 06:21:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-17 06:21:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:21:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-17 06:21:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:21:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-17 06:21:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:21:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-17 06:21:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:21:39] [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
[2024-10-17 06:21:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:21:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:21:53] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 06:21:53] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-10-17 06:21:53] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 06:21:53] [TRACE] [OmnipathR] Contains 1 files.
[2024-10-17 06:21:53] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-10-17 06:21:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:21:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:21:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 06:21:53] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-17 06:21:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-17 06:21:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:21:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-17 06:21:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:21:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-17 06:21:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:21:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-17 06:21:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:21:53] [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 ... ERROR
Running examples in ‘wppi-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: common_neighbors
> ### Title: Shared neighbors of connected vertices
> ### Aliases: common_neighbors
>
> ### ** Examples
>
> graph_op <- graph_from_op(wppi_omnipath_data())
[2024-10-17 06:22:13] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-10-17 06:22:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:22:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:13] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-10-17 06:22:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:22:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:13] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-10-17 06:22:13] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-10-17 06:22:13] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-10-17 06:22:13] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-10-17 06:22:14] [TRACE] [OmnipathR] HTTP 200
[2024-10-17 06:22:14] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-10-17 06:22:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:22:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:14] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
Error in `map_int()`:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `UseMethod()`:
! no applicable method for 'html_table' applied to an object of class "xml_missing"
Backtrace:
▆
1. ├─wppi::graph_from_op(wppi_omnipath_data())
2. │ └─op_data %>% ...
3. ├─dplyr::select(., -c(source_genesymbol, target_genesymbol))
4. ├─wppi::wppi_omnipath_data()
5. │ └─... %>% select(seq(10))
6. ├─dplyr::select(., seq(10))
7. ├─rlang::exec(., !!!omnipath_param)
8. ├─OmnipathR (local) `<fn>`(entity_type = "protein")
9. │ ├─rlang::exec(import_omnipath, !!!args)
10. │ └─OmnipathR (local) `<fn>`(...)
11. │ └─environment() %>% as.list %>% c(list(...)) %>% ...
12. ├─OmnipathR:::omnipath_check_param(.)
13. │ └─param$organisms %<>% map_int(ncbi_taxid)
14. ├─purrr::map_int(., ncbi_taxid)
15. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
16. │ ├─purrr:::with_indexed_errors(...)
17. │ │ └─base::withCallingHandlers(...)
18. │ ├─purrr:::call_with_cleanup(...)
19. │ └─OmnipathR (local) .f(.x[[i]], ...)
20. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
21. ├─purrr::map_int(., taxon_name, "ncbi")
22. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
23. │ ├─purrr:::with_indexed_errors(...)
24. │ │ └─base::withCallingHandlers(...)
25. │ ├─purrr:::call_with_cleanup(...)
26. │ └─OmnipathR (local) .f(.x[[i]], ...)
27. │ ├─... %>% if_null_len0(NA)
28. │ └─OmnipathR::get_db("organisms")
29. │ └─OmnipathR::load_db(key, param = param)
30. │ ├─rlang::exec(loader, !!!param)
31. │ └─OmnipathR (local) `<fn>`()
32. │ ├─... %>% ...
33. │ └─OmnipathR::ensembl_organisms()
34. │ ├─... %>% ...
35. │ └─OmnipathR::ensembl_organisms_raw()
36. │ └─... %>% html_table()
37. ├─OmnipathR:::if_null_len0(., NA)
38. │ └─value1 %>% is_empty_2 %>% if (value2) value1
39. ├─OmnipathR:::is_empty_2(.)
40. │ └─value %>% ...
41. ├─dplyr::first(.)
42. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
43. │ └─vctrs::vec_size(x)
44. ├─dplyr::pull(., name_type)
45. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
46. ├─dplyr::select(., -latin_name.x, -latin_name.y)
47. ├─dplyr::mutate(...)
48. ├─dplyr::full_join(...)
49. ├─dplyr::mutate(...)
