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sciruby's Introduction

SciRuby meta gem Build Status

Tools for Scientific Computing in Ruby

Description

This gem acts as a meta gem which collects and provides multiple scientific gems, including numeric and visualization libraries.

Getting started

Installation:

gem install sciruby
gem install sciruby-full

If you want to have a full-blown installation, install sciruby-full.

Start a notebook server:

iruby notebook

Enter commands:

require 'sciruby'
# Scientific gems are auto loaded, you can use them directly!
plot = Nyaplot::Plot.new
sc = plot.add(:scatter, [0,1,2,3,4], [-1,2,-3,4,-5])

Take a look at gems.yml or the list of gems for interesting gems which are included in sciruby-full.

License

Copyright (c) 2010 onward, The Ruby Science Foundation.

All rights reserved.

SciRuby is licensed under the BSD 3-clause license. See LICENSE for details.

Donations

Support a SciRuby Fellow via Pledgie.

sciruby's People

Contributors

agarie avatar audy avatar ck3gemproject avatar jtprince avatar mananshah99 avatar matthewrobertson avatar minad avatar translunar avatar

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sciruby's Issues

Sciruby installation failed on macOS Mojave

I am trying to install SciRuby on Mac machine but the installation failed. I have searched this issue but didn't help much and the issued were related to a different error.

when I used the command

gem install sciruby
Successfully installed sciruby-0.2.11
Parsing documentation for sciruby-0.2.11
Done installing documentation for sciruby after 0 seconds
1 gem installed

It successfully installed it. But when I used the command

gem install sciruby-full

I get this error

Building native extensions. This could take a while...
ERROR:  Error installing sciruby-full:
	ERROR: Failed to build gem native extension.

    current directory: /Library/Ruby/Gems/2.6.0/gems/ruby-minisat-2.2.0/ext/minisat
/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby -I /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0 -r ./siteconf20191203-21492-19ae7a3.rb extconf.rb
checking for -lminisat... no
checking for -lstdc++... yes
creating Makefile

current directory: /Library/Ruby/Gems/2.6.0/gems/ruby-minisat-2.2.0/ext/minisat
make "DESTDIR=" clean

current directory: /Library/Ruby/Gems/2.6.0/gems/ruby-minisat-2.2.0/ext/minisat
make "DESTDIR="
compiling minisat.c
compiling minisat-wrap.cpp
In file included from minisat-wrap.cpp:35:
In file included from ./../../minisat/minisat/core/Solver.h:24:
./../../minisat/minisat/mtl/Vec.h:99:97: warning: '&&' within '||' [-Wlogical-op-parentheses]
    if (add > INT_MAX - cap || ((data = (T*)::realloc(data, (cap += add) * sizeof(T))) == NULL) && errno == ENOMEM)
                            ~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
./../../minisat/minisat/mtl/Vec.h:99:97: note: place parentheses around the '&&' expression to silence this warning
    if (add > INT_MAX - cap || ((data = (T*)::realloc(data, (cap += add) * sizeof(T))) == NULL) && errno == ENOMEM)
                               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
In file included from minisat-wrap.cpp:35:
In file included from ./../../minisat/minisat/core/Solver.h:27:
./../../minisat/minisat/utils/Options.h:63:44: warning: '&&' within '||' [-Wlogical-op-parentheses]
            return test1 < 0 || test1 == 0 && strcmp(x->type_name, y->type_name) < 0;
                             ~~ ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./../../minisat/minisat/utils/Options.h:63:44: note: place parentheses around the '&&' expression to silence this warning
            return test1 < 0 || test1 == 0 && strcmp(x->type_name, y->type_name) < 0;
                                           ^
                                (                                                   )
In file included from minisat-wrap.cpp:35:
In file included from ./../../minisat/minisat/core/Solver.h:28:
./../../minisat/minisat/core/SolverTypes.h:50:16: error: friend declaration specifying a default argument must be a definition
    friend Lit mkLit(Var var, bool sign = false);
               ^
./../../minisat/minisat/core/SolverTypes.h:58:14: error: friend declaration specifying a default argument must be the only declaration
inline  Lit  mkLit     (Var var, bool sign) { Lit p; p.x = var + var + (int)sign; return p; }
             ^
./../../minisat/minisat/core/SolverTypes.h:50:16: note: previous declaration is here
    friend Lit mkLit(Var var, bool sign = false);
               ^
2 warnings and 2 errors generated.
make: *** [minisat-wrap.o] Error 1

make failed, exit code 2

Gem files will remain installed in /Library/Ruby/Gems/2.6.0/gems/ruby-minisat-2.2.0 for inspection.
Results logged to /Library/Ruby/Gems/2.6.0/extensions/universal-darwin-19/2.6.0/ruby-minisat-2.2.0/gem_make.out

I am using

ProductName: Mac OS X
ProductVersion: 10.15.1
ruby 2.6.3p62 (2019-04-16 revision 67580) [universal.x86_64-darwin19]
Apple clang version 11.0.0 (clang-1100.0.33.12)

feature request - move development discussion to Gitter

Since development is done on GitHub, I suggest using https://gitter.im/home/ as a discussion platform. It's very similar to Slack but without the limits on the number of users or messages. The Jupyter project is very active there and Daru has a "room" there as well (https://gitter.im/v0dro/daru). Like Slack, it offers a great platform for developers and users to communicate in real-time. A room could be created for each SciRuby repo or more if needed.

NMatrix::IO::MATLAB, parsing doubles

Hi, I tried loading some of my mat data like this:

require "nmatrix"
NMatrix::IO::Matlab::load_mat("r03_12_1.mat")

I was getting some strange values back, so I used some dummy data just for testing purposes. It seems that everything is fine as long as the original data only have integers, but as soon as any doubles are introduced, I get weird results.

For example, #load_mat is showing -1.5423487136706484e-180, but in MATLAB it's 1.1. Not sure if something is buggy or if I'm just missing something obvious.

Original data were from:

  • 64-bit Win7
  • MATLAB R2012a

Trying to parse the data on:

  • 64-bit Arch Linux
  • ruby 1.9.3-p286 rev 37165
  • nmatrix 0.0.2

Thanks!

public code

Thanks for initiating this project. It is much needed!
(I am a bioinformaticist using ruby)

I'm a bit surprised by the following statement in the manifesto: "Prime Directive
All published results obtained using our code must include online publication of any and all source code using our libraries. (This refers not to the constituent parts, but to SciRuby as a whole.)"

