Bioconductor Code: derfinderPlot

Graph of derfinderPlot

65847f5 (HEAD -> devel, origin/master, origin/devel, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 10:38:59 -0400;
23673da (origin/RELEASE_3_18, RELEASE_3_18) bump x.y.z version to even y prior to creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 10:38:59 -0400;
b96d9bb Update .github files, README, pkgdown config, ran dev/04_update.R by Leonardo Collado Torres <lcolladotor@gmail.com> 2023-05-07 01:07:10 -0400;
2aa4858 Update GHA to bioc 3.17 by Leonardo Collado Torres <lcolladotor@gmail.com> 2023-05-06 20:48:10 -0400;
28a3ccb bump x.y.z version to odd y following creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 10:35:05 -0400;
a4e6dde (origin/RELEASE_3_17, RELEASE_3_17) bump x.y.z version to even y prior to creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 10:35:05 -0400;
a63cb58 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 11:10:25 -0400;
9245bc5 (origin/RELEASE_3_16, RELEASE_3_16) 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 11:10:25 -0400;
4cf63c3 bump x.y.z version to odd y following creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:21:51 +0000;
4ebf7a9 (origin/RELEASE_3_15, RELEASE_3_15) bump x.y.z version to even y prior to creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:21:51 +0000;
62c9d98 (origin/RELEASE_3_14, RELEASE_3_14) v1.28.1 by Leonardo Collado Torres <lcolladotor@gmail.com> 2021-11-22 19:33:33 -0500;
c6ca8d2 v1.29.1 by Leonardo Collado Torres <lcolladotor@gmail.com> 2021-11-22 19:33:05 -0500;
8253c82 update biocthis with bioc 3.14 by Leonardo Collado Torres <lcolladotor@gmail.com> 2021-11-22 19:29:29 -0500;
e1e3ee5 Work-around https://github.com/lawremi/ggbio/issues/159 by Leonardo Collado Torres <lcolladotor@gmail.com> 2021-11-22 19:28:06 -0500;
0712071 update biocthis with bioc 3.14 by Leonardo Collado Torres <lcolladotor@gmail.com> 2021-11-22 19:29:29 -0500;
13d9e97 Work-around https://github.com/lawremi/ggbio/issues/159 by Leonardo Collado Torres <lcolladotor@gmail.com> 2021-11-22 19:28:06 -0500;
7e0f460 bump x.y.z version to odd y following creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 16:16:23 +0000;
16f8de2 bump x.y.z version to even y prior to creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 16:16:23 +0000;
5882387 try to resolve BiocCheck warnings from https://github.com/leekgroup/derfinderPlot/runs/3286040865?check_suite_focus=true#step:23:136 by Leonardo Collado Torres <lcolladotor@gmail.com> 2021-08-09 20:59:22 -0400;
1518bec match biocthis 1.3.7 after noticing https://github.com/ComunidadBioInfo/cdsb2021_scRNAseq/commit/7447618a7731d9ba13f358aceda926b195706c20 by Leonardo Collado Torres <lcolladotor@gmail.com> 2021-08-09 20:15:49 -0400;
3c919e3 err, fix my new typo by Leonardo Collado Torres <lcolladotor@gmail.com> 2021-08-05 13:50:22 -0400;
d544686 v1.27.1 -- match bioc 1.3.6 and fix https://github.com/lcolladotor/derfinder/pull/42 by Leonardo Collado Torres <lcolladotor@gmail.com> 2021-08-05 13:46:48 -0400;
1afbab8 bump x.y.z version to odd y following creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 16:08:11 +0000;
41d3249 (origin/RELEASE_3_13, RELEASE_3_13) bump x.y.z version to even y prior to creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 16:08:11 +0000;
8c36901 (origin/RELEASE_3_12, RELEASE_3_12) Fix citep -> Citep(); fix biblio by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-12-17 17:25:38 -0500;
36eede2 Fix citep -> Citep(); fix biblio by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-12-17 17:25:38 -0500;
adb0e95 v1.24.1 -- update to latest biocthis GHA; replace knitcitations with RefManageR by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-12-17 15:26:36 -0500;
ba957a6 v1.25.1 -- update to latest biocthis GHA; replace knitcitations with RefManageR by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-12-17 15:26:36 -0500;
602007a bump x.y.z version to odd y following creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 10:59:31 -0400;
b0d9a12 bump x.y.z version to even y prior to creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 10:59:31 -0400;
175c81b Update dev/ files by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-05-27 01:02:03 -0400;
6ea343c Update to match https://github.com/lcolladotor/biocthis/commit/3b96da142aef74df69f35664a13d1283359d5db5 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-05-27 00:53:14 -0400;
70ec1a7 Adding the latest dev files from https://github.com/lcolladotor/biocthis/commit/61e65ee854aff39d7c90f3df72ab842b77a15d10 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-05-10 12:18:40 -0400;
7653a15 v1.23.1 -- Update to match https://github.com/lcolladotor/biocthis/commit/61e65ee854aff39d7c90f3df72ab842b77a15d10 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-05-10 11:58:34 -0400;
0561966 bump x.y.z version to odd y following creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 18:43:44 +0000;
b1daeb6 (origin/RELEASE_3_11, RELEASE_3_11) bump x.y.z version to even y prior to creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 18:43:44 +0000;
