Step Five: Installing the tools

We will start with MikTex. I’ve downloaded that  exe file and now we need to install it. There are some options offered to you upon install. I installed it for all users and selected Letter as my desired paper size.  While it’s installing it will also go out and look for missing elements. I installed it to the default directory it offered  C:\Program Files (x86)\MiKTeX 2.9  We will need this later for modifying our path variable. Before the completion of the install I get the following message

Loading package database...
starting package maintenance...
installation directory: "C:\Program Files (x86)\MiKTeX 2.9"
package repository: C:\Users\steve\AppData\Local\Temp\mik24524
visiting repository C:\Users\steve\AppData\Local\Temp\mik24524...
repository type: local package repository
loading lightweight database...
lightweight database digest: 38c13d099f49452bb6a7ccd99210b201
going to install 9425 file(s) (157 package(s))
problem: C:\Program Files (x86)\MiKTeX 2.9\miktex/bin\MiKTeX209-core-PS.dll does not exist
problem: C:\Program Files (x86)\MiKTeX 2.9\miktex/bin\MiKTeX209-core.dll does not exist
problem: C:\Program Files (x86)\MiKTeX 2.9\miktex/bin\MiKTeX209-packagemanager-PS.dll does not exist
problem: C:\Program Files (x86)\MiKTeX 2.9\miktex/bin\MiKTeX209-packagemanager.dll does not exist
extracting files from ae.tar.lzma...
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updating package definition directory ("C:\Program Files (x86)\MiKTeX 2.9\tpm\packages")...
installed 2067 package definition files
visiting repository C:\Users\steve\AppData\Local\Temp\mik24524...
repository type: local package repository
loading lightweight database...
Registering root directories...
Removing fndb (C:\ProgramData\MiKTeX\2.9)...
Removing fndb ("C:\Program Files (x86)\MiKTeX 2.9")...
configuring fontconfig\config\fonts.conf
registering C:\Program Files (x86)\MiKTeX 2.9\miktex/bin\MiKTeX209-core.dll
registering C:\Program Files (x86)\MiKTeX 2.9\miktex/bin\MiKTeX209-core-PS.dll
registering C:\Program Files (x86)\MiKTeX 2.9\miktex/bin\MiKTeX209-packagemanager.dll
registering C:\Program Files (x86)\MiKTeX 2.9\miktex/bin\MiKTeX209-packagemanager-PS.dll
Skipping user root directory (C:\Users\steve\AppData\Roaming\MiKTeX\2.9)...
Skipping user root directory (C:\Users\steve\AppData\Local\MiKTeX\2.9)...
Creating fndb for common root directory (C:\ProgramData\MiKTeX\2.9)...
Creating fndb for common root directory ("C:\Program Files (x86)\MiKTeX 2.9")...
Making format links...
Making script links...
  C:\Program Files (x86)\MiKTeX 2.9\miktex/bin\miktex-taskbar-icon.exe
  C:\Program Files (x86)\MiKTeX 2.9\miktex/bin\miktex-update.exe
Creating language.dat, language.dat.lua and language.def...
Entering administrative mode...
Parsing config file "C:\Program Files (x86)\MiKTeX 2.9\miktex\config\updmap.cfg"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\tetex\dvips35.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\tetex\pdftex35.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\tetex\dvipdfm35.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\tetex\ps2pk35.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\amsfonts\cm.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\amsfonts\cmextra.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\amsfonts\cyrillic.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\amsfonts\euler.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\dvips\eurosym\eurosym.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\amsfonts\latxfont.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\rsfs\rsfs.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\amsfonts\symbols.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\xypic\xypic.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\psnfss\charter.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\psnfss\fpls.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\lm\lm.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\obsolete\mathpi.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\obsolete\mathpple-ext.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\psnfss\pazo.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\dvips\pslatex\pcrr8rn.map"...
