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setup general package framework and CI
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@@ -39,3 +39,5 @@ inst/doc | |
data-raw/*.rds | ||
.Rhistory | ||
.Rproj.user | ||
doc | ||
Meta |
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# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r | ||
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language: R | ||
cache: packages | ||
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after_success: | ||
- Rscript -e 'covr::codecov()' |
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@@ -4,17 +4,17 @@ Title: Read HotNet2 Results and Convert to Graph object | |
Version: 0.0.0.9000 | ||
Author: person(c("Joshua", "H"), "Cook", email = "[email protected]", | ||
role = c("aut", "cre")) | ||
Maintainer: Joshua Cook <[email protected]> | ||
Description: This package reads the results from HotNet2 for further analysis. | ||
It can return the results as a list of list of genes or transform them into | ||
`igraph` or `tidygraph` objects. | ||
License: file LICENSE | ||
Encoding: UTF-8 | ||
LazyData: true | ||
Depends: R (>= 3.5.0) | ||
Imports: | ||
dplyr (>= 0.8.0), | ||
ggplot2 (>= 3.1.0), | ||
magrittr (>= 1.5.0), | ||
purrr (>= 0.3.0), | ||
rlang (>= 0.3.0), | ||
tibble(>= 2.0.0) | ||
Suggests: | ||
knitr, | ||
rmarkdown, | ||
covr | ||
VignetteBuilder: knitr | ||
RoxygenNote: 6.1.1 |
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exportPattern("^[[:alpha:]]+") | ||
# Generated by roxygen2: do not edit by hand | ||
|
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--- | ||
title: "README.Rmd" | ||
author: "Joshua H. Cook" | ||
date: "2/22/2019" | ||
output: | ||
md_document: | ||
variant: markdown_github | ||
output: github_document | ||
--- | ||
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```{r setup, include=FALSE} | ||
knitr::opts_chunk$set(echo = TRUE) | ||
<!-- README.md is generated from README.Rmd. Please edit that file --> | ||
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```{r, include = FALSE} | ||
knitr::opts_chunk$set( | ||
collapse = TRUE, | ||
comment = "#>", | ||
fig.path = "man/figures/README-", | ||
out.width = "100%" | ||
) | ||
``` | ||
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# HotNetvieweR | ||
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**author: Joshua H. Cook** | ||
<!-- badges: start --> | ||
![CRAN_Release_Badge](https://www.r-pkg.org/badges/version/HotNetvieweR) | ||
[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) | ||
[![Travis build status](https://travis-ci.org/jhrcook/HotNetvieweR.svg?branch=master)](https://travis-ci.org/jhrcook/HotNetvieweR) | ||
[![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/jhrcook/HotNetvieweR?branch=master&svg=true)](https://ci.appveyor.com/project/jhrcook/HotNetvieweR) | ||
[![Codecov test coverage](https://codecov.io/gh/jhrcook/HotNetvieweR/branch/master/graph/badge.svg)](https://codecov.io/gh/jhrcook/HotNetvieweR?branch=master) | ||
<!-- badges: end --> | ||
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**date: 2019-02-22** | ||
The goal of HotNetvieweR is to ... | ||
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[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) | ||
![CRAN_Release_Badge](https://www.r-pkg.org/badges/version/HotNetvieweR) | ||
## Installation | ||
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You can install the released version of HotNetvieweR from [CRAN](https://CRAN.R-project.org) with: | ||
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``` r | ||
install.packages("HotNetvieweR") | ||
``` | ||
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Just started this package, but I have most of the pieces from my personal use. Should be able to get this up soon. | ||
And the development version from [GitHub](https://github.com/) with: | ||
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``` r | ||
# install.packages("devtools") | ||
devtools::install_github("jhrcook/HotNetvieweR") | ||
``` | ||
## Example | ||
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This is a basic example which shows you how to solve a common problem: | ||
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```{r example, eval=FALSE} | ||
library(HotNetvieweR) | ||
## basic example code | ||
``` |
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HotNetvieweR | ||
============ | ||
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**author: Joshua H. Cook** | ||
<!-- README.md is generated from README.Rmd. Please edit that file --> | ||
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**date: 2019-02-22** | ||
# HotNetvieweR | ||
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[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) ![CRAN\_Release\_Badge](https://www.r-pkg.org/badges/version/HotNetvieweR) | ||
<!-- badges: start --> | ||
