Adding CellNOptR_0.1, the Bioconductor-friendly version of CellNOptR, which excludes the 2 time points analysis and clean up all procedures and helps

git-svn-id: https://svn.ebi.ac.uk/sysbiomed/CNOR4Biocond/CellNOptR@89 be9b9435-a577-4725-b17d-0f23881b854c
Add current CellNOptR 4 Biocond directory -- version 0.99.6 is the current one, submitted to Bioc Oct22

git-svn-id: https://svn.ebi.ac.uk/sysbiomed/CNOR4Biocond/CellNOptR@177 be9b9435-a577-4725-b17d-0f23881b854c
Make a copy of CellNOptR from the latests release of Bioconductor to start a "real" trunk on which development can be carried on




git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@191 be9b9435-a577-4725-b17d-0f23881b854c
* Add verbose option
* add tag option to save filenames
* changed fileName into filename


git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@206 be9b9435-a577-4725-b17d-0f23881b854c
Fix readMIDAS NaN to NA conversion that was failing. The reason being that coed was changed to fit the needs of a reviewer (see Changelog from Camille related to version 0.99.6 So I switched back to the previous version (by default) putting a tryCatch to switch to the Camille's add-on code if it fails.

git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@210 be9b9435-a577-4725-b17d-0f23881b854c
add the multicore option

git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@211 be9b9435-a577-4725-b17d-0f23881b854c
Fix issue in the tryCatch when trying to print a message


git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@212 be9b9435-a577-4725-b17d-0f23881b854c
update some of the man/vignettes to reflect recent changes


git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@215 be9b9435-a577-4725-b17d-0f23881b854c
coming back to r191 (removing multicore)


git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@229 be9b9435-a577-4725-b17d-0f23881b854c
update the manual with respect to the changes made in the code (verbose, tag
options)


git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@230 be9b9435-a577-4725-b17d-0f23881b854c
add option (does not change the current behaviour) to switch off the plot
to be shown (only PDF is created) so that it can be run on a cluster.


git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@256 be9b9435-a577-4725-b17d-0f23881b854c
switching to 0.99.8 which will contain the 2 time points

git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@292 be9b9435-a577-4725-b17d-0f23881b854c
Adding the t2 functions

git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@293 be9b9435-a577-4725-b17d-0f23881b854c
Adding the help for t2 functions and t2 model and CNOlist objects

git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@294 be9b9435-a577-4725-b17d-0f23881b854c
Adding the t2 model and list data objects, and the t2 model sif file

git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@295 be9b9435-a577-4725-b17d-0f23881b854c
changing namespace file to include t2 functions

git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@296 be9b9435-a577-4725-b17d-0f23881b854c
Fix a bug in writeNetwork that prevents the function from stopping if a path is too long to be mapped, and prints a warning (if verbose=true)

git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@297 be9b9435-a577-4725-b17d-0f23881b854c
Change the help of writeNetwork to include the new verbose parameter

git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@298 be9b9435-a577-4725-b17d-0f23881b854c
Delete old vignette and replace by new one which contains t2 example

git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@299 be9b9435-a577-4725-b17d-0f23881b854c
change CNORwrap so it includes t2

git-svn-id: https://svn.ebi.ac.uk/sysbiomed/trunk/CellNOptR@300 be9b9435-a577-4725-b17d-0f23881b854c