gentoo auto-resync : 08:04:2024 - 12:31:06

5 files changed, 420 insertions, 8 deletions

diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index 058aac655eac..4ddf7671d460 100644
--- a/sci-libs/Manifest.gz
+++ b/sci-libs/Manifest.gz
diff --git a/sci-libs/hdf/Manifest b/sci-libs/hdf/Manifest
index 30b483f6e803..b25800bedf8b 100644
--- a/sci-libs/hdf/Manifest
+++ b/sci-libs/hdf/Manifest
@@ -1,6 +1,8 @@
+AUX 0001-simply-do-not-build-the-mfhdf-tools-ncgen-ncdump.patch 1028 BLAKE2B 6b5a88e903c1201138055fc73f3f850b7d0680de538a712640b75b718fe2b8c78a402b25687de378bcba47341a598598b4a61795cbf943b42c4aade3ec5d38e8 SHA512 8f6e82f7f693589d4ca0e4b4a1d4b4a09b8f58adcda3c314c74835eeba4d471b122c962ba41ecd9f50b3279fafe31b31d83eb577e790441b4f572c10c69f4dca
 AUX hdf-4.2.15-enable-fortran-shared.patch 1271 BLAKE2B bdeb5214a92618b0587472db79d6bef7677cf51ceeb77d9b8593fc374547ee4f63eb7e614c621043670236151731fcdcaac2f3e1fc18b4f577cceca24e38aa37 SHA512 daa6bf33cf5b0f9445c1e96c67907463f2a3813d2d6528a0fd19a57db98253794c3d147e736c3568766e87d01ff41a492ecd18fcef3d85af2adb77315d770be8
 AUX hdf-4.2.15-fix-rpch-location.patch 550 BLAKE2B a88448fa6f454fcac9567b05270f637d144dae5c88d4a88d19a5cc3897f7e20c61e36678dee730ee80bece1c05cd69514f87658e6a691826dce233cdbe9ff49e SHA512 77855e3e7562412fa18e102385264af42605d462690bbe4fbc867268c1cd1837eb012546294b433c4de8e98ddfdeb58c2a5480a7418252563579d6ee26808f88
+AUX hdf4-c99.patch 10535 BLAKE2B e90795c86561c6726fa099b5f55948529bc66cf40640110cbf199f9a8c86206ce6ffc3580446cbd85f123ff26d8c4c725a095b2dae0facbec4562c0e241db046 SHA512 e31eab185e4438e2e91114c7ffe0d3a713f2b736278b417f78c0cc6e6c808417d81e1607072cbcd8f9df7e50ffbeba25ed72e3347de760e6a2ba5d1e99ad90f4
 DIST hdf-4.2.15-arch-patches-1.tar.bz2 7187 BLAKE2B 461e3d7c5e3603fb909d59d6fb23b59f64ef6a6c4e58fe85ddf906a8f27918ac25d3928f5c705290d9d778e1ed07b009bd0602409c05d13a06905d58f2a2cfff SHA512 616c39d06fb6f479a7bed88a89828530ac32018dae827259b76d6e177e5b50378722b60532533a02ae534dddc445f4e360e7a19a28e2cf9728549e5ee27c3e67
 DIST hdf-4.2.15.tar.bz2 3647900 BLAKE2B b1d60ee880563bf64ae6eae4c66f86afe55f4c512f06c84c154de30034fa7a65cfa2b9bd68fbf8a055bb42b57215455ac8967f2a73ec88b361750aa07e0da5e6 SHA512 7d4037800ef8950ed74f225355ef5458444bed26fc189fbbd2ce7d36009998013ac1f6ba5d4e60834acf8f6f73550357238745acc35e162679919400a48191e9
-EBUILD hdf-4.2.15-r1.ebuild 2151 BLAKE2B 36829259b5fddef733086e3427f98cc575ce1cbe7e08d565f5f450e906f7ae4bfc8c42b18aceaa3019a07c2c563530385df20ac62417c1eabb96efb6679753b6 SHA512 8f16ee75c61ceb0522fa033e836120216936f87b4441a53f4606db6e0577535a320f921cd66edfab58ccba5662b362f6ea7b92eee979d0d9c7f4c3d9c5caeaa3
+EBUILD hdf-4.2.15-r2.ebuild 2470 BLAKE2B 782d1337d4a1d8105a0e4c596c07ebb3008621f9d0108d2744c5b80f4848d222b8f89f848ecc7e067d68f0232004e8c274b57934f7d405d4e1bf8fd331659b95 SHA512 7302ef8dd3df3fb2c9bd2fd6df4a83e75d391aeadcb57a39ba2520e6ac8626c0dbd89918bb9487e1297db79469e503145170e0fad530b084eb5db2971621f48b
 MISC metadata.xml 938 BLAKE2B 6fc9c080eaaf83ab22aab00a6645d5e9936479b65d11645c0e76ed28b0e137e1ef60326ddc638a3187018d11400f35e2e17df747b3621ff26c2394800d522322 SHA512 7a54140b8429dfc6b9b078c642875c70f15fc7b7f78710acd285ae306244e09b818f41ae73571a25c16f39530ef6e53d2e26d94f6fb952ba4d4d49f58038c00f
diff --git a/sci-libs/hdf/files/0001-simply-do-not-build-the-mfhdf-tools-ncgen-ncdump.patch b/sci-libs/hdf/files/0001-simply-do-not-build-the-mfhdf-tools-ncgen-ncdump.patch
new file mode 100644
index 000000000000..c57481a6cb84
--- /dev/null
+++ b/sci-libs/hdf/files/0001-simply-do-not-build-the-mfhdf-tools-ncgen-ncdump.patch
@@ -0,0 +1,30 @@
+From 5a93f7ba5bea12bd78616a2168035324054ed7b7 Mon Sep 17 00:00:00 2001
+From: Eli Schwartz <eschwartz93@gmail.com>
+Date: Sun, 7 Apr 2024 23:11:43 -0400
+Subject: [PATCH] simply do not build the mfhdf tools ncgen/ncdump
+
+They were removed upstream in:
+https://github.com/HDFGroup/hdf4/commit/57b87b9927f0127d0d04ab7cd6c93e01bf54e3ee
+
+With the note that people who want them can get them from... yup, you
+guessed it, netcdf.