4124541 Always use the latest remotes by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-27 10:01:51 -0400;
6736084 Try installing the dependencies in steps /nocache by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-27 09:59:02 -0400;
8695cbe See if the dev pkgdown works for recountWorkflow and recount as I get a similar error in https://github.com/LieberInstitute/recountWorkflow/runs/619097138?check_suite_focus=true#step:15:29 to https://github.com/r-lib/pkgdown/issues/1275 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-26 23:17:38 -0400;
2230fd2 Clean up a comment by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-26 23:06:31 -0400;
69d97f7 Add some messages so I can find the lines easier on the log files. /nocache by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-26 23:00:19 -0400;
59c296a edit a comment, just an excuse to use /nocache which I forgot in 464148c by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-26 21:14:42 -0400;
464148c Do the installation in even more granular steps by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-26 21:13:08 -0400;
058feee Try another test prior to responding to https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016680.html. Related to https://github.com/r-lib/remotes/issues/296. /nocache by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-26 20:00:48 -0400;
ea58939 Fix my earlier test at e0f61f5 for: try using remotes to find the dependencies, but install them with BiocManager::install() instead of remotes::install_deps() given https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html and https://github.com/r-lib/remotes/issues/296 /nocache by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-26 11:26:52 -0400;
8efd4b6 Just a minor change. I forgot to use /nocache on my previous commit message :P by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-26 11:16:41 -0400;
e0f61f5 Try using remotes to find the dependencies, but install them with BiocManager::install() instead of remotes::install_deps() given https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html and https://github.com/r-lib/remotes/issues/296 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-26 11:15:03 -0400;
bae121d Remove the windows R-devel hack I used plus other outdated code now that R 4.0 has been released /nocache by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-25 15:46:33 -0400;
3e056e2 Try with installing tibble manually first on Windows by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-25 14:56:49 -0400;
e6e2ed8 GenomeInfoDbData needs to be installed before TxDb.Hsapiens.UCSC.hg19.knownGene can be installed on macOS and Windows by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-25 14:07:48 -0400;
06095fb Add lots of comments, no longer use R-devel by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-25 12:54:07 -0400;
6e0bd3c Tiny change by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-21 19:49:08 -0400;
9ff0ca6 Update after running styler by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-21 01:51:06 -0400;
83990df v1.21.5 -- fix logic on Windows by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-21 01:20:37 -0400;
d586ae4 Fix BiocStyle syntax + fix Windows hack if + Fix link to BiocStyle by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-21 01:00:45 -0400;
a38d0e9 GenomeInfoDbData needs to be installed first by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-20 22:54:02 -0400;
413cebf Fix contrib urls. BioCann, BioCexp and BioCworkflows are only available from source by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-20 21:17:32 -0400;
306abfe Attempt messing with contrib by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-20 20:30:02 -0400;
6cc04ae try with http instead of https by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-20 18:28:35 -0400;
3dc8b60 Second attempt at fixing the syntax by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-20 17:49:24 -0400;
1205a93 Fix the syntax by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-20 17:47:13 -0400;
337a5d8 Try with the binary for Rhtslib from BioC 3.11 and R 4.0 -- it's really a workaround. Add conditional caching. Could be a solution to https://github.com/r-lib/actions/issues/86 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-20 17:44:51 -0400;
247f571 fix order by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-20 15:35:24 -0400;
cb9781b Attempt bypassing the Rhtslib issues on Windows by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-20 13:14:06 -0400;
628a4a7 Update to match https://github.com/LieberInstitute/recount3/commit/0f8c259 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-20 13:04:30 -0400;
94b7b25 Update to match https://github.com/LieberInstitute/recount3/commit/85339bd by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-20 13:01:53 -0400;
b1e7173 Revert "Hm... maybe R 4.0 is supported on Windows. Let's see" by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-19 18:59:00 -0400;
c0dcd8a Hm... maybe R 4.0 is supported on Windows. Let's see by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-19 18:18:58 -0400;
