Subject: bug#51351: closed (Re: [bug#51351] [PATCH] gnu: pplacer: Fix build.)

From: [email-masked] (GNU bug Tracking System)
Date: Tue, 16 Nov 2021 13:49:02 +0000

Your bug report

#51351: [PATCH] gnu: pplacer: Fix build.

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to [email-masked].

-- 
51351: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=51351
GNU Bug Tracking System
Contact [email-masked] with problems

Subject: Re: [bug#51351] [PATCH] gnu: pplacer: Fix build.
From: Efraim Flashner <[email-masked]>
To: Julien Lepiller <[email-masked]>
Cc: [email-masked]
Date: Tue, 16 Nov 2021 15:47:41 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

On Sat, Oct 23, 2021 at 04:30:08PM +0200, Julien Lepiller wrote:
> 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.

I ended up pushing this patch set for you. Thanks!

-- 
Efraim Flashner   <[email-masked]>   רנשלפ םירפא
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Subject: [PATCH] gnu: pplacer: Fix build.
From: Julien Lepiller <[email-masked]>
To: [email-masked]
Date: Sat, 23 Oct 2021 16:30:08 +0200
List-Id: <debbugs-submit.debbugs.gnu.org>

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.
>From 5a85894ee405d2fbe909b61fb3817aa44d6a08df Mon Sep 17 00:00:00 2001
Message-Id: <[email-masked]>
From: Julien Lepiller <[email-masked]>
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

>From b77fb136a6f1e4ecceb0ddbd2a0318af80721d50 Mon Sep 17 00:00:00 2001
Message-Id: <[email-masked]>
In-Reply-To: <[email-masked]>
References: <[email-masked]>
From: Julien Lepiller <[email-masked]>
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

>From 7b0144518fa422088477d764233c1278ce48573e Mon Sep 17 00:00:00 2001
Message-Id: <[email-masked]>
In-Reply-To: <[email-masked]>
References: <[email-masked]>
From: Julien Lepiller <[email-masked]>
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

>From e7413cc1b1759ad7049b044d3e6743f572ced836 Mon Sep 17 00:00:00 2001
Message-Id: <[email-masked]>
In-Reply-To: <[email-masked]>
References: <[email-masked]>
From: Julien Lepiller <[email-masked]>
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

>From 04a94967f5816b42277b099aa2b386b68d13cdee Mon Sep 17 00:00:00 2001
Message-Id: <[email-masked]>
In-Reply-To: <[email-masked]>
References: <[email-masked]>
From: Julien Lepiller <[email-masked]>
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

>From 9a5d8c50f30a25b5246d321d5331b72a88f587f9 Mon Sep 17 00:00:00 2001
Message-Id: <[email-masked]>
In-Reply-To: <[email-masked]>
References: <[email-masked]>
From: Julien Lepiller <[email-masked]>
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