I appreciate the effort at promoting open source code. But with such strong wording I think you may alienate some users.
For example, will pharma company X ban ruby because it doesn't want to have to publish the code it uses for its internal LIMS?

Gemfile: Repeated Code

The installation warning caused by some repeated code

"Your Gemfile lists the gem hoe (~> 2.12) more than once.
You should probably keep only one of them.
While it's not a problem now, it could cause errors if you change the version of just one of them later."

I have already created patch to fix this problem and pasted it to a gist though I did this locally.

Would it be better to clone this repository and make a pull request after applying the patch?

sciruby-full fails to install on Ubuntu 18.04

Here's the log https://gist.github.com/lokeshh/2965832ed4f1cb718723bfe2b709a6af

The Dockerfile I used:

FROM jupyter/base-notebook:latest

USER root

RUN apt-get update && \
    apt-get install -y build-essential \
        ruby2.5 ruby2.5-dev libzmq3-dev gnuplot-nox libgsl-dev libtool autoconf make \
        automake zlib1g-dev libsqlite3-dev libmagick++-dev imagemagick \
        libatlas-base-dev g++ libczmq-dev libffi-dev libtool-bin cmake git && \
        apt-get clean

# See https://github.com/methodmissing/rbczmq/issues/64
RUN CPPFLAGS='-Wno-error=deprecated-declarations' gem install rbczmq -v '1.7.9'

RUN gem update --no-document --system && gem install --no-document sciruby-full

USER $NB_UID

RUN iruby register --force

COPY . .

ENTRYPOINT jupyter-notebook

It seems to me the problem is with gsl gem.

GSoC related links in Wiki need to be updated

Since the GSoC 2016 is coming, the GSoC 2014 links in the Wiki's home need to be updated.
Also the Ideas Page link in GSoC 2016 Student Application page incorrectly points to the GSoC 2014 one, which needs to be fixed.

Complete set of common probability distributions

Claudio Bustos' distribution gem supplies the probability distributions for SciRuby.

Some of these have already been implemented (e.g., normal, chisquare, hypergeometric, logistic, F, exponential, binomial, bivariate normal, Poisson, Student's t, beta, gamma).

Others have not. For example, multivariate normal and lognormal are both needed.

See a list of already-implemented distributions. Make sure to look at existing distributions for a template. The goal is to eventually implement each in Java, pure Ruby, and C (i.e., GSL or statistics2).

One difficulty is license compatibility. If code is GPLed, it cannot go directly into SciRuby. Claudio's distribution gem is currently under the GPL, mainly because some of the distributions are derived from GSL code (which is itself GPL). It would be best to rewrite those distributions (eventually) based on academic papers or other material that isn't subject to the GPL, because we want to be moving toward BSD/MIT compatibility.

This goes for new distributions as well. If you can only get code from GSL, see if you can reach out to the original author of the code in question. Find out how he or she would feel about us incorporating it into SciRuby under a more liberal license. Please document any conversations you may have, particularly if you're able to reach an author and he or she gives permission.

One idea for finding a list of common probability distributions: seach arxiv.org for usage of the names of distributions, like so:
https://www.google.com/search?q=site%3Aarxiv.org+%22gamma+distribution%22

Gamma distribution is found 2500 times, but Poisson distribution is found over 10,000 times. You could use this to get an idea which distributions are most utilized.

Improvements needed for SciRuby::Plotter continuous evaluation

Continuous evaluation works fairly well if you're only dealing with one source file (call it A), but it breaks if your source file requires another (let's call that B). Specifically, changes to B don't trigger a plot update. You can force one with changes to A, but changes to B won't be included since B has already been required. In such a case you have to totally restart the plotter, which is not how it should be.

Additionally, the backtrace display for the plotter is totally borked. It was badly written to begin with. It cuts off certain error messages. Some are too long to display in an alert box. Perhaps a console of some sort is needed.

Interactive, 3D plots

Rubyvis is based on Protovis, which allows for a certain level of user interaction. Unfortunately, it's not clear how Rubyvis can be interactive in a way that is portable.

Let's say you render an SVG in SciRuby::Plotter. You could build a custom SVG rendering library which might allow elements to be re-sized or moved. But what if you wanted to display that SVG in a web browser? The interactive portion would be lost.

Alternatively, assume you render an SVG and send it to a browser, and then write Javascript to enable interactivity. Same problem as before, but in reverse: now you can't get the interactivity in SciRuby::Plotter, which doesn't understand Javascript. Plus, the user now has to write in Ruby and Javascript, which is annoying.

There is likely no easy solution to this sort of problem, short of finding a way to interpret Ruby in a web browser. But I include it in the issue tracker for either (a) that day when someone really wants a challenge, or (b) a future redesign of plotting.

Relatedly, Protovis has limited 3D capabilities. Perhaps someone can come up with a solution that enables rendering of 3D plots, written in pure Ruby, in a web browser.

Save and load .mat files (from Matlab)

SciRuby needs support for saving and loading .mat files, which are created by Matlab.

The framework already exists in the sparse branch of the repository (please ignore the sparse_matrix stuff, which is only there for testing purposes). In fact, .mat v5 loading is already mostly working, or appears to. It shouldn't take more than a little more work to get v5 saving to function properly.

  • MatFile5Reader needs to be renamed to MatFile5IO, probably.
  • The write routines for MatFile5Reader need to be fixed.
  • MatFile4Reader/MatFile4IO needs to be written.
  • Need to clean up the source (and document) a bit.

Originally I tried to derive it directly from SciPy. That won't work. The old SciPy code may need to be cleaned a bit.

Linear Equations

Those are use widely in science and I believe sciruby needs them too. I have a code, which can be rewritten to be used in sciruby for gauss method, lu decomposition, choleski decomposition, conjugate gradient method and preconditioned conjugate gradient method.

failed gem install sciruby

I have no idea why built failed. Could anyone please help me what failed and how to fix this issue?

โžœ  ~  gem install sciruby-full
Building native extensions.  This could take a while...
ERROR:  Error installing sciruby-full:
    ERROR: Failed to build gem native extension.

