[bug#56282] [PATCH 0/7] Update octave.

[bug#56282] [PATCH 0/7] Update octave.

[Greg Hogan]

This patchset updates octave and failing dependent packages, with the
exception of the currently failing r-ifultools.

Greg Hogan (7):
  gnu: octave: Update to 7.1.0.
  gnu: Add r-metadat.
  gnu: Add r-mathjaxr.
  gnu: r-metafor: Update to 3.4-0.
  gnu: gnuradio: Update to 3.10.3.0.
  gnu: gr-satellites: Update to 4.6.0.
  gnu: gnss-sdr: Update to 0.0.17.

 gnu/packages/cran.scm  | 46 +++++++++++++++++++++++++++++++++++++++---
 gnu/packages/maths.scm |  4 ++--
 gnu/packages/radio.scm | 21 ++++++++++++-------
 3 files changed, 59 insertions(+), 12 deletions(-)

-- 
2.36.1

[bug#56282] [PATCH 1/7] gnu: octave: Update to 7.1.0.

[Greg Hogan]

* gnu/packages/maths.scm (octave): Update to 7.1.0.
---
 gnu/packages/maths.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 5e8fd7ae2d..8268b8954e 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2657,7 +2657,7 @@ (define-public ceres-solver-benchmarks
 (define-public octave-cli
   (package
     (name "octave-cli")
-    (version "6.2.0")
+    (version "7.1.0")
     (source
      (origin
       (method url-fetch)
@@ -2665,7 +2665,7 @@ (define-public octave-cli
                           version ".tar.xz"))
       (sha256
        (base32
-        "06id09zspya24gshcwgp039cp35c06150mdlxysawgnbrhj16wkv"))))
+        "0wv26nsfi6cq80np6p4av4wfrvbaflca6szajf6c60mbpdg63m1z"))))
     (build-system gnu-build-system)
     (inputs
      `(("alsa-lib" ,alsa-lib)
-- 
2.36.1

[bug#56282] [PATCH 2/7] gnu: Add r-metadat.

[Greg Hogan]

* gnu/packages/cran.scm (r-metadat): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 96dca393e6..bb2519bcda 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -33438,3 +33438,24 @@ (define-public r-zoeppritz
 coefficients or scattering amplitudes, for seismological P and S-waves at an
 interface.")
     (license license:gpl2+)))
+
+(define-public r-metadat
+  (package
+    (name "r-metadat")
+    (version "1.2-0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "metadat" version))
+              (sha256
+               (base32
+                "1f7mb3pw5d0akr09jjva06ay223izhpzbr21bapnw99x1kiybk7h"))))
+    (properties `((upstream-name . "metadat")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-mathjaxr))
+    (home-page "https://github.com/wviechtb/metadat")
+    (synopsis "Meta-Analysis Datasets")
+    (description
+     "This package provides a collection of meta-analysis datasets for teaching
+purposes, illustrating/testing meta-analytic methods, and validating published
+analyses.")
+    (license license:gpl2+)))
-- 
2.36.1

[bug#56282] [PATCH 3/7] gnu: Add r-mathjaxr.

[Greg Hogan]

* gnu/packages/cran.scm (r-mathjaxr): New variable.
---
 gnu/packages/cran.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index bb2519bcda..b7387e444f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -33459,3 +33459,22 @@ (define-public r-metadat
 purposes, illustrating/testing meta-analytic methods, and validating published
 analyses.")
     (license license:gpl2+)))
+
+(define-public r-mathjaxr
+  (package
+    (name "r-mathjaxr")
+    (version "1.6-0")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "mathjaxr" version))
+              (sha256
+               (base32
+                "0yf1sfkb2kjsplipl2v4k2gp20li9xzsynclg228sy0v243pdi7c"))))
+    (properties `((upstream-name . "mathjaxr")))
+    (build-system r-build-system)
+    (home-page "https://github.com/wviechtb/mathjaxr")
+    (synopsis "Using 'Mathjax' in Rd Files")
+    (description
+     "This package provides 'MathJax' and macros to enable its use within Rd files for
+rendering equations in the HTML help files.")
+    (license license:gpl3)))
-- 
2.36.1

[bug#56282] [PATCH 4/7] gnu: r-metafor: Update to 3.4-0.

[Greg Hogan]

* gnu/packages/cran.scm (r-metafor): Update to 3.4-0.
[propagated-inputs]: Add r-mathjaxr r-metadat r-pbapply.
---
 gnu/packages/cran.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b7387e444f..3fa6101900 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -29149,18 +29149,18 @@ (define-public r-mlecens
 (define-public r-metafor
   (package
     (name "r-metafor")
-    (version "2.4-0")
+    (version "3.4-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "metafor" version))
        (sha256
         (base32
-         "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn"))))
+         "0vn244xfgq7yxwl6ykvadb305z360ssc9vzva7kbcdfiqhhvrqcj"))))
     (properties `((upstream-name . "metafor")))
     (build-system r-build-system)
     (propagated-inputs
-     (list r-matrix r-nlme))
+     (list r-mathjaxr r-matrix r-metadat r-nlme r-pbapply))
     (home-page "https://cran.r-project.org/web/packages/metafor/")
     (synopsis "Meta-analysis package for R")
     (description
-- 
2.36.1

[bug#56282] [PATCH 5/7] gnu: gnuradio: Update to 3.10.3.0.

