Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-30 12:37:33 -0400 (Thu, 30 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
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: 1.13.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wppi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wppi_1.13.0.tar.gz |
StartedAt: 2024-05-30 09:38:27 -0400 (Thu, 30 May 2024) |
EndedAt: 2024-05-30 09:41:22 -0400 (Thu, 30 May 2024) |
EllapsedTime: 174.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: wppi.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wppi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wppi_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘wppi/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘wppi’ version ‘1.13.0’ * 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 whether startup messages can be suppressed ... NOTE [2024-05-30 09:39:22] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-30 09:39:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 09:39:22] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-30 09:39:22] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-30 09:39:22] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-30 09:39:22] [TRACE] [OmnipathR] Contains 1 files. [2024-05-30 09:39:22] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-30 09:39:22] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-30 09:39:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 09:39:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-30 09:39:22] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-30 09:39:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-30 09:39:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 09:39:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-30 09:39:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 09:39:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-30 09:39:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 09:39:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-30 09:39:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 09:39:22] [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 [2024-05-30 09:39:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-30 09:39:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 09:39:56] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-30 09:39:56] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-30 09:39:56] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-30 09:39:56] [TRACE] [OmnipathR] Contains 1 files. [2024-05-30 09:39:56] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-30 09:39:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-30 09:39:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 09:39:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-30 09:39:56] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-30 09:39:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-30 09:39:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 09:39:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-30 09:39:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 09:39:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-30 09:39:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 09:39:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-30 09:39:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 09:39:56] [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()) [2024-05-30 09:40:48] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-05-30 09:40:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-30 09:40:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 09:40:48] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-05-30 09:40:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-30 09:40:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-30 09:40:48] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-05-30 09:40:48] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-05-30 09:40:48] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-05-30 09:40:48] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-05-30 09:40:55] [WARN] [OmnipathR] HTTP 403 [2024-05-30 09:40:55] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 403 [2024-05-30 09:41:00] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-05-30 09:41:00] [WARN] [OmnipathR] HTTP 403 [2024-05-30 09:41:00] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 403 [2024-05-30 09:41:05] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-05-30 09:41:05] [WARN] [OmnipathR] HTTP 403 [2024-05-30 09:41:05] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 403 Error in `map_int()`: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error: ! HTTP 403 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck/00check.log’ for details.
wppi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2024-05-29 12:48:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-29 12:48:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:48:50] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-29 12:48:50] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-29 12:48:50] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-29 12:48:50] [TRACE] [OmnipathR] Contains 1 files. [2024-05-29 12:48:50] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-29 12:48:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-29 12:48:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:48:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-29 12:48:50] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-29 12:48:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-29 12:48:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:48:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-29 12:48:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:48:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-29 12:48:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:48:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-29 12:48:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:48:51] [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 [2024-05-29 12:48:58] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-29 12:48:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:48:59] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-29 12:48:59] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-29 12:48:59] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-29 12:48:59] [TRACE] [OmnipathR] Contains 1 files. [2024-05-29 12:48:59] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-29 12:48:59] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-29 12:48:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:48:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-29 12:48:59] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-29 12:48:59] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-29 12:48:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:48:59] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-29 12:48:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:48:59] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-29 12:48:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:48:59] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-29 12:48:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:48:59] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-05-29 12:49:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-29 12:49:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:49:05] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-29 12:49:05] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-29 12:49:05] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-29 12:49:05] [TRACE] [OmnipathR] Contains 1 files. [2024-05-29 12:49:05] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-29 12:49:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-29 12:49:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:49:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-29 12:49:06] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-29 12:49:06] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-29 12:49:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:49:06] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-29 12:49:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:49:06] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-29 12:49:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:49:06] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-29 12:49:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 12:49:06] [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 |