From 633097ceda8e15b1d8e0cd2d01a8f10443774da3 Mon Sep 17 00:00:00 2001 From: Yuri05 Date: Thu, 25 Jul 2024 15:14:12 +0200 Subject: [PATCH] Review comments --- README.Rmd | 3 ++- README.md | 61 ++++++++++++++++++++++++++---------------------------- 2 files changed, 31 insertions(+), 33 deletions(-) diff --git a/README.Rmd b/README.Rmd index 1476ae447..0c63164cc 100644 --- a/README.Rmd +++ b/README.Rmd @@ -16,7 +16,8 @@ knitr::opts_chunk$set( # OSPSuite-R -[![Main-Workflow](https://github.com/Open-Systems-Pharmacology/OSPSuite-R/actions/workflows/main-workflow.yaml/badge.svg)](https://github.com/Open-Systems-Pharmacology/OSPSuite-R/actions/workflows/main-workflow.yaml) +[![](https://img.shields.io/github/actions/workflow/status/Open-Systems-Pharmacology/OSPSuite-R/main-workflow.yaml?branch=main&label=Build +)](https://github.com/Open-Systems-Pharmacology/OSPSuite-R/actions/workflows/main-workflow.yaml) [![Codecov test coverage](https://codecov.io/gh/Open-Systems-Pharmacology/OSPSuite-R/branch/main/graph/badge.svg)](https://app.codecov.io/gh/Open-Systems-Pharmacology/OSPSuite-R?branch=main) diff --git a/README.md b/README.md index e4a488f98..ff49dfd41 100644 --- a/README.md +++ b/README.md @@ -5,9 +5,9 @@ -[![R-CMD-check](https://github.com/Open-Systems-Pharmacology/OSPSuite-R/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Open-Systems-Pharmacology/OSPSuite-R/actions/workflows/R-CMD-check.yaml) +[![](https://img.shields.io/github/actions/workflow/status/Open-Systems-Pharmacology/OSPSuite-R/main-workflow.yaml?branch=main&label=Build)](https://github.com/Open-Systems-Pharmacology/OSPSuite-R/actions/workflows/main-workflow.yaml) [![Codecov test -coverage](https://codecov.io/gh/Open-Systems-Pharmacology/OSPSuite-R/branch/develop/graph/badge.svg)](https://app.codecov.io/gh/Open-Systems-Pharmacology/OSPSuite-R?branch=develop) +coverage](https://codecov.io/gh/Open-Systems-Pharmacology/OSPSuite-R/branch/main/graph/badge.svg)](https://app.codecov.io/gh/Open-Systems-Pharmacology/OSPSuite-R?branch=main) # Overview @@ -64,7 +64,8 @@ following order: # Installation The **ospsuite** package is compatible with R version 4.x.x and can be -used on [Windows](#on-windows) and [Linux](#on-linux) operating systems. +used on [Windows](#on-windows) and [Linux (Ubuntu)](#on-linux) operating +systems. `ospsuite` is not available on CRAN and also depends on packages from the OSP ecosystem that are not available on CRAN. Please follow the @@ -78,7 +79,7 @@ dependencies. The package requires additional software installations: - Latest Microsoft Visual C++ Redistributable for Visual Studio 2015, - 2017 and 2019 available + 2017, 2019 and 2022 available [here](https://support.microsoft.com/en-us/help/2977003/the-latest-supported-visual-c-downloads) - .NET 8 runtime available [here](https://dotnet.microsoft.com/download/dotnet/8.0/runtime). @@ -115,25 +116,23 @@ files provided with the When installing from such files, the CRAN dependencies need to be installed manually first. -``` r -# Install dependencies (e.g. R6) which are on CRAN -install.packages("data.table") -install.packages("dplyr") -install.packages("ggplot2") -install.packages("ggtext") -install.packages("jsonlite") -install.packages("lifecycle") -install.packages("openxlsx") -install.packages("patchwork") -install.packages("purrr") -install.packages("R6") -install.packages("rClr") -install.packages("readr") -install.packages("rlang") -install.packages("stringr") -install.packages("tidyr") -install.packages("xml2") -``` + #> Warning: package 'pacman' was built under R version 4.2.3 + # Install dependencies (e.g. R6) which are on CRAN + install.packages("data.table") + install.packages("dplyr") + install.packages("ggplot2") + install.packages("ggtext") + install.packages("jsonlite") + install.packages("lifecycle") + install.packages("openxlsx") + install.packages("patchwork") + install.packages("purrr") + install.packages("R6") + install.packages("readr") + install.packages("rlang") + install.packages("stringr") + install.packages("tidyr") + install.packages("xml2") #### Install non-CRAN dependencies @@ -176,16 +175,14 @@ install.packages(pathToOSPSuite.zip, repos = NULL) ## On Linux The **ospsuite** package has been tested under Linux distribution -**Ubuntu 22**. Installation under Linux requires several prerequisites, -the detailed instructions can be found in the Wiki: +**Ubuntu 22.04**. Installation under Linux requires several +prerequisites, the detailed instructions can be found in the Wiki: -- [Setup OSPSuite-R on - CentOS](https://github.com/Open-Systems-Pharmacology/OSPSuite-R/wiki/Setup-ospsuite-R-on-CentOS7) - [Setup OSPSuite-R on Ubuntu](https://github.com/Open-Systems-Pharmacology/OSPSuite-R/wiki/Setup-ospsuite-R-on-Ubuntu) -For other Linux distributions Docker containers can be used (Dockerfiles -based on CentOS 7 and Ubuntu 18 are available under +For other Linux distributions Docker containers can be used (Docker +container based on Ubuntu 22 is available under ) ## Build from source @@ -195,9 +192,9 @@ You can clone the GIT repository and build the package from source. ### How to update the libraries? The `{ospsuite}` package requires some shared libraries to get access to -PK-Sim functionality. To get the latest libraries(dll on Windows or so -on Linux), run the script file \`update_core_files.R’ provided with this -package. +PK-Sim functionality. To get the latest libraries(**.dll** on Windows or +**.so** on Linux), run the script file \`update_core_files.R’ provided +with this package. # Known issues