[Therion] The results of your email commands

Sat Jan 31 14:08:49 CET 2015

Hi  Friends
thank you for your interest my friends.
but i have an error in installing therion.

i use mac os 10.10.1 !

type the following brew in terminal :

the result is :

Macs-MacBook-Pro:~ yonesshariatmadari$ brew install
https://raw.githubusercontent.com/ladislavb/homebrew-science/master/therion.rb

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Warning: You have an outdated version of /usr/bin/install_name_tool
installed.

This will cause binary package installations to fail.

This can happen if you install osx-gcc-installer or RailsInstaller.

To restore it, you must reinstall OS X or restore the binary from

the OS packages.

*==>** Installing dependencies for therion: **libpng, freetype, libtool,
jpeg, xz, imagemagick, lcdf-typetools, boost, fontconfig, szip, hdf5,
libtiff, vtk, wxmac*

*==>** Installing therion dependency: **libpng*

*==>** Downloading
https://downloads.sf.net/project/machomebrew/Bottles/libpng-1.6.16.yosemite.bottle.tar.gz
<https://downloads.sf.net/project/machomebrew/Bottles/libpng-1.6.16.yosemite.bottle.tar.gz>*

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*==>** Pouring libpng-1.6.16.yosemite.bottle.tar.gz*

/usr/bin/install_name_tool: object:
/usr/local/Cellar/libpng/1.6.16/bin/pngfix malformed object (unknown load
command 9)

Error: Failed to fix install names

The formula built, but you may encounter issues using it or linking other

formula against it.

*==>** Summary*

🍺  /usr/local/Cellar/libpng/1.6.16: 17 files, 1.3M

*==>** Installing therion dependency: **freetype*

*==>** Downloading
https://downloads.sf.net/project/machomebrew/Bottles/freetype-2.5.5.yosemite.bottle.tar.gz
<https://downloads.sf.net/project/machomebrew/Bottles/freetype-2.5.5.yosemite.bottle.tar.gz>*

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*==>** Pouring freetype-2.5.5.yosemite.bottle.tar.gz*

/usr/bin/install_name_tool: object:
/usr/local/Cellar/freetype/2.5.5/lib/libfreetype.6.dylib malformed object
(unknown load command 8)

Error: Failed to fix install names

The formula built, but you may encounter issues using it or linking other

formula against it.

*==>** Summary*

🍺  /usr/local/Cellar/freetype/2.5.5: 60 files, 2.6M

*==>** Installing therion dependency: **libtool*

*==>** Downloading
https://downloads.sf.net/project/machomebrew/Bottles/libtool-2.4.5.yosemite.bottle.tar.gz
<https://downloads.sf.net/project/machomebrew/Bottles/libtool-2.4.5.yosemite.bottle.tar.gz>*

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*==>** Pouring libtool-2.4.5.yosemite.bottle.tar.gz*

*==>** Caveats*

In order to prevent conflicts with Apple's own libtool we have prepended a
"g"

so, you have instead: glibtool and glibtoolize.

/usr/bin/install_name_tool: object:
/usr/local/Cellar/libtool/2.4.5/lib/libltdl.7.dylib malformed object
(unknown load command 8)

Error: Failed to fix install names

The formula built, but you may encounter issues using it or linking other

formula against it.

*==>** Summary*

🍺  /usr/local/Cellar/libtool/2.4.5: 69 files, 3.8M

*==>** Installing therion dependency: **jpeg*

*==>** Downloading
https://downloads.sf.net/project/machomebrew/Bottles/jpeg-8d.yosemite.bottle.2.tar.gz
<https://downloads.sf.net/project/machomebrew/Bottles/jpeg-8d.yosemite.bottle.2.tar.gz>*

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*==>** Pouring jpeg-8d.yosemite.bottle.2.tar.gz*

/usr/bin/install_name_tool: object: /usr/local/Cellar/jpeg/8d/bin/cjpeg
malformed object (unknown load command 9)

Error: Failed to fix install names

The formula built, but you may encounter issues using it or linking other

formula against it.

