From 2112892f8acb0c4d40e63cc3cd2c002cbbbb4261 Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Fri, 5 Jul 2024 12:25:37 +0200 Subject: [PATCH 1/2] fix: added package anchors for links --- R/ArmadilloConnection.R | 12 ++++++------ R/ArmadilloDriver.R | 2 +- R/ArmadilloResult.R | 2 +- man/ArmadilloConnection-class.Rd | 2 +- man/ArmadilloDriver-class.Rd | 2 +- man/ArmadilloResult-class.Rd | 2 +- man/dsAssignResource-ArmadilloConnection-method.Rd | 2 +- man/dsDisconnect-ArmadilloConnection-method.Rd | 2 +- man/dsIsAsync-ArmadilloConnection-method.Rd | 2 +- man/dsListResources-ArmadilloConnection-method.Rd | 2 +- man/dsListTables-ArmadilloConnection-method.Rd | 2 +- 11 files changed, 16 insertions(+), 16 deletions(-) diff --git a/R/ArmadilloConnection.R b/R/ArmadilloConnection.R index 9f745c8..fea73ae 100644 --- a/R/ArmadilloConnection.R +++ b/R/ArmadilloConnection.R @@ -5,7 +5,7 @@ setOldClass("handle") #' Class ArmadilloConnection. #' #' An Armadillo connection implementing the DataSHIELD Interface (DSI) -#' \code{\link{DSConnection-class}}. +#' \code{\link[DSI]{DSConnection-class}}. #' #' @slot name The name of the connection #' @slot handle The handle used to connect with the server @@ -39,7 +39,7 @@ methods::setClass("ArmadilloConnection", #' character string). #' #' @importMethodsFrom DSI dsDisconnect -#' @seealso \code{\link{dsDisconnect}} +#' @seealso \code{\link[DSI]{dsDisconnect}} #' @export methods::setMethod( "dsDisconnect", "ArmadilloConnection", @@ -86,7 +86,7 @@ methods::setMethod( #' #' @return The fully qualified names of the tables. #' -#' @seealso \code{\link{dsListTables}} +#' @seealso \code{\link[DSI]{dsListTables}} #' @importMethodsFrom DSI dsListTables #' @export methods::setMethod( @@ -134,7 +134,7 @@ methods::setMethod( #' #' @return The fully qualified names of the resources. #' -#' @seealso \code{\link{dsListResources}} +#' @seealso \code{\link[DSI]{dsListResources}} #' @importMethodsFrom DSI dsListResources #' @export methods::setMethod( @@ -176,7 +176,7 @@ methods::setMethod( #' List of DataSHIELD operations on which Armadillo DataSHIELD Service supports #' asynchronicity. #' -#' When a \code{\link{DSResult-class}} object is returned on aggregation or +#' When a \code{\link[DSI]{DSResult-class}} object is returned on aggregation or #' assignment operation, the raw result can be accessed asynchronously, #' allowing parallelization of DataSHIELD calls over multpile servers. #' The returned named list of logicals will specify if asynchronicity is @@ -300,7 +300,7 @@ methods::setMethod( #' #' Assign a resource in the DataSHIELD R session. #' -#' @param conn An object that inherits from \code{\link{DSConnection-class}}. +#' @param conn An object that inherits from \code{\link[DSI]{DSConnection-class}}. #' @param symbol Name of the R symbol. #' @param resource Fully qualified name of a resource reference in the data #' repository. diff --git a/R/ArmadilloDriver.R b/R/ArmadilloDriver.R index c3fcb52..8ae6263 100644 --- a/R/ArmadilloDriver.R +++ b/R/ArmadilloDriver.R @@ -2,7 +2,7 @@ #' Class ArmadilloDriver with constructor armadillo #' #' An Armadillo DataSHIELD Service Driver implementing the DataSHIELD Interface -#' (DSI) \code{\link{DSDriver-class}}. This class should always be initialized +#' (DSI) \code{\link[DSI]{DSDriver-class}}. This class should always be initialized #' with the \code{\link{armadillo}} function. #' It returns a singleton that allows you to connect to Armadillo #' diff --git a/R/ArmadilloResult.R b/R/ArmadilloResult.R index 8fe75c1..00c774f 100644 --- a/R/ArmadilloResult.R +++ b/R/ArmadilloResult.R @@ -4,7 +4,7 @@ NULL #' Class ArmadilloResult. #' #' An Armadillo result implementing the DataSHIELD Interface (DSI) -#' \code{\link{DSResult-class}}. +#' \code{\link[DSI]{DSResult-class}}. #' #' @slot conn The connection used to create this result #' @slot rval The result diff --git a/man/ArmadilloConnection-class.Rd b/man/ArmadilloConnection-class.Rd index c182b82..be49a17 100644 --- a/man/ArmadilloConnection-class.Rd +++ b/man/ArmadilloConnection-class.Rd @@ -6,7 +6,7 @@ \title{Class ArmadilloConnection.