>From f1a3bc9dcfbe9091110aacf353d8224a88788292 Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <thomas.dancka...@gmail.com>
Date: Fri, 17 Jun 2016 10:51:38 +0200
Subject: [PATCH] gnu: Add hdf-eos5.
* gnu/packages/maths.scm (hdf-eos5): New variable.
* gnu/packages/patches/hdf-eos5-build-shared.patch: New file.
* gnu/packages/patches/hdf-eos5-remove-gctp.patch: New file.
* gnu/packages/patches/hdf-eos5-fix-szip.patch: New file.
---
gnu/packages/maths.scm | 45 ++++++++++++
gnu/packages/patches/hdf-eos5-build-shared.patch | 88 ++++++++++++++++++++++++
gnu/packages/patches/hdf-eos5-fix-szip.patch | 32 +++++++++
gnu/packages/patches/hdf-eos5-headers.patch | 14 ++++
gnu/packages/patches/hdf-eos5-remove-gctp.patch | 61 ++++++++++++++++
5 files changed, 240 insertions(+)
create mode 100644 gnu/packages/patches/hdf-eos5-build-shared.patch
create mode 100644 gnu/packages/patches/hdf-eos5-fix-szip.patch
create mode 100644 gnu/packages/patches/hdf-eos5-headers.patch
create mode 100644 gnu/packages/patches/hdf-eos5-remove-gctp.patch
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 0401cd3..1cc041d 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -42,6 +42,7 @@
#:use-module (guix build-system gnu)
#:use-module (guix build-system r)
#:use-module (gnu packages algebra)
+ #:use-module (gnu packages autotools)
#:use-module (gnu packages bison)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
@@ -483,6 +484,50 @@ extremely large and complex data collections.")
(license (license:x11-style
"http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING";))))
+(define-public hdf-eos5
+ (package
+ (name "hdf-eos5")
+ (version "1.15")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
+/edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
+ (sha256
+ (base32
+ "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
+ (patches (search-patches "hdf-eos5-build-shared.patch"
+ "hdf-eos5-remove-gctp.patch"
+ "hdf-eos5-fix-szip.patch"
+ "hdf-eos5-headers.patch"))))
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("libtool" ,libtool)))
+ (build-system gnu-build-system)
+ (inputs
+ `(("hdf5" ,hdf5)
+ ("zlib" ,zlib)
+ ("gctp" ,gctp)))
+ (arguments
+ `(#:configure-flags '("--enable-install-include")
+ #:phases
+ (modify-phases %standard-phases
+ (add-before
+ 'configure 'autogen
+ (lambda _ ; configure.ac was patched
+ (and (chmod "./configure" #o755)
+ (zero? (system* "autoreconf" "--install"))))))
+ #:parallel-tests? #f))
+ (synopsis
+ "HDF-EOS5: HDF5-based data format for NASA's Earth Observing System")
+ (description
+ "HDF-EOS5 is a software library built on HDF5 to support the construction
+of data structures used in NASA's Earth Observing System (Grid, Point and
+Swath).")
+ (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5";)
+ (license (license:bsd-style
+ "http://www.hdfeos.org/software/library.php#HDF-EOS5";))))
+
(define-public hdf5-parallel-openmpi
(package (inherit hdf5)
(name "hdf5-parallel-openmpi")
diff --git a/gnu/packages/patches/hdf-eos5-build-shared.patch b/gnu/packages/patches/hdf-eos5-build-shared.patch
new file mode 100644
index 0000000..d1b4806
--- /dev/null
+++ b/gnu/packages/patches/hdf-eos5-build-shared.patch
@@ -0,0 +1,88 @@
+Allow shared build.
+
+We remove all references to the 'testdrivers' directory. This directory is
+not included in the distributed source archive, and its absence trips up
+automake.
+
+---
+ Makefile.am | 6 ------
+ configure.ac | 12 ------------
+ include/HE5_HdfEosDef.h | 1 +
+ src/Makefile.am | 3 ++-
+ 4 files changed, 3 insertions(+), 19 deletions(-)
+
+diff --git a/Makefile.am b/Makefile.am
+index 363bcfb..01ed024 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -3,13 +3,7 @@
+ # Include boilerplate
+ include $(top_srcdir)/config/include.am
+
+-# List of subdirectories.
+-# Only build the testdrivers directory if configure detected that it's present.
+-if TESTDRIVERS_CONDITIONAL
+-TESTDRIVERS=testdrivers
+-else
+ TESTDRIVERS=
+-endif
+
+ if INSTALL_INCLUDE_CONDITIONAL
+ INCLUDE=include
+diff --git a/configure.ac b/configure.ac
+index 5d48b43..cfa9d4e 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -13,9 +13,6 @@ AC_CONFIG_AUX_DIR([config])
+ AM_INIT_AUTOMAKE([foreign])
+ AM_MAINTAINER_MODE
+
+-# Disable shared libraries (for now)
+-AC_DISABLE_SHARED
+-
+ AM_PROG_LIBTOOL
+
+ dnl ----------------------------------------------------------------------
+@@ -597,13 +594,4 @@ AC_CONFIG_FILES([Makefile
+ gctp/src/Makefile
+ samples/Makefile])
+
+-if test "X$TESTDRIVERS_DIR" = "Xyes"; then
+- AC_CONFIG_FILES([ testdrivers/Makefile
+- testdrivers/grid/Makefile
+- testdrivers/point/Makefile
+- testdrivers/swath/Makefile
+- testdrivers/threads/Makefile
+- testdrivers/za/Makefile])
+-fi
+-
+ AC_OUTPUT
+diff --git a/include/HE5_HdfEosDef.h b/include/HE5_HdfEosDef.h
+index 9ed7881..abf0a90 100755
+--- a/include/HE5_HdfEosDef.h
++++ b/include/HE5_HdfEosDef.h
+@@ -24,6 +24,7 @@
+ #ifndef HE5_HDFEOSDEF_H_
+ #define HE5_HDFEOSDEF_H_
+
++#define H5_USE_16_API 1 // required for compilation with recent HDF5
+ #include <hdf5.h>
+
+ #ifdef H5_USE_16_API
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 76b1d4c..daf7ad8 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -10,7 +10,8 @@ INCLUDES=-I$(top_srcdir)/include/
+
+ # Set LDFLAGS to allow the HDF-EOS library to use extern variables from
+ # HDF5
+-LDFLAGS=-Wl,-single_module
++LDFLAGS+= -shrext .so
++LIBS+= -lhdf5_hl -lhdf5 -lm
+
+ # Build HDF-EOS5
+ lib_LTLIBRARIES=libhe5_hdfeos.la
+--
+2.5.0
+
diff --git a/gnu/packages/patches/hdf-eos5-fix-szip.patch b/gnu/packages/patches/hdf-eos5-fix-szip.patch
new file mode 100644
index 0000000..f66ad51
--- /dev/null
+++ b/gnu/packages/patches/hdf-eos5-fix-szip.patch
@@ -0,0 +1,32 @@
+Fix compilation without szip.
