[PATCH] Add ApaptiveSparsity.

[PATCH] Add ApaptiveSparsity.

[Ricardo Wurmus]

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From b9ef283243b792ea7ac095a203e5aea3c221f78f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 17 Dec 2015 16:27:32 +0100
Subject: [PATCH 1/2] gnu: Add r-rcpparmadillo.

* gnu/packages/statistics.scm (r-rcpparmadillo): New variable.
---
 gnu/packages/statistics.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 95176aa..8beb8c8 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1411,3 +1411,31 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.")
 variety of formats.")
     (license license:gpl3+)))
 
+(define-public r-rcpparmadillo
+  (package
+    (name "r-rcpparmadillo")
+    (version "0.6.200.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "RcppArmadillo" version))
+              (sha256
+               (base32
+                "137wqqga776yj6synx5awhrzgkz7mmqnvgmggh9l4k6d99vwp9gj"))))
+    (properties `((upstream-name . "RcppArmadillo")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/RcppCore/RcppArmadillo")
+    (synopsis "Rcpp integration for the linear algebra library 'Armadillo'")
+    (description
+     "Armadillo is a templated C++ linear algebra library that aims towards a
+good balance between speed and ease of use.  Integer, floating point and
+complex numbers are supported, as well as a subset of trigonometric and
+statistics functions.  Various matrix decompositions are provided through
+optional integration with LAPACK and ATLAS libraries.  This package includes
+the header files from the templated Armadillo library.")
+    ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
+    ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
+    ;; later, as is the rest of 'Rcpp'.
+    (license license:gpl2+)))
+
-- 
2.1.0


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From 64e16086990806f2f30e651dbbf2ff62470b2fcc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 17 Dec 2015 16:28:25 +0100
Subject: [PATCH 2/2] gnu: Add AdaptiveSparsity.

* gnu/packages/machine-learning.scm (r-adaptivesparsity): New variable.
---
 gnu/packages/machine-learning.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index bfa88ac..030d60d 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -23,6 +23,7 @@
   #:use-module (guix download)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system r)
   #:use-module (gnu packages)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
@@ -290,3 +291,27 @@ combine multiple data representations, algorithm classes, and general purpose
 tools.  This enables both rapid prototyping of data pipelines and extensibility
 in terms of new algorithms.")
     (license license:gpl3+)))
+
+(define-public r-adaptivesparsity
+  (package
+    (name "r-adaptivesparsity")
+    (version "1.4")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "AdaptiveSparsity" version))
+              (sha256
+               (base32
+                "1az7isvalf3kmdiycrfl6s9k9xqk22k1mc6rh8v0jmcz402qyq8z"))))
+    (properties
+     `((upstream-name . "AdaptiveSparsity")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rcpp" ,r-rcpp)
+       ("r-rcpparmadillo" ,r-rcpparmadillo)))
+    (home-page "http://cran.r-project.org/web/packages/AdaptiveSparsity")
+    (synopsis "Adaptive sparsity models")
+    (description
+     "This package implements the Figueiredo machine learning algorithm for
+adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
+geometric models.")
+    (license license:lgpl3+)))
-- 
2.1.0

Re: [PATCH] Add ApaptiveSparsity.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> From b9ef283243b792ea7ac095a203e5aea3c221f78f Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 17 Dec 2015 16:27:32 +0100
> Subject: [PATCH 1/2] gnu: Add r-rcpparmadillo.
>
> * gnu/packages/statistics.scm (r-rcpparmadillo): New variable.

[...]

> +    (properties `((upstream-name . "RcppArmadillo")))
> +    (build-system r-build-system)
> +    (propagated-inputs
> +     `(("r-rcpp" ,r-rcpp)))
> +    (home-page "https://github.com/RcppCore/RcppArmadillo")
> +    (synopsis "Rcpp integration for the linear algebra library 'Armadillo'")

“for the Armadillo linear algebra library” maybe?