    /home/cooldudeabhi/.rvm/rubies/ruby-2.2.3/bin/ruby -r ./siteconf20151217-4634-15xzki5.rb extconf.rb
using C++ standard... c++11
g++ reports version... 5.2.1-22ubuntu2)
checking for main() in -lclapack... no
checking for main() in -llapack... no
checking for main() in -lcblas... no
checking for main() in -latlas... no
checking for atlas/cblas.h... no
checking for cblas.h... no
checking for clapack.h... no
checking for clapack_dgetrf() in atlas/clapack.h... no
checking for clapack_dgetri() in atlas/clapack.h... no
checking for dgesvd_() in clapack.h... no
checking for cblas_dgemm() in cblas.h... no
creating nmatrix_config.h
creating Makefile

make "DESTDIR=" clean

make "DESTDIR="
compiling nmatrix.cpp
In file included from nmatrix.cpp:59:0:
math/math.h:128:29: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline void syrk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                             ^
math/math.h:128:59: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline void syrk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                                                           ^
math/math.h:128:87: error: use of enum โ€˜CBLAS_TRANSPOSEโ€™ without previous declaration
 inline void syrk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                                                                                       ^
math/math.h:134:29: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline void herk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                             ^
math/math.h:134:59: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline void herk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                                                           ^
math/math.h:134:87: error: use of enum โ€˜CBLAS_TRANSPOSEโ€™ without previous declaration
 inline void herk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                                                                                       ^
math/math.h:140:29: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline void syrk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                             ^
math/math.h:140:59: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline void syrk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                                                           ^
math/math.h:140:87: error: use of enum โ€˜CBLAS_TRANSPOSEโ€™ without previous declaration
 inline void syrk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                                                                                       ^
math/math.h: In function โ€˜void nm::math::syrk(int, int, int, int, int, const DType*, const DType*, int, const DType*, DType*, int) [with DType = float]โ€™:
math/math.h:142:70: error: โ€˜cblas_ssyrkโ€™ was not declared in this scope
   cblas_ssyrk(Order, Uplo, Trans, N, K, *alpha, A, lda, *beta, C, ldc);
                                                                      ^
math/math.h: At global scope:
math/math.h:146:29: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline void syrk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                             ^
math/math.h:146:59: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline void syrk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                                                           ^
math/math.h:146:87: error: use of enum โ€˜CBLAS_TRANSPOSEโ€™ without previous declaration
 inline void syrk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                                                                                       ^
math/math.h: In function โ€˜void nm::math::syrk(int, int, int, int, int, const DType*, const DType*, int, const DType*, DType*, int) [with DType = double]โ€™:
math/math.h:148:70: error: โ€˜cblas_dsyrkโ€™ was not declared in this scope
   cblas_dsyrk(Order, Uplo, Trans, N, K, *alpha, A, lda, *beta, C, ldc);
                                                                      ^
math/math.h: At global scope:
math/math.h:152:29: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline void syrk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                             ^
math/math.h:152:59: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline void syrk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                                                           ^
math/math.h:152:87: error: use of enum โ€˜CBLAS_TRANSPOSEโ€™ without previous declaration
 inline void syrk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                                                                                       ^
math/math.h: In function โ€˜void nm::math::syrk(int, int, int, int, int, const DType*, const DType*, int, const DType*, DType*, int) [with DType = nm::Complex<float>]โ€™:
math/math.h:154:68: error: โ€˜cblas_csyrkโ€™ was not declared in this scope
   cblas_csyrk(Order, Uplo, Trans, N, K, alpha, A, lda, beta, C, ldc);
                                                                    ^
math/math.h: At global scope:
math/math.h:158:29: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline void syrk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                             ^
math/math.h:158:59: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline void syrk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                                                           ^
math/math.h:158:87: error: use of enum โ€˜CBLAS_TRANSPOSEโ€™ without previous declaration
 inline void syrk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                                                                                       ^
math/math.h: In function โ€˜void nm::math::syrk(int, int, int, int, int, const DType*, const DType*, int, const DType*, DType*, int) [with DType = nm::Complex<double>]โ€™:
math/math.h:160:68: error: โ€˜cblas_zsyrkโ€™ was not declared in this scope
   cblas_zsyrk(Order, Uplo, Trans, N, K, alpha, A, lda, beta, C, ldc);
                                                                    ^
math/math.h: At global scope:
math/math.h:165:29: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline void herk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                             ^
math/math.h:165:59: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline void herk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                                                           ^
math/math.h:165:87: error: use of enum โ€˜CBLAS_TRANSPOSEโ€™ without previous declaration
 inline void herk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                                                                                       ^
math/math.h: In function โ€˜void nm::math::herk(int, int, int, int, int, const DType*, const DType*, int, const DType*, DType*, int) [with DType = nm::Complex<float>]โ€™:
math/math.h:167:74: error: โ€˜cblas_cherkโ€™ was not declared in this scope
   cblas_cherk(Order, Uplo, Trans, N, K, alpha->r, A, lda, beta->r, C, ldc);
                                                                          ^
math/math.h: At global scope:
math/math.h:171:29: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline void herk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                             ^
math/math.h:171:59: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline void herk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                                                           ^
