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gnu: Add hdf-eos5.

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* 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/patches/hdf-eos5-fortrantests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add patches.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
This commit is contained in:
Thomas Danckaert 2016-06-17 10:51:38 +02:00 committed by Ludovic Courtès
parent b282c78192
commit 0f43f8354c
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GPG key ID: 090B11993D9AEBB5
6 changed files with 313 additions and 0 deletions
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4
gnu/local.mk
View file

@ -571,6 +571,10 @@ dist_patch_DATA = \
%D%/packages/patches/gtk3-respect-GUIX_GTK3_IM_MODULE_FILE.patch \
%D%/packages/patches/gtkglext-disable-disable-deprecated.patch \
%D%/packages/patches/hdf5-config-date.patch \
%D%/packages/patches/hdf-eos5-build-shared.patch \
%D%/packages/patches/hdf-eos5-remove-gctp.patch \
%D%/packages/patches/hdf-eos5-fix-szip.patch \
%D%/packages/patches/hdf-eos5-fortrantests.patch \
%D%/packages/patches/higan-remove-march-native-flag.patch \
%D%/packages/patches/hop-bigloo-4.0b.patch \
%D%/packages/patches/hop-linker-flags.patch \

37
gnu/packages/maths.scm
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@ -14,6 +14,7 @@
;;; Copyright © 2016 Kei Kebreau <kei@openmailbox.org>
;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
;;; Copyright © 2016 Thomas Danckaert <post@thomasdanckaert.be>
;;;
;;; This file is part of GNU Guix.
;;;
@ -483,6 +484,42 @@ (define-public hdf5
(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-fortrantests.patch"))))
(native-inputs
`(("gfortran" ,gfortran)))
(build-system gnu-build-system)
(inputs
`(("hdf5" ,hdf5)
("zlib" ,zlib)
("gctp" ,gctp)))
(arguments
`(#:configure-flags '("--enable-install-include" "--enable-shared"
"CC=h5cc -Df2cFortran" "LIBS=-lgctp")
#:parallel-tests? #f))
(synopsis "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")
;; Source files carry a permissive license header.
(license (license:non-copyleft home-page))))
(define-public hdf5-parallel-openmpi
(package (inherit hdf5)
(name "hdf5-parallel-openmpi")

31
gnu/packages/patches/hdf-eos5-build-shared.patch Normal file
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@ -0,0 +1,31 @@
Make shared library linking work.
---
src/Makefile.in | 5 +----
1 file changed, 1 insertion(+), 4 deletions(-)
diff --git a/src/Makefile.in b/src/Makefile.in
index 86880e5..24efffe 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -72,7 +72,7 @@ LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(DEFS) \
$(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \
$(AM_CFLAGS) $(CFLAGS) -DH5_USE_16_API
CCLD = $(CC)
-LINK = $(LIBTOOL) --mode=link --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
+LINK = HDF5_USE_SHLIB=yes $(LIBTOOL) --mode=link --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
$(AM_LDFLAGS) $(LDFLAGS) -o $@
SOURCES = $(libhe5_hdfeos_la_SOURCES)
DIST_SOURCES = $(libhe5_hdfeos_la_SOURCES)
@@ -124,9 +124,6 @@ INSTALL_PROGRAM = @INSTALL_PROGRAM@
INSTALL_SCRIPT = @INSTALL_SCRIPT@
INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
-# Set LDFLAGS to allow the HDF-EOS library to use extern variables from
-# HDF5
-LDFLAGS = -Wl,-single_module
LIBOBJS = @LIBOBJS@
LIBS = @LIBS@
LIBTOOL = @LIBTOOL@
--
2.10.0

30
gnu/packages/patches/hdf-eos5-fix-szip.patch Normal file
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@ -0,0 +1,30 @@
Ill-placed #endif causes missing symbol errors when compiling without
szip. Reported to upstream maintainer.
---
src/EHapi.c | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/src/EHapi.c b/src/EHapi.c
index 46a9b5c..208f447 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 */
/*----------------------------------------------------------------------------|
@@ -11509,8 +11510,6 @@ HE5_EHHEisHE5(char *filename)
}
}
-#endif /* H5_HAVE_FILTER_SZIP */
-
#ifndef __cplusplus
--
2.10.0

