R/zzz.R

In dendextend: Extending 'dendrogram' Functionality in R

# Copyright (C) Tal Galili
#
# This file is part of dendextend.
#
# dendextend is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
# dendextend is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
#  A copy of the GNU General Public License is available at
#  http://www.r-project.org/Licenses/



# https://stackoverflow.com/questions/10325231/when-writing-my-own-r-package-i-cant-seem-to-get-other-packages-to-import-corr
#' @importFrom viridis viridis

#' @import datasets





# Add myself to github:
# http://www.r-bloggers.com/rstudio-and-github/

# git remote add origin https://github.com/talgalili/dendextend.git
# git config remote.origin.url git@github.com:talgalili/dendextend.git
# git pull -u origin master
# git push -u origin master

# https://nathanj.github.io/gitguide/tour.html
# add "git@github.com:talgalili/dendextend.git"

# if the RStudio buttons are greyed out, then run the following in git shell:
# git push -u origin master
# source: http://www.r-bloggers.com/things-i-forget-pushpull-greyed-out-in-rstudio/
# this updates \\.git\\config with the following lines:
# [branch "master"]
#     remote = origin
#     merge = refs/heads/master


.onLoad <- function(libname, pkgname) {
  # Thanks for Romain: https://stackoverflow.com/questions/4369334/first-lib-idiom-in-r-packages

  # adding and removing menus from the Rgui when loading and detaching the library
  # setHook(packageEvent("installr", "attach"), {function(pkgname, libpath) {add.installr.GUI()}  } )
  # setHook(packageEvent("dendextend", "detach"), {function(pkgname, libpath) {remove_dendextend_options()}  } )

  # set default options for dendextend
  setHook(packageEvent("dendextend", "onLoad"), {
    function(pkgname, libpath) {
      assign_dendextend_options()
    }
  })

  # Does NOT work!
  # remove_dendextend_options is currently an empty function. In the future, it should
  # remove default options for dendextend when unloading
  setHook(packageEvent("dendextend", "onUnload"), {
    function(pkgname, libpath) {
      remove_dendextend_options()
    }
  })
  setHook(packageEvent("dendextend", "detach"), {
    function(pkgname, libpath) {
      remove_dendextend_options()
    }
  })

  # dendextend::dendextend_options()
}

# menus are added and removed as needed: !!


.onAttach <- function(lib, pkg, ...) {
  ####
  ### I decided to not use the following code since it will
  ###   always give a "masked" warning when loading
  ###   dendextend. But it IS an issue...
  ####
  # if ape is installed on this computer, it will be loaded FIRST!
  # This way I make sure to not have "rotate" masked by {ape}
  #     (they would still work though)

  # this would solve it, but it is not a "nice" way to do it...
  #    if("ape" %in% .packages(all.available = TRUE)) {
  #       library("ape", pos = which(search() %in% "package:dendextend")+1,
  #               warn.conflicts = FALSE,
  #               quietly = TRUE)
  #    }

  # The above line causes problems such as: 'library' or 'require' call not declared from: 'ape'

  #       search()
  #       unloadNamespace(ape")
  #       unloadNamespace("dendextend")
  #       require("dendextend", warn.conflicts = TRUE)
  #       require("dendextend", warn.conflicts = FALSE)
  # but it makes sure that "dendextend" does not "Depends" on ape"...

  # move some functions to the "options" so that they would later be overridden.
  #    create_dendextend_options()

  # details in dendextend_options.R
  # assign_dendextend_options()

  packageStartupMessage(dendextendWelcomeMessage())

  #    assign_dendextendRcpp_to_dendextend()
}




dendextendWelcomeMessage <- function() {
  # library(utils)