math/math.h:171:87: error: use of enum โ€˜CBLAS_TRANSPOSEโ€™ without previous declaration
 inline void herk(const enum CBLAS_ORDER Order, const enum CBLAS_UPLO Uplo, const enum CBLAS_TRANSPOSE Trans, const int N,
                                                                                       ^
math/math.h: In function โ€˜void nm::math::herk(int, int, int, int, int, const DType*, const DType*, int, const DType*, DType*, int) [with DType = nm::Complex<double>]โ€™:
math/math.h:173:74: error: โ€˜cblas_zherkโ€™ was not declared in this scope
   cblas_zherk(Order, Uplo, Trans, N, K, alpha->r, A, lda, beta->r, C, ldc);
                                                                          ^
math/math.h: At global scope:
math/math.h:178:29: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline void trmm(const enum CBLAS_ORDER order, const enum CBLAS_SIDE side, const enum CBLAS_UPLO uplo,
                             ^
math/math.h:178:59: error: use of enum โ€˜CBLAS_SIDEโ€™ without previous declaration
 inline void trmm(const enum CBLAS_ORDER order, const enum CBLAS_SIDE side, const enum CBLAS_UPLO uplo,
                                                           ^
math/math.h:178:87: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline void trmm(const enum CBLAS_ORDER order, const enum CBLAS_SIDE side, const enum CBLAS_UPLO uplo,
                                                                                       ^
math/math.h:179:29: error: use of enum โ€˜CBLAS_TRANSPOSEโ€™ without previous declaration
                  const enum CBLAS_TRANSPOSE ta, const enum CBLAS_DIAG diag, const int m, const int n, const DType* alpha,
                             ^
math/math.h:179:60: error: use of enum โ€˜CBLAS_DIAGโ€™ without previous declaration
                  const enum CBLAS_TRANSPOSE ta, const enum CBLAS_DIAG diag, const int m, const int n, const DType* alpha,
                                                            ^
math/math.h:185:29: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline void trmm(const enum CBLAS_ORDER order, const enum CBLAS_SIDE side, const enum CBLAS_UPLO uplo,
                             ^
math/math.h:185:59: error: use of enum โ€˜CBLAS_SIDEโ€™ without previous declaration
 inline void trmm(const enum CBLAS_ORDER order, const enum CBLAS_SIDE side, const enum CBLAS_UPLO uplo,
                                                           ^
math/math.h:185:87: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline void trmm(const enum CBLAS_ORDER order, const enum CBLAS_SIDE side, const enum CBLAS_UPLO uplo,
                                                                                       ^
math/math.h:186:29: error: use of enum โ€˜CBLAS_TRANSPOSEโ€™ without previous declaration
                  const enum CBLAS_TRANSPOSE ta, const enum CBLAS_DIAG diag, const int m, const int n, const float* alpha,
                             ^
math/math.h:186:60: error: use of enum โ€˜CBLAS_DIAGโ€™ without previous declaration
                  const enum CBLAS_TRANSPOSE ta, const enum CBLAS_DIAG diag, const int m, const int n, const float* alpha,
                                                            ^
math/math.h: In function โ€˜void nm::math::trmm(int, int, int, int, int, int, int, const DType*, const DType*, int, DType*, int) [with DType = float]โ€™:
math/math.h:188:72: error: โ€˜cblas_strmmโ€™ was not declared in this scope
   cblas_strmm(order, side, uplo, ta, diag, m, n, *alpha, A, lda, B, ldb);
                                                                        ^
math/math.h: At global scope:
math/math.h:192:29: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline void trmm(const enum CBLAS_ORDER order, const enum CBLAS_SIDE side, const enum CBLAS_UPLO uplo,
                             ^
math/math.h:192:59: error: use of enum โ€˜CBLAS_SIDEโ€™ without previous declaration
 inline void trmm(const enum CBLAS_ORDER order, const enum CBLAS_SIDE side, const enum CBLAS_UPLO uplo,
                                                           ^
math/math.h:192:87: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline void trmm(const enum CBLAS_ORDER order, const enum CBLAS_SIDE side, const enum CBLAS_UPLO uplo,
                                                                                       ^
math/math.h:193:29: error: use of enum โ€˜CBLAS_TRANSPOSEโ€™ without previous declaration
                  const enum CBLAS_TRANSPOSE ta, const enum CBLAS_DIAG diag, const int m, const int n, const double* alpha,
                             ^
math/math.h:193:60: error: use of enum โ€˜CBLAS_DIAGโ€™ without previous declaration
                  const enum CBLAS_TRANSPOSE ta, const enum CBLAS_DIAG diag, const int m, const int n, const double* alpha,
                                                            ^
math/math.h: In function โ€˜void nm::math::trmm(int, int, int, int, int, int, int, const DType*, const DType*, int, DType*, int) [with DType = double]โ€™:
math/math.h:195:72: error: โ€˜cblas_dtrmmโ€™ was not declared in this scope
   cblas_dtrmm(order, side, uplo, ta, diag, m, n, *alpha, A, lda, B, ldb);
                                                                        ^
math/math.h: At global scope:
math/math.h:199:29: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline void trmm(const enum CBLAS_ORDER order, const enum CBLAS_SIDE side, const enum CBLAS_UPLO uplo,
                             ^
math/math.h:199:59: error: use of enum โ€˜CBLAS_SIDEโ€™ without previous declaration
 inline void trmm(const enum CBLAS_ORDER order, const enum CBLAS_SIDE side, const enum CBLAS_UPLO uplo,
                                                           ^
math/math.h:199:87: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline void trmm(const enum CBLAS_ORDER order, const enum CBLAS_SIDE side, const enum CBLAS_UPLO uplo,
                                                                                       ^
math/math.h:200:29: error: use of enum โ€˜CBLAS_TRANSPOSEโ€™ without previous declaration
                  const enum CBLAS_TRANSPOSE ta, const enum CBLAS_DIAG diag, const int m, const int n, const Complex64* alpha,
                             ^
math/math.h:200:60: error: use of enum โ€˜CBLAS_DIAGโ€™ without previous declaration
                  const enum CBLAS_TRANSPOSE ta, const enum CBLAS_DIAG diag, const int m, const int n, const Complex64* alpha,
                                                            ^
math/math.h: In function โ€˜void nm::math::trmm(int, int, int, int, int, int, int, const DType*, const DType*, int, DType*, int) [with DType = nm::Complex<float>]โ€™:
math/math.h:202:71: error: โ€˜cblas_ctrmmโ€™ was not declared in this scope
   cblas_ctrmm(order, side, uplo, ta, diag, m, n, alpha, A, lda, B, ldb);
                                                                       ^
math/math.h: At global scope:
math/math.h:206:29: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline void trmm(const enum CBLAS_ORDER order, const enum CBLAS_SIDE side, const enum CBLAS_UPLO uplo,
                             ^
math/math.h:206:59: error: use of enum โ€˜CBLAS_SIDEโ€™ without previous declaration
 inline void trmm(const enum CBLAS_ORDER order, const enum CBLAS_SIDE side, const enum CBLAS_UPLO uplo,
                                                           ^
