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jefferislab / NBLAST_figures

R Markdown documents used to produce figures for Costa et al. (2014) NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases
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add instructions to install CMTK and X11 #1

Open mmc46 opened 9 years ago

mmc46 commented 9 years ago

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?

jefferis commented 9 years ago

Sent from my iPad

On 22 Mar 2015, at 13:36, mmc46 notifications@github.com wrote:

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

This means that CMTK command line tools are not installed on this machine or that nat cannot find them for some reason.

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)

cmtk is not an R package. Is this in a script?

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

As the message says CMTK needs to be installed from NITRC. Do you know if it has been?

mmc46 commented 9 years ago

After installing

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

it works fine. I'll add it to the pre-requisite downloads.

Maybe also add a link to your instructions to install the binaries? http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:compile_cmtk_tools

jefferis commented 9 years ago

I've done something, so pull before editing further. Best, G.

Sent from my iPad

On 22 Mar 2015, at 14:32, mmc46 notifications@github.com wrote:

After installing

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

it works fine. I'll add it to the pre-requisite downloads.

Maybe also add a link to your instructions to install the binaries? http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:compile_cmtk_tools

— Reply to this email directly or view it on GitHub.