hyperSpec

This is the new home for R package hyperSpec.

Issues and feature requests should go here!

Installation instructions

Option A, simple: Installation from CRAN

open R and use command install.packages("hyperSpec"). This installs the latest version available on CRAN.

Option B – build it yourself from source in this repo

Preparations

1. You will need git, git-lfs and GNU make (>= 3.80)

   NOTE: Windows users need to dowload and install Rtools(see this instructions). GNU make is included to Rtools, so you don't need to install it. See Troubleshooting below to check version of GNU make and update it if needed.

2. Clone or download hyperSpec source code from github
   git clone [email protected]:cbeleites/hyperSpec.git

Building hyperSpec

1. If you build hyperSpec for the first time, or run into trouble as the installed version on your computer is too old, run make bootstrap This will also check whether all dependencies and suggested packages (which are in fact dependencies for building) are installed and install them if not.
2. Execute make install. It creates a new tar.gz package with everything inside and installs it via R CMD INSTALL hyperSpec_vv-date.
3. Restart R to avoid trouble due to changes in the documentation data base.

NOTE: Windows users can run make commands in R using system: for example, system('make install'). But be sure that your wd is set to the root directory containing Makefile.

Troubleshooting

• Vignette building fails and you suspect that this is due to the installed version of hyperSpec being too old.

  Solution: Run make bootstrap to fix it.

• Vignette fileio needs lots of example files for testing import functions. These are managed by git lfs.

  Typical error: e.g. when building vignette chondro, import function complains Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : scan() expected 'a real', found 'version'
  or in vignette flu: Error in .spc.filehdr(f) : Wrong spc file format version (or no spc file at all). Only 'new' spc files (1996 file format) with LSB word order are supported.

  Solution: Execute git lfs pull to get them.

• Old versions of GNU make don't support order-only prerequisites (|).

  Typical erros: No rule to make target '|', needed by 'fileio.pdf'. Stop.

  Solution: Update version of GNU make. For Linux, just downloand last version from the link above. For Windows, run system('where make') and replace that file by make.exe from [here] (http://www.equation.com/servlet/equation.cmd?fa=make). To check version of GNU make use make -v.

• Default language of your R enviroment is not English.

  Typical error: inputenc Error: Unicode char \u8:árq not set up for use with LaTeX

  Solution: Set language of the session to English as suggested here.

• Issues of versions 5.0.1 - 6.0.0(?) of roxygen2.

  Typical error: unable to find required package 'roxygen_devtest'

  Solution: In order to avoid it update roxygen2 (version 6.0.1 works) or downgrade to version 5.0.1: run in R devtools::install_version(package = 'roxygen2', version = '5.0.1').