math/math.h:206:87: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline void trmm(const enum CBLAS_ORDER order, const enum CBLAS_SIDE side, const enum CBLAS_UPLO uplo,
                                                                                       ^
math/math.h:207:29: error: use of enum โ€˜CBLAS_TRANSPOSEโ€™ without previous declaration
                  const enum CBLAS_TRANSPOSE ta, const enum CBLAS_DIAG diag, const int m, const int n, const Complex128* alpha,
                             ^
math/math.h:207:60: error: use of enum โ€˜CBLAS_DIAGโ€™ without previous declaration
                  const enum CBLAS_TRANSPOSE ta, const enum CBLAS_DIAG diag, const int m, const int n, const Complex128* alpha,
                                                            ^
math/math.h: In function โ€˜void nm::math::trmm(int, int, int, int, int, int, int, const DType*, const DType*, int, DType*, int) [with DType = nm::Complex<double>]โ€™:
math/math.h:209:71: error: โ€˜cblas_ztrmmโ€™ was not declared in this scope
   cblas_ztrmm(order, side, uplo, ta, diag, m, n, alpha, A, lda, B, ldb);
                                                                       ^
math/math.h: At global scope:
math/math.h:540:29: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline int potrf(const enum CBLAS_ORDER order, const enum CBLAS_UPLO uplo, const int N, DType* A, const int lda) {
                             ^
math/math.h:540:59: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline int potrf(const enum CBLAS_ORDER order, const enum CBLAS_UPLO uplo, const int N, DType* A, const int lda) {
                                                           ^
math/math.h:881:30: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline void lauum(const enum CBLAS_ORDER order, const enum CBLAS_UPLO uplo, const int N, DType* A, const int lda) {
                              ^
math/math.h:881:60: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline void lauum(const enum CBLAS_ORDER order, const enum CBLAS_UPLO uplo, const int N, DType* A, const int lda) {
                                                            ^
math/math.h: In function โ€˜void nm::math::lauum(int, int, int, DType*, int)โ€™:
math/math.h:896:17: error: โ€˜CblasUpperโ€™ was not declared in this scope
     if (uplo == CblasUpper) {
                 ^
math/math.h:897:20: error: โ€˜CblasRowMajorโ€™ was not declared in this scope
       if (order == CblasRowMajor) {
                    ^
math/math.h:905:20: error: โ€˜CblasRowMajorโ€™ was not declared in this scope
       if (order == CblasRowMajor) {
                    ^
math/math.h:919:37: error: โ€˜CblasLowerโ€™ was not declared in this scope
                             uplo == CblasLower ? CblasConjTrans : CblasNoTrans,
                                     ^
math/math.h:919:50: error: โ€˜CblasConjTransโ€™ was not declared in this scope
                             uplo == CblasLower ? CblasConjTrans : CblasNoTrans,
                                                  ^
math/math.h:919:67: error: โ€˜CblasNoTransโ€™ was not declared in this scope
                             uplo == CblasLower ? CblasConjTrans : CblasNoTrans,
                                                                   ^
math/math.h:922:36: error: โ€˜CblasLeftโ€™ was not declared in this scope
       nm::math::trmm<DType>(order, CblasLeft, uplo, CblasConjTrans, CblasNonUnit, Nright, Nleft, &ONE, U1, lda, G, lda);
                                    ^
math/math.h:922:69: error: โ€˜CblasNonUnitโ€™ was not declared in this scope
       nm::math::trmm<DType>(order, CblasLeft, uplo, CblasConjTrans, CblasNonUnit, Nright, Nleft, &ONE, U1, lda, G, lda);
                                                                     ^
math/math.h:925:37: error: โ€˜CblasLowerโ€™ was not declared in this scope
                             uplo == CblasLower ? CblasTrans : CblasNoTrans,
                                     ^
math/math.h:925:50: error: โ€˜CblasTransโ€™ was not declared in this scope
                             uplo == CblasLower ? CblasTrans : CblasNoTrans,
                                                  ^
math/math.h:925:63: error: โ€˜CblasNoTransโ€™ was not declared in this scope
                             uplo == CblasLower ? CblasTrans : CblasNoTrans,
                                                               ^
math/math.h:928:36: error: โ€˜CblasLeftโ€™ was not declared in this scope
       nm::math::trmm<DType>(order, CblasLeft, uplo, CblasTrans, CblasNonUnit, Nright, Nleft, &ONE, U1, lda, G, lda);
                                    ^
math/math.h:928:65: error: โ€˜CblasNonUnitโ€™ was not declared in this scope
       nm::math::trmm<DType>(order, CblasLeft, uplo, CblasTrans, CblasNonUnit, Nright, Nleft, &ONE, U1, lda, G, lda);
                                                                 ^
math/math.h: At global scope:
math/math.h:969:37: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline int clapack_lauum(const enum CBLAS_ORDER order, const enum CBLAS_UPLO uplo, const int n, void* a, const int lda) {
                                     ^
math/math.h:969:67: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline int clapack_lauum(const enum CBLAS_ORDER order, const enum CBLAS_UPLO uplo, const int n, void* a, const int lda) {
                                                                   ^
math/math.h: In function โ€˜int nm::math::clapack_lauum(int, int, int, void*, int)โ€™:
math/math.h:973:15: error: โ€˜CblasUpperโ€™ was not declared in this scope
   if (uplo == CblasUpper) lauum<is_complex, DType>(order, uplo, n, reinterpret_cast<DType*>(a), lda);
               ^
math/math.h: At global scope:
math/math.h:1016:37: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline int clapack_potrf(const enum CBLAS_ORDER order, const enum CBLAS_UPLO uplo, const int n, void* a, const int lda) {
                                     ^
math/math.h:1016:67: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline int clapack_potrf(const enum CBLAS_ORDER order, const enum CBLAS_UPLO uplo, const int n, void* a, const int lda) {
                                                                   ^
math/math.h:1023:29: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline int potri(const enum CBLAS_ORDER order, const enum CBLAS_UPLO uplo, const int n, DType* a, const int lda) {
                             ^
math/math.h:1023:59: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline int potri(const enum CBLAS_ORDER order, const enum CBLAS_UPLO uplo, const int n, DType* a, const int lda) {
                                                           ^
math/math.h:1060:37: error: use of enum โ€˜CBLAS_ORDERโ€™ without previous declaration
 inline int clapack_potri(const enum CBLAS_ORDER order, const enum CBLAS_UPLO uplo, const int n, void* a, const int lda) {
                                     ^
math/math.h:1060:67: error: use of enum โ€˜CBLAS_UPLOโ€™ without previous declaration
 inline int clapack_potri(const enum CBLAS_ORDER order, const enum CBLAS_UPLO uplo, const int n, void* a, const int lda) {
                                                                   ^
In file included from nmatrix.cpp:297:0:
ruby_nmatrix.c: In function โ€˜VALUE nm_reshape_bang(VALUE, VALUE)โ€™:
ruby_nmatrix.c:1069:11: warning: unused variable โ€˜elemโ€™ [-Wunused-variable]
     void* elem = s->elements;
           ^
Makefile:241: recipe for target 'nmatrix.o' failed
make: *** [nmatrix.o] Error 1

