problem with cmaking the project

[Orlov, Nikita (NIH/NIA/IRP) [E]]

Hi,

 

I am having problem while trying to cmake this project.

Here is what I keep getting.

 

==========================

NIA-LG-01742679:bin orlovni$ cmake ..

-- Build type: Release

CMake Error at matlab/FindMatlab.cmake:125 (message):

  MATLAB_ROOT variable not provider by the user, and 'matlab' command not in

  the path either.  I do not know where to search for Matlab.

Call Stack (most recent call first):

  CMakeLists.txt:82 (find_package)

 

-- Configuring incomplete, errors occurred!

See also "…/gerardus/bin/CMakeFiles/CMakeOutput.log".

==========================

 

It is not like MATLAB_ROOT is a complete stranger to the environment:

 

==========================

NIA-LG-01742679:bin orlovni$ printenv

TERM_PROGRAM=Apple_Terminal

TERM=xterm-256color

SHELL=/bin/sh

TMPDIR=/var/folders/1f/_86m3sn57dz0qt4kmfdh67hh5s90th/T/

Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.se2CxQhSpd/Render

TERM_PROGRAM_VERSION=361.1

OLDPWD=…/gerardus

TERM_SESSION_ID=8C060517-8FA6-42B3-83D1-7B4E263827DD

USER=orlovni

SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.DI0ZaEjvd6/Listeners

__CF_USER_TEXT_ENCODING=0xB948350:0x0:0x0

PATH=/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin

PWD=…/gerardus/bin

LANG=en_US.UTF-8

XPC_FLAGS=0x0

XPC_SERVICE_NAME=0

HOME=/Users/orlovni

SHLVL=1

MATLAB_ROOT=/Applications/MATLAB_R2017a.app

LOGNAME=orlovni

DISPLAY=/private/tmp/com.apple.launchd.l3RBCB5OJk/org.macosforge.xquartz:0

SECURITYSESSIONID=186bb

_=/usr/bin/printenv

==========================

 

So, what do I do wrong? Any help is much appreciated.

 

Regards,

Nik

[Ramón Casero Cañas]

Hi Nik,

I don't have a Mac, and I'm not sure the project would build on one. So I'm afraid I cannot help very much. The error probably comes from some point in one of the CMakeLists.txt, where it's expecting to find a command called "matlab", or the Matlab directory be called in a certain way.

What are you trying to do more generally? What do you need from gerardus?

Best regards,

Ramon.

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Dr Ramón Casero, Post-Doctoral Researcher

 
MRC Harwell Institute, Biocomputing, Mammalian Genetics Unit

Harwell Campus, Oxfordshire, OX11 0RD, UK.
Tel: +44 (0)1235 841237 | www.har.mrc.ac.uk

[norlov]

Hi Ramon,

Thank you for your reply. 

I am not sure whether my problem is due to the particular system (Mac) though.

At one point, FindMatlab.cmake wants an access to mbuild (COMMAND grep " ver='" "${MATLAB_ROOT}/bin/mbuild") and fails with a message

"  grep: /bin/mbuild: No such file or directory "

Nope, in my distribution, I don't have Compiler (and thus, no mbuild). 

I commented this portion (lines 155:159) to see what's next.

The code now chokes on line 171 ( COMMAND xargs echo -n ):

" xargs: unterminated quote "

I don't have much skills to navigate myself through the shell scripting. Without expertise from others, I may abandon this project.

I saw instructions for Mac and Linux users, so I thought Mac installation would be feasable. 

As I understand, you personally don't have any experience with Mac installation. 

Do you have Mac users backfeed at all? Do I start a separate threat for Mac installation?

My interest to gerardus is to have a wrapper for ITK, and also to see what's available in given matlab functions. 

As I understand, matlab functions (w/o access to ITK) should be available, regardless of my misfortunates with cmake.

Thanks again --

Nik

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