Graph of OmnipathR
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  • 3877294 (HEAD -> devel, origin/master, origin/devel, origin/HEAD, master) `search`: added missing NSE variable initialisations by deeenes <turei.denes@gmail.com> 2023-03-22 14:52:55 +0100;
  • 015253b typo in a docstring example by deeenes <turei.denes@gmail.com> 2023-03-22 14:46:40 +0100;
  • 5b8e047 Bump version: 3.7.7 → 3.7.8 by deeenes <turei.denes@gmail.com> 2023-03-22 14:44:28 +0100;
  • 3fa4445 typo in a docstring example by deeenes <turei.denes@gmail.com> 2023-03-22 14:44:10 +0100;
  • 1cf2bba Bump version: 3.7.6 → 3.7.7 by deeenes <turei.denes@gmail.com> 2023-03-22 09:21:24 +0100;
  • a713dca `query_info` docstring example: added missing arg by deeenes <turei.denes@gmail.com> 2023-03-22 09:21:14 +0100;
  • 1cbeae5 Bump version: 3.7.5 → 3.7.6 by deeenes <turei.denes@gmail.com> 2023-03-21 22:45:32 +0100;
  • ee30490 fixed `dplyr::first` issue in `resources_colname` by deeenes <turei.denes@gmail.com> 2023-03-21 22:20:11 +0100;
  • c66697b `search`: log message about unfinished implementation by deeenes <turei.denes@gmail.com> 2023-03-21 22:10:46 +0100;
  • c0a1d67 Bump version: 3.7.4 → 3.7.5 by deeenes <turei.denes@gmail.com> 2023-03-21 16:32:38 +0100;
  • 27bb65f (origin/RELEASE_3_16, RELEASE_3_16) Bump version: 3.6.5 → 3.6.6 by deeenes <turei.denes@gmail.com> 2023-03-21 16:32:02 +0100;
  • 5488c9c fixed `dplyr::first` issue in `curated_ligand_receptor_interactions` by deeenes <turei.denes@gmail.com> 2023-03-21 16:31:32 +0100;
  • 29b6bec fixed `dplyr::first` issue in `curated_ligand_receptor_interactions` by deeenes <turei.denes@gmail.com> 2023-03-21 16:31:32 +0100;
  • 3a9959f Revert "to be reverted" by deeenes <turei.denes@gmail.com> 2023-03-21 16:25:47 +0100;
  • f0a805f Bump version: 3.6.4 → 3.6.5 by deeenes <turei.denes@gmail.com> 2023-03-21 16:24:08 +0100;
  • 0f404b3 `dplyr::first/last` does not work on `igraph` vertex sequences any more by deeenes <turei.denes@gmail.com> 2023-03-19 16:07:13 +0100;
  • 9014ad1 Bump version: 3.6.3 → 3.6.4 by deeenes <turei.denes@gmail.com> 2023-03-21 12:58:38 +0100;
  • bd98a30 Bump version: 3.7.3 → 3.7.4 by deeenes <turei.denes@gmail.com> 2023-03-21 12:58:04 +0100;
  • 85dcdf8 `taxonomy`: use `map_int` for ncbi tax ids by deeenes <turei.denes@gmail.com> 2023-03-21 12:54:19 +0100;
  • 1d5a30c fixed: new behaviour of `dplyr::first` broke `biomart_query` by deeenes <turei.denes@gmail.com> 2023-03-21 12:44:52 +0100;
  • b54259c `taxonomy`: use `map_int` for ncbi tax ids by deeenes <turei.denes@gmail.com> 2023-03-21 12:54:19 +0100;
  • a0e67e3 fixed: new behaviour of `dplyr::first` broke `biomart_query` by deeenes <turei.denes@gmail.com> 2023-03-21 12:44:52 +0100;
  • 1127927 Bump version: 3.7.2 → 3.7.3 by deeenes <turei.denes@gmail.com> 2023-03-19 16:07:47 +0100;
  • e4e551f `dplyr::first/last` does not work on `igraph` vertex sequences any more by deeenes <turei.denes@gmail.com> 2023-03-19 16:07:13 +0100;
  • 5bae9f7 Bump version: 3.6.2 → 3.6.3 by deeenes <turei.denes@gmail.com> 2023-03-19 14:53:27 +0100;
  • d57e398 `where` is not exported from (older?) `tidyselect` by deeenes <turei.denes@gmail.com> 2023-03-19 14:53:20 +0100;