[Greg Hogan]

* gnu/packages/radio.scm (gnuradio): Update to 3.10.3.0.
[native-inputs]: Add python-jsonschema and soapysdr.
[propagated-inputs]: Add spdlog.
[arguments]<#:configure-flags>: Add -DENABLE_GRC=ON.
---
 gnu/packages/radio.scm | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index c25cdbc20c..e014707e44 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -542,7 +542,7 @@ (define-public redsea
 (define-public gnuradio
   (package
     (name "gnuradio")
-    (version "3.9.2.0")
+    (version "3.10.3.0")
     (source
      (origin
        (method git-fetch)
@@ -551,7 +551,7 @@ (define-public gnuradio
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "01wyqazrpphmb0fl69j93k0w4vm4d1l4177m1fyg7qx8hzia0aaq"))))
+        (base32 "0xdhb2blzajxpi0f2ch23hh6bzdwz5q7syi3bmiqzdjlj2yjfzd4"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("doxygen" ,doxygen)
@@ -589,6 +589,7 @@ (define-public gnuradio
        ("python" ,python)
        ("python-click" ,python-click)
        ("python-click-plugins" ,python-click-plugins)
+       ("python-jsonschema" ,python-jsonschema)
        ("python-lxml" ,python-lxml)
        ("python-matplotlib" ,python-matplotlib)
        ("python-numpy" ,python-numpy)
@@ -600,8 +601,11 @@ (define-public gnuradio
        ("qtbase" ,qtbase-5)
        ("qwt" ,qwt)
        ("sdl" ,sdl)
+       ("soapysdr" ,soapysdr)
        ("volk" ,volk)
        ("zeromq" ,zeromq)))
+    (propagated-inputs
+     (list spdlog))
     (arguments
      `(#:modules ((guix build cmake-build-system)
                   ((guix build glib-or-gtk-build-system) #:prefix glib-or-gtk:)
@@ -612,7 +616,8 @@ (define-public gnuradio
                            (guix build glib-or-gtk-build-system)
                            (guix build python-build-system))
        #:configure-flags
-       (list (string-append "-DMATHJAX2_ROOT="
+       (list "-DENABLE_GRC=ON"
+             (string-append "-DMATHJAX2_ROOT="
                             (assoc-ref %build-inputs "js-mathjax")
                             "/share/javascript/mathjax"))
        #:phases
-- 
2.36.1

[bug#56282] [PATCH 6/7] gnu: gr-satellites: Update to 4.6.0.

[Greg Hogan]

* gnu/packages/radio.scm (gr-satellites): Update to 4.6.0.
---
 gnu/packages/radio.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index e014707e44..d7b7f60d97 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -847,7 +847,7 @@ (define-public gr-iqbal
 (define-public gr-satellites
   (package
     (name "gr-satellites")
-    (version "4.2.0")
+    (version "4.6.0")
     (source
      (origin
        (method git-fetch)
@@ -856,7 +856,7 @@ (define-public gr-satellites
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "01p9cnwjxas3pkqr9m5fnrgm45cji0sfdqqa51hzy7izx9vgzaf8"))))
+        (base32 "0mcrxwb27n2v8v8vmcmmm1pbmy3c02a22mz2wnpdsfb2163qpchw"))))
     (build-system cmake-build-system)
     (native-inputs
      (list pkg-config pybind11 python-six))
-- 
2.36.1

[bug#56282] [PATCH 7/7] gnu: gnss-sdr: Update to 0.0.17.

[Greg Hogan]

* gnu/packages/radio.scm (gnss-sdr): Update to 0.0.17.
[inputs]: Add fmt.
---
 gnu/packages/radio.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index d7b7f60d97..efee0e2f31 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -79,6 +79,7 @@ (define-module (gnu packages radio)
   #:use-module (gnu packages popt)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages protobuf)
+  #:use-module (gnu packages pretty-print)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
@@ -2506,7 +2507,7 @@ (define-public urh
 (define-public gnss-sdr
   (package
     (name "gnss-sdr")
-    (version "0.0.15")
+    (version "0.0.17")
     (source
      (origin
        (method git-fetch)
@@ -2515,7 +2516,7 @@ (define-public gnss-sdr
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1m41rnlfr1nrzbg382jfsk5x0by2ym48v3innd2rbc6phd85q223"))))
+        (base32 "0kxn98vmrsd2a157cf3hsmivi6p4k4a3907j5w8hmcs0nn92786i"))))
     (build-system cmake-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)
@@ -2527,6 +2528,7 @@ (define-public gnss-sdr
     (inputs
      (list armadillo
            boost
+           fmt
            gflags
            glog
            gmp
-- 
2.36.1

bug#56282: [PATCH 0/7] Update octave.

[Guillaume Le Vaillant]

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Patches pushed as 4eddce8ce9337fd4d8f4fd97b7d41ac3cef4e3f0 and
following.
Thanks.

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[bug#56282] [PATCH 3/7] gnu: Add r-mathjaxr.

[Maxime Devos]

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Greg Hogan schreef op di 28-06-2022 om 15:22 [+0000]:
> * gnu/packages/cran.scm (r-mathjaxr): New variable.

This patch was (will be?) reverted as mentioned on #guix because ...

> +    (source (origin
> +              (method url-fetch)
> +              (uri (cran-uri "mathjaxr" version))
> +              (sha256
> +               (base32
> +                "0yf1sfkb2kjsplipl2v4k2gp20li9xzsynclg228sy0v243pdi7c"))))

... it bundles mathjax, and it isn't built from source.

> +    (properties `((upstream-name . "mathjaxr")))
> +    (build-system r-build-system)
> +    (home-page "https://github.com/wviechtb/mathjaxr")
> +    (synopsis "Using 'Mathjax' in Rd Files")
> +    (description
> +     "This package provides 'MathJax' and macros to enable its use within Rd files for
> +rendering equations in the HTML help files.")
> +    (license license:gpl3)))

also, the license information is incorrect -- the mathjax is
Apache 2.0, and it's a rather important component, so I think it should
be listed.

Greetings,
Maxime.

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