Installation error messages and cadabra2-gtk not working on Mac OS X El Capitan

Question

Hi, I followed the instructions for installing Cadabra on Mac (I am using OS X El Capitan, version 10.11.6), and all went fine, except the almost final step (make), where I got the following messages:

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make --ignore-errors [ 1%] Built target cadabra2python [ 3%] Creating gauge_theory/instantons.py... [ 3%] Built target gauge_theory_instantons [ 3%] Creating package relativity... [ 3%] Built target relativity [ 3%] Creating relativity/schwarzschild.py... [ 3%] Built target relativity_schwarzschild [ 3%] Creating package gauge_theory... [ 3%] Built target gauge_theory [ 3%] Creating gauge_theory/init.py... [ 3%] Built target gauge_theory_init [ 4%] Creating relativity/init_.py... [ 4%] Built target relativityinit [ 75%] Built target cadabra2 [ 77%] Built target test_preprocessor [ 78%] Linking CXX shared library libcadabra_server.dylib ld: warning: ignoring file /opt/local/lib/libglibmm-2.4.dylib, file was built for i386 which is not the architecture being linked (x86_64): /opt/local/lib/libglibmm-2.4.dylib ld: warning: ignoring file /opt/local/lib/libsigc-2.0.dylib, file was built for i386 which is not the architecture being linked (x86_64): /opt/local/lib/libsigc-2.0.dylib Undefined symbols for architecture x86_64: "Glib::get_user_config_dir()", referenced from: snoop::SnoopImpl::get_user_uuid(std::1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in Snoop.cc.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) [ 81%] Built target cadabra_server [ 81%] Building CXX object client_server/CMakeFiles/cadabra_client.dir/ComputeThread.cc.o /Users/dario/cadabra2/client_server/ComputeThread.cc:182:19: error: no member named 'SPAWN_DEFAULT' in namespace 'Glib' ...Glib::SPAWN_DEFAULT|Glib::SPAWN_SEARCH_PATH,

1 error generated.
[ 81%] Linking CXX shared library libcadabra_client.dylib
clang: error: no such file or directory: 'CMakeFiles/cadabra_client.dir/ComputeThread.cc.o'
[ 85%] Built target cadabra_client
make[2]: *** No rule to make target `client_server/libcadabra_client.dylib', needed by `client_server/cadabra2cadabra'.  Stop.
[ 86%] Built target cadabra2cadabra
make[2]: *** No rule to make target `client_server/libcadabra_client.dylib', needed by `client_server/cadabra2html'.  Stop.
[ 88%] Built target cadabra2html
make[2]: *** No rule to make target `client_server/libcadabra_server.dylib', needed by `client_server/cadabra-server'.  Stop.
[ 88%] Built target cadabra-server
[ 90%] Built target texengine
[ 91%] Built target test_tex
[ 91%] Creating scalar_manipulations notebook...
/bin/sh: ../client_server/cadabra2cadabra: No such file or directory
-n
[ 91%] Built target scalar_manipulations_test
[ 93%] Creating kaluza_klein notebook...
/bin/sh: ../client_server/cadabra2cadabra: No such file or directory
-n
[ 93%] Built target kaluza_klein_test
[ 93%] Creating schwarzschild notebook...
/bin/sh: ../client_server/cadabra2cadabra: No such file or directory
-n
[ 93%] Built target schwarzschild_test
[ 93%] Creating fierz notebook...
/bin/sh: ../client_server/cadabra2cadabra: No such file or directory
-n
[ 93%] Built target fierz_test
[ 93%] Creating string_states notebook...
/bin/sh: ../client_server/cadabra2cadabra: No such file or directory
-n
[ 93%] Built target string_states_test
[ 95%] Creating poincare_algebra notebook...
/bin/sh: ../client_server/cadabra2cadabra: No such file or directory
-n
[ 95%] Built target poincare_algebra_test
[ 96%] Creating gamma_matrix_algebra notebook...
/bin/sh: ../client_server/cadabra2cadabra: No such file or directory
-n
[ 96%] Built target gamma_matrix_algebra_test
[ 98%] Creating bianchi_identities notebook...
/bin/sh: ../client_server/cadabra2cadabra: No such file or directory
-n
[ 98%] Built target bianchi_identities_test
[ 98%] Creating converge notebook...
/bin/sh: ../client_server/cadabra2cadabra: No such file or directory
-n
[ 98%] Built target converge_test
[ 98%] Creating for_previous_users notebook...
/bin/sh: ../client_server/cadabra2cadabra: No such file or directory
-n
[ 98%] Built target for_previous_users_test
[ 98%] Creating tensor_monomials notebook...
/bin/sh: ../client_server/cadabra2cadabra: No such file or directory
-n
[ 98%] Built target tensor_monomials_test
[ 98%] Creating beginners notebook...
/bin/sh: ../client_server/cadabra2cadabra: No such file or directory
-n
[ 98%] Built target beginners_test
[100%] Creating quickstart notebook...
/bin/sh: ../client_server/cadabra2cadabra: No such file or directory
-n
[100%] Built target quickstart_test