50. ├─dplyr::select(...)
51. ├─rvest::html_table(.)
52. └─base::.handleSimpleError(...)
53. └─purrr (local) h(simpleError(msg, call))
54. └─cli::cli_abort(...)
55. └─rlang::abort(...)
Execution halted
* 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
[2024-10-17 06:22:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:22:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:18] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 06:22:18] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-10-17 06:22:18] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 06:22:18] [TRACE] [OmnipathR] Contains 2 files.
[2024-10-17 06:22:18] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-10-17 06:22:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:22:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 06:22:18] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-17 06:22:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-17 06:22:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-17 06:22:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-17 06:22:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-17 06:22:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:18] [TRACE] [OmnipathR] Cache locked: FALSE
[2024-10-17 06:22:19] [INFO] [wppi] Executing WPPI workflow.
[2024-10-17 06:22:19] [INFO] [wppi] Collecting database knowledge.
[2024-10-17 06:22:19] [TRACE] [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2024-10-17 06:22:19] [INFO] [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2024-10-17 06:22:19] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2024-10-17 06:22:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:22:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:22:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:19] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2024-10-17 06:22:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2024-10-17 06:22:19] [INFO] [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2024-10-17 06:22:19] [TRACE] [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2024-10-17 06:22:39] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2024-10-17 06:22:39] [INFO] [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2024-10-17 06:22:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:22:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:39] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2024-10-17 06:22:40] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 312812 records
[2024-10-17 06:22:40] [TRACE] [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2024-10-17 06:22:40] [INFO] [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2024-10-17 06:22:40] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2024-10-17 06:22:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:22:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:22:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:40] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2024-10-17 06:22:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2024-10-17 06:22:40] [INFO] [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2024-10-17 06:22:40] [TRACE] [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2024-10-17 06:22:54] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2024-10-17 06:22:54] [INFO] [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1]
[2024-10-17 06:22:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:22:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:54] [INFO] [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`.
[2024-10-17 06:22:55] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 773774 records
[2024-10-17 06:22:55] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-10-17 06:22:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:22:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:55] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-10-17 06:22:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:22:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:55] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-10-17 06:22:55] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-10-17 06:22:55] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-10-17 06:22:55] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-10-17 06:22:55] [TRACE] [OmnipathR] HTTP 200
[2024-10-17 06:22:55] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-10-17 06:22:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 06:22:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 06:22:55] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
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 `UseMethod()`:
! no applicable method for 'html_table' applied to an object of class "xml_missing"
--- 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: 2 ERRORs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck/00check.log’
for details.
wppi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2024-10-16 16:21:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-16 16:21:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:43] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-10-16 16:21:43] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-16 16:21:43] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-10-16 16:21:43] [TRACE] [OmnipathR] Contains 1 files. [2024-10-16 16:21:43] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-16 16:21:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-16 16:21:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-10-16 16:21:43] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-10-16 16:21:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-16 16:21:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-16 16:21:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-16 16:21:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-16 16:21:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:43] [TRACE] [OmnipathR] Cache locked: FALSE Note: wrong number of arguments to '/' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2024-10-16 16:21:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-16 16:21:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:46] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-10-16 16:21:46] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-16 16:21:46] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-10-16 16:21:46] [TRACE] [OmnipathR] Contains 1 files. [2024-10-16 16:21:46] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-16 16:21:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-16 16:21:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-10-16 16:21:46] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-10-16 16:21:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-16 16:21:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-16 16:21:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-16 16:21:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-16 16:21:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:46] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-10-16 16:21:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-16 16:21:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:49] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-10-16 16:21:49] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-16 16:21:49] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-10-16 16:21:49] [TRACE] [OmnipathR] Contains 1 files. [2024-10-16 16:21:49] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-16 16:21:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-16 16:21:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-10-16 16:21:49] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-10-16 16:21:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-16 16:21:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-16 16:21:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-16 16:21:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-16 16:21:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:21:49] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi)
wppi.Rcheck/wppi-Ex.timings
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