Patchwork gnu: Add hdf4

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Submitter Thomas Danckaert
Date Oct. 11, 2016, 8:57 a.m.
Message ID <20161011.105744.1519945377775544087.post@thomasdanckaert.be>
Download mbox | patch
Permalink /patch/16419/
State New
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Comments

Thomas Danckaert - Oct. 11, 2016, 8:57 a.m.
Hi Guix,

this patch continues the work done by Jeremy Robst to package HDF4

(https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00069.html)

 - Back then, people reported occasional build failures. I've disabled
   parallel tests and don't have any problems on my system anymore
   (maybe someone else can test?).

 - I've added a patch to allow a shared build with Fortran interface,
   and some substitutions to remove bogus RPATH settings from the
   Makefiles (otherwise, build directories are included in the RPATH).

 - I've also added a variant “hdf4-alt”: by default, HDF4 includes a
   netCDF API to access HDF4 files, which clashes with the symbols in
   the real netCDF library when you try to use both libraries in your
   program.  This variant uses the “--disable-netcdf” configure flag
   to avoid this.  We could call it “hdf4-nonetcdf”, but the name
   “hdf4-alt” is used by Debian, so maybe it's good to use the same?

best,

Thomas
Ludovic Courtès - Oct. 12, 2016, 12:54 p.m.
Hello!

Thomas Danckaert <post@thomasdanckaert.be> skribis:

> this patch continues the work done by Jeremy Robst to package HDF4
>
> (https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00069.html)

Nice!

>  - Back then, people reported occasional build failures. I've disabled
>    parallel tests and don't have any problems on my system anymore
>    (maybe someone else can test?).

Will do.

>  - I've added a patch to allow a shared build with Fortran interface,
>    and some substitutions to remove bogus RPATH settings from the
>    Makefiles (otherwise, build directories are included in the RPATH).
>
>  - I've also added a variant “hdf4-alt”: by default, HDF4 includes a
>    netCDF API to access HDF4 files, which clashes with the symbols in
>    the real netCDF library when you try to use both libraries in your
>    program.  This variant uses the “--disable-netcdf” configure flag
>    to avoid this.  We could call it “hdf4-nonetcdf”, but the name
>    “hdf4-alt” is used by Debian, so maybe it's good to use the same?

Would “hdf4-minimal” sound appropriate here?  That’s a convention we use
in similar cases.  Otherwise “hdf4-alt” is fine with me.

> From dd7eca9a3cfec364a05aa0f52b941f09b4dea039 Mon Sep 17 00:00:00 2001
> From: Thomas Danckaert <thomas.danckaert@gmail.com>
> Date: Wed, 28 Sep 2016 10:34:58 +0200
> Subject: [PATCH] gnu: Add hdf4
>
> * gnu/packages/maths.scm (hdf4, hdf4-alt): New variables.
> * gnu/packages/patches/hdf4-reproducibility.patch: New file.
> * gnu/packages/patches/hdf4-shared-fortran.patch: New file.
> * gnu/local.mk (dist_patch_DATA): Add patches.

Please credit Jeremy in a “Co-authored-by” tag.

I only have cosmetic comments:

> +             (substitute*
> +                 (map (lambda (dir) (string-append dir "/Makefile.in"))
> +                      '("hdf" "hdf/examples" "hdf/fortran" "hdf/src"
> +                        "hdf/test" "hdf/util" "mfhdf" "mfhdf/dumper"
> +                        "mfhdf/examples" "mfhdf/fortran" "mfhdf/hdfimport"
> +                        "mfhdf/hdiff" "mfhdf/hrepack" "mfhdf/libsrc"
> +                        "mfhdf/ncgen" "mfhdf/ncdump" "mfhdf/nctest"
> +                        "mfhdf/test" "mfhdf/xdr"))

Maybe simply (find-files "." "^Makefile\\.in$")?

