From 8e9155b80bce6188ec007fda21b359760326bae7 Mon Sep 17 00:00:00 2001 From: Brandon Date: Tue, 14 Mar 2023 10:54:50 -0400 Subject: [PATCH] Purge old package name --- .Rbuildignore | 2 +- DESCRIPTION | 4 ++-- NAMESPACE | 1 + R/initializer.R | 2 +- R/updater.R | 4 ++-- R/utils.R | 2 +- R/zzz.R | 8 ++++---- README.md | 2 +- man/Enum.Rd | 14 ++++++++++++++ man/getCommitMetaData.Rd | 4 ++-- man/getDirFields.Rd | 16 ++++++++++++++++ man/initializeJars.Rd | 2 +- man/updateJars.Rd | 17 +++++++++++++++++ 13 files changed, 63 insertions(+), 15 deletions(-) create mode 100644 man/Enum.Rd create mode 100644 man/getDirFields.Rd create mode 100644 man/updateJars.Rd diff --git a/.Rbuildignore b/.Rbuildignore index 4f4107a..05050aa 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,2 +1,2 @@ -^bljars\.Rproj$ +^mgjars\.Rproj$ ^\.Rproj\.user$ diff --git a/DESCRIPTION b/DESCRIPTION index 90beb3a..8bd98c1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -14,7 +14,7 @@ Description: used in two packages generated by the Buckler Lab: rTASSEL and rPHG. License: `use_gpl3_license()` URL: - https://bitbucket.org/bucklerlab/bljars/src/master/ + https://github.com/maize-genetics/MGJars Depends: rJava Imports: @@ -23,7 +23,7 @@ Imports: Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.3 Suggests: testthat (>= 3.0.0) Config/testthat/edition: 3 diff --git a/NAMESPACE b/NAMESPACE index 3364ca2..4021b05 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,3 +1,4 @@ # Generated by roxygen2: do not edit by hand export(initializeJars) +export(updateJars) diff --git a/R/initializer.R b/R/initializer.R index cbbfaef..87b7f50 100644 --- a/R/initializer.R +++ b/R/initializer.R @@ -58,7 +58,7 @@ getCommitMetaData <- function( ## ---- -#' @title Initialize \code{BLJars}. +#' @title Initialize \code{MGJars}. #' #' @description Download jar files to designated directory #' diff --git a/R/updater.R b/R/updater.R index 1bdff41..71d4cb6 100644 --- a/R/updater.R +++ b/R/updater.R @@ -9,11 +9,11 @@ #' @export updateJars <- function(test = TRUE) { - paths <- BLJars:::getDirFields() + paths <- getDirFields() blVersions <- rJava::.jnew("net/maizegenetics/tassel/TasselVersions") if (test) { - metaDf <- read.csv("/home/btmonier/Temporary/test_rtassel/bljars_metadata_old.csv") + metaDf <- read.csv("/home/btmonier/Temporary/test_rtassel/mgjars_metadata_old.csv") } else { metaDf <- read.csv(metaPath) } diff --git a/R/utils.R b/R/utils.R index 0db0640..39b1e3a 100644 --- a/R/utils.R +++ b/R/utils.R @@ -9,7 +9,7 @@ getDirFields <- function(pkg = "MGJars", sep = "/") { pkgDir <- find.package(pkg) javaDir <- "java/" metaDir <- "extdata/" - metaFile <- "bljars_metadata.csv" + metaFile <- "mgjars_metadata.csv" return( list( diff --git a/R/zzz.R b/R/zzz.R index 9a21f97..0d0be76 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -12,17 +12,17 @@ fields <- getDirFields() if (!any(grepl("jar", list.files(fields$fullJava)))) { msg <- paste0( - "This looks like your first time running BLJars:", "\n", + "This looks like your first time running MGJars:", "\n", " * Please run 'initializeJars()'", "\n", " - This will download JAR files to the package.", "\n", - " * Once finished, please reload the BLJars package." + " * Once finished, please reload the MGJars package." ) } else { tasselVersions <- rJava::.jnew("net/maizegenetics/tassel/TasselVersions") msg <- paste0( - "BLJars package successfully loaded:", "\n", - " * BLJars version....... ", utils::packageVersion("BLJars"), "\n", + "MGJars package successfully loaded:", "\n", + " * MGJars version....... ", utils::packageVersion("MGJars"), "\n", " * PHG version.......... ", tasselVersions$phgVersion(), "\n", " * TASSEL version....... ", tasselVersions$tasselVersion(), "\n", " * Build date........... ", tasselVersions$tasselVersionDate(), "\n" diff --git a/README.md b/README.md index 6c2e907..1951311 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ experimental branches of `rTASSEL` and `rPHG`. In order to use this, the user will need to manually initialize: ``` -library(BLJars) +library(MGJars) ``` ...and then load `rTASSEL` and/or `rPHG`: diff --git a/man/Enum.Rd b/man/Enum.Rd new file mode 100644 index 0000000..0dc9832 --- /dev/null +++ b/man/Enum.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils.R +\name{Enum} +\alias{Enum} +\title{Create Enum collections and lock bindings} +\usage{ +Enum(l) +} +\arguments{ +\item{l}{List of elements to add to \code{Enum} instance} +} +\description{ +Create Enum collections and lock bindings +} diff --git a/man/getCommitMetaData.Rd b/man/getCommitMetaData.Rd index 6b2432d..089c71b 100644 --- a/man/getCommitMetaData.Rd +++ b/man/getCommitMetaData.Rd @@ -5,8 +5,8 @@ \title{Get TASSEL standalone JAR metadata} \usage{ getCommitMetaData( - - apiPath = "https://api.bitbucket.org/2.0/repositories/tasseladmin/tassel-5-standalone/src/master/", + apiPath = + "https://api.bitbucket.org/2.0/repositories/tasseladmin/tassel-5-standalone/src/master/", pageLen = 100 ) } diff --git a/man/getDirFields.Rd b/man/getDirFields.Rd new file mode 100644 index 0000000..de6e4a0 --- /dev/null +++ b/man/getDirFields.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils.R +\name{getDirFields} +\alias{getDirFields} +\title{Get directory fields for installed package} +\usage{ +getDirFields(pkg = "MGJars", sep = "/") +} +\arguments{ +\item{pkg}{Package name} + +\item{sep}{Directory separator character} +} +\description{ +Get directory fields for installed package +} diff --git a/man/initializeJars.Rd b/man/initializeJars.Rd index d29c329..743aaae 100644 --- a/man/initializeJars.Rd +++ b/man/initializeJars.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/initializer.R \name{initializeJars} \alias{initializeJars} -\title{Initialize \code{BLJars}.} +\title{Initialize \code{MGJars}.} \usage{ initializeJars() } diff --git a/man/updateJars.Rd b/man/updateJars.Rd new file mode 100644 index 0000000..517ef15 --- /dev/null +++ b/man/updateJars.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/updater.R +\name{updateJars} +\alias{updateJars} +\title{Update jar files.} +\usage{ +updateJars(test = TRUE) +} +\arguments{ +\item{test}{Debug.} +} +\value{ +void +} +\description{ +Updates jar files to designated directory +}