> +    (description
> +     "Armadillo is a templated C++ linear algebra library that aims towards a
> +good balance between speed and ease of use.  Integer, floating point and
> +complex numbers are supported, as well as a subset of trigonometric and
> +statistics functions.  Various matrix decompositions are provided through
> +optional integration with LAPACK and ATLAS libraries.  This package includes
> +the header files from the templated Armadillo library.")
> +    ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
> +    ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
> +    ;; later, as is the rest of 'Rcpp'.
> +    (license license:gpl2+)))

Does this package bundle a copy of Armadillo?  If yes, it would be great
if we could make a separate Armadillo package that r-rcpparmadillo would
depend on.

WDYT?

> From 64e16086990806f2f30e651dbbf2ff62470b2fcc Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 17 Dec 2015 16:28:25 +0100
> Subject: [PATCH 2/2] gnu: Add AdaptiveSparsity.
>
> * gnu/packages/machine-learning.scm (r-adaptivesparsity): New variable.

LGTM.

Thanks!

Ludo’.

Re: [PATCH] Add ApaptiveSparsity.

[Ricardo Wurmus]

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Ludovic Courtès <ludo@gnu.org> writes:

>> +    (synopsis "Rcpp integration for the linear algebra library 'Armadillo'")
>
> “for the Armadillo linear algebra library” maybe?

Okay.

>> +    (description
>> +     "Armadillo is a templated C++ linear algebra library that aims towards a
>> +good balance between speed and ease of use.  Integer, floating point and
>> +complex numbers are supported, as well as a subset of trigonometric and
>> +statistics functions.  Various matrix decompositions are provided through
>> +optional integration with LAPACK and ATLAS libraries.  This package includes
>> +the header files from the templated Armadillo library.")
>> +    ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
>> +    ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
>> +    ;; later, as is the rest of 'Rcpp'.
>> +    (license license:gpl2+)))
>
> Does this package bundle a copy of Armadillo?  If yes, it would be great
> if we could make a separate Armadillo package that r-rcpparmadillo would
> depend on.

It bundles the headers of a particular version (6.200.2, latest is
6.400.3) of Armadillo.  I just made a package for Armadillo 6.400.3 and
derived a package variant for 6.200.2 (both attached), used that as an
input and removed the includes from RcppArmadillo with a snippet.

The package builds, but there’s a linker problem that I don’t know how
to fix:

    ** testing if installed package can be loaded
    Error in dyn.load(file, DLLpath = DLLpath, ...) : 
      unable to load shared object '/gnu/store/vgnld4sl6ki7k1d70cjqk4rm68iimybp-r-rcpparmadillo-0.6.200.2.0/site-library/RcppArmadillo/libs/RcppArmadillo.so':
      /gnu/store/vgnld4sl6ki7k1d70cjqk4rm68iimybp-r-rcpparmadillo-0.6.200.2.0/site-library/RcppArmadillo/libs/RcppArmadillo.so: undefined symbol: wrapper_dgesv_
    Error: loading failed
    Execution halted
    ERROR: loading failed
    * removing ‘/gnu/store/vgnld4sl6ki7k1d70cjqk4rm68iimybp-r-rcpparmadillo-0.6.200.2.0/site-library/RcppArmadillo’
    phase `install' failed after 21.5 seconds

It’s probably something to do with linking to lapack or something, but I
don’t know how to address this.

The bundled includes in “inst/include/armadillo*” are almost identical
to those provided by the armadillo package.  The “config.hpp” file has
been patched to comment out a couple of defines and a cmake file was
added.

~~ Ricardo


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From 2500805d1aa6bf0890fb43d530da3f4ea6bb39f7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 21 Dec 2015 12:37:23 +0100
Subject: [PATCH 1/2] gnu: Add armadillo.