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Just started this package, but I have most of the pieces from my personal use. Should be able to get this up soon. | ||
![CRAN\_Release\_Badge](https://www.r-pkg.org/badges/version/HotNetvieweR) | ||
[![License: GPL | ||
v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) | ||
[![Travis build | ||
status](https://travis-ci.org/jhrcook/HotNetvieweR.svg?branch=master)](https://travis-ci.org/jhrcook/HotNetvieweR) | ||
[![AppVeyor build | ||
status](https://ci.appveyor.com/api/projects/status/github/jhrcook/HotNetvieweR?branch=master&svg=true)](https://ci.appveyor.com/project/jhrcook/HotNetvieweR) | ||
[![Codecov test | ||
coverage](https://codecov.io/gh/jhrcook/HotNetvieweR/branch/master/graph/badge.svg)](https://codecov.io/gh/jhrcook/HotNetvieweR?branch=master) | ||
<!-- badges: end --> | ||
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The goal of HotNetvieweR is to … | ||
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## Installation | ||
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||
You can install the released version of HotNetvieweR from | ||
[CRAN](https://CRAN.R-project.org) with: | ||
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``` r | ||
install.packages("HotNetvieweR") | ||
``` | ||
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And the development version from [GitHub](https://github.com/) with: | ||
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``` r | ||
# install.packages("devtools") | ||
devtools::install_github("jhrcook/HotNetvieweR") | ||
``` | ||
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## Example | ||
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This is a basic example which shows you how to solve a common problem: | ||
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``` r | ||
library(HotNetvieweR) | ||
## basic example code | ||
``` |
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destination: docs | ||
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template: | ||
params: | ||
bootswatch: flatly | ||
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navbar: | ||
structure: | ||
left: | ||
- home | ||
- intro | ||
- reference | ||
- articles | ||
- tutorials | ||
right: | ||
- news | ||
- github | ||
components: | ||
home: | ||
icon: fas fa-home fa-lg | ||
href: index.html | ||
reference: | ||
text: Reference | ||
href: reference/index.html | ||
articles: | ||
text: Articles | ||
menu: | ||
- text: HotNet2 Setup and Example | ||
href: articles/HotNet2-setup-and-example.html | ||
news: | ||
text: Versions | ||
href: news/index.html | ||
github: | ||
icon: fa-github fa-lg | ||
href: https://github.com/jhrcook/ggasym | ||
twitter: | ||
icon: fab fa-twitter fa-lg | ||
href: https://twitter.com/JoshDoesa |
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# DO NOT CHANGE the "init" and "install" sections below | ||
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# Download script file from GitHub | ||
init: | ||
ps: | | ||
$ErrorActionPreference = "Stop" | ||
Invoke-WebRequest https://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1" | ||
Import-Module '..\appveyor-tool.ps1' | ||
install: | ||
ps: Bootstrap | ||
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cache: | ||
- C:\RLibrary | ||
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environment: | ||
NOT_CRAN: true | ||
# env vars that may need to be set, at least temporarily, from time to time | ||
# see https://github.com/krlmlr/r-appveyor#readme for details | ||
# USE_RTOOLS: true | ||
# R_REMOTES_STANDALONE: true | ||
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# Adapt as necessary starting from here | ||
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build_script: | ||
- travis-tool.sh install_deps | ||
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test_script: | ||
- travis-tool.sh run_tests | ||
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on_failure: | ||
- 7z a failure.zip *.Rcheck\* | ||
- appveyor PushArtifact failure.zip | ||
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artifacts: | ||
- path: '*.Rcheck\**\*.log' | ||
name: Logs | ||
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- path: '*.Rcheck\**\*.out' | ||
name: Logs | ||
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- path: '*.Rcheck\**\*.fail' | ||
name: Logs | ||
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- path: '*.Rcheck\**\*.Rout' | ||
name: Logs | ||
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- path: '\*_*.tar.gz' | ||
name: Bits | ||
|
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- path: '\*_*.zip' | ||
name: Bits |
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comment: false | ||
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coverage: | ||
status: | ||
project: | ||
default: | ||
target: auto | ||
threshold: 1% | ||
patch: | ||
default: | ||
target: auto | ||
threshold: 1% |
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