From 2b0dbba61949ec8c8ca405a9797784dc6113cd60 Mon Sep 17 00:00:00 2001 From: Arni Magnusson Date: Thu, 15 Jun 2023 11:21:30 +1100 Subject: [PATCH 1/4] Remove gdata dependency --- DESCRIPTION | 6 +++--- NAMESPACE | 1 - README.md | 2 +- 3 files changed, 4 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8e8853a..c5d5e89 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,14 +2,14 @@ Package: elementR Type: Package Title: An Framework for Reducing Elemental LAICPMS Data from Solid Structures -Version: 1.3.7 -Date: 2020-09-01 +Version: 1.3.8 +Date: 2023-06-15 Author: Charlotte Sirot, Francois Guilhaumon Maintainer: Charlotte Sirot Description: Aims to facilitate the reduction of elemental microchemistry data from solid-phase LAICPMS analysis (laser ablation inductive coupled plasma mass spectrometry). The 'elementR' package provides a reactive and user friendly interface (based on a 'shiny' application) and a set of 'R6' classes for conducting all steps needed for an optimal data reduction while leaving maximum control for user. Repository: CRAN Depends: R (>= 3.2.3) -Imports: gdata, shiny,devtools, shinyjs, gnumeric, R6, shinydashboard, +Imports: shiny,devtools, shinyjs, gnumeric, R6, shinydashboard, abind, stringr, lmtest, tcltk,tcltk2, reader, readODS, readxl, EnvStats, outliers, zoo, colourpicker, stats, graphics, utils, httpuv diff --git a/NAMESPACE b/NAMESPACE index c26fe56..1e7f53d 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -10,7 +10,6 @@ importFrom(shinyjs, delay, useShinyjs, addClass) importFrom(gnumeric, read.gnumeric.sheet) importFrom(abind, abind) importFrom(tcltk2, tk2text) -importFrom(gdata, read.xls) importFrom(lmtest, dwtest, hmctest) importFrom(colourpicker, colourInput) importFrom("readODS", read.ods) diff --git a/README.md b/README.md index 8c087cb..6d63609 100644 --- a/README.md +++ b/README.md @@ -48,7 +48,7 @@ Alternatively, you can install the development version (not yet pushed on cran) ``` #Install elementR's dependencies -pkgs <- c("gdata", "shiny","devtools", "shinyjs", "gnumeric", "R6", "shinydashboard", +pkgs <- c("shiny","devtools", "shinyjs", "gnumeric", "R6", "shinydashboard", "abind", "stringr", "lmtest", "tcltk", "tcltk2", "reader", "readODS", "readxl", "outliers", "climtrends", "EnvStats", "colourpicker", "zoo", "httpuv") From 150ec7a5e6817c5fa78816487d07462309c0f173 Mon Sep 17 00:00:00 2001 From: Arni Magnusson Date: Thu, 15 Jun 2023 11:54:20 +1100 Subject: [PATCH 2/4] Fix help page: delementR_repStandard -> elementR_repStandard --- man/elementR_repStandard.Rd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/man/elementR_repStandard.Rd b/man/elementR_repStandard.Rd index c151454..77d9a2d 100644 --- a/man/elementR_repStandard.Rd +++ b/man/elementR_repStandard.Rd @@ -7,11 +7,11 @@ Object elementR_repStandard \description{ The \code{R6Class} object \code{elementR_repStandard} contains the main information needed for the filtration of a batch of standard replicates. } -\usage{delementR_repStandard} +\usage{elementR_repStandard} \format{ An \code{R6Class} generator object } -\section{Inheritance}{The \code{delementR_repStandard} object inherits from the \code{elementR_rep}.} +\section{Inheritance}{The \code{elementR_repStandard} object inherits from the \code{elementR_rep}.} \section{Fields}{ \describe{\item{\code{rep_type}}{A character string indicating the type of the batch considered (here, "standard")}} From 5ae423cad8388b1706a6f21e49c73f05f69786db Mon Sep 17 00:00:00 2001 From: Arni Magnusson Date: Thu, 15 Jun 2023 11:55:11 +1100 Subject: [PATCH 3/4] Fix https links --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 6d63609..bbb1839 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/elementR)](https://cran.r-project.org/package=elementR) [![Download_badge](http://cranlogs.r-pkg.org/badges/grand-total/elementR?color=brightgreen)](https://cran.r-project.org/package=elementR) [![Build Status](https://api.travis-ci.org/charlottesirot/elementR.svg?branch=master)](https://travis-ci.org/charlottesirot/elementR.svg?branch=master) -[![codecov](https://codecov.io/gh/charlottesirot/elementR/branch/master/graph/badge.svg)](https://codecov.io/gh/charlottesirot/elementR) +[![codecov](https://app.codecov.io/gh/charlottesirot/elementR/branch/master/graph/badge.svg)](https://app.codecov.io/gh/charlottesirot/elementR)
@@ -27,7 +27,7 @@ For more details on the project or on elementR, see [elementR website](https://c - a set of classes to handle LA-ICPMS data - a reactive user friendly interface running in the web browser to conduct all steps needed for an optimal data reduction while leaving maximum control to the user. -**elementR** implements [R6 R classes](https://github.com/wch/R6/) and is based on [Shiny](http://shiny.rstudio.com/) for it's GUI. +**elementR** implements [R6 R classes](https://github.com/r-lib/R6) and is based on [Shiny](https://shiny.posit.co/) for it's GUI. #### Before installation From ed66c7fd6a42f8e60cc5fff4109838f1739a39ed Mon Sep 17 00:00:00 2001 From: Arni Magnusson Date: Thu, 15 Jun 2023 11:56:30 +1100 Subject: [PATCH 4/4] Remove Travis - service stopped in 2021 --- .Rbuildignore | 2 -- .travis.yml | 21 --------------------- README.md | 1 - 3 files changed, 24 deletions(-) delete mode 100644 .travis.yml diff --git a/.Rbuildignore b/.Rbuildignore index 77372e0..dab355a 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,7 +1,5 @@ ^.*\.Rproj$ ^\.Rproj\.user$ -.travis.yml - ^README\.Rmd$ ^README-.*\.png$ diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index c8eabe5..0000000 --- a/.travis.yml +++ /dev/null @@ -1,21 +0,0 @@ -language: r -cache: packages - -#addons: -# sauce_connect: -# username: "fguilhaumon" -# access_key: "37bb8444-05bd-4508-bb15-f1720fbaf01d" - -r_packages: - - covr - -before_install: - - sudo apt-get update -qq - - sudo apt-get install -y tcl8.5 tcl8.5-dev - - "export DISPLAY=:99.0" - - "sh -e /etc/init.d/xvfb start" - - sleep 3 # give xvfb some time to start -# - rackup # start a Web server -# - sleep 3 # give Web server some time to bind to sockets, etc -after_success: - - Rscript -e 'library(covr);codecov()' \ No newline at end of file diff --git a/README.md b/README.md index bbb1839..efe0d20 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,6 @@ [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/elementR)](https://cran.r-project.org/package=elementR) [![Download_badge](http://cranlogs.r-pkg.org/badges/grand-total/elementR?color=brightgreen)](https://cran.r-project.org/package=elementR) - [![Build Status](https://api.travis-ci.org/charlottesirot/elementR.svg?branch=master)](https://travis-ci.org/charlottesirot/elementR.svg?branch=master) [![codecov](https://app.codecov.io/gh/charlottesirot/elementR/branch/master/graph/badge.svg)](https://app.codecov.io/gh/charlottesirot/elementR)