  • 53eeec6 to be reverted by deeenes <turei.denes@gmail.com> 2023-02-20 14:51:54 +0100;
  • b062d77 Bump version: 3.6.1 → 3.6.2 by deeenes <turei.denes@gmail.com> 2023-02-10 14:30:45 +0100;
  • 40ccd5d `hpo_download`: handle NAs only for character column -- compatible with new tidyselect behaviour; fixes <a href="#60">#60</a> and AnaGalhoz37/wppi#3 by deeenes <turei.denes@gmail.com> 2023-02-10 14:18:49 +0100;
  • c5f63b4 Bump version: 3.7.1 → 3.7.2 by deeenes <turei.denes@gmail.com> 2023-02-10 14:30:01 +0100;
  • f0d21c7 `hpo_download`: handle NAs only for character column -- compatible with new tidyselect behaviour; fixes <a href="#60">#60</a> and AnaGalhoz37/wppi#3 by deeenes <turei.denes@gmail.com> 2023-02-10 14:18:49 +0100;
  • 38e1dcc Bump version: 3.6.0 → 3.6.1 by deeenes <turei.denes@gmail.com> 2023-02-01 02:16:42 +0100;
  • da92af9 adjusted bumpversion to version increment by bioc by deeenes <turei.denes@gmail.com> 2023-02-01 02:16:34 +0100;
  • faf0bb7 do not pass named arguments in ellipsis to `purrr::map` by deeenes <turei.denes@gmail.com> 2023-02-01 02:12:47 +0100;
  • e057724 Bump version: 3.7.0 → 3.7.1 by deeenes <turei.denes@gmail.com> 2023-02-01 02:15:24 +0100;
  • 3a38753 adjusted bumpversion to version increment by bioc by deeenes <turei.denes@gmail.com> 2023-02-01 02:15:20 +0100;
  • 68e5aa0 do not pass named arguments in ellipsis to `purrr::map`; fixes <a href="#56">#56</a> by deeenes <turei.denes@gmail.com> 2023-02-01 02:12:47 +0100;
  • 42949d2 log message at the end of search index build by deeenes <turei.denes@gmail.com> 2023-02-01 01:56:54 +0100;
  • 76838e4 fixed all trivial issues with search index build by deeenes <turei.denes@gmail.com> 2022-12-10 00:16:55 +0100;
  • 48cea05 `database_summary`: removing empty elements from values; option to return data frame by deeenes <turei.denes@gmail.com> 2022-12-07 18:30:52 +0100;
  • 33709fa search index builders for each OmniPath database by deeenes <turei.denes@gmail.com> 2022-12-07 18:29:59 +0100;
  • 33b2590 `datasets_one_column`: for datasets in itneractions data frames, create a list of character vectors column instead of multiple logical columns by deeenes <turei.denes@gmail.com> 2022-12-07 17:34:06 +0100;
  • 8ba796a functions to access lists of interaction datasets or types directly by deeenes <turei.denes@gmail.com> 2022-12-07 16:41:53 +0100;
  • 8c99894 `extra_attrs` can be also an argument for `import_omnipath` by deeenes <turei.denes@gmail.com> 2022-12-07 15:24:05 +0100;
  • edf276b removed 2 stray `print` statements by deeenes <turei.denes@gmail.com> 2022-12-07 14:52:30 +0100;
  • 80c00c4 Merge branch 'master' of github.com:saezlab/OmnipathR by deeenes <turei.denes@gmail.com> 2022-12-07 14:29:37 +0100;
  • 05bf40c `database_summary`: access `annotations/intercell_summary` as a list by deeenes <turei.denes@gmail.com> 2022-12-05 19:39:52 +0100;
  • ae61e54 `safe_json`: some more log messages by deeenes <turei.denes@gmail.com> 2022-12-05 19:28:54 +0100;
  • 7b659e7 disabled `license` parameter for `summary` queries; `import_omnipath` passes `simplifyDataFrame = FALSE` to JSON loader by deeenes <turei.denes@gmail.com> 2022-12-05 19:28:17 +0100;
  • d8dd73f better access to metadata: `resource_info`, `query_info` by deeenes <turei.denes@gmail.com> 2022-12-05 16:02:08 +0100;
