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* [bug#51351] [PATCH] gnu: pplacer: Fix build.
@ 2021-10-23 14:30 Julien Lepiller
  2021-11-11 17:47 ` Ricardo Wurmus
                   ` (4 more replies)
  0 siblings, 5 replies; 7+ messages in thread
From: Julien Lepiller @ 2021-10-23 14:30 UTC (permalink / raw)
  To: 51351

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Hi Guix!

This patch series fixes pplacer. I noticed ocaml4.07-re was failing to
build, and others also failed, so this series fixes them, and pplacer.

[-- Attachment #2: 0001-gnu-Add-ocaml4.07-re.patch --]
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From 5a85894ee405d2fbe909b61fb3817aa44d6a08df Mon Sep 17 00:00:00 2001
Message-Id: <5a85894ee405d2fbe909b61fb3817aa44d6a08df.1634999221.git.julien@lepiller.eu>
From: Julien Lepiller <julien@lepiller.eu>
Date: Sat, 23 Oct 2021 15:22:11 +0200
Subject: [PATCH 1/6] gnu: Add ocaml4.07-re.

* gnu/packages/ocaml.scm (ocaml4.07-re): New variable.
---
 gnu/packages/ocaml.scm | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 660bc44bc7..412e9e339d 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -3353,6 +3353,7 @@ (define-public ocaml-re
      `(("ocaml-seq" ,ocaml-seq)))
     (native-inputs
      `(("ounit" ,ocaml-ounit)))
+    (properties `((ocaml4.07-variant . ,(delay ocaml4.07-re))))
     (home-page "https://github.com/ocaml/ocaml-re/")
     (synopsis "Regular expression library for OCaml")
     (description "Pure OCaml regular expressions with:
@@ -3365,6 +3366,19 @@ (define-public ocaml-re
 @end enumerate")
     (license license:expat)))
 
+(define-public ocaml4.07-re
+  (package-with-ocaml4.07
+    (package
+      (inherit ocaml-re)
+      (arguments
+       `(#:test-target "."
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'fix-dune-version
+             (lambda _
+               (delete-file "dune-project"))))))
+      (properties '()))))
+
 (define-public ocaml-ocplib-endian
   (package
     (name "ocaml-ocplib-endian")
-- 
2.33.0


[-- Attachment #3: 0002-gnu-Add-ocaml4.07-alcotest.patch --]
[-- Type: text/x-patch, Size: 2280 bytes --]

From b77fb136a6f1e4ecceb0ddbd2a0318af80721d50 Mon Sep 17 00:00:00 2001
Message-Id: <b77fb136a6f1e4ecceb0ddbd2a0318af80721d50.1634999221.git.julien@lepiller.eu>
In-Reply-To: <5a85894ee405d2fbe909b61fb3817aa44d6a08df.1634999221.git.julien@lepiller.eu>
References: <5a85894ee405d2fbe909b61fb3817aa44d6a08df.1634999221.git.julien@lepiller.eu>
From: Julien Lepiller <julien@lepiller.eu>
Date: Sat, 23 Oct 2021 15:26:54 +0200
Subject: [PATCH 2/6] gnu: Add ocaml4.07-alcotest.

* gnu/packages/ocaml.scm (ocaml4.07-alcotest): New variable.
---
 gnu/packages/ocaml.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 412e9e339d..a8f5faaf1d 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -2268,6 +2268,7 @@ (define-public ocaml-alcotest
        ("ocaml-stdlib-shims" ,ocaml-stdlib-shims)
        ("ocaml-uuidm" ,ocaml-uuidm)
        ("ocaml-uutf" ,ocaml-uutf)))
+    (properties `((ocaml4.07-variant . ,(delay ocaml4.07-alcotest))))
     (home-page "https://github.com/mirage/alcotest")
     (synopsis "Lightweight OCaml test framework")
     (description "Alcotest exposes simple interface to perform unit tests.  It
@@ -2278,6 +2279,30 @@ (define-public ocaml-alcotest
 simple (yet expressive) query language to select the tests to run.")
     (license license:isc)))
 
+(define-public ocaml4.07-alcotest
+  (package-with-ocaml4.07
+    (package
+      (inherit ocaml-alcotest)
+      (version "1.0.1")
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/mirage/alcotest")
+                      (commit version)))
+                (file-name (git-file-name "ocaml-alcotest" version))
+                (sha256
+                 (base32
+                  "1frwi185z4aadmaf0vp8xk5227nyg7nmh28ijj5l7ncjr5slvhz8"))))
+      (arguments
+       `(#:test-target "."
+         #:package "alcotest"
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'fix-dune-version
+             (lambda _
+               (delete-file "dune-project"))))))
+      (properties '()))))
+
 (define-public ocaml-ppx-tools
   (package
     (name "ocaml-ppx-tools")
-- 
2.33.0


