GNU bug report logs - #38184
[PATCH 0/4] Move r-{quadprog, pracma, subplex, desolve} to gnu/packages/cran.scm

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 0/4] Move r-{quadprog, pracma, subplex,
 desolve} to gnu/packages/cran.scm
Date: Tue, 12 Nov 2019 20:04:37 +0100

Dear,

This series move the packages from maths.scm to cran.scm. The copyright header
is modified accordingly. The packages which depend on are defined in files
already importing the cran module; the maths module cannot be removed of these
files because other packages import other maths packages.

All the best,
simon


zimoun (4):
  gnu: r-quadprog: Move to (gnu packages cran).
  gnu: r-pracma: Move to (gnu packages cran).
  gnu: r-subplex: Move to (gnu packages cran).
  gnu: r-desolve: Move to (gnu packages cran).

 gnu/packages/cran.scm  | 92 +++++++++++++++++++++++++++++++++++++++++-
 gnu/packages/maths.scm | 90 -----------------------------------------
 2 files changed, 91 insertions(+), 91 deletions(-)

-- 
2.23.0

Message #8 received at 38184 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 38184 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 1/4] gnu: r-quadprog: Move to (gnu packages cran).
Date: Tue, 12 Nov 2019 20:15:30 +0100

* gnu/packages/maths.scm (r-quadprog): Move from here...
* gnu/packages/cran.scm (r-quadprog): ...to here.
---
 gnu/packages/cran.scm  | 21 +++++++++++++++++++++
 gnu/packages/maths.scm | 21 ---------------------
 2 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 4662680b19..67959c9280 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15645,3 +15645,24 @@ unique identifiers, and whether it is a certain length.  In addition,
 files and to efficiently import multiple tabular data files into one
 data.table.")
     (license license:gpl3)))
+
+(define-public r-quadprog
+  (package
+    (name "r-quadprog")
+    (version "1.5-7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "quadprog" version))
+       (sha256
+        (base32
+         "0vg7i9p241bwvfdspjbydjrsvgipl6nsb8bjigp0hbbgvxbixx0s"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/quadprog")
+    (synopsis "Functions to solve quadratic programming problems")
+    (description
+     "This package contains routines and documentation for solving quadratic
+programming problems.")
+    (license license:gpl3+)))
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 16a9d97a47..a4452af93e 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2341,27 +2341,6 @@ sparse system of linear equations A x = b using Gaussian elimination.")
     (inputs
      (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
 
-(define-public r-quadprog
-  (package
-    (name "r-quadprog")
-    (version "1.5-7")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "quadprog" version))
-       (sha256
-        (base32
-         "0vg7i9p241bwvfdspjbydjrsvgipl6nsb8bjigp0hbbgvxbixx0s"))))
-    (build-system r-build-system)
-    (native-inputs
-     `(("gfortran" ,gfortran)))
-    (home-page "https://cran.r-project.org/web/packages/quadprog")
-    (synopsis "Functions to solve quadratic programming problems")
-    (description
-     "This package contains routines and documentation for solving quadratic
-programming problems.")
-    (license license:gpl3+)))
-
 (define-public r-pracma
   (package
     (name "r-pracma")
-- 
2.23.0

Message #11 received at 38184 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 38184 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH] gnu: r-desolve: Move to (gnu packages cran).
Date: Tue, 12 Nov 2019 20:15:29 +0100

* gnu/packages/maths.scm (r-desolve): Move from here...
* gnu/packages/cran.scm (r-desolve): ...to here.
---
 gnu/packages/cran.scm  | 30 ++++++++++++++++++++++++++++++
 gnu/packages/maths.scm | 29 -----------------------------
 2 files changed, 30 insertions(+), 29 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 48ddaadd8d..c62b8eb730 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15710,3 +15710,33 @@ It solves unconstrained optimization problems using a simplex method on
 subspaces.  The method is well suited for optimizing objective functions that
 are noisy or are discontinuous at the solution.")
     (license license:gpl3+)))
+
+(define-public r-desolve
+  (package
+    (name "r-desolve")
+    (version "1.24")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "deSolve" version))
+       (sha256
+        (base32
+         "0hkvspq0fp8j64l9zayab2l2nazazhwfgfym0jllh0xv5a12r99s"))))
+    (properties `((upstream-name . "deSolve")))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://desolve.r-forge.r-project.org/")
+    (synopsis "Solvers for initial value problems of differential equations")
+    (description
+     "This package provides functions that solve initial
+value problems of a system of first-order ordinary differential equations (ODE),
+of partial differential equations (PDE), of differential algebraic equations
+(DAE), and of delay differential equations.  The functions provide an interface
+to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
+to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
+the Runge-Kutta family with fixed or variable time steps.  The package contains
+routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
+differential equations (PDE) that have been converted to ODEs by numerical
+differencing.")
+    (license license:gpl2+)))
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 77bd5d246b..80645f47b9 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4343,35 +4343,6 @@ analysed.")
     (arguments
      '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF")))))
 
