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2012-08-18 23:04:02 +0200 answered a question Can't get Sage to build: Clean install Ubuntu 12.04, iPython Error

benjaminfjones (44 mins ago) was right - OpenSSL was the problem - once OpenSSL was installed and I re-ran `make it worked. (sudo apt-get install libssl-dev).

For the benefit of anyone with this problem - the complete list of installed packages for my (apparently successful) build in Ubuntu 12.04 is as follows. Im sure these arent all necessary! (but this could be used in troubleshooting by generating a similar list with dpkg --get-selections and running the `diff command):

accountsservice install acl install acpi-support install acpid install activity-log-manager-common install activity-log-manager-control-center install adduser install adium-theme-ubuntu install aisleriot install alsa-base install alsa-utils install anacron install apg install app-install-data install app-install-data-partner install apparmor install appmenu-gtk install appmenu-gtk3 install appmenu-qt install apport install apport-gtk install apport-symptoms install apt install apt-transport-https install apt-utils install apt-xapian-index install aptdaemon install aptdaemon-data install apturl install apturl-common install aspell install aspell-en install at install at-spi2-core install avahi-autoipd install avahi-daemon install avahi-utils install bamfdaemon install baobab install base-files install base-passwd install bash install bash-completion install bc install bind9-host install binutils install bluez install bluez-alsa install bluez-cups install bluez-gstreamer install branding-ubuntu install brasero install brasero-cdrkit install brasero-common install brltty install bsdmainutils install bsdutils install build-essential install busybox-initramfs install busybox-static install bzip2 install ca-certificates install checkbox install checkbox-qt install cmap-adobe-japan2 install colord install command-not-found install command-not-found-data install compiz install compiz-core install compiz-gnome install compiz-plugins-default install compiz-plugins-main-default install compizconfig-backend-gconf install console-setup install consolekit install coreutils install cpio install cpp install cpp-4.6 install crda install cron install cryptsetup-bin install cups install cups-bsd install cups-client install cups-common install cups-filters install cups-ppdc install dash install dbus install dbus-x11 install dc install dconf-gsettings-backend install dconf-service install debconf install debconf-i18n install debianutils install deja-dup install desktop-file-utils install dictionaries-common install diffutils install dkms install dmidecode install dmsetup install dmz-cursor-theme install dnsmasq-base install dnsutils install doc-base install dosfstools install dpkg install dpkg-dev install duplicity install dvd+rw-tools install dvipng install e2fslibs install e2fsprogs install ed install eject install elyxer install emacs install emacs23 install emacs23-bin-common install emacs23-common install emacsen-common install empathy install empathy-common install enchant install eog install espeak install espeak-data install evince install evince-common install evolution-data-server install evolution-data-server-common install example-content install fakeroot install file install file-roller install findutils install firefox install firefox-globalmenu install firefox-gnome-support install firefox-locale-en install flashplugin-installer install folks-common install fontconfig install fontconfig-config install fonts-kacst install fonts-kacst-one install fonts-khmeros-core install fonts-lao install fonts-liberation install fonts-nanum install fonts-opensymbol install fonts-takao-pgothic install fonts-thai-tlwg install fonts-tlwg-garuda install fonts-tlwg-kinnari install fonts-tlwg-loma install fonts-tlwg-mono install fonts-tlwg-norasi install fonts-tlwg-purisa install fonts-tlwg-sawasdee install fonts-tlwg-typewriter install fonts-tlwg-typist install fonts-tlwg-typo install fonts-tlwg-umpush install fonts-tlwg-waree install foomatic-db-compressed-ppds install foomatic-db-engine install foomatic-filters install freepats install friendly-recovery install ftp install fuse install g++ install g++-4.6 install gcalctool install gcc install gcc-4.6 install gcc-4.6-base install gconf-service install gconf-service-backend install gconf2 install gconf2-common install gdb install gedit install gedit-common install genisoimage install geoclue install geoclue-ubuntu-geoip install geoip-database install gettext install gettext-base install gfortran install gfortran-4.6 install ghostscript install ghostscript-cups install ghostscript-x install ginn install gir1.2-appindicator3-0.1 install gir1.2-atk-1.0 install gir1.2-atspi-2.0 install gir1 ... (more)

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2012-08-18 20:39:52 +0200 commented question Can't get Sage to build: Clean install Ubuntu 12.04, iPython Error

When I do the the grep -li "^Error installing" thing on the logs the only package mentioned: sagenb-0.9.1.log.

2012-08-18 20:39:02 +0200 commented question Can't get Sage to build: Clean install Ubuntu 12.04, iPython Error

Not sure what you mean - I don't have a .ipython director that I see in my home directory.

2012-08-18 15:41:45 +0200 asked a question Can't get Sage to build: Clean install Ubuntu 12.04, iPython Error

I'm trying to get Sage to work on a clean install of Ubuntu 12.04 Desktop running through Virtualbox on Windows 7.

What am I missing? What have I done wrong?

I've seen a number of problems with iPython - I know Sage can conflict with iPython but does it happen with the default settings for Ubuntu?

Previously I was using Fedora and didn't have a problem...