  # paste("\n",
  #       "Welcome to dendextend version ", utils::packageDescription("dendextend")$Version, "\n",
  #       "\n",
  #       "Type ?dendextend to access the overall documentation and\n",
  #       "browseVignettes(package = 'dendextend') for the package vignette.\n",
  #       "You can execute a demo of the package via: demo(dendextend)\n",
  #       "\n",
  #       "More information is available on the dendextend project web-site:\n",
  #       "https://github.com/talgalili/dendextend/\n",
  #       "\n",
  #       "Contact: <tal.galili@gmail.com>\n",
  #       "Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues\n",
  #       "\n",
  #       "\t\t\tTo suppress this message use:\n",
  #       "\t\t\tsuppressPackageStartupMessages(library(dendextend))\n",
  #       sep="")
  #
  paste0(
    "\n",
    "---------------------\n",
    "Welcome to dendextend version ", utils::packageDescription("dendextend")$Version, "\n",
    # "\n",
    "Type citation('dendextend') for how to cite the package.\n",
    "\n",
    "Type browseVignettes(package = 'dendextend') for the package vignette.\n",
    "The github page is: ",
    "https://github.com/talgalili/dendextend/\n",
    "\n",
    "Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues\n",
    "You may ask questions at stackoverflow, use the r and dendextend tags: \n\t https://stackoverflow.com/questions/tagged/dendextend\n",
    "\n",
    "\tTo suppress this message use:  ", "suppressPackageStartupMessages(library(dendextend))\n",
    "---------------------\n"
  )
}





# using "zzz.r" like in devtools...

# When adding new files, make sure they are listed in DESCRIPTION:
# Collate:
#    'create.global.library.r'
# 'install.r'
# 'updateR.r'




# library(dendextend)
# environmentIsLocked(as.environment("package:dendextend"))
# lockEnvironment(env=as.environment("package:dendextend"), bindings = FALSE)
# lockEnvironment(env=as.environment("package:dendextend"), bindings = TRUE)


# IMPORTANT NOTICE: this will add Collate to the DESCRIPTION file, and if any new r file is added - it will need to be updated.
# Collate:
# +    'create.global.library.r'
# +    'install.r'
# +    'updateR.r'
# +    'zzz.r'


############
## OLD
# Steps:
# http://r.789695.n4.nabble.com/vignettes-problems-with-PDF-compaction-td4664909.html
# 1) install gs - http://www.ghostscript.com/download/gsdnld.html
# 2) find where it is, and update R_GSCMD:
# Sys.setenv(R_GSCMD="C:\\Program Files\\gs\\gs9.10\\bin\\gswin64c.exe")
# Sys.setenv(R_GSCMD="C:\\Program Files\\gs\\gs9.14\\bin\\gswin64c.exe")
# Sys.setenv(R_GSCMD="D:\\temp\\qpdf-5.1.2\\bin\\qpdf.exe")
# Sys.getenv("R_GSCMD")
# 3) Check that it works:
# system2(Sys.getenv("R_GSCMD"), args="--version")
# 4) use:
# library(tools)
# tools::compactPDF("inst\\doc\\dendextend-tutorial.pdf", gs_quality="printer")
# tools::compactPDF("inst\\doc\\dendextend-tutorial.pdf",
# qpdf = "D:\\temp\\qpdf-5.1.2\\bin\\qpdf.exe", gs_cmd = "C:\\Program Files\\gs\\gs9.14\\bin\\gswin64c.exe")
#### tools::compactPDF("inst\\doc\\dendextend-tutorial.pdf", gs_quality="ebook")
#### tools::compactPDF("inst\\doc\\dendextend-tutorial.pdf", gs_quality="screen")
#### tools::compactPDF("vignettes\\dendextend-tutorial.pdf")
###   compacted 'dendextend-tutorial.pdf' from 964Kb to 737Kb
#### tools::compactPDF("vignettes\\dendextend-tutorial.pdf", gs_quality="ebook")

# For checking:
# 1) get qpdf
#     http://sourceforge.net/projects/qpdf/files/
# 2) put it somewhere
# 3) set R_QPDF
#  Sys.setenv(R_QPDF="C:\\Rtools\\qpdf-5.1.1\\bin\\qpdf.exe")
#  Sys.which(Sys.getenv("R_QPDF", "qpdf"))

# Also, make sure to add:
# options(repos=c("http://cran.rstudio.com", "http://www.stats.ox.ac.uk/pub/RWin" ))
# to D:\R\R-devel\etc\Rprofile.site

##############







##########
##########
##########
##########
## NEW
# How to deal with compression:
# 1) Download the latest qpdf: http://sourceforge.net/projects/qpdf/files/  (and place it somewhere)
# 2) Install gs - http://www.ghostscript.com/download/gsdnld.html
# 3) Run the following:

# tools::compactPDF("inst\\doc\\dendextend-tutorial.pdf",
#                   qpdf = "C:\\Program Files (x86)\\qpdf-5.1.2\\bin\\qpdf.exe",
#                   gs_cmd = "C:\\Program Files\\gs\\gs9.14\\bin\\gswin64c.exe",
#                   gs_quality="ebook")

##########
##########
##########



# https://stat.ethz.ch/pipermail/r-help/2010-September/251194.html
# tools::showNonASCII( readLines("vignettes\\FAQ.Rmd"))
#





####### Cool stuff to add:
# library(devtools)
# use_code_of_conduct()
# use_cran_badge()
# use_coveralls()
# #



# install.packages("C:\\Dropbox\\aaaa good R code\\AA - My packages\\dendextend_1.0.0.tar.gz", repos = NULL, type="source")

#
# # Run once:
# shell('set PATH=%PATH%;"C:\\Program%20Files%20(x86)\\Git\\bin"', intern = TRUE)
# shell("echo %PATH% ", intern= TRUE)
#
# system('set PATH=%PATH%;C:\\xampp\\php')
#
#
#
# # Creating a changelog using git
# First make sure git is in the path. Run the
# following using cmd.exe, as admin:
# setx PATH "C:\\Program Files (x86)\\Git\\bin"
#
# Then - run the script to create the ChangeLog before shipping the package.
# # https://stackoverflow.com/questions/10330425/how-do-i-export-a-git-log-to-a-text-file
# # https://stackoverflow.com/questions/3523534/good-ways-to-manage-a-changelog-using-git
# # http://www.commandlinefu.com/commands/view/12420/generate-a-change-log-with-git
# shell("git log --decorate > ChangeLog", intern = T)

# Modify it using: http://git-scm.com/book/en/Git-Basics-Viewing-the-Commit-History
#         https://stackoverflow.com/questions/9007181/custom-log-format-omits-newline-at-end-of-output
# shell('git log --graph --stat --date=iso > ChangeLog', intern = TRUE)
# use this:
# shell('git log --graph --stat --date=short --pretty=format:"%ad(%an) %s |%h" > ChangeLog', intern = TRUE)
#
# system.PATH()
# shell("path")


# shell("echo %PATH% ", intern= TRUE)
# library(rmarkdown)
# rmarkdown::render("NEWS",clean = TRUE,output_format = "html_document")








# when a function is renamed, its document in man must be removed - otherwise it may cause problems with the built check (it will try to run the code in the example, and will fail.)
# When all is done, run:
# library(devtools)
# check()
# browseURL(tempdir())
### http://www.rstudio.com/ide/docs/packages/build_options
#
# check(build_args="--no-build-vignettes --no-manual", args = "--no-examples --no-build-vignettes --no-manual",  cran = FALSE, cleanup = FALSE)
# devtools::check(build_args="--no-build-vignettes --no-manual", args = " --no-build-vignettes --no-manual",  cran = FALSE, cleanup = FALSE)
# check(build_args="--no-build-vignettes --no-manual", args = "--no-build-vignettes --no-manual",  cran = FALSE, cleanup = FALSE)
# check(build_args="--no-build-vignettes ", args = "--no-build-vignettes",  cran = FALSE, cleanup = FALSE)
# devtools::check(args="--as-cran")
# devtools::check("C:/Dropbox/aaaa good R code/AA - My packages/dendextend", args="--as-cran")
#                 Thanks to: https://stackoverflow.com/questions/10017702/r-cmd-check-options-for-more-rigorous-testing-2-15-0


# Adding github actions:
# https://www.tidyverse.org/blog/2022/06/actions-2-0-0/

# spelling::spell_check_package()
# shell('git log --graph --stat --date=short --pretty=format:"%ad(%an) %s |%h" > ChangeLog', intern = TRUE)
# For linux:
# system('git log --graph --stat --date=short --pretty=format:"%ad(%an) %s |%h" > ChangeLog', intern = TRUE)
# pkgdown::build_site(run_dont_run = FALSE)
#  pkgdown::build_home()
#  pkgdown::build_news()
#  pkgdown::build_site()
#  pkgdown::build_articles()
# devtools::check_win_release()
# devtools::check_win_devel()
# release()