-(define-public r-desolve
-  (package
-    (name "r-desolve")
-    (version "1.24")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (cran-uri "deSolve" version))
-        (sha256
-         (base32
-          "0hkvspq0fp8j64l9zayab2l2nazazhwfgfym0jllh0xv5a12r99s"))))
-    (properties `((upstream-name . "deSolve")))
-    (build-system r-build-system)
-    (native-inputs
-     `(("gfortran" ,gfortran)))
-    (home-page "https://desolve.r-forge.r-project.org/")
-    (synopsis "Solvers for initial value problems of differential equations")
-    (description "This package provides functions that solve initial
-value problems of a system of first-order ordinary differential equations (ODE),
-of partial differential equations (PDE), of differential algebraic equations
-(DAE), and of delay differential equations.  The functions provide an interface
-to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
-to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
-the Runge-Kutta family with fixed or variable time steps.  The package contains
-routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
-differential equations (PDE) that have been converted to ODEs by numerical
-differencing.")
-    (license license:gpl2+)))
-
 (define-public tcalc
   (package
   (name "tcalc")
-- 
2.23.0

Message #14 received at 38184 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 38184 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 2/4] gnu: r-pracma: Move to (gnu packages cran).
Date: Tue, 12 Nov 2019 20:15:31 +0100

* gnu/packages/maths.scm (r-pracma): Move from here...
* gnu/packages/cran.scm (r-pracma): ...to here.
---
 gnu/packages/cran.scm  | 23 ++++++++++++++++++++++-
 gnu/packages/maths.scm | 18 ------------------
 2 files changed, 22 insertions(+), 19 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 67959c9280..ed416c4a8e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado <at> elephly.net>
 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben <at> gmail.com>
-;;; Copyright © 2017, 2018 Roel Janssen <roel <at> gnu.org>
+;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel <at> gnu.org>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me <at> tobias.gr>
 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo <at> gmail.com>
 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12 <at> gmail.com>
@@ -15666,3 +15666,24 @@ data.table.")
      "This package contains routines and documentation for solving quadratic
 programming problems.")
     (license license:gpl3+)))
+
+(define-public r-pracma
+  (package
+    (name "r-pracma")
+    (version "2.2.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "pracma" version))
+       (sha256
+        (base32
+         "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g"))))
+    (build-system r-build-system)
+    (home-page "https://cran.r-project.org/web/packages/pracma/")
+    (synopsis "Practical numerical math functions")
+    (description
+     "This package provides functions for numerical analysis and
+linear algebra, numerical optimization, differential equations, plus some
+special functions.  It uses Matlab function names where appropriate to simplify
+porting.")
+    (license license:gpl3+)))
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index a4452af93e..3565b99e05 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2341,24 +2341,6 @@ sparse system of linear equations A x = b using Gaussian elimination.")
     (inputs
      (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
 
-(define-public r-pracma
-  (package
-    (name "r-pracma")
-    (version "2.2.5")
-    (source (origin
-      (method url-fetch)
-      (uri (cran-uri "pracma" version))
-      (sha256
-        (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g"))))
-    (build-system r-build-system)
-    (home-page "https://cran.r-project.org/web/packages/pracma/")
-    (synopsis "Practical numerical math functions")
-    (description "This package provides functions for numerical analysis and
-linear algebra, numerical optimization, differential equations, plus some
-special functions.  It uses Matlab function names where appropriate to simplify
-porting.")
-    (license license:gpl3+)))
-
 (define-public ruby-asciimath
   (package
     (name "ruby-asciimath")
-- 
2.23.0

Message #17 received at 38184 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 38184 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 3/4] gnu: r-subplex: Move to (gnu packages cran).
Date: Tue, 12 Nov 2019 20:15:32 +0100

* gnu/packages/maths.scm (r-subplex): Move from here...
* gnu/packages/cran.scm (r-subplex): ...to here.
---
 gnu/packages/cran.scm  | 23 +++++++++++++++++++++++
 gnu/packages/maths.scm | 22 ----------------------
 2 files changed, 23 insertions(+), 22 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ed416c4a8e..48ddaadd8d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15687,3 +15687,26 @@ linear algebra, numerical optimization, differential equations, plus some
 special functions.  It uses Matlab function names where appropriate to simplify
 porting.")
     (license license:gpl3+)))
+
+(define-public r-subplex
+  (package
+    (name "r-subplex")
+    (version "1.5-4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "subplex" version))
+       (sha256
+        (base32
+         "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://cran.r-project.org/web/packages/subplex")
+    (synopsis "Unconstrained optimization using the subplex algorithm")
+    (description
+     "This package implements the Subplex optimization algorithm.
+It solves unconstrained optimization problems using a simplex method on
+subspaces.  The method is well suited for optimizing objective functions that
+are noisy or are discontinuous at the solution.")
+    (license license:gpl3+)))
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 3565b99e05..77bd5d246b 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4343,28 +4343,6 @@ analysed.")
     (arguments
      '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF")))))
 