*==>** Summary*

🍺  /usr/local/Cellar/jpeg/8d: 18 files, 776K

*==>** Installing therion dependency: **xz*

*==>** Downloading
https://downloads.sf.net/project/machomebrew/Bottles/xz-5.2.0.yosemite.bottle.tar.gz
<https://downloads.sf.net/project/machomebrew/Bottles/xz-5.2.0.yosemite.bottle.tar.gz>*

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*==>** Pouring xz-5.2.0.yosemite.bottle.tar.gz*

/usr/bin/install_name_tool: object: /usr/local/Cellar/xz/5.2.0/bin/lzmadec
malformed object (unknown load command 9)

Error: Failed to fix install names

The formula built, but you may encounter issues using it or linking other

formula against it.

*==>** Summary*

🍺  /usr/local/Cellar/xz/5.2.0: 59 files, 1.7M

*==>** Installing therion dependency: **imagemagick*

*==>** Downloading
https://downloads.sf.net/project/machomebrew/Bottles/imagemagick-6.9.0-3.yosemite.bottle.tar.gz
<https://downloads.sf.net/project/machomebrew/Bottles/imagemagick-6.9.0-3.yosemite.bottle.tar.gz>*

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*==>** Pouring imagemagick-6.9.0-3.yosemite.bottle.tar.gz*

/usr/bin/install_name_tool: object:
/usr/local/Cellar/imagemagick/6.9.0-3/bin/animate malformed object (unknown
load command 9)

Error: Failed to fix install names

The formula built, but you may encounter issues using it or linking other

formula against it.

*==>** Summary*

🍺  /usr/local/Cellar/imagemagick/6.9.0-3: 1440 files, 22M

*==>** Installing therion dependency: **lcdf-typetools*

couldn't understand kern.osversion `14.0.0'

*==>** Downloading http://www.lcdf.org/type/lcdf-typetools-2.104.tar.gz
<http://www.lcdf.org/type/lcdf-typetools-2.104.tar.gz>*

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*==>** ./configure --prefix=/usr/local/Cellar/lcdf-typetools/2.104
--without-kpathsea*

*==>** make install*

🍺  /usr/local/Cellar/lcdf-typetools/2.104: 29 files, 4.3M, built in 5.5
minutes

*==>** Installing therion dependency: **boost*

*==>** Downloading
https://downloads.sf.net/project/machomebrew/Bottles/boost-1.57.0.yosemite.bottle.tar.gz
<https://downloads.sf.net/project/machomebrew/Bottles/boost-1.57.0.yosemite.bottle.tar.gz>*

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*==>** Pouring boost-1.57.0.yosemite.bottle.tar.gz*

/usr/bin/install_name_tool: object:
/usr/local/Cellar/boost/1.57.0/lib/libboost_atomic-mt.dylib malformed
object (unknown load command 8)

Error: Failed to fix install names

The formula built, but you may encounter issues using it or linking other

formula against it.

*==>** Summary*

🍺  /usr/local/Cellar/boost/1.57.0: 10572 files, 439M

*==>** Installing therion dependency: **fontconfig*

*==>** Downloading
https://downloads.sf.net/project/machomebrew/Bottles/fontconfig-2.11.1.yosemite.bottle.3.tar.gz
<https://downloads.sf.net/project/machomebrew/Bottles/fontconfig-2.11.1.yosemite.bottle.3.tar.gz>*

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*==>** Pouring fontconfig-2.11.1.yosemite.bottle.3.tar.gz*

/usr/bin/install_name_tool: object:
/usr/local/Cellar/fontconfig/2.11.1/bin/fc-cache malformed object (unknown
load command 9)

Error: Failed to fix install names

The formula built, but you may encounter issues using it or linking other

formula against it.