* gnu/packages/maths.scm (armadillo): New variable.
---
 gnu/packages/maths.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 0c0f013..0d66b9f 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1422,6 +1422,35 @@ output to TeX, and a browser for Maxima's manual including command index and
 full text searching.")
     (license license:gpl2+)))
 
+(define-public armadillo
+  (package
+    (name "armadillo")
+    (version "6.400.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/arma/armadillo-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "0bsgrmldlx77w5x26n3axj1hg6iw6csyw0dwl1flrbdwl51f9701"))))
+    (build-system cmake-build-system)
+    (arguments `(#:tests? #f)) ;no test target
+    (inputs
+     `(("openblas" ,openblas)
+       ("lapack" ,lapack)
+       ("arpack" ,arpack-ng)))
+    (home-page "http://arma.sourceforge.net/")
+    (synopsis "C++ linear algebra library")
+    (description
+     "Armadillo is a C++ linear algebra library, aiming towards a good balance
+between speed and ease of use.  It is useful for algorithm development
+directly in C++, or quick conversion of research code into production
+environments.  It can be used for machine learning, pattern recognition,
+signal processing, bioinformatics, statistics, econometrics, etc.  The library
+provides efficient classes for vectors, matrices and cubes, as well as 150+
+associated functions (eg. contiguous and non-contiguous submatrix views).")
+    (license license:mpl2.0)))
+
 (define-public muparser
   (package
     (name "muparser")
-- 
2.1.0


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From 9017b290c126143598eb6bb5e1c82e899d01b858 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 21 Dec 2015 12:37:38 +0100
Subject: [PATCH 2/2] gnu: Add armadillo 6.200.2.

* gnu/packages/maths.scm (armadillo-for-rcpparmadillo): New variable.
---
 gnu/packages/maths.scm | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 0d66b9f..e7a7b7c 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1451,6 +1451,17 @@ provides efficient classes for vectors, matrices and cubes, as well as 150+
 associated functions (eg. contiguous and non-contiguous submatrix views).")
     (license license:mpl2.0)))
 
+(define-public armadillo-for-rcpparmadillo
+  (package (inherit armadillo)
+    (version "6.200.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge/arma/armadillo-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1f69rlqhnf2wv8khyn2a8vi6gx1i72qgfy8b9b760ssk85dcl763"))))))
+
 (define-public muparser
   (package
     (name "muparser")
-- 
2.1.0

Re: [PATCH] Add ApaptiveSparsity.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> It bundles the headers of a particular version (6.200.2, latest is
> 6.400.3) of Armadillo.  I just made a package for Armadillo 6.400.3 and
> derived a package variant for 6.200.2 (both attached), used that as an
> input and removed the includes from RcppArmadillo with a snippet.

Perfect.

> The package builds, but there’s a linker problem that I don’t know how
> to fix:
>
>     ** testing if installed package can be loaded
>     Error in dyn.load(file, DLLpath = DLLpath, ...) : 
>       unable to load shared object '/gnu/store/vgnld4sl6ki7k1d70cjqk4rm68iimybp-r-rcpparmadillo-0.6.200.2.0/site-library/RcppArmadillo/libs/RcppArmadillo.so':
>       /gnu/store/vgnld4sl6ki7k1d70cjqk4rm68iimybp-r-rcpparmadillo-0.6.200.2.0/site-library/RcppArmadillo/libs/RcppArmadillo.so: undefined symbol: wrapper_dgesv_
>     Error: loading failed
>     Execution halted
>     ERROR: loading failed
>     * removing ‘/gnu/store/vgnld4sl6ki7k1d70cjqk4rm68iimybp-r-rcpparmadillo-0.6.200.2.0/site-library/RcppArmadillo’
>     phase `install' failed after 21.5 seconds
>
> It’s probably something to do with linking to lapack or something, but I
> don’t know how to address this.

Sounds like the command that built RcppArmadillo.so lacked a -llapack or
something (not sure which library provides ‘wrapper_dgesv_’), no?