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Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\avantgar\uag.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\bookman\ubk.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\courier\ucr.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\helvetic\uhv.map"...
Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\ncntrsbk\unc.map"...
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Parsing "C:\Program Files (x86)\MiKTeX 2.9\fonts\map\dvips\zapfding\uzd.map"...
Writing C:\ProgramData\MiKTeX\2.9\dvips\config\ps2pk.map...
Writing C:\ProgramData\MiKTeX\2.9\dvips\config\download35.map...
Writing C:\ProgramData\MiKTeX\2.9\dvips\config\builtin35.map...
Writing C:\ProgramData\MiKTeX\2.9\dvips\config\psfonts_t1.map...
Writing C:\ProgramData\MiKTeX\2.9\dvips\config\psfonts_pk.map...
Writing C:\ProgramData\MiKTeX\2.9\pdftex\config\pdftex_ndl14.map...
Writing C:\ProgramData\MiKTeX\2.9\pdftex\config\pdftex_dl14.map...
Writing C:\ProgramData\MiKTeX\2.9\dvipdfm\config\dvipdfm_dl14.map...
Writing C:\ProgramData\MiKTeX\2.9\dvipdfm\config\dvipdfm_ndl14.map...
Copying C:\ProgramData\MiKTeX\2.9\dvips\config\psfonts_t1.map
     to C:\ProgramData\MiKTeX\2.9\dvips\config\psfonts.map...
Copying C:\ProgramData\MiKTeX\2.9\dvipdfm\config\dvipdfm_dl14.map
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Copying C:\ProgramData\MiKTeX\2.9\pdftex\config\pdftex_dl14.map
     to C:\ProgramData\MiKTeX\2.9\pdftex\config\pdftex.map...
C:/Windows/Fonts: skipping, existing cache is valid: 917 fonts, 0 dirs
C:/Program Files (x86)/MiKTeX 2.9/fonts/type1: caching, new cache contents: 0 fonts, 5 dirs
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C:/Program Files (x86)/MiKTeX 2.9/fonts/type1/public/amsfonts/euler: caching, new cache contents: 22 fonts, 0 dirs
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C:/Program Files (x86)/MiKTeX 2.9/fonts/type1/public/amsfonts/symbols: caching, new cache contents: 12 fonts, 0 dirs
C:/Program Files (x86)/MiKTeX 2.9/fonts/type1/public/cbcoptic: caching, new cache contents: 2 fonts, 0 dirs
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C:/Program Files (x86)/MiKTeX 2.9/fonts/type1/public/lm: caching, new cache contents: 92 fonts, 0 dirs
C:/Program Files (x86)/MiKTeX 2.9/fonts/type1/public/rsfs: caching, new cache contents: 3 fonts, 0 dirs
C:/Program Files (x86)/MiKTeX 2.9/fonts/type1/public/xypic: caching, new cache contents: 23 fonts, 0 dirs
C:/Program Files (x86)/MiKTeX 2.9/fonts/type1/urw: caching, new cache contents: 0 fonts, 9 dirs
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C:/ProgramData/MiKTeX/2.9/fontconfig/cache: cleaning cache directory
C:\Program Files (x86)\MiKTeX 2.9\miktex\bin\fc-cache.EXE: succeeded
Skipping user root directory (C:\Users\steve\AppData\Roaming\MiKTeX\2.9)...
Skipping user root directory (C:\Users\steve\AppData\Local\MiKTeX\2.9)...
Creating fndb for common root directory (C:\ProgramData\MiKTeX\2.9)...
Creating fndb for common root directory ("C:\Program Files (x86)\MiKTeX 2.9")...
MiKTeX: 2.9
Invokers: explorer/chrome/basic-miktex-2.9.4146
SystemAdmin: yes
PowerUser: no
OS: Microsoft Windows 7 Home Premium Edition, 64-bit (build 7600)
Root0: C:\Users\steve\AppData\Roaming\MiKTeX\2.9
Root1: C:\Users\steve\AppData\Local\MiKTeX\2.9
Root2: C:\ProgramData\MiKTeX\2.9
Root3: C:\Program Files (x86)\MiKTeX 2.9
UserInstall: C:\Users\steve\AppData\Roaming\MiKTeX\2.9
UserData: C:\Users\steve\AppData\Local\MiKTeX\2.9
UserConfig: C:\Users\steve\AppData\Roaming\MiKTeX\2.9
CommonInstall: C:\Program Files (x86)\MiKTeX 2.9
CommonData: C:\ProgramData\MiKTeX\2.9
CommonConfig: C:\ProgramData\MiKTeX\2.9