*==>** /usr/local/Cellar/fontconfig/2.11.1/bin/fc-cache -frv*

^\Warning: The post-install step did not complete successfully

You can try again using `brew postinstall fontconfig`

*==>** Summary*

🍺  /usr/local/Cellar/fontconfig/2.11.1: 448 files, 3.6M

*==>** Installing therion dependency: **szip*

couldn't understand kern.osversion `14.0.0'

*==>** Downloading
http://www.hdfgroup.org/ftp/lib-external/szip/2.1/src/szip-2.1.tar.gz
<http://www.hdfgroup.org/ftp/lib-external/szip/2.1/src/szip-2.1.tar.gz>*

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*==>** ./configure --prefix=/usr/local/Cellar/szip/2.1*

*==>** make install*

🍺  /usr/local/Cellar/szip/2.1: 9 files, 132K, built in 28 seconds

*==>** Installing therion dependency: **hdf5*

*==>** Downloading
https://downloads.sf.net/project/machomebrew/Bottles/science/hdf5-1.8.14.yosemite.bottle.tar.gz
<https://downloads.sf.net/project/machomebrew/Bottles/science/hdf5-1.8.14.yosemite.bottle.tar.gz>*

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*==>** Pouring hdf5-1.8.14.yosemite.bottle.tar.gz*

/usr/bin/install_name_tool: object:
/usr/local/Cellar/hdf5/1.8.14/bin/gif2h5 malformed object (unknown load
command 9)

Error: Failed to fix install names

The formula built, but you may encounter issues using it or linking other

formula against it.

*==>** Summary*

🍺  /usr/local/Cellar/hdf5/1.8.14: 118 files, 9.9M

*==>** Installing therion dependency: **libtiff*

*==>** Downloading
https://downloads.sf.net/project/machomebrew/Bottles/libtiff-4.0.3.yosemite.bottle.tar.gz
<https://downloads.sf.net/project/machomebrew/Bottles/libtiff-4.0.3.yosemite.bottle.tar.gz>*

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*==>** Pouring libtiff-4.0.3.yosemite.bottle.tar.gz*

/usr/bin/install_name_tool: object:
/usr/local/Cellar/libtiff/4.0.3/bin/bmp2tiff malformed object (unknown load
command 9)

Error: Failed to fix install names

The formula built, but you may encounter issues using it or linking other

formula against it.

*==>** Summary*

🍺  /usr/local/Cellar/libtiff/4.0.3: 254 files, 3.8M

*==>** Installing therion dependency: **vtk*

*==>** Downloading
https://downloads.sf.net/project/machomebrew/Bottles/science/vtk-6.1.0_1.yosemite.bottle.tar.gz
<https://downloads.sf.net/project/machomebrew/Bottles/science/vtk-6.1.0_1.yosemite.bottle.tar.gz>*

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*==>** Pouring vtk-6.1.0_1.yosemite.bottle.tar.gz*

*==>** Caveats*

Even without the --with-qt option, you can display native VTK render windows

from python. Alternatively, you can integrate the RenderWindowInteractor

in PyQt, PySide, Tk or Wx at runtime. Read more:

    import vtk.qt4; help(vtk.qt4) or import vtk.wx; help(vtk.wx)

Python modules have been installed and Homebrew's site-packages is not

in your Python sys.path, so you will not be able to import the modules

this formula installed. If you plan to develop with these modules,

please run:

  mkdir -p
/Users/yonesshariatmadari/Library/Python/2.7/lib/python/site-packages

  echo 'import site;
site.addsitedir("/usr/local/lib/python2.7/site-packages")' >>
/Users/yonesshariatmadari/Library/Python/2.7/lib/python/site-packages/homebrew.pth

/usr/bin/install_name_tool: object:
/usr/local/Cellar/vtk/6.1.0_1/bin/vtkHashSource-6.1 malformed object
(unknown load command 9)

Error: Failed to fix install names

The formula built, but you may encounter issues using it or linking other

formula against it.

*==>** Summary*

🍺  /usr/local/Cellar/vtk/6.1.0_1: 3005 files, 123M

*==>** Installing therion dependency: **wxmac*

*==>** Downloading
https://downloads.sf.net/project/machomebrew/Bottles/wxmac-3.0.2.yosemite.bottle.9.tar.gz
<https://downloads.sf.net/project/machomebrew/Bottles/wxmac-3.0.2.yosemite.bottle.9.tar.gz>*

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*==>** Pouring wxmac-3.0.2.yosemite.bottle.9.tar.gz*

/usr/bin/install_name_tool: for architecture i386 object:
/usr/local/Cellar/wxmac/3.0.2/bin/wxrc-3.0 malformed object (unknown load
command 9)

Error: Failed to fix install names

The formula built, but you may encounter issues using it or linking other

formula against it.

