Groups 213 of 99+ julia-users › Unable to install IJulia 10 posts by 3 authors Ismael Venegas Castelló 2/3/14 First I got a segmentation fault when trying to install IJulia, I have tried several times, sometimes I get another error, I'm trying to reproduce again: fish: Job 1, 'julia' terminated by signal SIGSEGV (Address boundary error) I have reinstalled julia several times, each time I removed the .julia folder to start anew, but with no luck. ismaelvc@toybox ~> julia _ _ _ _(_)_ | A fresh approach to technical computing (_) | (_) (_) | Documentation: http://docs.julialang.org _ _ _| |_ __ _ | Type "help()" to list help topics | | | | | | |/ _` | | | | |_| | | | (_| | | Version 0.3.0-prerelease+1367 (2014-02-03 08:34 UTC) _/ |\__'_|_|_|\__'_| | Commit 793d769* (0 days old master) |__/ | i686-pc-linux-gnu julia> Pkg.update() INFO: Initializing package repository /home/ismaelvc/.julia/v0.3 INFO: Cloning METADATA from git://github.com/JuliaLang/METADATA.jl INFO: Updating METADATA... INFO: Computing changes... INFO: No packages to install, update or remove julia> Pkg.add("IJulia") ERROR: access to undefined reference My machine info: ismaelvc@toybox ~> uname -a Linux toybox 3.12.9-1-ARCH #1 SMP PREEMPT Sun Jan 26 09:15:23 CET 2014 i686 GNU/Linux Using the package manager to clone manually IJulia and it's dependencies, doesnt work either, I'm trying to reproduce that issue. Ismael Venegas Castelló 2/3/14 I just tried building it again using the Arch AUR PKGBUILD, got segfault, when building Nettle: ismaelvc@toybox ~> julia _ _ _ _(_)_ | A fresh approach to technical computing (_) | (_) (_) | Documentation: http://docs.julialang.org _ _ _| |_ __ _ | Type "help()" to list help topics | | | | | | |/ _` | | | | |_| | | | (_| | | Version 0.3.0-prerelease+1367 (2014-02-03 08:34 UTC) _/ |\__'_|_|_|\__'_| | Commit 793d769* (0 days old master) |__/ | i686-pc-linux-gnu julia> Pkg.update() INFO: Initializing package repository /home/ismaelvc/.julia/v0.3 INFO: Cloning METADATA from git://github.com/JuliaLang/METADATA.jl INFO: Updating METADATA... INFO: Computing changes... INFO: No packages to install, update or remove julia> Pkg.add("IJulia") INFO: Cloning cache of BinDeps from git://github.com/JuliaLang/BinDeps.jl.git INFO: Cloning cache of IJulia from git://github.com/JuliaLang/IJulia.jl.git INFO: Cloning cache of JSON from git://github.com/JuliaLang/JSON.jl.git INFO: Cloning cache of Nettle from git://github.com/staticfloat/Nettle.jl.git INFO: Cloning cache of REPLCompletions from git://github.com/loladiro/REPLCompletions.jl.git INFO: Cloning cache of URIParser from git://github.com/loladiro/URIParser.jl.git INFO: Cloning cache of ZMQ from git://github.com/JuliaLang/ZMQ.jl.git INFO: Installing BinDeps v0.2.12 INFO: Installing IJulia v0.1.1 INFO: Installing JSON v0.3.3 INFO: Installing Nettle v0.1.3 INFO: Installing REPLCompletions v0.0.0 INFO: Installing URIParser v0.0.1 INFO: Installing ZMQ v0.1.8 INFO: Building Nettle fish: Job 1, 'julia' terminated by signal SIGSEGV (Address boundary error) ismaelvc@toybox ~ [139]> Keno Fischer 2/3/14 Re: [julia-users] Re: Unable to install IJulia What version of LLVM is Arch using? Given their reputation, I can see that they may have switched to 3.4, where we're still experiencing problems. - show quoted text - João Felipe Santos 2/3/14 Re: [julia-users] Re: Unable to install IJulia I'm running Arch also, LLVM 3.4 is what we have in the official repositories. I always build Julia straight from the Git repo without using system libraries as it is prone to problems such as this one. Did you use any system libraries when building Julia yourself (instead of using the AUR pkgbuild)? -- João Felipe Santos - show