Hi Guys I have officially put the therion brew into the science project brew install homebrew/science/therion For now therion still needs VTK5. While by default it tries to install VTK6. best Chris
On 31 Jan 2015, at 14:08, Yones Shariatmadari <yonessh2@gmail.com> wrote:
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.... <https://raw.githubusercontent.com/ladislavb/homebrew-science/master/therion.rb> ######################################################################## 100.0% Warning: You have an outdated version of /usr/bin/install_name_tool installed.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.... <https://downloads.sf.net/project/machomebrew/Bottles/libpng-1.6.16.yosemite.bottle.tar.gz> ######################################################################## 100.0% ==> 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... <https://downloads.sf.net/project/machomebrew/Bottles/freetype-2.5.5.yosemite.bottle.tar.gz> ######################################################################## 100.0% ==> 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.... <https://downloads.sf.net/project/machomebrew/Bottles/libtool-2.4.5.yosemite.bottle.tar.gz> ######################################################################## 100.0% ==> 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... <https://downloads.sf.net/project/machomebrew/Bottles/jpeg-8d.yosemite.bottle.2.tar.gz> ######################################################################## 100.0% ==> 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.bottl... <https://downloads.sf.net/project/machomebrew/Bottles/xz-5.2.0.yosemite.bottle.tar.gz> ######################################################################## 100.0% ==> 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.yos... <https://downloads.sf.net/project/machomebrew/Bottles/imagemagick-6.9.0-3.yosemite.bottle.tar.gz> ######################################################################## 100.0% ==> 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> ######################################################################## 100.0% ==> ./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.b... <https://downloads.sf.net/project/machomebrew/Bottles/boost-1.57.0.yosemite.bottle.tar.gz> ######################################################################## 100.0% ==> 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.yosem... <https://downloads.sf.net/project/machomebrew/Bottles/fontconfig-2.11.1.yosemite.bottle.3.tar.gz> ######################################################################## 100.0% ==> 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> ######################################################################## 100.0% ==> ./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.yos... <https://downloads.sf.net/project/machomebrew/Bottles/science/hdf5-1.8.14.yosemite.bottle.tar.gz> ######################################################################## 100.0% ==> 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.... <https://downloads.sf.net/project/machomebrew/Bottles/libtiff-4.0.3.yosemite.bottle.tar.gz> ######################################################################## 100.0% ==> 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.yos... <https://downloads.sf.net/project/machomebrew/Bottles/science/vtk-6.1.0_1.yosemite.bottle.tar.gz> ######################################################################## 100.0% ==> 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.bo... <https://downloads.sf.net/project/machomebrew/Bottles/wxmac-3.0.2.yosemite.bottle.9.tar.gz> ######################################################################## 100.0% ==> 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> ######################################################################## 100.0% ==> Downloading http://www.lblazek.cz/osx_vtk6.patch <http://www.lblazek.cz/osx_vtk6.patch> ######################################################################## 100.0% ==> 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 <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@mac.com <mailto:martinsluka@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.... <https://raw.githubusercontent.com/ladislavb/homebrew-science/master/therion.rb>
m.s.
30. 1. 2015 v 22:23, Yones Shariatmadari <yonessh2@gmail.com <mailto:yonessh2@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@mac.com <mailto:martinsluka@mac.com>> wrote:
30. 1. 2015 v 12:05, Yones Shariatmadari <yonessh2@gmail.com <mailto:yonessh2@gmail.com>>:
what should i do? please help me
Hi,
try to use HomeBrew instalation:
- download and install HomeBrew - http://brew.sh <http://brew.sh/>
- in terminal: brew install therion
m.
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-- 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@speleo.sk <mailto:Therion@speleo.sk> http://mailman.speleo.sk/mailman/listinfo/therion <http://mailman.speleo.sk/mailman/listinfo/therion>
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-- 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@speleo.sk http://mailman.speleo.sk/mailman/listinfo/therion