I'm trying to install vim and nvim as a replacement for Notational Velocity. I recently migrated to Ubuntu (14.04) and I'm very new to how everything works. The instructions for installing nvim are kind of elliptic and not entirely clear to me as a beginner. I manage to get it running if I enter vim and then type :Nvim inside the directory where I store my .txt notes. However, the notes aren't visible in nvim and here's where I run into trouble. As a beginner I simply do not understand the instructions regarding PATH and :python that are given on the installation page. I've tried (successfully, I think) to install xapian as well (after having installed vim) but nothing changed. That is, I cannot specify a PATH for my nvim and I cannot get the nvim script to work as a command anywhere in the terminal.
More consequentially, when I type
:python nvimdb.rebuild_database()
inside vim, I get:
Traceback (most recent call last):
File "", line 1, in
NameError: name 'nvimdb' is not defined
What I would like to ask for are step by step instructions for making nvim work with an existing library of .txt notes targeted at the vim and linux novice.
The program looks great and appears to be exactly what I need for my note taking needs, and I would really appreciate your help! Thank you so much.
I believe this is probably because you haven't installed the xapian library as that is a required mentioned by nvim. You need to install the package xapian-core I believe, you can do that in ubuntu with something like this : sudo apt-get install xapian-core
Related
I'm trying to use the Python interface for LHAPDF, but I receive the following error message:
Traceback (most recent call last):
File "test.py", line 2, in <module>
import lhapdf
ImportError: /home/n17182559/LHAPDF/lib/python2.7/site-packages/lhapdf.so: undefined symbol: _ZN6LHAPDF6ConfigD1Ev
I'm running on Ubuntu 17.04, using Python 2.7, have Boost installed and have a working C++ compiler (g++). I believe I have successfully installed LHAPDF, as I followed the instructions on their website and got no error message (only warnings that auto_ptr is deprecated, but I don't think I have control over that). I did add the ~/LHAPDF/lib/python2.7/sitepackages/ directory to $PYTHONPATH and ~/LHAPDF/bin/ directory to $PATH. I am using LHAPDF 6.1.6 (latest version as of writing this).
I get this error message from a test.py file that merely contains
#!/usr/bin/python
import lhapdf
If it can help you help me, I have found someone with a similar problem, but the cause seems not to be the same thing (I don't have Anaconda installed). As they solved their problem by removing Anaconda from $PATH, here are my $PATH and $PYTHONPATH as they might be the source of the problem (although I don't see how):
$PATH
/home/n17182559/LHAPDF/bin:/opt/applications/geant4/geant4.10.02-install/bin:/home/n17182559/ROOT/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:
$PYTHONPATH
/home/n17182559/ROOT/lib:/home/n17182559/LHAPDF/lib/python2.7/site-packages:
Hope you guys can help!
I solved it (with external help), if anyone wants the solution. The problem was that the main LHAPDF lib directory was not linked to my LD_LIBRARY_PATH. This command line solved it:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/LHAPDF/lib/libLHAPDF.so
(which I added to my ~/.bashrc file).
I can't speak to your specific problem, but when I get this class of error, it stems from a version mismatch between packages: lhapdf depends on another package to define that arcane "semi-hidden" symbol, but the package on which it depends is of a version different from the one expected; the older/newer version doesn't provide that symbol.
It is a version mismatch (of Python), which is likely caused by upgrading Python after LHAPDF is installed.
Therefore you may have to reinstall LHAPDF, or you could install a second LHAPDF if you use two versions of Python (as of now I am not aware of a solution other than this).
Let us assume you use LHAPDF of version 6.2 or higher, which is much simpler. First you would like to set the path in your shell profile so that it points to the version of Python you want to install LHAPDF for. For bash, you could do
export PATH=path/to/python
then you would like to follow the instruction and do
tar xf LHAPDF-6.X.Y.tar.gz
cd LHAPDF-6.X.Y
./configure --prefix=/path/for/installation
make
make install
After the installation is done, you can add LHAPDF to the path by
export PYTHONPATH=path/to/lhapdf/lib/pythonx.y/site-packages/
export LD_LIBRARY_PATH=path/to/lhapdf/lib
export PATH=path/to/lhapdf/bin/:$PATH
export LHAPDF_DATA_PATH=path/to/lhapdf/share/LHAPDF
I am trying to install python through cygwin on a windows machine in order to make use of a statistical program that can only be implemented using python in a linux environment.
I have run setup-x86_64.exe and installed all python related cygwin packages in an attempt to install python, but when I open a terminal and type python I just get
$ python
-bash: python: command not found
which is the same for all python commands I try so clearly the installation has not occurred. However, I have found a path to Python-2.7.9 which appears to contain the files required to build python from source.