156
gnu/packages/patches/hdf-eos5-fortrantests.patch Normal file
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@ -0,0 +1,156 @@
Fix fortran line length/indentation issues in Fortran test programs.
Reported to upstream maintainer.
diff --git a/samples/he5_gd_writedataF_32.f b/samples/he5_gd_writedataF_32.f
index 515edf9..9c86299 100755
--- a/samples/he5_gd_writedataF_32.f
+++ b/samples/he5_gd_writedataF_32.f
@@ -77,26 +77,26 @@ c ------------------------------
attr4 = "ABCDEFGH"
count(1) = 8
- status = he5_gdwrattr(gdid,"GLOBAL_CHAR_ATTR",HE5T_NATIVE_CHAR,
- 1 count,attr4)
+ status = he5_gdwrattr(gdid,"GLOBAL_CHAR_ATTR"
+ & ,HE5T_NATIVE_CHAR,count,attr4)
write(*,*) 'Status returned by he5_gdwrattr(): ',status
attr4 = "111"
count(1) = 3
- status = he5_gdwrgattr(gdid,"GLOBAL_CHAR_ATTR_1",HE5T_NATIVE_CHAR,
- 1 count,attr4)
+ status = he5_gdwrgattr(gdid,"GLOBAL_CHAR_ATTR_1"
+ & ,HE5T_NATIVE_CHAR,count,attr4)
write(*,*) 'Status returned by he5_gdwrgattr(): ',status
attr4 = "222222"
count(1) = 6
- status = he5_ehwrglatt(gdfid,"GLOBAL_CHAR_ATTR_2",HE5T_NATIVE_CHAR,
- 1 count,attr4)
+ status = he5_ehwrglatt(gdfid,"GLOBAL_CHAR_ATTR_2"
+ & ,HE5T_NATIVE_CHAR,count,attr4)
write(*,*) 'Status returned by he5_ehwrglatt(): ',status
attr5 = "abcdefgh111111111111"
count(1) = 20
- status = he5_gdwrlattr(gdid,"Vegetation","LocalAttribute_0",
- 1 HE5T_NATIVE_CHAR,count,attr5)
+ status = he5_gdwrlattr(gdid,"Vegetation"
+ & ,"LocalAttribute_0",HE5T_NATIVE_CHAR,count,attr5)
write(*,*) 'Status returned by he5_gdwrlattr(): ',status
endif
diff --git a/samples/he5_gd_writedataF_64.f b/samples/he5_gd_writedataF_64.f
index eff04f5..62a7398 100755
--- a/samples/he5_gd_writedataF_64.f
+++ b/samples/he5_gd_writedataF_64.f
@@ -77,26 +77,26 @@ c ------------------------------
attr4 = "ABCDEFGH"
count(1) = 8
- status = he5_gdwrattr(gdid,"GLOBAL_CHAR_ATTR",HE5T_NATIVE_CHAR,
- 1 count,attr4)
+ status = he5_gdwrattr(gdid,"GLOBAL_CHAR_ATTR"
+ & ,HE5T_NATIVE_CHAR,count,attr4)
write(*,*) 'Status returned by he5_gdwrattr(): ',status
attr4 = "111"
count(1) = 3
- status = he5_gdwrgattr(gdid,"GLOBAL_CHAR_ATTR_1",HE5T_NATIVE_CHAR,
- 1 count,attr4)
+ status = he5_gdwrgattr(gdid,"GLOBAL_CHAR_ATTR_1"
+ & ,HE5T_NATIVE_CHAR,count,attr4)
write(*,*) 'Status returned by he5_gdwrgattr(): ',status
attr4 = "222222"
count(1) = 6
- status = he5_ehwrglatt(gdfid,"GLOBAL_CHAR_ATTR_2",HE5T_NATIVE_CHAR,
- 1 count,attr4)
+ status = he5_ehwrglatt(gdfid,"GLOBAL_CHAR_ATTR_2"
+ & ,HE5T_NATIVE_CHAR,count,attr4)
write(*,*) 'Status returned by he5_ehwrglatt(): ',status
attr5 = "abcdefgh111111111111"
count(1) = 20
- status = he5_gdwrlattr(gdid,"Vegetation","LocalAttribute_0",
- 1 HE5T_NATIVE_CHAR,count,attr5)
+ status = he5_gdwrlattr(gdid,"Vegetation"
+ & ,"LocalAttribute_0",HE5T_NATIVE_CHAR,count,attr5)
write(*,*) 'Status returned by he5_gdwrlattr(): ',status
endif
diff --git a/samples/he5_sw_writedataF_32.f b/samples/he5_sw_writedataF_32.f
index 7abab9b..fedd49a 100755
--- a/samples/he5_sw_writedataF_32.f
+++ b/samples/he5_sw_writedataF_32.f
@@ -173,20 +173,21 @@ c Write Global Attribute
c ----------------------
attr4 = "ABCDEFGH"
count(1) = 8
- status = he5_swwrattr(swid,"GLOBAL_CHAR_ATTR",HE5T_NATIVE_CHAR,
- 1 count,attr4)
+ status = he5_swwrattr(swid,"GLOBAL_CHAR_ATTR"
+ & ,HE5T_NATIVE_CHAR,count,attr4)
write(*,*) 'Status returned by he5_swwrattr(): ',status
attr4 = "111"
count(1) = 3
- status = he5_swwrgattr(swid,"GLOBAL_CHAR_ATTR_1",HE5T_NATIVE_CHAR,
- 1 count,attr4)
+ status = he5_swwrgattr(swid,"GLOBAL_CHAR_ATTR_1"
+ & ,HE5T_NATIVE_CHAR,count,attr4)
write(*,*) 'Status returned by he5_swwrgattr(): ',status
attr4 = "222222"
count(1) = 6
- status = he5_ehwrglatt(swfid,"GLOBAL_CHAR_ATTR_2",HE5T_NATIVE_CHAR,
- 1 count,attr4)
+ status = he5_ehwrglatt(swfid
+ & ,"GLOBAL_CHAR_ATTR_2",HE5T_NATIVE_CHAR
+ & ,count,attr4)
write(*,*) 'Status returned by he5_ehwrglatt(): ',status
c Write Local Attribute
diff --git a/samples/he5_sw_writedataF_64.f b/samples/he5_sw_writedataF_64.f
index 79e34bd..e5d74cb 100755
--- a/samples/he5_sw_writedataF_64.f
+++ b/samples/he5_sw_writedataF_64.f
@@ -162,25 +162,27 @@ c Write Global Attribute
c ----------------------
attr4 = "ABCDEFGH"
count(1) = 8
- status = he5_swwrattr(swid,"GLOBAL_CHAR_ATTR",HE5T_NATIVE_CHAR,
- 1 count,attr4)
+ status = he5_swwrattr(swid,"GLOBAL_CHAR_ATTR"
+ & ,HE5T_NATIVE_CHAR,count,attr4)
attr4 = "111"
count(1) = 3
- status = he5_swwrgattr(swid,"GLOBAL_CHAR_ATTR_1",HE5T_NATIVE_CHAR,
- 1 count,attr4)
+ status = he5_swwrgattr(swid,"GLOBAL_CHAR_ATTR_1"
+ & ,HE5T_NATIVE_CHAR,count,attr4)
attr4 = "222222"
count(1) = 6
- status = he5_ehwrglatt(swfid,"GLOBAL_CHAR_ATTR_2",HE5T_NATIVE_CHAR,
- 1 count,attr4)
+ status = he5_ehwrglatt(swfid
+ & ,"GLOBAL_CHAR_ATTR_2",HE5T_NATIVE_CHAR
+ & ,count,attr4)
c Write Local Attribute
c ---------------------
attr5 = "abababababababababab"
count(1) = 20
- status = he5_swwrlattr(swid,"Density","LocalAttribute_0",
- 1 HE5T_NATIVE_CHAR,count,attr5)
+ status = he5_swwrlattr(swid,"Density"
+ & ,"LocalAttribute_0",HE5T_NATIVE_CHAR,count
+ & ,attr5)
endif
--
2.10.0