make failed, exit code 2

Gem files will remain installed in /home/cooldudeabhi/.rvm/gems/ruby-2.2.3/gems/nmatrix-0.1.0 for inspection.
Results logged to /home/cooldudeabhi/.rvm/gems/ruby-2.2.3/extensions/x86_64-linux/2.2.0/nmatrix-0.1.0/gem_make.out
โžœ  ~          

Create SciRuby Guides

This is an idea for when we have better documentation and development on the subprojects.

We could use guides showing how to use the various parts of SciRuby, e.g. how to solve linear systems, interpolation, statistics, etc. It'd be similar to RailsGuides.

I'll write something using NMatrix, but this should be done for all the projects and for various simple recurrent problems.

Obs: This is the same as saying "we need better documentation". We need better documentation. Even the examples on statsample and the specs on nmatrix, distribution, etc aren't enough.

What is the purpose of this gem?

There is some code which hasn't been changed since 2011. Why is that? Shouldn't this be some kind of meta gem?

Is there a list of all sci gems that are currently under development?

Update list of gems

The list of gems is kept in the gems.yml

  • Add version constraints (version: '~> ...')
  • Remove obsolete gems
  • Add missing gems
  • Improve descriptions
  • Improve categories
  • Test all gems, autoloading of modules etc.

ping @SciRuby/owners

SciRuby::Plotter alternate UI library bindings (JRuby, MacRuby, etc.)

Plotter is currently written using green shoes, which requires a number of external libraries. As a result, it probably doesn't work in JRuby, MacRuby, or really anywhere other than MRI.

Additionally, green_shoes is known to not work with macruby.

The short term solution:

  • Implement a version of SciRuby::Plotter with continuous evaluation that displays and updates the output in a web browser instead of the native window manager.

The long term solution:

  • Adapt green_shoes to work with MacRuby, JRuby, etc., or implement alternate versions of Plotter to function in these environments.

Modify save file window in Plotter

Right now, the save dialog box is the Green Shoes native save dialog. It'd be nice if there was a note in there about how you could save to other formats just by changing the file extension.

Menus and shortcut key combinations for saving in Plotter

A simple menu would be nice in Plotter, since not everyone knows they can press 's' to save their plots.

It'd also better if users had to press ctrl+s instead of s to save. I couldn't get this to work; it may be a Green Shoes bug.

GSL version mismatch

Trying to install sciruby-full-0.2.11 on macOS Sierra: For some reason the gem installer forces the gsl-2.1.0 gem, while that gem version is not compatible with the recent version of the GSL library (2.3). Homebrew can only install the latest version of GSL on Mac, so for now it is not possible to install sciruby-full on a Mac if one uses Homebrew for installing library requirements.

Btw, gsl-2.1.0.2 gem adds a patch to fix the issue.

Random numbers

It would be probably a good idea to support those. Probably methods to get a single random number from a set of probability distributions, but also an array of random numbers, maybe using ziggurat algorithm(faster than getting n random numbers one by one)

Suggestion to Update "Build Instructions for OS X" for Mountain Lion

I run OS X Mountain Lion and have been experimenting with installing SciRuby. I followed the instructions in the Wiki in Build Instructions for OS X but found that they did not cover all the issues I ran into. When installing SciRuby (I cloned the repo then ran bundle install), I had issues with the following dependency gems (in addition to the gsl gem, which is already mentioned):

  • gtksourceview2
  • rmagick

The problem with gtksourceview2 was that the pkg-config gem, invoked during installation, was unable to find libxml2, which is a dependency of gtksourceview2. This was due to a missing libxml-2.0.pc file in /usr/lib/pkgconfig. See here and here for more information on this. Basically Mountain Lion dropped a few .pc files from /usr/lib/pkgconfig for reasons I don't understand, even though the libraries (at least libxml2) are still packaged with Mountain Lion. The only way I was able to get gtksourceview2 to install was to brew install libxml2 and symlink the libxml-2.0.pc file that comes with it into /usr/local/pkgconfig using

sudo ln -s /usr/local/Cellar/libxml2/2.9.0/lib/pkgconfig/libxml-2.0.pc /usr/lib/pkgconfig

This directs gtksourceview to the libxml version installed via Homebrew rather than the system version-- not sure if that will cause any problems. I'm sure there's a cleaner way to fix this but I don't know what it is.

The issue with rmagick was that a simple brew install imagemagick seemed to create an incompatible imagemagick installation. I had to brew remove imagemagick and then brew install imagemagick --disable-openmp --build-from-source, as per this StackOverflow question.

Anyway, just hoping to spare others on Mountain Lion my pain...

Algorithms gem

Why do we need a forked gem for algorithms and DS implementation?
Can't Sciruby build this on its own? I'm sure it'll be more optimised.
I looked into the gem and saw ruby handling all the code for all the algorithms and DS. A C library handling the processing for the input will be much better I think, since Sciruby is meant to work for small and large datasets.
I can help contribute building it, if needed.

BTW kudos to the maintainers for building this meta-gem ๐Ÿ‘

conflicting dependency on install

$ gem install sciruby-full
ERROR: While executing gem ... (Gem::DependencyResolutionError)
conflicting dependencies nmatrix (= 0.2.0) and nmatrix (> 0.1)
Activated nmatrix-0.1.0 via:
nmatrix-0.1.0 (
> 0.1), sciruby-full-0.2.8 (= 0.2.8)
instead of (= 0.2.0) via:
nmatrix-lapacke-0.2.0 (> 0.2.0), mixed_models-0.1.1 (> 0.1), sciruby-full-0.2.8 (= 0.2.8)

install sciruby gem failed on

Here is the output:

1 stardiviner@dark ~ % gem install sciruby                                                                             :(
Building native extensions.  This could take a while...
ERROR:  Error installing sciruby:
        ERROR: Failed to build gem native extension.