  • efb50d2 Create CNAME by deeenes <turei.denes@gmail.com> 2022-12-02 00:46:55 +0100;
  • aa2c26f replaced `class() ==` with `class() %>% equals` to see if it triggers bioccheck warning by deeenes <turei.denes@gmail.com> 2022-11-02 16:13:54 +0100;
  • 1a13d8c bump x.y.z version to odd y following creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:20:45 -0400;
  • 6188f30 bump x.y.z version to even y prior to creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:20:45 -0400;
  • 2a734a1 Bump version: 3.5.24 → 3.5.25 by deeenes <turei.denes@gmail.com> 2022-10-22 23:10:29 +0200;
  • 766eca9 fixed precedence issue in `import_all_interaction` by deeenes <turei.denes@gmail.com> 2022-10-22 23:10:22 +0200;
  • 72501ae Bump version: 3.5.23 → 3.5.24 by deeenes <turei.denes@gmail.com> 2022-10-19 20:58:59 +0200;
  • dd6b6fb restored accidentally deleted package data (required for vignettes) by deeenes <turei.denes@gmail.com> 2022-10-19 20:58:47 +0200;
  • 3b982a1 drug targets vignette: fixed super ugly formatting by deeenes <turei.denes@gmail.com> 2022-10-19 20:52:29 +0200;
  • d7afef6 Bump version: 3.5.22 → 3.5.23 by deeenes <turei.denes@gmail.com> 2022-10-18 00:13:29 +0200;
  • ff2369f new function to add the omnipath domain to urls by deeenes <turei.denes@gmail.com> 2022-10-18 00:13:10 +0200;
  • 56b7772 removed old bootstraps by deeenes <turei.denes@gmail.com> 2022-10-16 16:58:38 +0200;
  • 88e5e8c added bootstrap `5.1.3` by deeenes <turei.denes@gmail.com> 2022-10-16 16:57:26 +0200;
  • a485b3c website rebuild by deeenes <turei.denes@gmail.com> 2022-10-16 16:51:10 +0200;
  • dcf356b Bump version: 3.5.21 → 3.5.22 by deeenes <turei.denes@gmail.com> 2022-10-16 15:45:33 +0200;
  • 033f9f5 site rebuild by deeenes <turei.denes@gmail.com> 2022-10-16 15:45:17 +0200;
  • deaa6f1 UniProt: completely removed `www` and `pir3` subdomains - now only the legacy api is supported by deeenes <turei.denes@gmail.com> 2022-10-16 15:45:02 +0200;
  • da03dea checking for buildserver: moved to a function by deeenes <turei.denes@gmail.com> 2022-10-15 18:34:32 +0200;
  • fd6742c (origin/RELEASE_3_15, RELEASE_3_15) v3.4.7 - workaround for Bioc build server cache lock issue by deeenes <turei.denes@gmail.com> 2022-10-15 18:41:33 +0200;
  • fa0ebfa unlocking the cache on build servers (ignoring lock) at package load: workaround for the issue with Bioc servers merida1 and nebbiolo1 by deeenes <turei.denes@gmail.com> 2022-10-15 18:40:38 +0200;
  • 75bb1f7 checking for buildserver: moved to a function by deeenes <turei.denes@gmail.com> 2022-10-15 18:34:32 +0200;
  • 762b061 pkgdown site rebuild by deeenes <turei.denes@gmail.com> 2022-10-15 18:30:25 +0200;
  • efc250e v3.4.6: backported regnetwork SSL error workaround by deeenes <turei.denes@gmail.com> 2022-10-14 23:22:27 +0200;
  • c8aabe4 `regnetwork`: message and handling of missing server cert error by deeenes <turei.denes@gmail.com> 2022-10-14 23:18:16 +0200;
  • 44e4f86 `download_base`: returning the error object, not only the message by deeenes <turei.denes@gmail.com> 2022-10-14 23:17:39 +0200;
  • e396894 Bump version: 3.5.20 → 3.5.21 by deeenes <turei.denes@gmail.com> 2022-10-14 23:18:43 +0200;