55
gnu/packages/patches/hdf-eos5-remove-gctp.patch Normal file
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@ -0,0 +1,55 @@
Don't build/install/use bundled gctp code/headers.
* cproj.h, proj.h: part of GCTP, therefore already present.
* HE5_config.h, tutils.h: used for library building and testing.
diff --git a/Makefile.in b/Makefile.in
index f160d0d..367b537 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -206,7 +206,7 @@ LIBGCTP = $(top_builddir)/gctp/src/libGctp.la
@TESTDRIVERS_CONDITIONAL_TRUE@TESTDRIVERS = testdrivers
@INSTALL_INCLUDE_CONDITIONAL_FALSE@INCLUDE =
@INSTALL_INCLUDE_CONDITIONAL_TRUE@INCLUDE = include
-SUBDIRS = gctp src $(INCLUDE) samples $(TESTDRIVERS)
+SUBDIRS = src $(INCLUDE) samples $(TESTDRIVERS)
all: all-recursive
.SUFFIXES:
diff --git a/samples/Makefile.in b/samples/Makefile.in
index 59331dd..64fda89 100644
--- a/samples/Makefile.in
+++ b/samples/Makefile.in
@@ -206,7 +206,6 @@ he5_gd_datainfo_SOURCES = he5_gd_datainfo.c
he5_gd_datainfo_OBJECTS = he5_gd_datainfo.$(OBJEXT)
he5_gd_datainfo_LDADD = $(LDADD)
am__DEPENDENCIES_1 = $(top_builddir)/src/libhe5_hdfeos.la
-am__DEPENDENCIES_2 = $(top_builddir)/gctp/src/libGctp.la
he5_gd_datainfo_DEPENDENCIES = $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_2)
he5_gd_defexternalfld_SOURCES = he5_gd_defexternalfld.c
@@ -1093,7 +1092,7 @@ sharedstatedir = @sharedstatedir@
sysconfdir = @sysconfdir@
target_alias = @target_alias@
LIBHDFEOS5 = $(top_builddir)/src/libhe5_hdfeos.la
-LIBGCTP = $(top_builddir)/gctp/src/libGctp.la
+LIBGCTP =
# Boilerplate definitions file
diff --git a/include/Makefile.in b/include/Makefile.in
index a572128..64dabb5 100644
--- a/include/Makefile.in
+++ b/include/Makefile.in
@@ -190,8 +190,7 @@ LIBGCTP = $(top_builddir)/gctp/src/libGctp.la
# Boilerplate include
# 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
all: HE5_config.h
$(MAKE) $(AM_MAKEFLAGS) all-am
--
2.10.0