jefferislab / nblast_figures Goto Github PK

see http://docs.travis-ci.com/user/deployment/releases/

On start-up:
Loading required package: rgl
Some nat functions depend on a CMTK installation. See ?cmtk and README.md for details.

Trying to install cmtk:
install.packages("cmtk")
Warning in install.packages :
package ‘cmtk’ is not available (as a binary package for R version 3.1.3)

Knitting NBLAST-algorithm fig:
Quitting from lines 39-51 (NBLAST_algorithm.Rmd)
Error in cmtk.bindir(check = TRUE) :
Cannot find CMTK. Please install from http://www.nitrc.org/projects/cmtk and make sure that it is your path!
Calls: ... xformpoints -> xformpoints.cmtkreg -> file.path -> cmtk.bindir

Can we add instructions to pre-install CMTK?

http://www.nitrc.org/frs/?group_id=212
CMTK-3.2.2-MacOSX-10.4-i686.dmg

Add also X11 for mac?
http://xquartz.macosforge.org/landing/

And is there an equivalent for windows?

It downloaded many other neurons ok for APClustering.Rmd, but got an error on this one.

Quitting from lines 52-57 (APClustering.Rmd)
Error in download.file(url = paste0(attr(fh, "remote"), missing[i]), destfile = file.path(objDir, :
cannot open URL 'http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/flycircuit/data/5f83690feefa91617352393239ebdf6c'
Calls: ... tryCatchOne -> -> fillMissing -> download.file
Execution halted

Knitting NBLAST_search.Rmd:
Quitting from lines 45-49 (NBLAST_search.Rmd)
Error in fc_attach_bigmat(scoremat) :
Cannot find file: /Users/Carta/Library/Application Support/rpkg-flycircuit/data/bigmatrix/allbyallblastcv4.5.desc
Calls: ... sort -> fc_nblast -> fc_subscoremat -> fc_attach_bigmat
Execution halted

It currently assumes the presence of the all by all search matrix (which is really a bit big for convenient downloads) and all the neurons. I have made a new git repo that includes what seem to be the minimal set of neurons (see https://github.com/jefferislab/dpscanon).

Now it's necessary to switch this to smaller objects. @mmc46 just wanted to check whether you are working on this?