Help in setup and debugging

[Shekhar Prasad Rajak]

Hello all, I am trying to setup `daru` in my system. I have read several docs and blogs on `daru`. To setup the development version I did : 

gem install bundler
bundle install
bundle exec rake compile
bundle exec rake spec
 inside the daru cloned repo. But I got some errors. 
Something like : 

ERROR:  Error installing rmagick:
ERROR: Failed to build gem native extension.

Let me know if I am doing something wrong. I haven't seen any installation instruction in the docs (If it is somewhere then please share the link). Also please suggest a good debugger for the Ruby.

Thanks,
Shekhar

[Lokesh Sharma]

Try this

sudo apt-get install libmagickwand-dev imagemagick

This should fix it.

[Shekhar Prasad Rajak]

Thanks Lokesh for reply. I tried to install it using `brew` in my mac system. Also tried some different ways , but still I am getting error. I think I am missing something. I will try again and search for the ans.

--

Shekhar

[Lokesh Sharma]

Somewhere I read this might help

brew link --overwrite imagemagick

[Shekhar Prasad Rajak]

Thanks Lokesh for reply. There was a different problem in installation. rmagick is compatible with imagemagick 6.x.x version the latest version 7.x.x have some new updation in file names, so it was not working. I installed the 6.x.x version then did `gem install rmagick` it worked.

