Ana Galhoz
| Snapshot Date: 2025-01-30 13:00 -0500 (Thu, 30 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: RELEASE_3_20 |
| git_last_commit: 240f65a |
| git_last_commit_date: 2024-10-29 10:58:10 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-02-03 12:12 -0500 (Mon, 03 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4494 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4400 |
| 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 2269/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.14.0 (landing page) Ana Galhoz
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: wppi |
| Version: 1.14.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings wppi_1.14.0.tar.gz |
| StartedAt: 2025-01-31 11:30:08 -0000 (Fri, 31 Jan 2025) |
| EndedAt: 2025-01-31 11:41:00 -0000 (Fri, 31 Jan 2025) |
| EllapsedTime: 652.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: wppi.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings wppi_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.14.0’
* 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
[2025-01-31 11:30:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 11:30:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-31 11:30:48] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 11:30:48] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 11:30:48] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 11:30:48] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-31 11:30:48] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-31 11:30:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 11:30:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-31 11:30:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 11:30:48] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-01-31 11:30:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 11:30:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-31 11:30:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 11:30:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-31 11:30:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 11:30:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-31 11:30:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 11:30:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-31 11:30:48] [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
[2025-01-31 11:31:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 11:31:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-31 11:31:09] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 11:31:09] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 11:31:09] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 11:31:09] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-31 11:31:09] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-31 11:31:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 11:31:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-31 11:31:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 11:31:09] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-01-31 11:31:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 11:31:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-31 11:31:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 11:31:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-31 11:31:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 11:31:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-31 11:31:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 11:31:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-31 11:31:09] [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())
Warning in (function (...) : 'function (...)
{
.Deprecated("post_translational")
post_translational(...)
}' is deprecated.
Use 'post_translational' instead.
See help("Deprecated")
[2025-01-31 11:31:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [entity_types=protein,query_type=interactions]
[2025-01-31 11:31:40] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-01-31 11:31:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 11:31:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-31 11:31:40] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-01-31 11:31:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 11:31:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-31 11:31:40] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-01-31 11:31:40] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-01-31 11:31:40] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-01-31 11:31:40] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-31 11:34:42] [WARN] [OmnipathR] HTTP 404
[2025-01-31 11:34:42] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2025-01-31 11:34:47] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-31 11:37:49] [WARN] [OmnipathR] HTTP 404
[2025-01-31 11:37:49] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404
[2025-01-31 11:37:54] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-31 11:40:56] [WARN] [OmnipathR] HTTP 404
[2025-01-31 11:40:56] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404
Error in `map_int()`:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error:
! HTTP 404
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. │ └─OmnipathR::post_translational(...)
10. │ ├─rlang::exec(omnipath_query, !!!args)
11. │ └─OmnipathR (local) `<fn>`(...)
12. │ └─environment() %>% as.list %>% c(list(...)) %>% ...
13. ├─OmnipathR:::omnipath_check_param(.)
14. │ └─param$organisms %<>% map_int(ncbi_taxid)
15. ├─purrr::map_int(., ncbi_taxid)
16. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
17. │ ├─purrr:::with_indexed_errors(...)
18. │ │ └─base::withCallingHandlers(...)
19. │ ├─purrr:::call_with_cleanup(...)
20. │ └─OmnipathR (local) .f(.x[[i]], ...)
21. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
22. ├─purrr::map_int(., taxon_name, "ncbi")
23. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
24. │ ├─purrr:::with_indexed_errors(...)
25. │ │ └─base::withCallingHandlers(...)
26. │ ├─purrr:::call_with_cleanup(...)
27. │ └─OmnipathR (local) .f(.x[[i]], ...)
28. │ ├─... %>% if_null_len0(NA)
29. │ └─OmnipathR::get_db("organisms")
30. │ └─OmnipathR::load_db(key, param = param)
31. │ ├─rlang::exec(loader, !!!param)
32. │ └─OmnipathR (local) `<fn>`()
33. │ ├─... %>% ...
34. │ └─OmnipathR::ensembl_organisms()
35. │ ├─... %>% ...
36. │ └─OmnipathR::ensembl_organisms_raw()
37. │ └─... %>% html_table()
38. ├─OmnipathR:::if_null_len0(., NA)
39. │ └─value1 %>% is_empty_2 %>% if (value2) value1
40. ├─OmnipathR:::is_empty_2(.)
41. │ └─value %>% ...
42. ├─dplyr::first(.)
43. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
44. │ └─vctrs::vec_size(x)
45. ├─dplyr::pull(., name_type)
46. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
47. ├─dplyr::select(., -latin_name.x, -latin_name.y)
48. ├─dplyr::mutate(...)
49. ├─dplyr::full_join(...)
50. ├─dplyr::mutate(...)
51. ├─dplyr::select(...)
52. ├─rvest::html_table(.)
53. ├─rvest::html_element(., "table")
54. ├─xml2::read_html(.)
55. ├─OmnipathR:::download_to_cache(., req_headers = user_agent())
56. │ └─OmnipathR:::download_base(...)
57. │ └─base::stop(result)
58. └─purrr (local) `<fn>`(`<smplErrr>`)
59. └─cli::cli_abort(...)
60. └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 3 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck/00check.log’
for details.
wppi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.2/site-library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2025-01-30 20:43:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-30 20:43:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:44] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-30 20:43:44] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-30 20:43:44] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-30 20:43:44] [TRACE] [OmnipathR] Contains 1 files. [2025-01-30 20:43:44] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-30 20:43:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-30 20:43:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-30 20:43:44] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-01-30 20:43:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-30 20:43:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-30 20:43:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-30 20:43:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-30 20:43:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:44] [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 [2025-01-30 20:43:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-30 20:43:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:49] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-30 20:43:49] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-30 20:43:49] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-30 20:43:49] [TRACE] [OmnipathR] Contains 1 files. [2025-01-30 20:43:49] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-30 20:43:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-30 20:43:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-30 20:43:49] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-01-30 20:43:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-30 20:43:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-30 20:43:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-30 20:43:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-30 20:43:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:49] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-01-30 20:43:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-30 20:43:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:53] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-30 20:43:53] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-30 20:43:53] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-30 20:43:53] [TRACE] [OmnipathR] Contains 1 files. [2025-01-30 20:43:53] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-30 20:43:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-30 20:43:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-30 20:43:53] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-01-30 20:43:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-30 20:43:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-30 20:43:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-30 20:43:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-30 20:43:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-30 20:43:53] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi)
wppi.Rcheck/wppi-Ex.timings
| name | user | system | elapsed |