} \description{ An Armadillo connection implementing the DataSHIELD Interface (DSI) -\code{\link{DSConnection-class}}. +\code{\link[DSI]{DSConnection-class}}. } \section{Slots}{ diff --git a/man/ArmadilloDriver-class.Rd b/man/ArmadilloDriver-class.Rd index 90c4037..7f9026d 100644 --- a/man/ArmadilloDriver-class.Rd +++ b/man/ArmadilloDriver-class.Rd @@ -6,7 +6,7 @@ \title{Class ArmadilloDriver with constructor armadillo} \description{ An Armadillo DataSHIELD Service Driver implementing the DataSHIELD Interface -(DSI) \code{\link{DSDriver-class}}. This class should always be initialized +(DSI) \code{\link[DSI]{DSDriver-class}}. This class should always be initialized with the \code{\link{armadillo}} function. It returns a singleton that allows you to connect to Armadillo } diff --git a/man/ArmadilloResult-class.Rd b/man/ArmadilloResult-class.Rd index 762874c..00f8e9c 100644 --- a/man/ArmadilloResult-class.Rd +++ b/man/ArmadilloResult-class.Rd @@ -6,7 +6,7 @@ \title{Class ArmadilloResult.} \description{ An Armadillo result implementing the DataSHIELD Interface (DSI) -\code{\link{DSResult-class}}. +\code{\link[DSI]{DSResult-class}}. } \section{Slots}{ diff --git a/man/dsAssignResource-ArmadilloConnection-method.Rd b/man/dsAssignResource-ArmadilloConnection-method.Rd index 8afcca9..7a9541f 100644 --- a/man/dsAssignResource-ArmadilloConnection-method.Rd +++ b/man/dsAssignResource-ArmadilloConnection-method.Rd @@ -7,7 +7,7 @@ \S4method{dsAssignResource}{ArmadilloConnection}(conn, symbol, resource, async = TRUE) } \arguments{ -\item{conn}{An object that inherits from \code{\link{DSConnection-class}}.} +\item{conn}{An object that inherits from \code{\link[DSI]{DSConnection-class}}.} \item{symbol}{Name of the R symbol.} diff --git a/man/dsDisconnect-ArmadilloConnection-method.Rd b/man/dsDisconnect-ArmadilloConnection-method.Rd index af29f22..297009c 100644 --- a/man/dsDisconnect-ArmadilloConnection-method.Rd +++ b/man/dsDisconnect-ArmadilloConnection-method.Rd @@ -19,5 +19,5 @@ If a workspace ID is provided, the DataSHIELD R session will be saved before being destroyed. } \seealso{ -\code{\link{dsDisconnect}} +\code{\link[DSI]{dsDisconnect}} } diff --git a/man/dsIsAsync-ArmadilloConnection-method.Rd b/man/dsIsAsync-ArmadilloConnection-method.Rd index 6e2ddc2..7938ac0 100644 --- a/man/dsIsAsync-ArmadilloConnection-method.Rd +++ b/man/dsIsAsync-ArmadilloConnection-method.Rd @@ -17,7 +17,7 @@ List of DataSHIELD operations on which Armadillo DataSHIELD Service supports asynchronicity. } \details{ -When a \code{\link{DSResult-class}} object is returned on aggregation or +When a \code{\link[DSI]{DSResult-class}} object is returned on aggregation or assignment operation, the raw result can be accessed asynchronously, allowing parallelization of DataSHIELD calls over multpile servers. The returned named list of logicals will specify if asynchronicity is diff --git a/man/dsListResources-ArmadilloConnection-method.Rd b/man/dsListResources-ArmadilloConnection-method.Rd index 7ccf059..3450c27 100644 --- a/man/dsListResources-ArmadilloConnection-method.Rd +++ b/man/dsListResources-ArmadilloConnection-method.Rd @@ -17,5 +17,5 @@ List Armadillo DataSHIELD Service resources that may be accessible for performing DataSHIELD operations. } \seealso{ -\code{\link{dsListResources}} +\code{\link[DSI]{dsListResources}} } diff --git a/man/dsListTables-ArmadilloConnection-method.Rd b/man/dsListTables-ArmadilloConnection-method.Rd index dce0ae9..6941c05 100644 --- a/man/dsListTables-ArmadilloConnection-method.Rd +++ b/man/dsListTables-ArmadilloConnection-method.Rd @@ -17,5 +17,5 @@ List Armadillo DataSHIELD Service tables that may be accessible for performing DataSHIELD operations. } \seealso{ -\code{\link{dsListTables}} +\code{\link[DSI]{dsListTables}} } From 2083165feed205e1f24683f25ce6c80d5757d04d Mon Sep 17 00:00:00 2001 From: Tim Cadman <41470917+timcadman@users.noreply.github.com> Date: Fri, 5 Jul 2024 15:33:29 +0200 Subject: [PATCH 2/2] chore: bumped version number --- DESCRIPTION | 2 +- cran-comments.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 864403c..0869c7a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: DSMolgenisArmadillo Type: Package -Version: 2.0.8 +Version: 2.0.9 Title: 'DataSHIELD' Client for 'MOLGENIS Armadillo' Description: 'DataSHIELD' is an infrastructure and series of R packages that enables the remote and 'non-disclosive' analysis of sensitive research data. diff --git a/cran-comments.md b/cran-comments.md index eafa38b..dc576d2 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,4 +1,4 @@ -## 2.0.8 +## 2.0.9 * fix: align error handling with opal * fix: datashield.pkg_status, datashield.methods and datashield.workspaces now return same format as opal