> --- /dev/null
> +++ b/gnu/packages/patches/hdf4-reproducibility.patch
> @@ -0,0 +1,47 @@
> +Remove/patch unreproducible config data.
> +---
> + configure           | 9 ++++++++-
> + libhdf4.settings.in | 6 +++---
> + 2 files changed, 11 insertions(+), 4 deletions(-)
> +
> +diff --git a/configure b/configure
> +index eb9f346..ebab94d 100755
> +--- a/configure
> ++++ b/configure
> +@@ -23163,7 +23163,14 @@ H4_VERSION="`cut -d' ' -f3 $srcdir/README.txt | head -1`"
> + 
> + 
> + ## Configuration date
> +- CONFIG_DATE="`date`"
> ++CONFIG_DATE="`date -u`"
> ++if test -n "$SOURCE_DATE_EPOCH"; then
> ++  CONFIG_DATE=`date -u -d "@$SOURCE_DATE_EPOCH" 2>/dev/null \
> ++               || date -u -r "$SOURCE_DATE_EPOCH" 2>/dev/null`
> ++  if test -z "$CONFIG_DATE"; then
> ++    as_fn_error $? "malformed SOURCE_DATE_EPOCH" "$LINENO" 5
> ++  fi
> ++fi

It’d be enough to just do:

- CONFIG_DATE="`date`"
+ CONFIG_DATE="$SOURCE_DATE_EPOCH"

The smaller the patch, the better.  :-)

Otherwise LGTM.  Could you send an updated patch?

Thank you!

Ludo’.

Patch

From dd7eca9a3cfec364a05aa0f52b941f09b4dea039 Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <thomas.danckaert@gmail.com>
Date: Wed, 28 Sep 2016 10:34:58 +0200
Subject: [PATCH] gnu: Add hdf4

* gnu/packages/maths.scm (hdf4, hdf4-alt): New variables.
* gnu/packages/patches/hdf4-reproducibility.patch: New file.
* gnu/packages/patches/hdf4-shared-fortran.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add patches.
---
 gnu/local.mk                                    |  2 +
 gnu/packages/maths.scm                          | 65 +++++++++++++++++++++++++
 gnu/packages/patches/hdf4-reproducibility.patch | 47 ++++++++++++++++++
 gnu/packages/patches/hdf4-shared-fortran.patch  | 25 ++++++++++
 4 files changed, 139 insertions(+)
 create mode 100644 gnu/packages/patches/hdf4-reproducibility.patch
 create mode 100644 gnu/packages/patches/hdf4-shared-fortran.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 1ce95f2..1b65e74 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -570,6 +570,8 @@  dist_patch_DATA =						\
   %D%/packages/patches/gtk3-respect-GUIX_GTK3_PATH.patch	\
   %D%/packages/patches/gtk3-respect-GUIX_GTK3_IM_MODULE_FILE.patch \
   %D%/packages/patches/gtkglext-disable-disable-deprecated.patch \
+  %D%/packages/patches/hdf4-shared-fortran.patch 		\
+  %D%/packages/patches/hdf4-reproducibility.patch 		\
   %D%/packages/patches/hdf5-config-date.patch			\
   %D%/packages/patches/hdf-eos5-build-shared.patch 		\
   %D%/packages/patches/hdf-eos5-remove-gctp.patch		\
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index d5e82bb..72abe58 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -445,6 +445,71 @@  computations.")
     (home-page "https://github.com/OkoSanto/GCTP")
     (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
 