  • 0781110 `regnetwork`: message and handling of missing server cert error by deeenes <turei.denes@gmail.com> 2022-10-14 23:18:16 +0200;
  • 83b7016 `download_base`: returning the error object, not only the message by deeenes <turei.denes@gmail.com> 2022-10-14 23:17:39 +0200;
  • 6e4ff7e v3.4.5: backported: scholarly metadata: adjusted for compatibility with 4 years old pandoc of BioC build servers by deeenes <turei.denes@gmail.com> 2022-10-12 18:55:10 +0200;
  • 10245cd scholarly metadata: adjusted for compatibility with 4 years old pandoc of BioC build servers by deeenes <turei.denes@gmail.com> 2022-10-12 18:49:32 +0200;
  • ede6eaa Bump version: 3.5.19 → 3.5.20 by deeenes <turei.denes@gmail.com> 2022-10-12 18:49:51 +0200;
  • bcc2f28 scholarly metadata: adjusted for compatibility with 4 years old pandoc of BioC build servers by deeenes <turei.denes@gmail.com> 2022-10-12 18:49:32 +0200;
  • 41d8d04 v3.4.4 - backported bugfixes from the devel (BioC 3.16) branch by deeenes <turei.denes@gmail.com> 2022-10-12 16:25:50 +0200;
  • f297b3d docs rebuild by deeenes <turei.denes@gmail.com> 2022-10-12 16:23:32 +0200;
  • 3e19886 `pubmed_open`: handling if `browser` is empty string by deeenes <turei.denes@gmail.com> 2022-10-12 15:29:54 +0200;
  • 67f0692 merge: `misc`: more specific checks for empty or null values by deeenes <turei.denes@gmail.com> 2022-10-12 15:29:11 +0200;
  • 7489939 fixed RegNetwork URL: server introduced mandatory TLS, but the `www.` subdomain is not in the certificate by deeenes <turei.denes@gmail.com> 2022-10-11 23:27:39 +0200;
  • 1fc76fd merge: added `rmarkdown` to imports by deeenes <turei.denes@gmail.com> 2022-10-11 21:40:04 +0200;
  • eb7125e updated HPO URL by deeenes <turei.denes@gmail.com> 2022-10-11 19:23:41 +0200;
  • 7908c54 merge: log message with pandoc version on build servers by deeenes <turei.denes@gmail.com> 2022-10-11 19:18:08 +0200;
  • 6f858ea scholarly metadata lua script: fixed version comparison that failed with the old pandoc on the BioC Linux build machine by deeenes <turei.denes@gmail.com> 2022-10-11 19:17:15 +0200;
  • 5fc0466 some more Rbuildignore items by deeenes <turei.denes@gmail.com> 2022-10-11 19:15:58 +0200;
  • 31f2ccd merge: req headers should be unlisted for `add_headers` by deeenes <turei.denes@gmail.com> 2022-10-10 21:28:29 +0200;
  • 3318655 removed hardcoded URL from `resources.R` by deeenes <turei.denes@gmail.com> 2022-10-10 20:22:31 +0200;
  • fd44537 Rbuildignore: added docs and attic directories by deeenes <turei.denes@gmail.com> 2022-10-10 18:21:10 +0200;
  • 4499a0e updated scholarly metadata pandoc plugin by deeenes <turei.denes@gmail.com> 2022-10-10 15:07:12 +0200;
  • b0b2078 updated arg name for `safe_json` in `get_resources` - this issue disabled all `import_omnipath_...` functions by deeenes <turei.denes@gmail.com> 2022-10-10 14:39:28 +0200;
  • b74b536 missing newline at the end of `magic_bytes.json` by deeenes <turei.denes@gmail.com> 2022-10-07 17:05:52 +0200;
  • cd4ff34 merge: wrapper around `jsonlite::fromJSON`: `safe_json` - prints warning and returns empty list by deeenes <turei.denes@gmail.com> 2022-10-07 17:04:56 +0200;
  • c0554b8 Bump version: 3.5.18 → 3.5.19 by deeenes <turei.denes@gmail.com> 2022-10-12 15:30:23 +0200;