Bioconductor Code: Browse

Graph ofOmnipathR

38e1dcc (origin/RELEASE_3_16, RELEASE_3_16) 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 (HEAD -> master, origin/master, origin/HEAD) 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;
f030e69 `pubmed_open`: handling if `browser` is empty string by deeenes <turei.denes@gmail.com> 2022-10-12 15:29:54 +0200;
22ea47e `misc`: more specific checks for empty or null values by deeenes <turei.denes@gmail.com> 2022-10-12 15:29:11 +0200;
0d13274 Bump version: 3.5.17 → 3.5.18 by deeenes <turei.denes@gmail.com> 2022-10-11 23:27:46 +0200;
f4cdf42 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;
30b3f5a some missing NSE vs. R CMD check workarounds by deeenes <turei.denes@gmail.com> 2022-10-11 23:02:06 +0200;
84e9127 Bump version: 3.5.16 → 3.5.17 by deeenes <turei.denes@gmail.com> 2022-10-11 22:15:04 +0200;
649ccbb added `.bumpversion.cfg` to rbuildignore by deeenes <turei.denes@gmail.com> 2022-10-11 22:14:59 +0200;
c81661b removed `rmarkdown` from Suggests, as it is in Imports now by deeenes <turei.denes@gmail.com> 2022-10-11 22:14:36 +0200;
f63c487 Bump version: 3.5.15 → 3.5.16 by deeenes <turei.denes@gmail.com> 2022-10-11 21:40:09 +0200;
3b23c49 added `rmarkdown` to imports by deeenes <turei.denes@gmail.com> 2022-10-11 21:40:04 +0200;
0877461 Bump version: 3.5.14 → 3.5.15 by deeenes <turei.denes@gmail.com> 2022-10-11 19:23:47 +0200;
0a72936 updated HPO URL by deeenes <turei.denes@gmail.com> 2022-10-11 19:23:41 +0200;
93e8d80 Bump version: 3.5.13 → 3.5.14 by deeenes <turei.denes@gmail.com> 2022-10-11 19:18:14 +0200;
c07b2e0 log message with pandoc version on build servers by deeenes <turei.denes@gmail.com> 2022-10-11 19:18:08 +0200;
e4510f6 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;
291d9af some more Rbuildignore items by deeenes <turei.denes@gmail.com> 2022-10-11 19:15:58 +0200;
a3d3193 Bump version: 3.5.12 → 3.5.13 by deeenes <turei.denes@gmail.com> 2022-10-10 21:30:28 +0200;
46b699b fixed Vinayagam URL <a href="#48">#48</a> by deeenes <turei.denes@gmail.com> 2022-10-10 21:28:29 +0200;
3d48745 Bump version: 3.5.11 → 3.5.12 by deeenes <turei.denes@gmail.com> 2022-10-10 20:22:49 +0200;
ee9b8a7 removed hardcoded URL from `resources.R` by deeenes <turei.denes@gmail.com> 2022-10-10 20:22:31 +0200;
84901be added all missing R CMD check vs. NSE workarounds by deeenes <turei.denes@gmail.com> 2022-10-10 20:14:11 +0200;
e5ed8c8 Bump version: 3.5.10 → 3.5.11 by deeenes <turei.denes@gmail.com> 2022-10-10 19:53:02 +0200;
110958c `readr`/`vroom` fails to recognize gzip compression bc it checks for file name ending instead of magic bytes by deeenes <turei.denes@gmail.com> 2022-10-10 19:52:39 +0200;
89bdb38 bump2version config by deeenes <turei.denes@gmail.com> 2022-10-10 18:40:17 +0200;
d2a6c42 Bump version: 3.5.9 → 3.5.10 by deeenes <turei.denes@gmail.com> 2022-10-10 18:39:10 +0200;
68beada disabled export of half-ready functions by deeenes <turei.denes@gmail.com> 2022-10-10 18:31:11 +0200;
df94201 added `topology` arg to `intercell_consensus_filter` docs by deeenes <turei.denes@gmail.com> 2022-10-10 18:25:17 +0200;
b592099 Rbuildignore: added docs and attic directories by deeenes <turei.denes@gmail.com> 2022-10-10 18:21:10 +0200;
3c1e2ae added ellipsis to `get_db` docs by deeenes <turei.denes@gmail.com> 2022-10-10 18:20:47 +0200;
e774464 fixed `biomart_query` example by deeenes <turei.denes@gmail.com> 2022-10-10 18:08:46 +0200;
8e13572 docs rebuild by deeenes <turei.denes@gmail.com> 2022-10-10 18:04:40 +0200;