%%%%%%%%%

I thn get similar error messages for sudo make install, and at the end I am able to run cadabra2 in the terminal, but not cadabra2-gtk. I get the following message:

-bash: cadabra2-gtk: command not found

Any idea how to solve these issues?

Answer 1

Can you try

brew update

and see If that updates the gtk libraries?

Comments

Done already, and tried make again, but nothing changed.

Answer 2

if it can be useful, "brew doctor" gives me this:

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Warning: "config" scripts exist outside your system or Homebrew directories. ./configure scripts often look for *-config scripts to determine if software packages are installed, and what additional flags to use when compiling and linking.

Having additional scripts in your path can confuse software installed via Homebrew if the config script overrides a system or Homebrew provided script of the same name. We found the following "config" scripts: /sw/bin/apt-config /sw/bin/ncurses5-config /opt/local/bin/freetype-config /opt/local/bin/libpng-config /opt/local/bin/libpng16-config /opt/local/bin/ncurses6-config /opt/local/bin/ncursesw5-config /opt/local/bin/ncursesw6-config /opt/local/bin/pcre++-config /opt/local/bin/pcre-config /opt/local/bin/pkg-config /opt/local/bin/python2.5-config /opt/local/bin/python2.6-config /opt/local/bin/python2.7-config /opt/local/bin/rarian-sk-config /opt/local/bin/scrollkeeper-config /opt/local/bin/xft-config /opt/local/bin/xml2-config /opt/local/bin/xslt-config

Warning: gettext files detected at a system prefix. These files can cause compilation and link failures, especially if they are compiled with improper architectures. Consider removing these files: /usr/local/include/libintl.h /usr/local/include/libintl.h

Warning: You have MacPorts or Fink installed: /opt/local/bin/port, /sw/bin/fink

This can cause trouble. You don't have to uninstall them, but you may want to temporarily move them out of the way, e.g.

sudo mv /opt/local ~/macports

Warning: Unbrewed dylibs were found in /usr/local/lib. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted.

Unexpected dylibs: /usr/local/lib/libasprintf.0.0.0.dylib /usr/local/lib/libfreetype.6.3.12.dylib /usr/local/lib/libgdraw.1.0.14.dylib /usr/local/lib/libgettextlib-0.14.5.dylib /usr/local/lib/libgettextpo.0.1.0.dylib /usr/local/lib/libgettextsrc-0.14.5.dylib /usr/local/lib/libgunicode.2.0.3.dylib /usr/local/lib/libintl.3.4.3.dylib /usr/local/lib/libMagick++.10.0.7.dylib /usr/local/lib/libMagick.10.0.7.dylib /usr/local/lib/libuninameslist-fr.0.0.1.dylib /usr/local/lib/libuninameslist.0.0.1.dylib /usr/local/lib/libWand.10.0.7.dylib

Warning: Unbrewed header files were found in /usr/local/include. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted.