[-- Attachment #4: 0003-gnu-ocaml-lwt-Remove-unneeded-input.patch --]
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From 7b0144518fa422088477d764233c1278ce48573e Mon Sep 17 00:00:00 2001
Message-Id: <7b0144518fa422088477d764233c1278ce48573e.1634999221.git.julien@lepiller.eu>
In-Reply-To: <5a85894ee405d2fbe909b61fb3817aa44d6a08df.1634999221.git.julien@lepiller.eu>
References: <5a85894ee405d2fbe909b61fb3817aa44d6a08df.1634999221.git.julien@lepiller.eu>
From: Julien Lepiller <julien@lepiller.eu>
Date: Sat, 23 Oct 2021 16:07:46 +0200
Subject: [PATCH 3/6] gnu: ocaml-lwt: Remove unneeded input.

* gnu/packages/ocaml.scm (ocaml-lwt)[native-inputs]: Remove
ocaml-bisect-ppx.
---
 gnu/packages/ocaml.scm | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index a8f5faaf1d..43011a0aab 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -2427,8 +2427,7 @@ (define-public ocaml-lwt
     (arguments
      `(#:package "lwt"))
     (native-inputs
-     `(("ocaml-bisect-ppx" ,ocaml-bisect-ppx)
-       ("ocaml-cppo" ,ocaml-cppo)
+     `(("ocaml-cppo" ,ocaml-cppo)
        ("pkg-config" ,pkg-config)))
     (inputs
      `(("glib" ,glib)))
-- 
2.33.0


[-- Attachment #5: 0004-gnu-Add-ocaml4.07-bisect-ppx.patch --]
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From e7413cc1b1759ad7049b044d3e6743f572ced836 Mon Sep 17 00:00:00 2001
Message-Id: <e7413cc1b1759ad7049b044d3e6743f572ced836.1634999221.git.julien@lepiller.eu>
In-Reply-To: <5a85894ee405d2fbe909b61fb3817aa44d6a08df.1634999221.git.julien@lepiller.eu>
References: <5a85894ee405d2fbe909b61fb3817aa44d6a08df.1634999221.git.julien@lepiller.eu>
From: Julien Lepiller <julien@lepiller.eu>
Date: Sat, 23 Oct 2021 15:27:56 +0200
Subject: [PATCH 4/6] gnu: Add ocaml4.07-bisect-ppx.

* gnu/packages/ocaml.scm (ocaml4.07-bisect-ppx): New variable.
---
 gnu/packages/ocaml.scm | 30 +++++++++++++++++++++++++++++-
 1 file changed, 29 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 43011a0aab..87429b92ac 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -6625,7 +6625,8 @@ (define-public ocaml-bisect-ppx
     (arguments
      ;; Tests require ocamlformat which would lead to circular dependencies
      '(#:tests? #f))
-    (properties '((upstream-name . "bisect_ppx")))
+    (properties `((upstream-name . "bisect_ppx")
+                  (ocaml4.07-variant . ,(delay ocaml4.07-bisect-ppx))))
     (home-page "https://github.com/aantron/bisect_ppx")
     (synopsis "Code coverage for OCaml")
     (description "Bisect_ppx helps you test thoroughly.  It is a small
@@ -6637,6 +6638,33 @@ (define-public ocaml-bisect-ppx
 then run the Bisect_ppx report tool on the generated visitation files.")
     (license license:mpl2.0)))
 
+(define-public ocaml4.07-bisect-ppx
+  (package-with-ocaml4.07
+    (package
+      (inherit ocaml-bisect-ppx)
+      (version "2.4.0")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/aantron/bisect_ppx")
+               (commit version)))
+         (file-name (git-file-name "ocaml-bisect-ppx" version))
+         (sha256
+          (base32
+           "1njs8xc108rrpx5am5zhhcn6vjva7rsphm8034qp5lgyvnhfgh7q"))))
+      (propagated-inputs
+       `(("ocaml-migrate-parsetree" ,ocaml-migrate-parsetree)
+         ("ocaml-ppx-tools-versioned" ,ocaml-ppx-tools-versioned)
+         ,@(package-propagated-inputs ocaml-bisect-ppx)))
+      (native-inputs
+       `(("ocaml-ounit2" ,ocaml-ounit2)))
+      (arguments
+       `(#:test-target "."
+         ;; tests require git and network
+         #:tests? #f))
+      (properties '()))))
+
 (define-public ocaml-odoc
   (package
     (name "ocaml-odoc")
-- 
2.33.0