quoted text - Ismael Venegas Castelló 2/3/14 I did try first to install manually, using make, I don't know if now I have a mess of libraries, should I remove every dependency with pacman? I will try again doing it manually and post back any issue. ismaelvc@toybox ~ [1]> pacman -Qs llvm local/clang 3.4-1 C language family frontend for LLVM local/llvm 3.4-1 Low Level Virtual Machine local/llvm-libs 3.4-1 Low Level Virtual Machine (runtime library) ismaelvc@toybox ~> João Felipe Santos 2/3/14 Re: [julia-users] Re: Unable to install IJulia You should not need to. A manual install should download, compile, and install all the dependencies in the julia directory, not the system directories. I have LLVM/clang 3.4 and lots of other libraries used by Julia on my system path and they do not seem to interfere in Julia's functionality. For IJulia, however, you will need to install IPython. I got it working with Arch's ipython2 package (you'll need to install python2-tornado and python2-zmq manually as they are not required by the ipython2 package), with Anaconda's IPython, and with a manually installed IPython2.0.0-dev Hope it helps! -- João Felipe Santos - show quoted text - Ismael Venegas Castelló 2/3/14 Ok I'm starting fresh, it seems its going to build just a few deps, so I imagine it detects the rest from packages installed by pacman, should I remove all the packages listed here installed by pacman too?: https://github.com/JuliaLang/julia#Required-Build-Tools-External-Libraries Here is the AUR PKGBUILD: https://aur.archlinux.org/packages/ju/julia-git/PKGBUILD ismaelvc@toybox ~/Devel> git clone git://github.com/JuliaLang/julia.git Cloning into 'julia'... remote: Reusing existing pack: 85027, done. remote: Counting objects: 14, done. remote: Compressing objects: 100% (14/14), done. remote: Total 85041 (delta 4), reused 0 (delta 0) Receiving objects: 100% (85041/85041), 29.58 MiB | 413.00 KiB/s, done. Resolving deltas: 100% (63564/63564), done. Checking connectivity... done. ismaelvc@toybox ~/Devel> ls julia/ ismaelvc@toybox ~/Devel> cd julia/ ismaelvc@toybox ~/D/julia (master)> ls base/ deps/ etc/ Makefile README.md test/ Windows.inc contrib/ DISTRIBUTING.md examples/ Make.inc README.windows.md ui/ CONTRIBUTING.md doc/ LICENSE.md NEWS.md src/ VERSION ismaelvc@toybox ~/D/julia (master)> make which: no gtar in (/usr/local/sbin:/usr/local/bin:/usr/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl) which: no gtar in (/usr/local/sbin:/usr/local/bin:/usr/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl) Submodule 'deps/Rmath' (git://github.com/JuliaLang/Rmath.git) registered for path 'deps/Rmath' Submodule 'deps/libuv' (git://github.com/JuliaLang/libuv.git) registered for path 'deps/libuv' Submodule 'deps/openlibm' (git://github.com/JuliaLang/openlibm.git) registered for path 'deps/openlibm' Submodule 'deps/openspecfun' (git://github.com/JuliaLang/openspecfun.git) registered for path 'deps/openspecfun' Submodule 'doc/juliadoc' (git://github.com/JuliaLang/JuliaDoc.git) registered for path 'doc/juliadoc' Cloning into 'deps/Rmath'... remote: Reusing existing pack: 332, done. remote: Total 332 (delta 0), reused 0 (delta 0) Receiving objects: 100% (332/332), 247.59 KiB | 321.00 KiB/s, done. Resolving deltas: 100% (217/217), done. Checking connectivity... done. Submodule path 'deps/Rmath': checked out '004e056e4562a8e8459b3d283f7de2f655f99a8b' Cloning into 'deps/libuv'... João Felipe Santos 2/3/14 Re: [julia-users] Re: Unable to install IJulia If you did not define any of the USE_SYSTEM_* flags when calling make, it will download and compile everything locally. You don't need to worry about removing system packages. -- João Felipe Santos - show quoted text - Ismael Venegas Castelló 2/3/14 This seems to be all I have installed: local/automake 1.14.1-1 (base-devel) A GNU tool for automatically creating Makefiles local/make 4.0-2 (base-devel) GNU make utility to maintain groups of programs local/perl 5.18.2-2 (base) A highly capable, feature-rich programming language local/sip 4.15.4-1 A tool that makes it easy to create Python bindings for C and C++ libraries ismaelvc@toybox ~ > pacman -Qs gcc local/gcc 4.8.2-7 (base-devel) The GNU Compiler Collection - C and C++ frontends local/gcc-fortran 4.8.2-7 Fortran front-end for GCC local/gcc-libs 4.8.2-7 (base) Runtime libraries shipped by GCC ismaelvc@toybox ~> pacman -Qs clang local/clang 3.4-1 C language family frontend for LLVM ismaelvc@toybox ~> pacman -Qs wget local/wget 1.15-1 A network utility to retrieve files from the Web ismaelvc@toybox ~> pacman -Qs curl local/curl 7.35.0-1 An URL retrieval utility and library ismaelvc@toybox ~> pacman -Qs m4 local/m4 1.4.17-1 (base-devel) The GNU macro processor ismaelvc@toybox ~> pacman -Qs patch local/diffutils 3.3-1 (base) Utility programs used for creating patch files local/kdesdk-kompare 4.12.1-1 (kde kdesdk) Diff/Patch Frontend local/patch 2.7.1-2 (base-devel) A utility to apply patch files to original sources local/speech-dispatcher 0.8-2 High-level device independent layer for speech synthesis interface ismaelvc@toybox ~> pacman -Qs readline local/perl 5.18.2-2 (base) A highly capable, feature-rich programming language local/readline 6.2.004-2 GNU readline library ismaelvc@toybox ~> pacman -Qs libuv ismaelvc@toybox ~ [1]> pacman -Qs femto ismaelvc@toybox ~ [1]> pacman -Qs openlibm ismaelvc@toybox ~ [1]> pacman -Qs open spec local/mesa 10.0.2-1 an open-source implementation of the OpenGL specification local/unixodbc 2.3.2-1 ODBC is an open specification for providing application developers with a predictable API with which to access Data Sources ismaelvc@toybox ~> pacman -Qs dsfmt ismaelvc@toybox ~ [1]> pacman -Qs blas local/blas 3.5.0-1 Basic Linear Algebra Subprograms ismaelvc@toybox ~> pacman -Qs openblas ismaelvc@toybox ~ [1]> pacman -Qs lapak ismaelvc@toybox ~ [1]> pacman -Qs mkl ismaelvc@toybox ~ [1]> pacman -Qs amos ismaelvc@toybox ~ [1]> pacman -Qs arpack local/arpack 3.1.2-2 Fortran77 subroutines designed to solve large scale eigenvalue problems ismaelvc@toybox ~> pacman -Qs fftw local/fftw 3.3.3-2 A library for computing the discrete Fourier transform (DFT) ismaelvc@toybox ~> pacman -Qs pcre local/pcre 8.34-2 A library that implements Perl 5-style regular expressions ismaelvc@toybox ~> pacman -Qs gmp local/gmp 5.1.3-2 A free library for arbitrary precision arithmetic ismaelvc@toybox ~> pacman -Qs mpfr local/mpfr 3.1.2.p5-1 Multiple-precision floating-point library ismaelvc@toybox ~> pacman -Qs suitesparce ismaelvc@toybox ~ [1]> pacman -Qs double conversion ismaelvc@toybox ~ [1]> Ismael Venegas Castelló 2/3/14 Re: [julia-users] Re: Unable to install IJulia I have installed all the opt-depends listed by pacman for using the notebook with ipython2, which are: Dep. opcionales : wxpython: needed for ipythonx and ipython-wx twisted: networking-related tasks python2-foolscap: for IPython's parallel computing features python2-pexpect: for irunner python2-nose: if you want to run IPython's test suite python2-pyqt4: for ipython-qtconsole python2-sip: for ipython-qtconsole python2-pygments: for ipython-qtconsole python2-pyzmq: for ipython-qtconsole python2-tornado: for ipython notebook python2-jinja: for ipython notebook haskell-pandoc: ipython notebook conversion I also have the same for ipython3, but in Arch python3 is default for "python" in /usr/bin. - show quoted text -