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Where to find your R packages

R must be installed on your computer. Here is the R project site: R project
The packages Goulphar uses are marray, limma, convert et hexbin. They are available on the on the Bioconductor project site

How to install your R packages

R must be installed on your computer. The process is quite the same on Windows, MacOS or Linux if your are using the command line.
  • Launch R
  • Type these command lines:
    • source("http://bioconductor.org/biocLite.R")
    • biocLite()
    • biocLite("convert")
  • The biocLite() command performs the installation of the most common Bioconductor packages such as limma and marray. Then, the biocLite("convert") command performs the installation of convert.
If you use R on Windows or MacOS, you can use the Packages tab facilities in the Menu bar. It is easier if your not familiar with command lines and very quick.
  • Launch R
  • Go to the Packages tab
  • Choose the site you want to install the package from and follow the indications.
WARNING! If you use the basic procedure to install BioConductor as describe on their webpage. The latest distributions do not include the convert package and you need to install it manually. See the "problem encounter" section of this page.

Problems encountered

  • the version of limma has to be upper than 1.8.17. It works with version 1.8.21.
  • I use Windows and Goulphar cannot make any pdf or png file: you have to install Ghostscript
    • Search for AFLP Ghostscript on sourceforge and download it on your computer (8.50 version was tested and works)
    • Install it on your computer
    • You now have to create an environment variable in Windows
      • Open the Control Panel
      • Go to the System tab
      • Go to the Advanced tab
      • Click on the Environment Variable button
      • Create a new system variable
      • Its name is R_GSCMD
      • Its path corresponds to where gswinc.exe is installed. It should be something like "C:\Program Files\gs\gs8.50\bin\gswinc.exe"
      • Save your changes

  • Convert can't get installed (Error in library(convert): there is no package called 'convert'):
    • First, if you are using the graphical interface, use the package installer and select "BioConductor sources". Install the convert package using the interface.
    • If this is not working, get the sources of the package manually: on BioConductor repository
    • Using the command line interface, uncompress them with winzip or Unzip and put the Convert directory in the R library sub-directory
    • Alternatively using the graphic interface, when you download the source use the "package" menu to directly install the package using the compressed archive
  • If you use Mac OS X.2, the graphic device cannot build png files. This problem may be solved for later Mac OS X versions.
  • If you encounter the following error: "Error in sub(pattern, replacement, x, ignore.case, extended, fixed) : input string 1 is invalid in this locale", in the latest version the GPR headers are imported by the program and all file paths that contains special encoding caracters like accent create this error. So do not use special caracter in your folder and file names

Download Goulphar

Goulphar is a free R script. You can redistribute it and/or modify it under the terms of the GNU General Public License. Be careful, the script needs a parameter file located in the same directory to work properly.
Download example files (right or control clic on these links to save thess files on your computer):
To test a Genepix result file: To test a Spot result file:

  Goulphar is a lighthouse located in Belle-ile, a southern brittany island. It was built from 1824 to 1836.

Last page update: January 28th, 2008 - 16:18 | For any questions or comments send an e-mail to the Goulphar team