When I run ./configure it is successful, but when I then input make it fails due to:
File "build/temp.cygwin-1.7.35-x86_64-2.7/libffi/fficonfig.py", line 33, in <module>
ffi_sources += ffi_platforms['X86_WIN64']
KeyError: 'X86_WIN64'
Makefile:488: recipe for target 'sharedmods' failed
make: *** [sharedmods] Error 1
Anyone know why make won't work?
The options in ./configure --help are unfamiliar to me, could any of these options allow for successful installation?
Any ideas would be greatly appreciated, thank you.
Cygwin comes with an installer, called setup.exe or setup-x86_64.exe. Just run it and type python to the search box. Then let it install it for you.
python language interpreter is the basic package you need.
So, this question is 3 years old, but this error still happens with most recent versions of Python 2 (tested with 2.7.13 and 2.7.15)
I was able to get python to build by modifying the following file in the build directory.
--- build/temp.cygwin-2.11.1-x86_64-2.7/libffi/fficonfig.py~ 2018-11-03 14:51:53.290000000 -0400
+++ build/temp.cygwin-2.11.1-x86_64-2.7/libffi/fficonfig.py 2018-11-03 14:53:41.793000000 -0400
## -9,6 +9,7 ##
'X86': ['src/x86/ffi.c', 'src/x86/sysv.S', 'src/x86/win32.S'],
'X86_FREEBSD': ['src/x86/ffi.c', 'src/x86/freebsd.S'],
'X86_WIN32': ['src/x86/ffi.c', 'src/x86/win32.S'],
+ 'X86_WIN64': ['src/x86/ffi.c', 'src/x86/win64.S'],
'SPARC': ['src/sparc/ffi.c', 'src/sparc/v8.S', 'src/sparc/v9.S'],
'ALPHA': ['src/alpha/ffi.c', 'src/alpha/osf.S'],
'IA64': ['src/ia64/ffi.c', 'src/ia64/unix.S'],
The source files, in particular src/x86/win64.S, are present in the source tree. For some reason, ./configure does not seem to be properly adding the option to the dictionary in the fficonfig.py file, which causes the KeyError posted in the question. After making this modification, make and make install completed successfully and I was able to install an alternate version of python in addition to the normal Cygwin package.
I'm not yet sure why this happens, but I thought I would attempt to provide a solution to the question actually asked rather than just telling the asker to install a pre-compiled version using the package manager.
Since building Python from source was said to be a bad idea, I assumed my Cygwin was broken. I attempted to uninstall Cygwin following the instructions on the Cygwin website, but I was unable to remove it due to permission difficulties (I use a university-supplied Windows machine). My last resort was to run the Cygwin installation wizard setup-x86_64.exe and uninstall all packages, then run the wizard once more and select the necessary packages again as if starting from new. Miraculously, installing the required packages from scratch solved the problem and I am now running Python through my Cygwin terminal with no errors.
If you want to run Python on Cygwin, you might need to build it from source.
download the source
unpack it to the directory you could delete later, eg: build
run Cygwin, type: cd /path/to/build
run ./configure --help and read the help about the options you'll need
./configure #options
make
I am trying to install Jedi for emacs using marmalade package manager by following instructions here -- http://tkf.github.io/emacs-jedi/latest/. The package manger installs Jedi along with its dependencies. But I cannot install python server using:
M-x jedi:install-server
because that command is not available even after restarting emacs after jedi installation. The only available commands are:
Possible completions are:
jedi:ac-setup jedi:complete
jedi:dot-complete jedi:get-in-function-call
jedi:goto-definition jedi:goto-definition-next
jedi:goto-definition-pop-marker jedi:setup
jedi:show-doc jedi:show-jedi-version
jedi:start-dedicated-server jedi:stop-server
jedi:toggle-debug-server
My .emacs has the following:
(autoload 'jedi:setup "jedi" nil t)
(add-hook 'python-mode-hook 'jedi:setup)
(setq jedi:complete-on-dot t)
I am using emacs on Mac OS X.
