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Improve documentation and package imports #308

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f3bcb06
resolve tidyomics conflicts and docs clean up
chilampoon Sep 16, 2023
bd82a3c
rm ggplot2 dep and add .Rinstignore
chilampoon Sep 17, 2023
4d8a45b
Merge remote-tracking branch 'upstream/master'
chilampoon Sep 17, 2023
89b106f
try to find the warning source
chilampoon Sep 17, 2023
d7690dd
update R ver and check-bioc
chilampoon Sep 19, 2023
8709db9
imports conflict
chilampoon Sep 19, 2023
b6fdbc4
set _R_CHECK_FORCE_SUGGESTS_ to false
chilampoon Sep 19, 2023
0c1670a
add pkgconfig
chilampoon Sep 19, 2023
1a0c713
Merge branch 'master' into master
stemangiola Sep 19, 2023
c564934
Set automatic Bioconductor and R build-check versions
william-hutchison Jan 4, 2024
243532c
Replace check-bioc with rworkflows workflow file
william-hutchison Jan 4, 2024
25c605d
Update workflow branch triggers
william-hutchison Jan 4, 2024
bfe5ac8
Update function imports
william-hutchison Jan 5, 2024
c98891b
Update EPIC and EGSEA function imports
william-hutchison Jan 5, 2024
5188581
Fix vignette error
william-hutchison Jan 8, 2024
02dfccc
Remove unneeded files
william-hutchison Jan 8, 2024
50a94ab
Update suggested packages
william-hutchison Jan 8, 2024
a162b8e
Replace README example data
william-hutchison Jan 8, 2024
d8862e2
Update README tidyomics ecosystem links
william-hutchison Jan 8, 2024
225c005
Version up
william-hutchison Jan 8, 2024
eea34de
Remove EGSEA import
william-hutchison Jan 8, 2024
d59b0a4
Version up
william-hutchison Jan 8, 2024
0f60ddd
Remove unneeded whole package imports
william-hutchison Jan 9, 2024
fd170a8
Remove unneeded whole dplyr import
william-hutchison Jan 9, 2024
9a9542e
Replace EPIC import with message
william-hutchison Jan 9, 2024
9baac9c
Version up
william-hutchison Jan 9, 2024
7af3822
Update README
william-hutchison Jan 9, 2024
2193a71
Version up
william-hutchison Jan 9, 2024
989009a
Merge branch 'master' into chilampoon-improve-documentation
stemangiola Jan 9, 2024
c54b441
Merge branch 'master' into chilampoon-improve-documentation
stemangiola Feb 7, 2024
6671ed2
Merge remote-tracking branch 'stemangiola/master' into chilampoon-imp…
chilampoon Feb 12, 2024
e174749
resovle line char notes and some warnings
chilampoon Feb 12, 2024
fba863a
resolve doc warnings
chilampoon Feb 12, 2024
89c2244
merge try 1
chilampoon Feb 12, 2024
59862f2
Merge branch 'master' into chilampoon-improve-documentation
stemangiola Feb 12, 2024
2d2b508
replace one_of in functions.R
chilampoon Feb 12, 2024
ea0072b
resolve doc warnings and pull udpates
chilampoon Feb 12, 2024
e3f50e7
Merge branch 'chilampoon-improve-documentation'
william-hutchison Sep 3, 2024
6ba2954
Remove merge resolution comment
william-hutchison Sep 3, 2024
6f2b55a
Merge branch 'master' into chilampoon-improve-documentation
stemangiola Oct 16, 2024
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1 change: 1 addition & 0 deletions .Rinstignore
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
dev/
2 changes: 0 additions & 2 deletions .coveralls.yml

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278 changes: 0 additions & 278 deletions .github/workflows/check-bioc.yml

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47 changes: 47 additions & 0 deletions .github/workflows/rworkflows.yml
Original file line number Diff line number Diff line change
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name: rworkflows
on:
push:
pull_request:
jobs:
rworkflows:
permissions: write-all
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
container: ${{ matrix.config.cont }}
strategy:
fail-fast: ${{ false }}
matrix:
config:
- os: ubuntu-latest
bioc: devel
r: auto
cont: ghcr.io/bioconductor/bioconductor_docker:devel
rspm: ~
- os: macOS-latest
bioc: release
r: auto
cont: ~
rspm: ~
- os: windows-latest
bioc: release
r: auto
cont: ~
rspm: ~
steps:
- uses: neurogenomics/rworkflows@master
with:
run_bioccheck: ${{ false }}
run_rcmdcheck: ${{ true }}
as_cran: ${{ true }}
run_vignettes: ${{ true }}
has_testthat: ${{ true }}
run_covr: ${{ true }}
run_pkgdown: ${{ true }}
has_runit: ${{ false }}
has_latex: ${{ false }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run_docker: ${{ false }}
DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
runner_os: ${{ runner.os }}
cache_version: cache-v1
docker_registry: ghcr.io
24 changes: 0 additions & 24 deletions .gitignore

This file was deleted.

16 changes: 0 additions & 16 deletions .travis.yml

This file was deleted.

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