[-- Attachment #6: 0005-gnu-ocaml4.07-odoc-Fix-inputs.patch --]
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From 04a94967f5816b42277b099aa2b386b68d13cdee Mon Sep 17 00:00:00 2001
Message-Id: <04a94967f5816b42277b099aa2b386b68d13cdee.1634999221.git.julien@lepiller.eu>
In-Reply-To: <5a85894ee405d2fbe909b61fb3817aa44d6a08df.1634999221.git.julien@lepiller.eu>
References: <5a85894ee405d2fbe909b61fb3817aa44d6a08df.1634999221.git.julien@lepiller.eu>
From: Julien Lepiller <julien@lepiller.eu>
Date: Sat, 23 Oct 2021 15:28:54 +0200
Subject: [PATCH 5/6] gnu: ocaml4.07-odoc: Fix inputs.

* gnu/packages/ocaml.scm (ocaml4.07-odoc): Fix inputs.
---
 gnu/packages/ocaml.scm | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 87429b92ac..f0c46a9b4b 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -6751,6 +6751,12 @@ (define-public ocaml4.07-odoc
         (file-name (git-file-name name version))
         (sha256
          (base32 "0z2nisg1vb5xlk41hqw8drvj90v52wli7zvnih6a844cg6xsvvj2"))))
+    (inputs
+     `(("ocaml-alcotest" ,ocaml-alcotest)
+       ("ocaml-markup" ,ocaml-markup)
+       ("ocaml-sexplib" ,ocaml-sexplib)
+       ("ocaml-re" ,ocaml-re)
+       ("ocaml-uutf" ,ocaml-uutf)))
      (properties '()))))
 
 (define-public ocaml4.07-fftw3
-- 
2.33.0


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From 9a5d8c50f30a25b5246d321d5331b72a88f587f9 Mon Sep 17 00:00:00 2001
Message-Id: <9a5d8c50f30a25b5246d321d5331b72a88f587f9.1634999221.git.julien@lepiller.eu>
In-Reply-To: <5a85894ee405d2fbe909b61fb3817aa44d6a08df.1634999221.git.julien@lepiller.eu>
References: <5a85894ee405d2fbe909b61fb3817aa44d6a08df.1634999221.git.julien@lepiller.eu>
From: Julien Lepiller <julien@lepiller.eu>
Date: Sat, 23 Oct 2021 15:30:04 +0200
Subject: [PATCH 6/6] gnu: pplacer: Fix build.

* gnu/packages/bioinformatics.scm (pplacer): Add missing input.
---
 gnu/packages/bioinformatics.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 63b391683c..41a2e52ac8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -141,6 +141,7 @@ (define-module (gnu packages bioinformatics)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages shells)
   #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages sqlite)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages swig)
   #:use-module (gnu packages tbb)
@@ -13501,7 +13502,8 @@ (define-public pplacer
          ("ocaml-sqlite3" ,(package-with-ocaml4.07 ocaml-sqlite3))
          ("ocaml-xmlm" ,(package-with-ocaml4.07 ocaml-xmlm))
          ("ocaml-mcl" ,(package-with-ocaml4.07 ocaml-mcl))
-         ("ocaml-gsl" ,ocaml4.07-gsl-1)))
+         ("ocaml-gsl" ,ocaml4.07-gsl-1)
+         ("sqlite:static" ,sqlite "static")))
       (native-inputs
        `(("cddlib-src" ,(package-source cddlib))
          ("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild))
-- 
2.33.0


^ permalink raw reply related	[flat|nested] 7+ messages in thread
end of thread, other threads:[~2021-11-16 13:49 UTC | newest]

Thread overview: 7+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2021-10-23 14:30 [bug#51351] [PATCH] gnu: pplacer: Fix build Julien Lepiller
2021-11-11 17:47 ` Ricardo Wurmus
2021-11-15 13:22   ` zimoun
2021-11-15 13:39 ` Efraim Flashner
2021-11-15 13:40 ` Efraim Flashner
2021-11-15 13:42 ` Efraim Flashner
2021-11-16 13:47 ` bug#51351: " Efraim Flashner

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