At this current state when I open any python file (I use python 2.7), I see the following appear automatically in the minibuffer:
deferred error : (error Server may raise an error : Traceback (most recent call last):
File "/Users/t_nithyanandan/.emacs.d/elpa/jedi-0.1.2/jediepcserver.py", line 302, in <module>
main()
File "/Users/t_nithyanandan/.emacs.d/elpa/jedi-0.1.2/jediepcserver.py", line 298, in main
jedi_epc_server(**vars(ns))
File "/Users/t_nithyanandan/.emacs.d/elpa/jedi-0.1.2/jediepcserver.py", line 210, in jedi_epc_server
import_jedi()
File "/Users/t_nithyanandan/.emacs.d/elpa/jedi-0.1.2/jediepcserver.py", line 249, in import_jedi
import jedi
ImportError: No module named jedi
)
I tried installing jedi using other methods such as el-get and also manually but those seem to not even go this far. I see that the jedi commands available are even lesser than listed above.
Could someone help point out what I am missing?
Thanks.
Edit: The primary purpose I would like to use Jedi is to use auto-completion features for python programming although I believe Jedi has many powerful features. For such a purpose, is the python server essential or could one work around it? Eventually, of course, I'd like to take advantage of many more features in Jedi.
I managed to fix the problem thanks to help from Chris and syohex from emacs-jedi github. Credit goes to them in tracing this to Jedi version.
I am just linking the discussion on emacs-jedi issue #177 and pasting the workaround I found including other problems I encountered along the way.
I was using the Marmalade version which installs a much older version. So I uninstalled jedi and associated dependencies. I set my repository to MELPA and installed a much more recent version of jedi. This made the command
M-x jedi:install-server
available which wasn't the case earlier.
However, issuing that command gave an error
python-environment--make-with-runner: Program named "virtualenv" does not exist.
I made sure I added the location of virtualenv to PATH in my .bashrc.
So I looked up emacs-jedi issue #158 which suggests installing exec-path-from-shell. I installed it from MELPA and added the lines
(when (memq window-system '(mac ns))
(exec-path-from-shell-initialize))
following instructions.
Restarting Emacs with the above lines gave an error:
Symbol's function definition is void: exec-path-from-shell-initialize
So I looked up Autoload issue #3 under exec-path-from-shell development (the link to this can be found in the link for emacs-jedi issue #177). Following one of the solutions, I restarted my computer, uninstalled and reinstalled exec-path-from-shell which magically did solve the problem that existed before the reboot.
Now I checked in emacs if virtualenv could be found using
M-! which virtualenv
It gave the right location.
Then I ran:
M-x jedi:install-server
which now seemed to run without trouble. The first time, there were messages about setting up a
default virtual environment under
/Users/XXX/.emacs.d/.python-environments
besides
Running: pip install --upgrade /Users/XXX/.emacs.d/elpa/jedi-20140321.1323/...Done
but in subsequent trials only the pip upgrade message was displayed.
Having seen that the server installed without trouble, I closed and restarted Emacs and opened a python script file. When I started editing, I got these messages in the minibuffers:
Error (jedi): Failed to start Jedi EPC server.
*** You may need to run "M-x jedi:install-server". ***
This could solve the problem especially if you haven't run the command yet
since Jedi.el installation or update and if the server complains about
Python module imports.
and
auto-complete error: (error Server may raise an error. Use "M-x epc:pop-to-last-server-process-buffer RET" to see full traceback:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can't open file '/Users/XXX/.emacs.d/elpa/jedi-0.1.2/jediepcserver.py': [Errno 2] No such file or directory`
)
Thus, I realized that I have to issue the command:
M-x jedi:install-server
every time I start Emacs before opening any python file. Then I was finally able to see the auto-completion features being available during editing.
Though I can run the above command every time manually, I wanted to automate it from my .emacs whenever Emacs is launched. It turned out that I had the following line in my .emacs
(setq jedi:server-command (list "python" "/Users/XXX/.emacs.d/elpa/jedi-0.1.2/jediepcserver.py"))
Upon removing this line in my .emacs, the problem went away and jedi is functional now.
Marmalade currently contains jedi version 0.1.2, but you're looking at documentation for version 0.2.0alpha2.
The documentation for 0.1.2 has different instructions:
package.el (Marmalade or MELPA)
You can install Jedi.el using package.el interface from Marmalade or MELPA. As package.el does not support installing non-elisp packages, you need to install Python part manually (see the next section).
And then in that next section, the imporant bit:
Install Jedi and python-epc by
make requirements (no need for root privileges) or
pip install -r requirements.txt if you want to determine where to install Python modules. You need root privileges (i.e., sudo) to install it in system directory.
You should be able to do make requirements from the ~/.emacs.d/elpa/jedi-0.1.2/ directory, but something like pip install epc jedi should work too.
I'm fairly new to programming. I'm trying to install biopython on mac os x 10.5.
This is what I did so far. 1. installed xcode 2. installed numpy 3. ran these commands in terminal python setup.py build python setup.py test
test reported back one fail.
test_Tutorial ... FAIL
ERROR: Run tutorial doctests.