    /home/stardiviner/.rbenv/versions/2.2.0/bin/ruby -r ./siteconf20150507-29215-1t0s8z8.rb extconf.rb
checking gsl version... 1.16
checking gsl cflags... -I/usr/include
checking for main() in -lcblas... yes
checking for main() in -latlas... no
checking gsl libs... -L/usr/lib -lgsl -lgslcblas -lm
checking for round()... yes
checking for rngextra/rngextra.h... no
checking for qrngextra/qrngextra.h... no
checking for ool/ool_version.h... no
checking for tensor/tensor.h... no
checking for jacobi.h... no
checking for gsl/gsl_cqp.h... no
checking for gsl/gsl_multimin_fsdf.h... no
checking for gsl_poly_solve_quartic() in -lgsl... no
checking for gsl_eigen_francis() in -lgsl... yes
checking for ndlinear/gsl_multifit_ndlinear.h... no
checking for alf/alf.h... no
checking rb-gsl version...1.14.7
checking ruby version... 2.2.0
checking for graph... yes
*** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers.  Check the mkmf.log file for more details.  You may
need configuration options.

Provided configuration options:
        --with-opt-dir
        --without-opt-dir
        --with-opt-include
        --without-opt-include=${opt-dir}/include
        --with-opt-lib
        --without-opt-lib=${opt-dir}/lib
        --with-make-prog
        --without-make-prog
        --srcdir=.
        --curdir
        --ruby=/home/stardiviner/.rbenv/versions/2.2.0/bin/$(RUBY_BASE_NAME)
        --with-cblas-dir
        --without-cblas-dir
        --with-cblas-include
        --without-cblas-include=${cblas-dir}/include
        --with-cblas-lib
        --without-cblas-lib=${cblas-dir}/lib
        --with-atlas-dir
        --without-atlas-dir
        --with-atlas-include
        --without-atlas-include=${atlas-dir}/include
        --with-atlas-lib
        --without-atlas-lib=${atlas-dir}/lib
        --with-cblaslib
        --without-cblaslib
        --with-atlaslib
        --without-atlaslib
        --with-gsllib
        --without-gsllib
        --with-gsllib
        --without-gsllib
        --with-narray-dir
        --without-narray-dir
        --with-narray-include
        --without-narray-include=${narray-dir}/include
        --with-narray-lib
        --without-narray-lib=${narray-dir}/lib
extconf.rb:245:in `<main>': undefined method `searcher' for Gem:Module (NoMethodError)

extconf failed, exit code 1

Gem files will remain installed in /home/stardiviner/.rbenv/versions/2.2.0/lib/ruby/gems/2.2.0/gems/gsl-1.14.7 for inspection.
Results logged to /home/stardiviner/.rbenv/versions/2.2.0/lib/ruby/gems/2.2.0/extensions/x86_64-linux/2.2.0-static/gsl-1.14.7/gem_make.out
gem install sciruby  6.79s user 0.40s system 26% cpu 27.285 total

seems error happens on extconf and gsl.
I'm using Arch Linux, and installed package gsl.

kernel dies iruby notebook

I am completely noob in SciRuby. For the first time I am using SciRuby. I am following this video to get an overview of how to use SciRuby and plot graphs, charts etc. When I go to localhost:8888 and I create new notebooks from right drop down(Ruby 2.2.3)

I am in home(~) dir

notebook

Then at first it says Kernel connecting and then dead kernel message pops up again and again(within gap of few seconds). Nothing happens and the commands I am writing seems to have no effect. Please get this issue solved thanks a lot.

kernel


$ iruby notebook
Could not load bundler: Could not locate Gemfile or .bundle/ directory
[TerminalIPythonApp] WARNING | Subcommand `ipython notebook` is deprecated and will be removed in future versions.
[TerminalIPythonApp] WARNING | You likely want to use `jupyter notebook`... continue in 5 sec. Press Ctrl-C to quit now.
[I 01:13:51.976 NotebookApp] Serving notebooks from local directory: /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin
[I 01:13:51.976 NotebookApp] 0 active kernels 
[I 01:13:51.976 NotebookApp] The Jupyter Notebook is running at: http://localhost:8888/
[I 01:13:51.977 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
Gtk-Message: Failed to load module "pantheon-filechooser-module"

(firefox:8219): Gtk-WARNING **: Unable to locate theme engine in module_path: "pixmap",

(firefox:8219): Gtk-WARNING **: Unable to locate theme engine in module_path: "pixmap",

(firefox:8219): Gtk-WARNING **: Unable to locate theme engine in module_path: "pixmap",

(firefox:8219): Gtk-WARNING **: Unable to locate theme engine in module_path: "pixmap",