*==>** Summary*

🍺  /usr/local/Cellar/wxmac/3.0.2: 777 files, 41M

*==>** Installing **therion*

couldn't understand kern.osversion `14.0.0'

*==>** Downloading http://therion.speleo.sk/downloads/therion-5.3.15.tar.gz
<http://therion.speleo.sk/downloads/therion-5.3.15.tar.gz>*

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*==>** Downloading http://www.lblazek.cz/osx_vtk6.patch
<http://www.lblazek.cz/osx_vtk6.patch>*

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*==>** Patching*

patching file loch/lxData.cxx

Hunk #1 succeeded at 540 (offset 5 lines).

Hunk #2 succeeded at 582 (offset 5 lines).

patching file loch/Makefile

*==>** make config-macosx*

*==>** make*

couldn't understand kern.osversion `14.0.0'

loch/lxFile.cxx: In member function ‘void lxFile::ImportPLT(const char*)’:

loch/lxFile.cxx:755: error: ‘getline’ was not declared in this scope

make: *** [extern/lxFile.o] Error 1

make: *** Waiting for unfinished jobs....

couldn't understand kern.osversion `14.0.0'

READ THIS: http://git.io/brew-troubleshooting

*what should i do for this error, please help me.*

*thank you *
*Y.SH*

On Sat, Jan 31, 2015 at 2:03 AM, Martin Sluka <martinsluka at mac.com> wrote:

> It is on my computer (OSX 10.8.5):
>
> as written in wiki:
>
> brew tap homebrew/science
> brew install
> https://raw.githubusercontent.com/ladislavb/homebrew-science/master/therion.rb
>
>
>
> m.s.
>
>
> 30. 1. 2015 v 22:23, Yones Shariatmadari <yonessh2 at gmail.com>:
>
> *Hi*
>
> *i use homebrew , it is very good for checking but that error is in
> terminal !!!*
> *problem not solve.*
>
> *please check this:*
>
> Macs-MacBook-Pro:therion yonesshariatmadari$ brew install therion
> Error: No available formula for therion
> Searching formulae...
> Searching taps...
>
>
> On Fri, Jan 30, 2015 at 3:37 PM, Martin Sluka <martinsluka at mac.com> wrote:
>
>>
>> 30. 1. 2015 v 12:05, Yones Shariatmadari <yonessh2 at gmail.com>:
>>
>> what should i do?
>> please help me
>>
>>
>> Hi,
>>
>> try to use HomeBrew instalation:
>>
>> - download and install HomeBrew - http://brew.sh
>>
>> - in terminal: brew install therion
>>
>> m.
>>
>> _______________________________________________
>> Therion mailing list
>> Therion at speleo.sk
>> http://mailman.speleo.sk/mailman/listinfo/therion
>>
>>
>
>
> --
> Yones Shariatmadari
> Master Student , Department of BioStatistics
> School of Paramedical Science (PMS) <http://pms.sbmu.ac.ir/>
> Shahid Beheshti University of Medical Sciences (S.B.M.U)
> <http://www.sbmu.ac.ir/>
> Tehran, Iran
>  _______________________________________________
> Therion mailing list
> Therion at speleo.sk
> http://mailman.speleo.sk/mailman/listinfo/therion
>
>
>
> _______________________________________________
> Therion mailing list
> Therion at speleo.sk
> http://mailman.speleo.sk/mailman/listinfo/therion
>
>

-- 
Yones Shariatmadari
Master Student , Department of BioStatistics
School of Paramedical Science (PMS) <http://pms.sbmu.ac.ir>
Shahid Beheshti University of Medical Sciences (S.B.M.U)
<http://www.sbmu.ac.ir/>
Tehran, Iran
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