Traceback (most recent call last): File "test_Tutorial.py", line 152, in test_doctests ValueError: 4 Tutorial doctests failed: test_from_line_05671, test_from_line_06030, test_from_line_06190, test_from_line_06479
Thanks for any help or advice.
That file test_Tutorial.py runs marked examples in the source for the main Biopython Tutorial and Cookbook ( http://biopython.org/DIST/docs/tutorial/Tutorial.html / http://biopython.org/DIST/docs/tutorial/Tutorial.pdf ) to check the examples work as expected. Internally this uses the same library as Python's doctest examples.
The fact that test_Tutorial.py failed is probably a harmless issue with a couple of examples.
Which version of Biopython are you using? If this was an official release that failure is unexpected. If it was a snapshot from the git repository then that is unfortunate. If you are curious, you could try this to see more information:
$ cd Tests
$ python test_Tutorial.py
This kind of issue might be more easily discussed on the Biopython mailing list http://biopython.org/wiki/Mailing_lists
I've found that the easiest way to set up a good programming environment is to use MacPorts, as it has a great way of ensuring that all dependencies are satisfied when installing things. You'll need to be familiar with Terminal and the command line, though.
Install MacPorts for OSX 10.5. Read the documentation too.
Restart.
Open Terminal.app and enter sudo port selfupdate to make sure the portfile definitions are up to date.
Run sudo port install py27-biopython to install the latest version of Python 2 (2.7.3), numpy, and biopython. This will take a while.
Run echo $PATH and make sure that /opt/local/bin and /opt/local/sbin` are at the beginning. They should be.
Run which python and ensure it returns /opt/local/bin/python. If it doesn't, run sudo port install python_select and follow its instructions to select your default python version.
Hopefully, at this point you can run python to enter the interactive interpreter, and import Bio won't give any errors.
Good luck!
I'm using ubuntu x64, after two days and searching all the net, still i've not been able to install Megam,
i've read all information in this page http://www.cs.utah.edu/~hal/megam/
and installed x64 version of o'calm from http://packages.ubuntu.com/precise/ocaml
but when i want to use "megam" as a classifier in python, it says:
"NLTK was unable to find the megam file! Use software specific
configuration paramaters or set the MEGAM environment variable.
could anybody tell me how can i install and make use of it in python?
i've downloaded "ocaml-3.12.1.tar.gz" but the "make" command doesn't work (as it's said in its readme).
i've downloaded "megam_i686.opt" too, but it's not executable and i cannot run it
any help?
thanks in advance
For the future users:
megam is now available on MAC through brew:
$brew tap homebrew/science
$brew install megam
Use config_megam() to tell NLTK where the Megam executable is located. See: http://nltk.googlecode.com/svn/trunk/doc/api/nltk.classify.megam-module.html for details and documentation.
You also need to build MEGAM with the right 32/64 bit setting for your system. "megam_i686.opt" is for x86 iirc, so you should compile it for 64 bit. It is a while since I did this, but a simple build on an x64 system was all I needed: "Make doesn't work" is not very useful: I'm sure it gave you a few error messages...? Probably paths not set or are read only?
Edit: Looks like the above link is currently broken. The main Megam site can be found at:
http://www.umiacs.umd.edu/~hal/megam/
although it hasn't been updated for a while.
Answer given by Hugh Perkins, helped me resolve the issue (due to low reputation can't add a comment to that answer). After downloading the zip file (from http://thinknook.com/wp-content/uploads/2012/11/MEGAM.zip), I needed to tell python where it was, and that was done by adding it in os.environ as:
os.environ["MEGAM"] = '<<Complete path followed by file name>>/megam-64'
I downloaded from http://thinknook.com/wp-content/uploads/2012/11/MEGAM.zip , which was linked from http://thinknook.com/nltk-megam-maximum-entropy-library-on-64-bit-linux-2012-11-27/ This worked ok for me, on ubuntu 14.04
I manged to get megam to run on my docker instance running debian 9.7 following the steps below. Based on steps for MacOS install steps suggested by Jack Hong here.
apt-get install make
apt-get install ocaml-nox (or apt-get install ocaml, if you want x window support)
download source from here
unzip source creating a megam_0.92 directory
Edit the Makefile in megam_0.92 and make the following changes. (The
first change was already done in my particular instance):
WITHCLIBS=-I /usr/local/lib/ocaml/caml
WITHSTR =str.cma -cclib -lcamlstr
Save the changes and run make inside your megam_0.92 directory
add nltk.config_megam('//megam_0.92/megam') to your script and all should be well.