+
+An ill-placed #endif causes missing symbols when the library is compiled
+without szip.
+
+---
+ src/EHapi.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/EHapi.c b/src/EHapi.c
+index 46a9b5c..504d8f2 100755
+--- a/src/EHapi.c
++++ b/src/EHapi.c
+@@ -11379,6 +11379,7 @@ int HE5_szip_can_encode(void )
+ return(-1);
+ }
+
++#endif /* H5_HAVE_FILTER_SZIP */
+
+
+ /*----------------------------------------------------------------------------|
+@@ -11509,7 +11510,6 @@ HE5_EHHEisHE5(char *filename)
+ }
+ }
+
+-#endif /* H5_HAVE_FILTER_SZIP */
+
+
+ #ifndef __cplusplus
+--
+2.5.0
+
diff --git a/gnu/packages/patches/hdf-eos5-headers.patch b/gnu/packages/patches/hdf-eos5-headers.patch
new file mode 100644
index 0000000..84fd90c
--- /dev/null
+++ b/gnu/packages/patches/hdf-eos5-headers.patch
@@ -0,0 +1,14 @@
+Do not install unnecessary headers.
+
+diff --git a/include/Makefile.am b/include/Makefile.am
+index 3de93db..52246af 100755
+--- a/include/Makefile.am
++++ b/include/Makefile.am
+@@ -4,6 +4,5 @@
+ include $(top_srcdir)/config/include.am
+
+ # Headers to install
+-include_HEADERS = HE5_GctpFunc.h HE5_HdfEosDef.h HE5_config.h cproj.h ease.h \
+- isin.h proj.h tutils.h cfortHdf.h
++include_HEADERS = HE5_GctpFunc.h HE5_HdfEosDef.h ease.h isin.h cfortHdf.h
+
diff --git a/gnu/packages/patches/hdf-eos5-remove-gctp.patch b/gnu/packages/patches/hdf-eos5-remove-gctp.patch
new file mode 100644
index 0000000..359d486
--- /dev/null
+++ b/gnu/packages/patches/hdf-eos5-remove-gctp.patch
@@ -0,0 +1,61 @@
+Do not build/install the bundled GCTP and link shared -lgctp.
+
+---
+ Makefile.am | 2 +-
+ config/include.am | 1 -
+ configure.ac | 3 ---
+ include/Makefile.am | 3 +--
+ src/Makefile.am | 2 +-
+ 5 files changed, 3 insertions(+), 8 deletions(-)
+
+diff --git a/Makefile.am b/Makefile.am
+index 01ed024..ef325ac 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -11,5 +11,5 @@ else
+ INCLUDE=
+ endif
+
+-SUBDIRS=gctp src $(INCLUDE) samples $(TESTDRIVERS)
++SUBDIRS=src $(INCLUDE) samples $(TESTDRIVERS)
+
+diff --git a/config/include.am b/config/include.am
+index b82fae9..a1e0332 100644
+--- a/config/include.am
++++ b/config/include.am
+@@ -4,5 +4,4 @@
+ ## shared definitions.
+
+ LIBHDFEOS5=$(top_builddir)/src/libhe5_hdfeos.la
+-LIBGCTP=$(top_builddir)/gctp/src/libGctp.la
+
+diff --git a/configure.ac b/configure.ac
+index cfa9d4e..860da1c 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -589,9 +589,6 @@ AM_CONDITIONAL([SZIP_ENCODER_CONDITIONAL], [test "X$USE_SZIP_ENCODER" = "Xyes"])
+ AC_CONFIG_FILES([Makefile
+ include/Makefile
+ src/Makefile
+- gctp/Makefile
+- gctp/include/Makefile
+- gctp/src/Makefile
+ samples/Makefile])
+
+ AC_OUTPUT
+diff --git a/src/Makefile.am b/src/Makefile.am
+index daf7ad8..f4828cb 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -11,7 +11,7 @@ INCLUDES=-I$(top_srcdir)/include/
+ # Set LDFLAGS to allow the HDF-EOS library to use extern variables from
+ # HDF5
+ LDFLAGS+= -shrext .so
+-LIBS+= -lhdf5_hl -lhdf5 -lm
++LIBS+= -lgctp -lhdf5_hl -lhdf5 -lm
+
+ # Build HDF-EOS5
+ lib_LTLIBRARIES=libhe5_hdfeos.la
+--
+2.5.0
+
--
2.10.0