> From 2500805d1aa6bf0890fb43d530da3f4ea6bb39f7 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Mon, 21 Dec 2015 12:37:23 +0100
> Subject: [PATCH 1/2] gnu: Add armadillo.
>
> * gnu/packages/maths.scm (armadillo): New variable.

[...]

> +    (arguments `(#:tests? #f)) ;no test target
> +    (inputs
> +     `(("openblas" ,openblas)
> +       ("lapack" ,lapack)
> +       ("arpack" ,arpack-ng)))

Since this is a header-only library, are these useful at all?

Also, if they are included in the installed headers, should they be
propagated?

Otherwise LGTM.

> From 9017b290c126143598eb6bb5e1c82e899d01b858 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Mon, 21 Dec 2015 12:37:38 +0100
> Subject: [PATCH 2/2] gnu: Add armadillo 6.200.2.
>
> * gnu/packages/maths.scm (armadillo-for-rcpparmadillo): New variable.

OK.  I would do this as part of the patch that adds RcppArmadillo, but
no big deal.

Thanks!

Ludo’.

Re: [PATCH] Add ApaptiveSparsity.

[Ricardo Wurmus]

Ludovic Courtès <ludo@gnu.org> writes:

>> The package builds, but there’s a linker problem that I don’t know how
>> to fix:
>>
>>     ** testing if installed package can be loaded
>>     Error in dyn.load(file, DLLpath = DLLpath, ...) : 
>>       unable to load shared object '/gnu/store/vgnld4sl6ki7k1d70cjqk4rm68iimybp-r-rcpparmadillo-0.6.200.2.0/site-library/RcppArmadillo/libs/RcppArmadillo.so':
>>       /gnu/store/vgnld4sl6ki7k1d70cjqk4rm68iimybp-r-rcpparmadillo-0.6.200.2.0/site-library/RcppArmadillo/libs/RcppArmadillo.so: undefined symbol: wrapper_dgesv_
>>     Error: loading failed
>>     Execution halted
>>     ERROR: loading failed
>>     * removing ‘/gnu/store/vgnld4sl6ki7k1d70cjqk4rm68iimybp-r-rcpparmadillo-0.6.200.2.0/site-library/RcppArmadillo’
>>     phase `install' failed after 21.5 seconds
>>
>> It’s probably something to do with linking to lapack or something, but I
>> don’t know how to address this.
>
> Sounds like the command that built RcppArmadillo.so lacked a -llapack or
> something (not sure which library provides ‘wrapper_dgesv_’), no?

It lacked “-larmadillo”.  Turns out that the armadillo package produces
a shared library to wrap some lapack/arpack/openblas features.

>> From 2500805d1aa6bf0890fb43d530da3f4ea6bb39f7 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Mon, 21 Dec 2015 12:37:23 +0100
>> Subject: [PATCH 1/2] gnu: Add armadillo.
>>
>> * gnu/packages/maths.scm (armadillo): New variable.
>
> [...]
>
>> +    (arguments `(#:tests? #f)) ;no test target
>> +    (inputs
>> +     `(("openblas" ,openblas)
>> +       ("lapack" ,lapack)
>> +       ("arpack" ,arpack-ng)))
>
> Since this is a header-only library, are these useful at all?

They are optional inputs, and it seems that an actual shared library is
produced (only when they are present?).

>> From 9017b290c126143598eb6bb5e1c82e899d01b858 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Mon, 21 Dec 2015 12:37:38 +0100
>> Subject: [PATCH 2/2] gnu: Add armadillo 6.200.2.
>>
>> * gnu/packages/maths.scm (armadillo-for-rcpparmadillo): New variable.
>
> OK.  I would do this as part of the patch that adds RcppArmadillo, but
> no big deal.

Okay, I’ve merged this patch with the one for r-rcpparmadillo.
Thanks for the review!

~~ Ricardo