+(define-public hdf4
+  (package
+    (name "hdf4")
+    (version "4.2.11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
+                           version "/src/hdf-" version ".tar.bz2"))
+       (sha256
+        (base32 "16yr50j845zlfx20skmw3y75ww77akk9gg0affjqkg66ih5r03mv"))
+       (patches (search-patches "hdf4-reproducibility.patch"
+                                "hdf4-shared-fortran.patch"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("gfortran" ,gfortran)
+       ("bison" ,bison)
+       ("flex" ,flex)))
+    (inputs
+     `(("zlib" ,zlib)
+       ("libjpeg" ,libjpeg)))
+    (arguments
+     `(#:parallel-tests? #f
+       #:configure-flags '("--enable-shared")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'patchbuild
+           (lambda _
+             (substitute*
+                 '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
+               (("/bin/rm") "rm")
+               (("/bin/mkdir") "mkdir"))
+             (substitute*
+                 (map (lambda (dir) (string-append dir "/Makefile.in"))
+                      '("hdf" "hdf/examples" "hdf/fortran" "hdf/src"
+                        "hdf/test" "hdf/util" "mfhdf" "mfhdf/dumper"
+                        "mfhdf/examples" "mfhdf/fortran" "mfhdf/hdfimport"
+                        "mfhdf/hdiff" "mfhdf/hrepack" "mfhdf/libsrc"
+                        "mfhdf/ncgen" "mfhdf/ncdump" "mfhdf/nctest"
+                        "mfhdf/test" "mfhdf/xdr"))
+               (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
+-R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
+               (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
+-R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
+-R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") "")))))))
+    (home-page "https://www.hdfgroup.org/products/hdf4/")
+    (synopsis
+     "Library and multi-object file format for storing and managing data")
+    (description "HDF4 is a library and multi-object file format for storing
+and managing data between machines.  HDF4 is an older hierarchical data format,
+incompatible with HDF5.")
+    (license
+     (license:non-copyleft
+      "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
+
+(define-public hdf4-alt
+  (package
+    (inherit hdf4)
+    (name "hdf4-alt")
+    (arguments
+     (substitute-keyword-arguments (package-arguments hdf4)
+       ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
+    (synopsis
+     "HDF4 without netCDF API, can be combined with the regular netCDF library")))
+
 (define-public hdf5
   (package
     (name "hdf5")
diff --git a/gnu/packages/patches/hdf4-reproducibility.patch b/gnu/packages/patches/hdf4-reproducibility.patch
new file mode 100644
index 0000000..2c66bec
--- /dev/null
+++ b/gnu/packages/patches/hdf4-reproducibility.patch
@@ -0,0 +1,47 @@ 
+Remove/patch unreproducible config data.
+---
+ configure           | 9 ++++++++-
+ libhdf4.settings.in | 6 +++---
+ 2 files changed, 11 insertions(+), 4 deletions(-)
+
+diff --git a/configure b/configure
+index eb9f346..ebab94d 100755
+--- a/configure
++++ b/configure
+@@ -23163,7 +23163,14 @@ H4_VERSION="`cut -d' ' -f3 $srcdir/README.txt | head -1`"
+ 
+ 
+ ## Configuration date
+- CONFIG_DATE="`date`"
++CONFIG_DATE="`date -u`"
++if test -n "$SOURCE_DATE_EPOCH"; then
++  CONFIG_DATE=`date -u -d "@$SOURCE_DATE_EPOCH" 2>/dev/null \
++               || date -u -r "$SOURCE_DATE_EPOCH" 2>/dev/null`
++  if test -z "$CONFIG_DATE"; then
++    as_fn_error $? "malformed SOURCE_DATE_EPOCH" "$LINENO" 5
++  fi
++fi
+ 
+ ## User doing the configuration
+  CONFIG_USER="`whoami`@`hostname`"
+diff --git a/libhdf4.settings.in b/libhdf4.settings.in
+index 1d9bbb9..4180d72 100644
+--- a/libhdf4.settings.in
++++ b/libhdf4.settings.in
+@@ -5,10 +5,10 @@ General Information:
+ -------------------
+ 		   HDF4 Version: @H4_VERSION@
+ 		  Configured on: @CONFIG_DATE@
+-		  Configured by: @CONFIG_USER@
++		  Configured by: guix
+ 		 Configure mode: @CONFIG_MODE@
+-		    Host system: @host_cpu@-@host_vendor@-@host_os@
+-              Uname information: @UNAME_INFO@
++		    Host system: guix
++              Uname information: guix
+ 		      Libraries: @STATIC_SHARED@
+ 	     Installation point: @prefix@
+ 
+-- 
+2.10.0
+
diff --git a/gnu/packages/patches/hdf4-shared-fortran.patch b/gnu/packages/patches/hdf4-shared-fortran.patch
new file mode 100644
index 0000000..60db355
--- /dev/null
+++ b/gnu/packages/patches/hdf4-shared-fortran.patch
@@ -0,0 +1,25 @@ 
+Allow building a shared library with Fortran.
+---
+ configure | 6 ------
+ 1 file changed, 6 deletions(-)
+
+diff --git a/configure b/configure
+index f37d2fa..eb9f346 100755
+--- a/configure
++++ b/configure
+@@ -6141,12 +6141,6 @@ if test "X${enable_shared}" != "Xyes"; then
+     enable_shared="no"
+ fi
+ 
+-if test "X${enable_shared}" = "Xyes"; then
+-    if test "X${BUILD_FORTRAN}" = "Xyes"; then
+-        as_fn_error $? "Cannot build shared fortran libraries. Please configure with --disable-fortran flag." "$LINENO" 5
+-    fi
+-fi
+-
+ 
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ln -s works" >&5
+ $as_echo_n "checking whether ln -s works... " >&6; }
+-- 
+2.10.0
+
-- 
2.10.0