This page was last updated on Sunday, 09-Nov-2014 16:00:46 CST

Installation notes for SeqGrapheR version 0.4.8.3 (and 0.4.7.0)

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Prerequisites

R

GTK2

1. $ sudo apt-get install libgtk2.0-dev

GGobi

1. $ sudo apt-get install ggobi

Installation Version 0.4.8.3

1. $ sudo R
2. This command will fail unless run in an X session
   > install.packages('SeqGrapheR', dep=TRUE)
3. To run the program
   > library(SeqGrapheR)
4. > SeqGrapheR()

Installation Version 0.4.7.0

1. $ ver="0.4.7.0"
2. $ cd /programinstallers/
3. $ wget -N http://w3lamc.umbr.cas.cz/lamc/resources/SeqGrapheR_programs.tar.gz
4. $ tar -zxvf SeqGrapheR_programs.tar.gz
   

   data/
   data/CL7_reads.fas
   data/CL7.GL
   programs/
   programs/SeqGrapheR_manual.pdf
   programs/fgclust_manual.txt
   programs/README.txt
   programs/fgclust4.4.r
   programs/SeqGrapheR_0.4.7.0.tar.gz
   

5. Extracts to a folder named programs and data
   $ cd programs
6. $ tar -zxvf SeqGrapheR_$ver.tar.gz
7. $ sudo R
8. Note: the following is correct, but spelled incorrectly in documentation
   > install.packages('RGtk2', dep=TRUE)
9. > install.packages('igraph', dep=TRUE)
10. > install.packages('rggobi', dep=TRUE)
11. This one must be installed while in an X session, otherwise the following error occurs
    > install.packages('cairoDevice', dep=TRUE)
    …
    

    ** testing if installed package can be loaded
    Error : .onLoad failed in loadNamespace() for 'cairoDevice', details:
    call: fun(libname, pkgname)
    error: GDK display not found - please make sure X11 is running
    Error: loading failed

    …
12. Alternatively, this works in a terminal session
    > install.packages('cairoDevice', dep=TRUE, INSTALL_opts='--no-test-load')
13. > install.packages('gWidgetsRGtk2', dep=TRUE)
14. Note: the following is correct, but spelled incorrectly in documentation
    > install.packages('gWidgets', dep=TRUE)
    …
    

    ** preparing package for lazy loading
    Warning in fun(libname, pkgname) :
    no DISPLAY variable so Tk is not available
    Warning in tclRequire("ttk::theme::plastik") :
    Tcl package 'ttk::theme::plastik' not found
    Warning in tclRequire("ttk::theme::keramik") :
    Tcl package 'ttk::theme::keramik' not found
    Warning in tclRequire("ttk::theme::keramik_alt") :
    Tcl package 'ttk::theme::keramik_alt' not found
    Error in structure(.External("dotTclObjv", objv, PACKAGE = "tcltk"), class = "tclObj") :
    [tcl] invalid command name "font".
    Error : unable to load R code in package `gWidgetstcltk`
    ERROR: lazy loading failed for package `gWidgetstcltk`
    * removing `/usr/lib64/R/library/gWidgetstcltk`
    The downloaded packages are in
    `/tmp/RtmpUBVaLA/downloaded_packages`
    Updating HTML index of packages in '.Library'
    Making packages.html ... done
    Warning message:
    In install.packages("gWidgets", dep = TRUE) :
    installation of package `gWidgetstcltk` had non-zero exit status

    …
15. I could successfully install GWidgets on the actual computer, however, so some problem with connection to X session?
16. An undocumented dependency for fgclust
    > install.packages('getopt', dep=TRUE)
17. A bioconductor package
    > source("http://bioconductor.org/biocLite.R")
18. > biocLite("Biostrings")
19. And finally (this had to be installed on the actual computer also):
    > install.packages('/programinstallers/programs/SeqGrapheR_0.4.7.0.tar.gz', repos=NULL)
20. To run the program
    > library(SeqGrapheR)
21. > SeqGrapheR()