Unexpected header files: /usr/local/include/autosprintf.h /usr/local/include/freetype2/freetype/ftxf86.h /usr/local/include/ft2build.h /usr/local/include/gettext-po.h /usr/local/include/libintl.h /usr/local/include/libwmf/gd/gd.h /usr/local/include/libwmf/gd/gd_clip.h /usr/local/include/libwmf/gd/gdio.h /usr/local/include/libwmf/gd/gdcache.h /usr/local/include/libwmf/gd/gdfontg.h /usr/local/include/libwmf/gd/gdfontl.h /usr/local/include/libwmf/gd/gdfontmb.h /usr/local/include/libwmf/gd/gdfonts.h /usr/local/include/libwmf/gd/gdfontt.h /usr/local/include/magick/animate.h /usr/local/include/magick/annotate.h /usr/local/include/magick/api.h /usr/local/include/magick/blob.h /usr/local/include/magick/cache-view.h /usr/local/include/magick/cache.h /usr/local/include/magick/client.h /usr/local/include/magick/coder.h /usr/local/include/magick/color.h /usr/local/include/magick/colorspace.h /usr/local/include/magick/compare.h /usr/local/include/magick/composite.h /usr/local/include/magick/compress.h /usr/local/include/magick/configure.h /usr/local/include/magick/constitute.h /usr/local/include/magick/decorate.h /usr/local/include/magick/delegate.h /usr/local/include/magick/deprecate.h /usr/local/include/magick/display.h /usr/local/include/magick/draw.h /usr/local/include/magick/effect.h /usr/local/include/magick/enhance.h /usr/local/include/magick/exception.h /usr/local/include/magick/fx.h /usr/local/include/magick/gem.h /usr/local/include/magick/geometry.h /usr/local/include/magick/hashmap.h /usr/local/include/magick/identify.h /usr/local/include/magick/image.h /usr/local/include/magick/ImageMagick.h /usr/local/include/magick/layer.h /usr/local/include/magick/list.h /usr/local/include/magick/locale.h /usr/local/include/magick/log.h /usr/local/include/magick/magic.h /usr/local/include/magick/magick-config.h /usr/local/include/magick/magick-type.h /usr/local/include/magick/magick.h /usr/local/include/magick/MagickCore.h /usr/local/include/magick/memory.h /usr/local/include/magick/methods.h /usr/local/include/magick/mime.h /usr/local/include/magick/module.h /usr/local/include/magick/monitor.h /usr/local/include/magick/montage.h /usr/local/include/magick/option.h /usr/local/include/magick/paint.h /usr/local/include/magick/pixel.h /usr/local/include/magick/prepress.h /usr/local/include/magick/PreRvIcccm.h /usr/local/include/magick/profile.h /usr/local/include/magick/property.h /usr/local/include/magick/quantize.h /usr/local/include/magick/quantum.h /usr/local/include/magick/random.h /usr/local/include/magick/registry.h /usr/local/include/magick/resize.h /usr/local/include/magick/resource.h /usr/local/include/magick/segment.h /usr/local/include/magick/semaphore.h /usr/local/include/magick/shear.h /usr/local/include/magick/signature.h /usr/local/include/magick/splay-tree.h /usr/local/include/magick/statistic.h /usr/local/include/magick/stream.h /usr/local/include/magick/string.h /usr/local/include/magick/threshold.h /usr/local/include/magick/timer.h /usr/local/include/magick/token.h /usr/local/include/magick/transform.h /usr/local/include/magick/type.h /usr/local/include/magick/utility.h /usr/local/include/magick/version.h /usr/local/include/magick/widget.h /usr/local/include/magick/xml-tree.h /usr/local/include/magick/xwindow.h /usr/local/include/Magick++/Blob.h /usr/local/include/Magick++/CoderInfo.h /usr/local/include/Magick++/Color.h /usr/local/include/Magick++/Drawable.h /usr/local/include/Magick++/Exception.h /usr/local/include/Magick++/Geometry.h /usr/local/include/Magick++/Image.h /usr/local/include/Magick++/Include.h /usr/local/include/Magick++/Montage.h /usr/local/include/Magick++/Pixels.h /usr/local/include/Magick++/STL.h /usr/local/include/Magick++/TypeMetric.h /usr/local/include/Magick++.h /usr/local/include/plot.h /usr/local/include/plotcompat.h /usr/local/include/plotter.h /usr/local/include/ublio.h /usr/local/include/uninameslist.h /usr/local/include/wand/animate.h /usr/local/include/wand/compare.h /usr/local/include/wand/composite.h /usr/local/include/wand/conjure.h /usr/local/include/wand/convert.h /usr/local/include/wand/display.h /usr/local/include/wand/drawing-wand.h /usr/local/include/wand/identify.h /usr/local/include/wand/import.h /usr/local/include/wand/magick-image.h /usr/local/include/wand/magick-property.h /usr/local/include/wand/magick-wand.h /usr/local/include/wand/magick_wand.h /usr/local/include/wand/MagickWand.h /usr/local/include/wand/mogrify.h /usr/local/include/wand/montage.h /usr/local/include/wand/pixel-iterator.h /usr/local/include/wand/pixel-wand.h /usr/local/include/wand/stream.h /usr/local/include/wand/wand-config.h