Next,  I’ll install the Windows HTML Help Workshop. When you downloaded the file It may have already launched an installer. If not, then install it at this time. The install prompts you to create a HTML Help Workshop folder if you don’t have one. In addition, on my computer the install informs me that I have a newer version on my computer. Proceeding with the install, we note where the files are located  C:\Program Files (x86)\HTML Help Workshop.   We will need this for updating our PATH  as well.

Next we will install RTools. This is where things got a bit confusing for me. Lets start with the instructions we get during the Install

  Rtools Collection 2.13.0.1901

This is the Rtools.txt file, which will be installed in the main
Rtools directory. See also the README.txt file there, which describes
the origin of some of the tools. The tools installed in the
Rtools\MinGW directory are from the MinGW distribution.  

                                CYGWIN

Some of the R tools use the Cygwin DLLs, which are included.  If you
already have Cygwin installed, you should not install these (but see
"EXISTING CYGWIN INSTALLATIONS" below).

                           REMAINING TASKS

This installer doesn't install all of the tools necessary to build R
or R packages, because of license or size limitations.  The remaining
tools are all available online (at no charge) as described below.

TO BUILD R PACKAGES, you may optionally want items 1 and 2 below
(LaTeX and the HTML Help Workshop).

TO BUILD R, you need these plus item 3 below (Inno Setup).

Finally, the Rtools installer will optionally edit your PATH variable as follows:

PATH=c:\Rtools\bin;c:\Rtools\MinGW\bin;c:\R\bin;<others>

(where you will substitute appropriate directories for the ones listed
above, but please keep the path in the same order as shown. LaTeX and
the HTML Help Workshop should be installed among the "others".)

                           REMAINING ITEMS

1. You may install LaTeX, available from

  http://www.miktex.org

LaTeX is used to build .pdf forms of documentation.

2. You need the Inno Setup installer, available from

  http://www.innosetup.com

to build the R installer.

                               VERSIONS

This installer includes the following versions of the MinGW packages, obtained from
http://sourceforge.net/projects/mingw/files/:

     binutils-2.20.51-1-mingw32-bin.tar.lzma
     gcc-c++-4.5.0-1-mingw32-bin.tar.lzma
     gcc-core-4.5.0-1-mingw32-bin.tar.lzma
     gcc-fortran-4.5.0-1-mingw32-bin.tar.lzma
     libgcc-4.5.0-1-mingw32-dll-1.tar.lzma
     libgmp-5.0.1-1-mingw32-dll-10.tar.lzma
     libgomp-4.5.0-1-mingw32-dll-1.tar.lzma
     libmpc-0.8.1-1-mingw32-dll-2.tar.lzma
     libmpfr-2.4.1-1-mingw32-dll-1.tar.lzma
     libssp-4.5.0-1-mingw32-dll-0.tar.lzma
     mingwrt-3.18-mingw32-dev.tar.gz
     mingwrt-3.18-mingw32-dll.tar.gz
     w32api-3.15-1-mingw32-dev.tar.lzma

Vanilla Perl is from build 7 of that package.

The Cygwin tools and DLLs were updated on March 25, 2011.  They are taken from

    base-files 4.0-6
    coreutils 8.10-1
    cygwin 1.7.8-1
    diffutils 2.9-1
    findutils 4.5.9-1
    gawk 3.1.8-1
    grep 2.6.3-1
    gzip 1.4-1
    texinfo 4.13-3

The bitmap libraries are based on the following versions:

    jpegsrc.v8c
    libpng-1.5.1
    tiff-3.9.1

Tcl/Tk is version 8.5.8.

tar is a locally modified version of tar version 1.21.

                    EXISTING CYGWIN INSTALLATIONS

If you already have a full Cygwin installation, then you should not
install our Cygwin DLLs in the Rtools/bin directory.  You should make
sure your existing cygwin/bin directory is on the path (*after* all
the other entries listed above) and use the DLLs from there.

However, this may not work if your Cygwin installation is too old.  In
that case the Rtools utilities will fail to run.  To fix this, you
should update the Cygwin installation, or (with great care!) replace
the DLLs with the ones from the Rtools distribution.  Be very careful,
because if you have incompatible DLLs, your Cygwin tools will stop
working.

That’s not entirely clear, especially the bits about Cygwin. Do I need Cygwin to create a package that has no other code than R source. As the instructions are written they say that some of the tools require Cygwin. Are these tools I need? Do the compilers require Cygwin?

http://www.cygwin.com/

Since  I’m not sure, I’ll install it anyway. But first I noted that I had no existing installation of of Cygwin.

Note the install screens below and the options that I select.

 

Please Note that in the Path I have a path to the R binaries. This is a critical item. Otherwise your R command will not work from the console. If your Path doesnt contain a statement like ..R 2.13\bin\x64.. then you will need to add that to your path. see step 6. This is VITAL.

 

Step  6.