(firefox:8219): Gtk-WARNING **: Unable to locate theme engine in module_path: "pixmap",
Gtk-Message: Failed to load module "canberra-gtk-module"
[I 01:14:32.931 NotebookApp] 302 GET / (127.0.0.1) 0.69ms
[I 01:14:39.766 NotebookApp] Creating new file in 
[I 01:14:53.999 NotebookApp] Creating new notebook in 
[I 01:14:56.223 NotebookApp] Kernel started: 463b14e0-9f3d-49c0-bd3d-6dd19e7b43d9
W, [2016-03-13T01:14:56.726775 #8272]  WARN -- : Could not load bundler: Could not locate Gemfile or .bundle/ directory
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:163:in `rescue in root'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:159:in `root'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:71:in `bundle_path'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:401:in `configure_gem_home_and_path'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:57:in `configure'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:118:in `definition'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:109:in `check_bundler'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:67:in `run_kernel'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
You should install rbczmq or ffi_rzmq before running iruby notebook. See README.
F, [2016-03-13T01:14:56.821066 #8272] FATAL -- : Kernel died: uninitialized constant IRuby::Kernel::Session
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/kernel.rb:18:in `initialize'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `new'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `run_kernel'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/kernel.rb:18:in `initialize': uninitialized constant IRuby::Kernel::Session (NameError)
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `new'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `run_kernel'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
[I 01:14:59.223 NotebookApp] KernelRestarter: restarting kernel (1/5)
W, [2016-03-13T01:14:59.619447 #8309]  WARN -- : Could not load bundler: Could not locate Gemfile or .bundle/ directory
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:163:in `rescue in root'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:159:in `root'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:71:in `bundle_path'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:401:in `configure_gem_home_and_path'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:57:in `configure'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:118:in `definition'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:109:in `check_bundler'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:67:in `run_kernel'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
You should install rbczmq or ffi_rzmq before running iruby notebook. See README.
F, [2016-03-13T01:14:59.696087 #8309] FATAL -- : Kernel died: uninitialized constant IRuby::Kernel::Session
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/kernel.rb:18:in `initialize'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `new'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `run_kernel'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/kernel.rb:18:in `initialize': uninitialized constant IRuby::Kernel::Session (NameError)
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `new'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `run_kernel'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
[I 01:15:02.231 NotebookApp] KernelRestarter: restarting kernel (2/5)
W, [2016-03-13T01:15:02.619460 #8312]  WARN -- : Could not load bundler: Could not locate Gemfile or .bundle/ directory
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:163:in `rescue in root'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:159:in `root'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:71:in `bundle_path'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:401:in `configure_gem_home_and_path'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:57:in `configure'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:118:in `definition'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:109:in `check_bundler'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:67:in `run_kernel'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
You should install rbczmq or ffi_rzmq before running iruby notebook. See README.
F, [2016-03-13T01:15:02.703792 #8312] FATAL -- : Kernel died: uninitialized constant IRuby::Kernel::Session
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/kernel.rb:18:in `initialize'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `new'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `run_kernel'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/kernel.rb:18:in `initialize': uninitialized constant IRuby::Kernel::Session (NameError)
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `new'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `run_kernel'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
[I 01:15:05.239 NotebookApp] KernelRestarter: restarting kernel (3/5)
W, [2016-03-13T01:15:05.714227 #8316]  WARN -- : Could not load bundler: Could not locate Gemfile or .bundle/ directory
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:163:in `rescue in root'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:159:in `root'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:71:in `bundle_path'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:401:in `configure_gem_home_and_path'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:57:in `configure'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:118:in `definition'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:109:in `check_bundler'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:67:in `run_kernel'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
You should install rbczmq or ffi_rzmq before running iruby notebook. See README.
F, [2016-03-13T01:15:05.788401 #8316] FATAL -- : Kernel died: uninitialized constant IRuby::Kernel::Session
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/kernel.rb:18:in `initialize'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `new'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `run_kernel'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/kernel.rb:18:in `initialize': uninitialized constant IRuby::Kernel::Session (NameError)
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `new'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `run_kernel'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
[W 01:15:06.731 NotebookApp] Timeout waiting for kernel_info reply from 463b14e0-9f3d-49c0-bd3d-6dd19e7b43d9
[I 01:15:08.247 NotebookApp] KernelRestarter: restarting kernel (4/5)
WARNING:root:kernel 463b14e0-9f3d-49c0-bd3d-6dd19e7b43d9 restarted
W, [2016-03-13T01:15:08.701757 #8318]  WARN -- : Could not load bundler: Could not locate Gemfile or .bundle/ directory
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:163:in `rescue in root'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:159:in `root'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:71:in `bundle_path'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:401:in `configure_gem_home_and_path'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:57:in `configure'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:118:in `definition'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:109:in `check_bundler'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:67:in `run_kernel'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
You should install rbczmq or ffi_rzmq before running iruby notebook. See README.
F, [2016-03-13T01:15:08.779382 #8318] FATAL -- : Kernel died: uninitialized constant IRuby::Kernel::Session
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/kernel.rb:18:in `initialize'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `new'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `run_kernel'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/kernel.rb:18:in `initialize': uninitialized constant IRuby::Kernel::Session (NameError)
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `new'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `run_kernel'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
[W 01:15:11.256 NotebookApp] KernelRestarter: restart failed
[W 01:15:11.257 NotebookApp] Kernel 463b14e0-9f3d-49c0-bd3d-6dd19e7b43d9 died, removing from map.
ERROR:root:kernel 463b14e0-9f3d-49c0-bd3d-6dd19e7b43d9 restarted failed!
[W 01:15:11.329 NotebookApp] Kernel deleted before session
[W 01:15:11.330 NotebookApp] 410 DELETE /api/sessions/2709e672-f333-42d4-a84b-0c3ab68d3864 (127.0.0.1) 2.11ms referer=http://localhost:8888/notebooks/Untitled.ipynb?kernel_name=ruby
ryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:159:in `root'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:71:in `bundle_path'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:401:in `configure_gem_home_and_path'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:57:in `configure'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:118:in `definition'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:109:in `check_bundler'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:67:in `run_kernel'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
You should install rbczmq or ffi_rzmq before running iruby notebook. See README.
F, [2016-03-13T01:15:02.703792 #8312] FATAL -- : Kernel died: uninitialized constant IRuby::Kernel::Session
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/kernel.rb:18:in `initialize'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `new'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `run_kernel'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/kernel.rb:18:in `initialize': uninitialized constant IRuby::Kernel::Session (NameError)
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `new'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:70:in `run_kernel'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/bin/iruby:5:in `<top (required)>'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `load'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/iruby:23:in `<main>'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `eval'
    from /home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/bin/ruby_executable_hooks:15:in `<main>'
[I 01:15:05.239 NotebookApp] KernelRestarter: restarting kernel (3/5)
W, [2016-03-13T01:15:05.714227 #8316]  WARN -- : Could not load bundler: Could not locate Gemfile or .bundle/ directory
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:163:in `rescue in root'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:159:in `root'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:71:in `bundle_path'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:401:in `configure_gem_home_and_path'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:57:in `configure'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/bundler-1.11.2/lib/bundler.rb:118:in `definition'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:109:in `check_bundler'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:67:in `run_kernel'
/home/abhimanyuaryan/.rvm/gems/ruby-2.2.3/gems/iruby-0.2.8/lib/iruby/command.rb:34:in `run'
/home/abhimanyuarya[I 01:15:53.124 NotebookApp] Saving file at /Untitled.ipynb

Numeric array and matrix spec

In an rspec, document minimum expectations for the following:

  • 1D array
  • 2D array
  • vector
  • matrix
  • data frame

Lean toward current GSL syntax.

John Prince began the spec: https://github.com/SciRuby/sciruby/blob/generic_numeric_array/spec/sciruby/nvector_spec.rb

However, we first need to decide on a unified interface for matrices and vectors. For example, should 2D arrays be matrices? Should all arrays and matrices be fundamentally the same type?

See the following threads:

sciruby-plotter and old code

Hi @MohawkJohn,

I just closed all the old issues concerning the sciruby-plotter and the sciruby tool. I am wondering about it and the work that went into it - should we copy the code to some subproject or was everything somehow reused/scattered over the various gems that we have now? Maybe you would also like to keep it somewhere for historical reasons? ;)

Setup bank account for Pledgie

Paypal will give an error to Pledgie which users cannot decipher until we setup a bank account for the Paypal deposits.

Transfer iruby to sciruby?

Hi would you be interested in that? I still want to continue to maintain it, but maybe it is better to transfer it to your organization?

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