Comments

(continued...)

Warning: Unbrewed .la files were found in /usr/local/lib. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted.

Unexpected .la files: /usr/local/lib/libasprintf.la /usr/local/lib/libfreetype.la /usr/local/lib/libgdraw.la /usr/local/lib/libgettextlib.la /usr/local/lib/libgettextpo.la /usr/local/lib/libgettextsrc.la /usr/local/lib/libgunicode.la /usr/local/lib/libintl.la /usr/local/lib/libMagick++.la /usr/local/lib/libMagick.la /usr/local/lib/libplot.la /usr/local/lib/libplotter.la /usr/local/lib/libuninameslist-fr.la /usr/local/lib/libuninameslist.la /usr/local/lib/libWand.la /usr/local/lib/libwmf.la /usr/local/lib/libwmflite.la

Warning: Unbrewed .pc files were found in /usr/local/lib/pkgconfig. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted.

Unexpected .pc files: /usr/local/lib/pkgconfig/fontforge.pc /usr/local/lib/pkgconfig/ImageMagick++.pc /usr/local/lib/pkgconfig/ImageMagick.pc /usr/local/lib/pkgconfig/Wand.pc

Warning: Unbrewed static libraries were found in /usr/local/lib. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted.

Unexpected static libraries: /usr/local/lib/libasprintf.a /usr/local/lib/libgettextpo.a /usr/local/lib/libintl.a /usr/local/lib/libMagick++.a /usr/local/lib/libMagick.a /usr/local/lib/libplot.a /usr/local/lib/libplotter.a /usr/local/lib/libWand.a /usr/local/lib/libwmf.a /usr/local/lib/libwmflite.a

Warning: You have unlinked kegs in your Cellar Leaving kegs unlinked can lead to build-trouble and cause brews that depend on those kegs to fail to run properly once built. Run brew link on these: ghostscript plotutils

Warning: Homebrew's sbin was not found in your PATH but you have installed formulae that put executables in /usr/local/sbin. Consider setting the PATH for example like so echo 'export PATH="/usr/local/sbin:$PATH"' >> ~/.bash_profile

Warning: You have a non-Homebrew 'pkg-config' in your PATH: /opt/local/bin/pkg-config

./configure may have problems finding brew-installed packages using this other pkg-config.

