From 2ceed67ef9f50766d61e2f6afe8301590d02935f Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 9 Jun 2020 16:13:11 +0100 Subject: [PATCH 1/2] Added 'v6.0.1-dev' and 'v6.1-dev' --- README.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index c5d39e7b..b6358e98 100644 --- a/README.md +++ b/README.md @@ -8,9 +8,10 @@ DataSHIELD client side base R library. | Branch | dsBase status | dsBaseClient status | dsBaseClient tests | | -------- | ------------ | ------------------- | ------------------ | -| Master | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=master)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=3&branchName=master) | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=master)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=master) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/master/latest/) | -| v6.0-dev | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=v6.0-dev)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=3&branchName=v6.0-dev) | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=v6.0-dev)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.0-dev) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/v6.0-dev/latest/) | - +| Master | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=master)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=master) | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=master)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=master) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/master/latest/) | +| v6.0-dev | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=v6.0-dev)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.0-dev) | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=v6.0-dev)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.0-dev) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/v6.0-dev/latest/) | +| v6.0.1-dev | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=v6.0.1-dev)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.0.1-dev) | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=v6.0.1-dev)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.0.1-dev) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/v6.0.1-dev/latest/) | +| v6.1-dev | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=v6.1-dev)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.1-dev) | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=v6.1-dev)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.1-dev) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/v6.1-dev/latest/) | [![License](https://img.shields.io/badge/license-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.html) From 64365c02b60886a03bcaa86c227ee42e0cfdbdea Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Thu, 25 Jun 2020 19:00:37 +0100 Subject: [PATCH 2/2] Remove 'ds.acme' --- NAMESPACE | 1 - R/ds.acme.R | 46 ---------------------------------------------- man/ds.acme.Rd | 33 --------------------------------- 3 files changed, 80 deletions(-) delete mode 100644 R/ds.acme.R delete mode 100644 man/ds.acme.Rd diff --git a/NAMESPACE b/NAMESPACE index bd67b50c..5b15b758 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,7 +1,6 @@ # Generated by roxygen2: do not edit by hand export(ds.Boole) -export(ds.acme) export(ds.asCharacter) export(ds.asDataMatrix) export(ds.asFactor) diff --git a/R/ds.acme.R b/R/ds.acme.R deleted file mode 100644 index 17c58284..00000000 --- a/R/ds.acme.R +++ /dev/null @@ -1,46 +0,0 @@ -#' -#' @title ds.acme function template -#' @description example aggregate function template -#' @details Client-side acme example aggregate function template -#' This file is to be placed in server-sides R directory. -#' @param name a character vector containing "a name" -#' @param datasources specifies the particular 'connection object(s)' to use. -#' @return character vector containing "a message" -#' @author Ever, Who. -#' @export -#' - -ds.acme <- function(model, Set, type.data = "SummarizedExperiment", threshold = NULL, - reference = NULL, datasources=NULL) -{ - # if no opal login details are provided look for 'opal' objects in the environment - if (is.null(datasources)) - { - datasources <- DSI::datashield.connections_find() - } - type <- charmatch(type.data, c("SummarizedExperiment", "matrix", "htseq")) - - if(is.na(type)) - { - stop("type.data must be 'SummarizedExperiment', 'matrix', 'htseq'") - } - - mt <- all.vars(model) - variable_names <- mt[1] - - if (length(mt)>1) - { - covariable_names <- paste(mt[-1], collapse=",") - } - - else - { - covariable_names <- NULL - } - - # call the server side function - calltext <- call("acmeDS",Set, variable_names, covariable_names,type, threshold, reference) - output <- datashield.aggregate(datasources, calltext) - return(output) -} -#ds.acme diff --git a/man/ds.acme.Rd b/man/ds.acme.Rd deleted file mode 100644 index 2dba1fc0..00000000 --- a/man/ds.acme.Rd +++ /dev/null @@ -1,33 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/ds.acme.R -\name{ds.acme} -\alias{ds.acme} -\title{ds.acme function template} -\usage{ -ds.acme( - model, - Set, - type.data = "SummarizedExperiment", - threshold = NULL, - reference = NULL, - datasources = NULL -) -} -\arguments{ -\item{datasources}{specifies the particular 'connection object(s)' to use.} - -\item{name}{a character vector containing "a name"} -} -\value{ -character vector containing "a message" -} -\description{ -example aggregate function template -} -\details{ -Client-side acme example aggregate function template -This file is to be placed in server-sides R directory. -} -\author{ -Ever, Who. -}