Here's everything I've done:

  • Clean install Ubuntu 12.04
  • Download source

Here's most of the commands from my .bash_history

Additional package installs

sudo apt-get install tk8.5-dev
sudo apt-get install xdvi (error?)
sudo apt-get install dvipng
sudo apt-get install build-essential
sudo apt-get install xpdf
sudo apt-get install evince
sudo apt-get install make
sudo apt-get install m4
sudo apt-get install libgfortran3
sudo apt-get install texlive
sudo apt-get install tcl-dev
sudo apt-get install tcl8.5-dev
sudo apt-get install tcl8.5

Build commands:

tar xvf sage-5.2.tar




ImportError                               Traceback (most recent call last)

/home/justin/Downloads/sage-5.2/local/bin/<string> in <module>()

/home/justin/Downloads/sage-5.2/local/lib/python2.7/site-packages/sage/misc/ in <module>()
      6 ###########################################################################
----> 8 import sage.misc.interpreter
     10 import preparser

/home/justin/Downloads/sage-5.2/local/lib/python2.7/site-packages/sage/misc/ in <module>()
    104 import os
--> 105 import log
    106 import re

/home/justin/Downloads/sage-5.2/local/lib/python2.7/site-packages/sage/misc/ in <module>()
     64 import interpreter
---> 65 import latex
     66 import misc

/home/justin/Downloads/sage-5.2/local/lib/python2.7/site-packages/sage/misc/ in <module>()
     55 import types
---> 57 from misc import tmp_dir, graphics_filename
     58 import sage_eval
     59 from sage.misc.sage_ostools import have_program

/home/justin/Downloads/sage-5.2/local/lib/python2.7/site-packages/sage/misc/ in <module>()
   2162     return "0"*(size-len(str(s))) + str(s)
-> 2164 import
   2166 def embedded():

/home/justin/Downloads/sage-5.2/local/lib/python2.7/site-packages/sage/server/ in <module>()
     17 import sage.misc.pager
---> 19 import sage.misc.sagedoc as sagedoc
     20 import sage.misc.sageinspect as sageinspect

/home/justin/Downloads/sage-5.2/local/lib/python2.7/site-packages/sage/misc/ in <module>()
     38 from sage.misc.viewer import browser
     39 from sage.misc.misc import SAGE_DOC, tmp_dir
---> 40 from sagenb.misc.sphinxify import sphinxify
     41 import sage.version

ImportError: No module named sagenb.misc.sphinxify
WARNING: Failure executing code: 'import sage.misc.preparser_ipython;  sage.misc.preparser_ipython.magma_colon_equals=True'
ImportError                               Traceback (most recent call last)

/home/justin/Downloads/sage-5.2/local/lib/python2.7/site-packages/IPython/ipmaker.pyc in force_import(modname, force_reload)
     61         reload(sys.modules[modname])
     62     else:
---> 63         __import__(modname)

/home/justin/Downloads/sage-5.2/local/bin/ in <module>()
      1 import os
      2 if 'SAGE_CLEAN' not in os.environ:
----> 3     import sage.misc.misc ...
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2012-07-25 22:17:13 +0200 answered a question Can't Access Functions After Install R Additional Package

Turns out the step I was missing is that you must load the library using the r function r.library (i.e., r.library('SampleSizeMeans').

Therefore, step-by-step for loading and then using new R packages:

  1. Use r.install_packages('PackageName')
  2. Restart Sage
  3. Use r.library('PackageName') to load the package prior to use.

It's worth noting that although it recommends that you restart Sage, it seemed to work immediately for the packages I tried so it may not be strictly necessary which is very handy!

2012-07-25 21:07:20 +0200 asked a question Can't Access Functions After Install R Additional Package


I'm trying to install an additional package for R, "SampleSizeMeans." In the Notebook, I type r.install_packages('SampleSizeMeans') and it seems to install properly (output pasted below). Note I do this with "Sage" as the worksheet type at the top.

I've quit Sage completely and restarted the notebook, but none of the functions are available. I switch the Type in the Sage notebook to "R" and type "mu.acc(len=0.2, alpha=2, beta=2, n0=10)" (one of the examples) but it says "Error: could not find function "mu.acc".

Am I missing something or is this a bug?

Thanks very much,


0.00user 0.00system 0:00.00elapsed 0%CPU (0avgtext+0avgdata 2528maxresident)k 0inputs+0outputs (0major+204minor)pagefaults 0swaps

R version 2.14.0 (2011-10-31) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

options(repos=""); install.packages("SampleSizeMeans") trying URL '' Content type 'application/x-gzip' length 14807 bytes (14 Kb)

opened URL

downloaded 14 Kb

  • installing source package ‘SampleSizeMeans’ ... * R * preparing package for lazy loading * help ** installing help indices * building package indices ... * testing if installed package can be loaded

  • DONE (SampleSizeMeans)

The downloaded packages are in ‘/tmp/RtmpG4jlho/downloaded_packages’

Please restart Sage in order to use 'SampleSizeMeans'.

2012-07-22 15:53:12 +0200 commented answer Plot Series of 3D Direction Vectors (Not All from Origen)

Thanks very much!

2012-07-22 14:52:05 +0200 asked a question Plot Series of 3D Direction Vectors (Not All from Origen)


I'm trying to plot a series of vectors. I've pasted what I have below. The problem is that I want to plot the second vector, starting from the end of the first vector. If I run the commands below, I get two vectors plotted as I want (with arrows) but they are both from the origin.

I tried looking at MATPLOTLIB to see what to do but I got stuck.

Is there an easy way to plot a series of vectors in the way that I want?

aPlot=plot(a, legend_label='Vector a')
bPlot=plot(b, legend_label='Vector b')