8087c72 oops, I was wrong :/ https://github.com/r-lib/xml2/issues/296#issuecomment-616048078. I do need the devel version of xml2 on macOS by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-19 17:38:08 -0400;
2c52021 Update to match https://github.com/LieberInstitute/recount3/commit/25ad619 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-19 16:33:54 -0400;
cc96a88 Update to match https://github.com/LieberInstitute/recount3/commit/a7e66f6 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-19 16:11:33 -0400;
8728db6 Update to match https://github.com/LieberInstitute/recount3/commit/141a7fd by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-19 14:14:27 -0400;
c936a8a Update to match https://github.com/LieberInstitute/recount3/commit/3057bda by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-19 12:58:59 -0400;
a964db2 Try using https://github.com/lcolladotor/actions/commit/79f49f42fa95734d3c215d521c5c9bf39525c084 to run windows with r-devel + clean up as in https://github.com/LieberInstitute/recount3/commit/1d4e9de by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-19 01:29:39 -0400;
df4938e Test without using the devel version of xml2 after setting XML_CONFIG to point to the version from homebrew by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-19 00:13:56 -0400;
9ba5458 Clean up by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-18 23:55:23 -0400;
ae39a45 Also try another combination that sets more variables by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-18 22:43:42 -0400;
fc284eb Try a combination that seems to work locally by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-18 22:42:47 -0400;
ba28659 fix typos, try also setting XML_CONFIG like it's suggested at https://stackoverflow.com/questions/47540782/cannot-install-xml-package-in-r-rstudio/51115831 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-18 21:57:41 -0400;
e477acf Try with set-env by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-18 21:56:59 -0400;
04fcc39 Try with the brew recommendations from https://github.com/LieberInstitute/recount3/runs/598556681?check_suite_focus=true by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-18 19:34:21 -0400;
e00fa1c Try with brew install libxml2. Seems to work locally on my macOS laptop with R 4.1 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-18 18:55:38 -0400;
48e875c try without sudo by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-18 18:13:38 -0400;
7b8c0e6 Try installing xml2 with the instructions from http://mac.r-project.org/libs-4/ by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-18 17:49:00 -0400;
34709e3 Adapt interesting additions (xml2, imagemagick) from https://github.com/r-lib/usethis/commit/9741c470ab75655136d473aabd1d649e1ebfe486. Related also to https://community.rstudio.com/t/github-actions-failing-on-mac-devel-because-xml2-is-not-available/61537/3 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-18 16:57:14 -0400;
4d88465 Attempt to fix the bioc version setup for macOS by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-18 15:12:06 -0400;
b8427e4 Force re-installing BiocCheck by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-18 14:59:16 -0400;
b636c72 try R devel instead of 4.0 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-18 14:41:42 -0400;
073934a Add missing $ by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-18 14:10:53 -0400;
e5d6e66 Try implementing the code duplication idea I mentioned at https://github.com/r-lib/actions/issues/84#issuecomment-615903587 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-18 14:07:40 -0400;
bdcab5a Fix an if I noticed when writing https://github.com/r-lib/actions/issues/84#issue-602222491 by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-17 19:12:15 -0400;
49a6712 v1.21.4 -- test the hopefully final GitHub Action workflow (using the cache from the successful build from the last commit) by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-17 16:06:00 -0400;
5e4ade5 setup the GITHUB_PAT too by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-17 11:23:30 -0400;
256c3a9 Try setting the user email and name by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-17 11:06:59 -0400;
456184f Specify the shell used for the r_lib_var step by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-17 10:25:51 -0400;
a689861 set the GITHUB token by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-17 10:09:18 -0400;
d446381 Another attempt to fix BiocCheck by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-17 09:14:38 -0400;
cf3aad1 Now BiocCheck fails to find Biobase. So I'll use .libPaths()[2] for all of BiocCheck's dependencies by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-17 08:30:49 -0400;
edd8884 Try installing BiocCheck on the second .libPaths() given the new bug when using a volume with the biocdocker by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-17 02:04:23 -0400;
7797986 hm... new bug by Leonardo Collado Torres <lcolladotor@gmail.com> 2020-04-17 01:09:02 -0400;