-(define-public r-subplex
-  (package
-    (name "r-subplex")
-    (version "1.5-4")
-    (source
-    (origin
-      (method url-fetch)
-      (uri (cran-uri "subplex" version))
-      (sha256
-       (base32
-        "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
-    (build-system r-build-system)
-    (native-inputs
-     `(("gfortran" ,gfortran)))
-    (home-page "https://cran.r-project.org/web/packages/subplex")
-    (synopsis "Unconstrained optimization using the subplex algorithm")
-    (description "This package implements the Subplex optimization algorithm.
-It solves unconstrained optimization problems using a simplex method on
-subspaces.  The method is well suited for optimizing objective functions that
-are noisy or are discontinuous at the solution.")
-    (license license:gpl3+)))
-
 (define-public r-desolve
   (package
     (name "r-desolve")
-- 
2.23.0

Message #20 received at 38184 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 38184 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 4/4] gnu: r-desolve: Move to (gnu packages cran).
Date: Tue, 12 Nov 2019 20:15:33 +0100

* gnu/packages/maths.scm (r-desolve): Move from here...
* gnu/packages/cran.scm (r-desolve): ...to here.
---
 gnu/packages/cran.scm  | 30 ++++++++++++++++++++++++++++++
 gnu/packages/maths.scm | 29 -----------------------------
 2 files changed, 30 insertions(+), 29 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 48ddaadd8d..c62b8eb730 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -15710,3 +15710,33 @@ It solves unconstrained optimization problems using a simplex method on
 subspaces.  The method is well suited for optimizing objective functions that
 are noisy or are discontinuous at the solution.")
     (license license:gpl3+)))
+
+(define-public r-desolve
+  (package
+    (name "r-desolve")
+    (version "1.24")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "deSolve" version))
+       (sha256
+        (base32
+         "0hkvspq0fp8j64l9zayab2l2nazazhwfgfym0jllh0xv5a12r99s"))))
+    (properties `((upstream-name . "deSolve")))
+    (build-system r-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (home-page "https://desolve.r-forge.r-project.org/")
+    (synopsis "Solvers for initial value problems of differential equations")
+    (description
+     "This package provides functions that solve initial
+value problems of a system of first-order ordinary differential equations (ODE),
+of partial differential equations (PDE), of differential algebraic equations
+(DAE), and of delay differential equations.  The functions provide an interface
+to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
+to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
+the Runge-Kutta family with fixed or variable time steps.  The package contains
+routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
+differential equations (PDE) that have been converted to ODEs by numerical
+differencing.")
+    (license license:gpl2+)))
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 77bd5d246b..80645f47b9 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4343,35 +4343,6 @@ analysed.")
     (arguments
      '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF")))))
 
-(define-public r-desolve
-  (package
-    (name "r-desolve")
-    (version "1.24")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (cran-uri "deSolve" version))
-        (sha256
-         (base32
-          "0hkvspq0fp8j64l9zayab2l2nazazhwfgfym0jllh0xv5a12r99s"))))
-    (properties `((upstream-name . "deSolve")))
-    (build-system r-build-system)
-    (native-inputs
-     `(("gfortran" ,gfortran)))
-    (home-page "https://desolve.r-forge.r-project.org/")
-    (synopsis "Solvers for initial value problems of differential equations")
-    (description "This package provides functions that solve initial
-value problems of a system of first-order ordinary differential equations (ODE),
-of partial differential equations (PDE), of differential algebraic equations
-(DAE), and of delay differential equations.  The functions provide an interface
-to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
-to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
-the Runge-Kutta family with fixed or variable time steps.  The package contains
-routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
-differential equations (PDE) that have been converted to ODEs by numerical
-differencing.")
-    (license license:gpl2+)))
-
 (define-public tcalc
   (package
   (name "tcalc")
-- 
2.23.0

Message #25 received at 38184-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: 38184-done <at> debbugs.gnu.org
Subject: Re: [bug#38184] [PATCH 0/4] Move r-{quadprog, pracma, subplex,
 desolve} to gnu/packages/cran.scm
Date: Wed, 27 Nov 2019 18:33:52 +0100

Hi simon,

> This series move the packages from maths.scm to cran.scm. The copyright header
> is modified accordingly. The packages which depend on are defined in files
> already importing the cran module; the maths module cannot be removed of these
> files because other packages import other maths packages.

Thank you for this!

I’ve applied these patches (or rather recreations of them due to various
little problems that are not your fault) and also removed (gnu
build-system r) from (gnu packages maths) with commit f3640e7395.

--
Ricardo

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