Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-05-18 11:37:32 -0400 (Sat, 18 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 2282/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.12.0  (landing page)
Ana Galhoz
Snapshot Date: 2024-05-17 14:00:11 -0400 (Fri, 17 May 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)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for wppi on palomino3


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.

raw results


Summary

Package: wppi
Version: 1.12.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings wppi_1.12.0.tar.gz
StartedAt: 2024-05-18 07:54:59 -0400 (Sat, 18 May 2024)
EndedAt: 2024-05-18 07:56:40 -0400 (Sat, 18 May 2024)
EllapsedTime: 101.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: wppi.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings wppi_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'wppi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'wppi' version '1.12.0'
* 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 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 whether startup messages can be suppressed ... NOTE
[2024-05-18 07:55:29] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 07:55:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 07:55:29] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-18 07:55:29] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-18 07:55:29] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-18 07:55:29] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-18 07:55:30] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-18 07:55:30] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 07:55:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 07:55:30] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-18 07:55:30] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-18 07:55:30] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-18 07:55:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 07:55:30] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-18 07:55:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 07:55:30] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-18 07:55:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 07:55:30] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-18 07:55:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 07:55:30] [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
[2024-05-18 07:55:48] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 07:55:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 07:55:48] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-18 07:55:48] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-18 07:55:48] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-18 07:55:48] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-18 07:55:48] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-18 07:55:48] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 07:55:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 07:55:48] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-18 07:55:48] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-18 07:55:48] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-18 07:55:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 07:55:48] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-18 07:55:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 07:55:48] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-18 07:55:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 07:55:48] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-18 07:55:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 07:55:48] [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())
[2024-05-18 07:56:17] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-18 07:56:17] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 07:56:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 07:56:17] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-18 07:56:17] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 07:56:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 07:56:17] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-05-18 07:56:17] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-05-18 07:56:17] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-18 07:56:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-18 07:56:18] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-18 07:56:23] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-18 07:56:23] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
[2024-05-18 07:56:28] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-18 07:56:28] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
Error in `map_int()`:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `curl::curl_fetch_disk()`:
! schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.
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. ├─rvest::html_element(., "table")
 53. ├─xml2::read_html(.)
 54. ├─OmnipathR:::download_to_cache(.)
 55. │ └─OmnipathR:::download_base(...)
 56. │   └─base::stop(result)
 57. └─purrr (local) `<fn>`(`<smplErrr>`)
 58.   └─cli::cli_abort(...)
 59.     └─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
  'F:/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck/00check.log'
for details.


Installation output

wppi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'wppi' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2024-05-17 16:22:10] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-17 16:22:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:10] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-17 16:22:10] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-17 16:22:10] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-17 16:22:10] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-17 16:22:10] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-17 16:22:10] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-17 16:22:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:10] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-17 16:22:10] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-17 16:22:10] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-17 16:22:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:10] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-17 16:22:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:11] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-17 16:22:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:11] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-17 16:22:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:11] [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
[2024-05-17 16:22:16] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-17 16:22:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:16] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-17 16:22:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-17 16:22:16] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-17 16:22:16] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-17 16:22:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-17 16:22:16] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-17 16:22:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:16] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-17 16:22:17] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-17 16:22:17] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-17 16:22:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:17] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-17 16:22:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:17] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-17 16:22:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:17] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-17 16:22:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:17] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:20] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:20] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 16:22:20] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (wppi)

Tests output


Example timings

wppi.Rcheck/wppi-Ex.timings

nameusersystemelapsed