Warning: Broken symlinks were found. Remove them with brew prune: /usr/local/share/ghostscript/9.07/Resource/Font/logo10.pfb /usr/local/share/ghostscript/9.07/Resource/Font/logo8.pfb /usr/local/share/ghostscript/9.07/Resource/Font/logo9.pfb /usr/local/share/ghostscript/9.07/Resource/Font/logobf10.pfb /usr/local/share/ghostscript/9.07/Resource/Font/logod10.pfb /usr/local/share/ghostscript/9.07/Resource/Font/logosl10.pfb /usr/local/share/ghostscript/9.07/Resource/Font/logosl8.pfb /usr/local/share/ghostscript/9.07/Resource/Font/logosl9.pfb /usr/local/share/ghostscript/9.07/Resource/Font/manfnt.pfb /usr/local/share/ghostscript/9.07/Resource/Font/wasy10.pfb /usr/local/share/ghostscript/9.07/Resource/Font/wasy5.pfb /usr/local/share/ghostscript/9.07/Resource/Font/wasy6.pfb /usr/local/share/ghostscript/9.07/Resource/Font/wasy7.pfb /usr/local/share/ghostscript/9.07/Resource/Font/wasy8.pfb /usr/local/share/ghostscript/9.07/Resource/Font/wasy9.pfb /usr/local/share/ghostscript/9.07/Resource/Font/wasyb10.pfb /usr/local/share/ghostscript/9.10/Resource/Font/logo10.pfb /usr/local/share/ghostscript/9.10/Resource/Font/logo8.pfb /usr/local/share/ghostscript/9.10/Resource/Font/logo9.pfb /usr/local/share/ghostscript/9.10/Resource/Font/logobf10.pfb /usr/local/share/ghostscript/9.10/Resource/Font/logod10.pfb /usr/local/share/ghostscript/9.10/Resource/Font/logosl10.pfb /usr/local/share/ghostscript/9.10/Resource/Font/logosl8.pfb /usr/local/share/ghostscript/9.10/Resource/Font/logosl9.pfb /usr/local/share/ghostscript/9.10/Resource/Font/manfnt.pfb /usr/local/share/ghostscript/9.10/Resource/Font/wasy10.pfb /usr/local/share/ghostscript/9.10/Resource/Font/wasy5.pfb /usr/local/share/ghostscript/9.10/Resource/Font/wasy6.pfb /usr/local/share/ghostscript/9.10/Resource/Font/wasy7.pfb /usr/local/share/ghostscript/9.10/Resource/Font/wasy8.pfb /usr/local/share/ghostscript/9.10/Resource/Font/wasy9.pfb /usr/local/share/ghostscript/9.10/Resource/Font/wasyb10.pfb /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraKakuPro-W3 /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraKakuPro-W6 /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraKakuProN-W3 /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraKakuProN-W6 /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraKakuStd-W8 /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraKakuStdN-W8 /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraMaruPro-W4 /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraMaruProN-W4 /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraMinPro-W3 /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraMinPro-W6 /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraMinProN-W3 /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraMinProN-W6 /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraginoSansGB-W3 /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraginoSansGB-W6 /usr/local/share/ghostscript/9.16/Resource/CIDFont/YuMin-Demibold /usr/local/share/ghostscript/9.16/Resource/CIDFont/YuMin-Medium

%%%%%%%%%%%

---

It's possible that some of those issues are causing the problem, but I won't be able to check this on a clean system until Tuesday. Your problem is that the gtk version which is picked up by cadabra does not have some expected functionality, even though the version in brew has it. I'll get back to you on Tuesday.

---

I can't reproduce this problem on my machine here, and it also doesn't occur on the Travis build machines. I suspect that the /opt/local/bin/pkg-config on your machine leads cadabra to pick up a library installation which is not coming from homebrew. You can try to rename that temporarily to something else, then doing a clean installation of cadabra (erase the build directory first to avoid any left-overs from previous attempts).

The other brew doctor remarks seem relatively harmless at least for a cadabra build, but if the problem persists I would try to clean that up first so at least your homebrew installation works as it should.

Feel free to ask again if you get stuck.

---

One more thing: the two libraries which are mentioned in the make log,

/opt/local/lib/libglibmm-2.4.dylib
/opt/local/lib/libsigc-2.0.dylib

are suspicious: the build process claims that these are 32-bit libraries and are therefore not used. That would certainly not happen if these were installed by homebrew. You may want to try to uninstall and reinstall gtkmm3 with

brew uninstall libsigc++
brew uninstall gtkmm3
brew install gtkmm3

If that changes the errors you are almost certainly on the right track (and of course there is the possibility that this will make the build complete without errors, fingers crossed).

---

thanks for the help, the first suggestion worked! I renamed /opt/local/bin/pkg-config and reinstalled cadabra, this time without error messages. But... cadabra2-gtk is still not found, although during installation I got the message "[ 93%] Built target cadabra2-gtk". Does it make sense?

---

What else do the make and sudo make install steps spit out?

---

ha! excited by the successful elimination of the previous errors I forgot the last step...I had not done sudo make install !:-) Having done that, cadabra2-gtk works very fine. Thanks again!