The problem I am getting, when I run `bundle install ` is :

```

An error occurred while installing gsl (2.1.0.1), and Bundler cannot continue.

Make sure that `gem install gsl -v '2.1.0.1'` succeeds before bundling.

I tried few things but still not able to fix. I hope I will find a solution soon.

--

Shekhar

[Sameer Deshmukh]

Did you try installing rb-gsl individually? Can you post the error it gave you?

[Shekhar Prasad Rajak]

Thanks Sameer for reply. Yes I tried to install it manually. I followed these commands : 

curl -O http://mirror.veriportal.com/gnu/gsl/gsl-1.14.tar.gz
tar xvzf gsl-1.14.tar.gz
cd gsl-1.14
./configure
make
sudo make install
sudo gem install --conservative --no-ri --no-rdoc gsl

or

gem install gsl

and get this error :

Building native extensions.  This could take a while...

ERROR:  Error installing gsl:

ERROR: Failed to build gem native extension.

    current directory: /Users/.rvm/rubies/ruby-2.4.0/lib/ruby/gems/2.4.0/gems/gsl-2.1.0.1/ext/gsl_native

/Users/.rvm/rubies/ruby-2.4.0/bin/ruby -r ./siteconf20170125-34982-gd9cdo.rb extconf.rb

*** ERROR: missing required library to compile this module: Ruby/GSL requires gsl-1.15 or later.

*** 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.

When I tried to install it the tar file , I get this : 

#include <architecture/ppc/fp_regs.h> 

         ^

1 error generated.

make[1]: *** [fp.lo] Error 1

make: *** [install-recursive] Error 1

I am searching for the solution.

--

Shekhar

[Sameer Deshmukh]

You're installing GSL v.1.14. You'll need GSL 2.0 for installing the gem.

On Sunday, January 22, 2017 at 12:00:54 PM UTC+5:30, Shekhar Prasad Rajak wrote:

[Shekhar Prasad Rajak]

Yes, I also tried with 2.3 version, that time also I was getting similar problem. After some effort I am not getting that error. But after installing  gsl-2.0 using  tar file and then running `gem install gsl` is giving this error :

checking gsl version... 2.3

checking gsl cflags... -I/usr/local/include

checking gsl libs... -L/usr/local/lib -lgsl -lgslcblas

checking for round()... yes

checking for alf/alf.h... no

checking for qrngextra/qrngextra.h... no

checking for rngextra/rngextra.h... no

checking for tensor/tensor.h... no

checking for gsl/gsl_multimin_fsdf.h... no

checking for gsl/gsl_cqp.h... no

checking for jacobi.h... no

checking for ndlinear/gsl_multifit_ndlinear.h... no

checking for ool/ool_version.h... no

checking for gsl_eigen_francis() in -lgsl... yes

checking for gsl_eigen_francis()... yes

checking for gsl_poly_solve_quartic() in -lgsl... no

checking for graph... no

checking for tamu_anova/tamu_anova.h... no

checking for gsl_multifit_fdfsolver.J in gsl/gsl_multifit_nlin.h... no

checking for gsl_sf_mathieu_a_e() in gsl/gsl_sf_mathieu.h... yes

checking for gsl_sf_mathieu_b_e() in gsl/gsl_sf_mathieu.h... yes

checking for gsl_sf_mathieu_ce_e() in gsl/gsl_sf_mathieu.h... yes

checking for gsl_sf_mathieu_se_e() in gsl/gsl_sf_mathieu.h... yes

checking for gsl_sf_mathieu_Mc_e() in gsl/gsl_sf_mathieu.h... yes

checking for gsl_sf_mathieu_Ms_e() in gsl/gsl_sf_mathieu.h... yes

creating gsl_config.h

creating Makefile

To see why this extension failed to compile, please check the mkmf.log which can be found here:

  /Users/.rvm/gems/ruby-2.4.0/extensions/x86_64-darwin-16/2.4.0/gsl-2.1.0.1/mkmf.log

current directory: /Users/.rvm/gems/ruby-2.4.0/gems/gsl-2.1.0.1/ext/gsl_native

make "DESTDIR=" clean

current directory: /Users/.rvm/gems/ruby-2.4.0/gems/gsl-2.1.0.1/ext/gsl_native

make "DESTDIR="

compiling alf.c

compiling array.c

compiling array_complex.c

compiling blas.c

compiling blas1.c

compiling blas2.c

compiling blas3.c

compiling block.c

compiling bspline.c

compiling bundle.c

compiling cdf.c

compiling cheb.c

compiling combination.c

compiling common.c

common.c:78:10: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]

  len0 = strlen(s0);

       ~ ^~~~~~~~~~

common.c:79:10: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]

  len1 = strlen(s1);

       ~ ^~~~~~~~~~

common.c:89:10: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]

  len0 = strlen(s0);

       ~ ^~~~~~~~~~

common.c:90:10: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]

  len1 = strlen(s1);

       ~ ^~~~~~~~~~

4 warnings generated.

compiling complex.c

compiling const.c

compiling const_additional.c

compiling cqp.c

compiling deriv.c

compiling dht.c

dht.c:225:45: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]

        val = t->j[n+1]*gsl_dht_x_sample(t, m)/t->xmax;

                        ~~~~~~~~~~~~~~~~    ^

dht.c:234:41: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]

    val = t->j[n+1]*gsl_dht_x_sample(t, m)/t->xmax;

                    ~~~~~~~~~~~~~~~~    ^

dht.c:256:70: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]

        val = gsl_sf_bessel_Jnu(t->nu, t->j[n+1]*gsl_dht_x_sample(t, m)/t->xmax);

                                                 ~~~~~~~~~~~~~~~~    ^

dht.c:265:66: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]

    val = gsl_sf_bessel_Jnu(t->nu, t->j[n+1]*gsl_dht_x_sample(t, m)/t->xmax);

                                             ~~~~~~~~~~~~~~~~    ^

dht.c:333:70: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]

        val = gsl_sf_bessel_Jnu(t->nu, t->j[n+1]*gsl_dht_x_sample(t, m)/t->xmax);

                                                 ~~~~~~~~~~~~~~~~    ^

dht.c:343:66: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]

    val = gsl_sf_bessel_Jnu(t->nu, t->j[n+1]*gsl_dht_x_sample(t, m)/t->xmax);

                                             ~~~~~~~~~~~~~~~~    ^

6 warnings generated.

compiling diff.c

compiling dirac.c

compiling eigen.c

compiling error.c

error.c:83:66: error: use of undeclared identifier 'rb_cFixnum'

  pgsl_error[-2] = rb_define_class_under(mgsl_error, "CONTINUE", rb_cFixnum);

                                                                 ^

error.c:85:64: error: use of undeclared identifier 'rb_cFixnum'

  pgsl_error[0] = rb_define_class_under(mgsl_error, "SUCCESS", rb_cFixnum);

                                                               ^

2 errors generated.

make: *** [error.o] Error 1

make failed, exit code 2

I am trying check the error. Thanks for reply.

--

Shekhar

[Shekhar Prasad Rajak]

Anyone knows why I am getting this error during installation of nmatrix :

make "DESTDIR="

compiling nmatrix.cpp

g++-4.8: error: unrecognized command line option '-Wdivision-by-zero'

g++-4.8: error: unrecognized command line option '-Wextra-tokens'

make: *** [nmatrix.o] Error 1

--

Shekhar

[Sameer Deshmukh]

Ah. The problem is that you're using Ruby 2.4 and the gem that's currently on rubygems is not compatible with that. I will release a new gem soon and let you know. Meanwhile you can pull the gem directly from the github repo.

[Shekhar Prasad Rajak]

In first problem (rmagick issue during bundle install), solution :  we need to use imagemagick 6.x.x version then run `gem install rmagick` .

2nd problem (gsl issue) , solution: daru uses gsl 1.16 so the gsl tar file version must be 1.16 and ruby version must be 2.3.x . 

After fixing these issue when I do `bundle install` (in ruby version 2.3.1, fixed above problem) I get nmatrix error (previous post issue) :  

