From 2d7274af824d301f05ad5a866ad8a89851ca8524 Mon Sep 17 00:00:00 2001
From: Jim Thorson <50178738+James-Thorson-NOAA@users.noreply.github.com>
Date: Tue, 2 Apr 2024 08:59:39 -0700
Subject: [PATCH] further fix

---
 NAMESPACE                     |  1 -
 R/utils.R                     | 80 -----------------------------------
 man/checkDepPackageVersion.Rd | 28 ------------
 man/reinstalling.Rd           | 44 -------------------
 4 files changed, 153 deletions(-)
 delete mode 100644 R/utils.R
 delete mode 100644 man/checkDepPackageVersion.Rd
 delete mode 100644 man/reinstalling.Rd

diff --git a/NAMESPACE b/NAMESPACE
index c094211..aedd77b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -41,5 +41,4 @@ importFrom(stats,sd)
 importFrom(stats,simulate)
 importFrom(stats,time)
 importFrom(stats,vcov)
-importFrom(utils,packageVersion)
 useDynLib(dsem, .registration = TRUE)
diff --git a/R/utils.R b/R/utils.R
deleted file mode 100644
index 18dbd49..0000000
--- a/R/utils.R
+++ /dev/null
@@ -1,80 +0,0 @@
-#' @title Check for version mismatch in dependent binary packages
-#' @description Copied from glmmTMB with permission
-#' @param dep_pkg upstream package
-#' @param this_pkg downstream package
-#' @param write_file (logical) write version file and quit?
-#' @param warn give warning?
-#' @return logical: TRUE if the binary versions match
-#' @importFrom utils packageVersion
-#checkDepPackageVersion <- function(dep_pkg = "TMB",
-#                                   this_pkg = "dsem",
-#                                   write_file = FALSE,
-#                                   warn = TRUE) {
-#    cur_dep_version <- as.character(packageVersion(dep_pkg))
-#    fn <- sprintf("%s-version", dep_pkg)
-#    if (write_file) {
-#        cat(sprintf("current %s version=%s: writing file\n", dep_pkg, cur_dep_version))
-#        writeLines(cur_dep_version, con = fn)
-#        return(cur_dep_version)
-#    }
-#    fn <- system.file(fn, package=this_pkg)
-#    built_dep_version <- scan(file=fn, what=character(), quiet=TRUE)
-#    result_ok <- identical(built_dep_version, cur_dep_version)
-#    if(warn && !result_ok) {
-#        warning(
-#            "Package version inconsistency detected.\n",
-#            sprintf("%s was built with %s version %s",
-#                    this_pkg, dep_pkg, built_dep_version),
-#            "\n",
-#            sprintf("Current %s version is %s",
-#                    dep_pkg, cur_dep_version),
-#            "\n",
-#            sprintf("Please re-install %s from source ", this_pkg),
-#            "or restore original ",
-#            sQuote(dep_pkg), " package (see '?reinstalling' for more information)"
-#        )
-#    }
-#    return(result_ok)
-#}
-
-#' @name reinstalling
-#' @rdname reinstalling
-#' @title Reinstalling binary dependencies
-#'
-#' @description The \code{dsem} package depends on several upstream packages, which it
-#' uses in a way that depends heavily on their internal (binary) structure.
-#' Sometimes, therefore, installing an update to one of these packages will
-#' require that you re-install a \emph{binary-compatible} version of \code{dsem},
-#' i.e. a version that has been compiled with the updated version of the upstream
-#' package.
-#' \itemize{
-#' \item If you have development tools (compilers etc.) installed, you
-#' should be able to re-install a binary-compatible version of the package by running
-#' \code{install.packages("dsem", type="source")}. If you want to install
-#' the development version of \code{dsem} instead, you can use
-#' \code{remotes::install_github("James-Thorson-NOAA/dsem")}.
-#' (On Windows, you can install development tools following the instructions at
-#' \url{https://cran.r-project.org/bin/windows/Rtools/}; on MacOS, see
-#' \url{https://mac.r-project.org/tools/}.)