```

make "DESTDIR="

compiling nmatrix.cpp

g++-4.8: error: unrecognized command line option '-Wdivision-by-zero'

g++-4.8: error: unrecognized command line option '-Wextra-tokens'

make: *** [nmatrix.o] Error 1

```

I have added a comment in the issue also : https://github.com/SciRuby/nmatrix/issues/426#issuecomment-275828218

To install it manually I followed this : https://github.com/SciRuby/nmatrix/wiki/Installation#mac-os-x and tried `bundle install` but I get the same error. 

Also same error in this : https://github.com/SciRuby/nmatrix/wiki/Installation#standard-installation-procedure  

Need to check some dependencies. I am searching for the solution.

--

Shekhar

[Pjotr Prins]

Sigh.

On Sat, Jan 28, 2017 at 09:25:04AM -0800, Shekhar Prasad Rajak wrote:
> In first problem (rmagick issue during bundle install), solution :  we
> need to use imagemagick 6.x.x version then run `gem install rmagick` .
> 2nd problem (gsl issue) , solution: daru uses gsl 1.16 so the gsl tar file
> version must be 1.16 and ruby version must be 2.3.x . 
> After fixing these issue when I do `bundle install` (in ruby version
> 2.3.1, fixed above problem) I get nmatrix error (previous post issue) :  
> ```
>
> make "DESTDIR="
>
> compiling nmatrix.cpp
>
> g++-4.8: error: unrecognized command line option '-Wdivision-by-zero'
>
> g++-4.8: error: unrecognized command line option '-Wextra-tokens'
>
> make: *** [nmatrix.o] Error 1
>
> ```
>
> I have added a comment in the issue also

> : [1]https://github.com/SciRuby/nmatrix/issues/426#issuecomment-275828218

>
> To install it manually I followed this

> : [2]https://github.com/SciRuby/nmatrix/wiki/Installation#mac-os-x and

> tried `bundle install` but I get the same error. 
>
> Also same error in this :

> [3]https://github.com/SciRuby/nmatrix/wiki/Installation#standard-installation-procedure  

> --
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>
> References
>
> Visible links
> 1. https://github.com/SciRuby/nmatrix/issues/426#issuecomment-275828218
> 2. https://github.com/SciRuby/nmatrix/wiki/Installation#mac-os-x
> 3. https://github.com/SciRuby/nmatrix/wiki/Installation#standard-installation-procedure
> 4. mailto:sciruby-dev...@googlegroups.com
> 5. https://groups.google.com/d/optout


--

[Pjotr Prins]

The solution to deployment dependencies is by using GNU Guix which can
nowadays be installed without admin privileges. We'll need to package
a number of gems to make Sciruby deployment as simple as running an
install script.

Is anyone interested in helping me package these gems? It should not
be too hard, but I don't want to do it on my own. You'll learn about
deployment and get some LISP thrown in.

Pj.

> To unsubscribe from this group and stop receiving emails from it, send an email to sciruby-dev...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.

--

[Sameer Deshmukh]

Pjotr,

Can that be a GSOC project? Packaging SciRuby tools with Guix? Maybe get Guix contributors on board as mentors?

I recently asked the package management question to a panel at Ruby Conf India and nobody seemed to know what exactly should be done :\

> >    4. mailto:sciruby-dev+unsub...@googlegroups.com

[Pjotr Prins]

On Sun, Jan 29, 2017 at 01:28:38AM -0800, Sameer Deshmukh wrote:
> Pjotr,
>
> Can that be a GSOC project? Packaging SciRuby tools with Guix? Maybe get
> Guix contributors on board as mentors?
>
> I recently asked the package management question to a panel at Ruby Conf
> India and nobody seemed to know what exactly should be done :\

I put in a proposal 2 years ago. Maybe now the time is ripe :)

Pj.

[Sameer Deshmukh]

Shekhar,

Until I take care of rb-gsl, you can simply clone the daru source code, comment out the GSL dependency in the gemspec and begin contributing. GSL is not a hard dependency on daru and none of our current objectives depend on it in any way.

[Shekhar Prasad Rajak]

Thanks Sameer for reply. Now `bundle install` is going smooth. But when I try to do `bundle exec rake compile`

it returns with these error :

```

rake aborted!

Don't know how to build task 'compile' (see --tasks)

/Users/.rvm/gems/ruby-2.4.0/bin/ruby_executable_hooks:15:in `eval'

/Users/.rvm/gems/ruby-2.4.0/bin/ruby_executable_hooks:15:in `<main>'

(See full trace by running task with --trace)

```

It seems there is some problem in Rakefile. I am searching for the solution.

--

Shekhar

[Lokesh Sharma]

You don't need to run `bundle exec rake compile`. Read here https://github.com/SciRuby/daru/blob/master/CONTRIBUTING.md

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[Shekhar Prasad Rajak]

Thanks for reply. It seems there is some problem in my installation of rvm . I will try in rbenv. 

--

Shekhar

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