-#'
-#' \item If you do \emph{not} have development tools and can't/don't want to
-#' install them (and so can't install packages with compiled code from source),
-#' you can revert the upstream package(s) to their previous binary version. For example, using the
-#' \code{checkpoint} package:
-#' \preformatted{
-#' ## load (installing if necessary) the checkpoint package
-#' while (!require("checkpoint")) install.packages("checkpoint")
-#' ## retrieve build date of installed version of dsem
-#' bd <- as.character(asDateBuilt(
-#'       packageDescription("dsem",fields="Built")))
-#' oldrepo <- getOption("repos")
-#' use_mran_snapshot(bd) ## was setSnapshot() pre-checkpoint v1.0.0
-#' install.packages("TMB")
-#' options(repos=oldrepo) ## restore original repo
-#' }
-#' A similar recipe (substituting \code{Matrix} for \code{TMB} and \code{TMB} for \code{dsem})
-#' can be used if you get warnings about an incompatibility between \code{TMB} and \code{Matrix}.
-#' }
-#' @details Copied from glmmTMB with permission
-NULL
-
diff --git a/man/checkDepPackageVersion.Rd b/man/checkDepPackageVersion.Rd
deleted file mode 100644
index 1a4a61b..0000000
--- a/man/checkDepPackageVersion.Rd
+++ /dev/null
@@ -1,28 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{checkDepPackageVersion}
-\alias{checkDepPackageVersion}
-\title{Check for version mismatch in dependent binary packages}
-\usage{
-checkDepPackageVersion(
-  dep_pkg = "TMB",
-  this_pkg = "dsem",
-  write_file = FALSE,
-  warn = TRUE
-)
-}
-\arguments{
-\item{dep_pkg}{upstream package}
-
-\item{this_pkg}{downstream package}
-
-\item{write_file}{(logical) write version file and quit?}
-
-\item{warn}{give warning?}
-}
-\value{
-logical: TRUE if the binary versions match
-}
-\description{
-Copied from glmmTMB with permission
-}
diff --git a/man/reinstalling.Rd b/man/reinstalling.Rd
deleted file mode 100644
index 9e2ad3a..0000000
--- a/man/reinstalling.Rd
+++ /dev/null
@@ -1,44 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{reinstalling}
-\alias{reinstalling}
-\title{Reinstalling binary dependencies}
-\description{
-The \code{dsem} package depends on several upstream packages, which it
-uses in a way that depends heavily on their internal (binary) structure.
-Sometimes, therefore, installing an update to one of these packages will
-require that you re-install a \emph{binary-compatible} version of \code{dsem},
-i.e. a version that has been compiled with the updated version of the upstream
-package.
-\itemize{
-\item If you have development tools (compilers etc.) installed, you
-should be able to re-install a binary-compatible version of the package by running
-\code{install.packages("dsem", type="source")}. If you want to install
-the development version of \code{dsem} instead, you can use
-\code{remotes::install_github("James-Thorson-NOAA/dsem")}.
-(On Windows, you can install development tools following the instructions at
-\url{https://cran.r-project.org/bin/windows/Rtools/}; on MacOS, see
-\url{https://mac.r-project.org/tools/}.)
-
-\item If you do \emph{not} have development tools and can't/don't want to
-install them (and so can't install packages with compiled code from source),
-you can revert the upstream package(s) to their previous binary version. For example, using the
-\code{checkpoint} package:
-\preformatted{
-## load (installing if necessary) the checkpoint package
-while (!require("checkpoint")) install.packages("checkpoint")
-## retrieve build date of installed version of dsem
-bd <- as.character(asDateBuilt(
-      packageDescription("dsem",fields="Built")))
-oldrepo <- getOption("repos")
-use_mran_snapshot(bd) ## was setSnapshot() pre-checkpoint v1.0.0
-install.packages("TMB")
-options(repos=oldrepo) ## restore original repo
-}
-A similar recipe (substituting \code{Matrix} for \code{TMB} and \code{TMB} for \code{dsem})
-can be used if you get warnings about an incompatibility between \code{TMB} and \code{Matrix}.
-}
-}
-\details{
-Copied from glmmTMB with permission
-}