+---
+ mfhdf/Makefile.am | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/mfhdf/Makefile.am b/mfhdf/Makefile.am
+index d62d3af..0963923 100644
+--- a/mfhdf/Makefile.am
++++ b/mfhdf/Makefile.am
+@@ -17,7 +17,7 @@ FORTRAN_DIR =
+ endif
+ 
+ # src folder in root Makefile, build other folders now
+-SUBDIRS = $(XDR_DIR) libsrc $(FORTRAN_DIR) test ncdump ncgen dumper hdfimport hdiff hrepack nctest
++SUBDIRS = $(XDR_DIR) libsrc $(FORTRAN_DIR) test dumper hdfimport hdiff hrepack nctest
+ 
+ DIST_SUBDIRS = xdr libsrc fortran test ncdump ncgen dumper hdfimport hdiff hrepack nctest examples
+ 
+-- 
+2.43.2
+
diff --git a/sci-libs/hdf/files/hdf4-c99.patch b/sci-libs/hdf/files/hdf4-c99.patch
new file mode 100644
index 000000000000..de5f5d07847d
--- /dev/null
+++ b/sci-libs/hdf/files/hdf4-c99.patch
@@ -0,0 +1,371 @@
+From a3d4d30fe457fc9a85fce5508119dffd3ace54c1 Mon Sep 17 00:00:00 2001
+From: Eli Schwartz <eschwartz93@gmail.com>
+Date: Sun, 7 Apr 2024 21:28:39 -0400
+Subject: [PATCH 01/11] fix tests omitting required header
+
+sys/time.h is not time.h.
+
+Purports to be fixed by https://github.com/HDFGroup/hdf4/commit/276e2c205b767d31f9d0b757f53a36aee1e1f9b2
+which however doesn't directly include time.h, as of the current
+version. In later releases it does.
+---
+ hdf/test/buffer.c | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/hdf/test/buffer.c b/hdf/test/buffer.c
+index c7990e7..9f0f06f 100644
+--- a/hdf/test/buffer.c
++++ b/hdf/test/buffer.c
+@@ -50,6 +50,7 @@
+ #ifdef H4_HAVE_SYS_TIME_H
+ #include <sys/time.h>
+ #endif
++#include <time.h>
+ #include "tutils.h"
+ #include "hfile.h"
+ 
+-- 
+2.43.2
+
+
+From 02ec8e25e096241e20664acfc6596767f050ec86 Mon Sep 17 00:00:00 2001
+From: Eli Schwartz <eschwartz93@gmail.com>
+Date: Sun, 7 Apr 2024 20:41:06 -0400
+Subject: [PATCH 02/11] fix util omitting required header
+
+sys/wait.h is POSIX, but for some godforsaken reason upstream has
+decided to only include it behind random OS identifier macros. In a
+newer upstream version, they at least migrate over to including it
+whenever the header exists.
+
+https://github.com/HDFGroup/hdf4/commit/67e11955e41471c8892acc3c8930ea538f719a03
+---
+ hdf/util/he_file.c | 2 --
+ 1 file changed, 2 deletions(-)
+
+diff --git a/hdf/util/he_file.c b/hdf/util/he_file.c
+index 8686e2f..d6c5e7f 100644
+--- a/hdf/util/he_file.c
++++ b/hdf/util/he_file.c
+@@ -17,9 +17,7 @@
+ #include "he.h"
+ 
+ /* get the prototype for the wait() func. */
+-#if defined SUN | defined HP9000 | defined IRIX | defined UNIX386
+ #include <sys/wait.h>
+-#endif /* SUN | HP9000 */
+ #ifdef H4_HAVE_UNISTD_H
+ #include <unistd.h>
+ #endif
+-- 
+2.43.2
+
+
+From 60223f44459e7b43a26bdccf473804f1f0fd710f Mon Sep 17 00:00:00 2001
+From: Eli Schwartz <eschwartz93@gmail.com>
+Date: Sun, 7 Apr 2024 20:46:48 -0400
+Subject: [PATCH 03/11] another POSIX function with a missing header
+
+For this one it is not immediately apparent to me that it's fixed
+upstream at all. Will check later.
+---
+ mfhdf/libsrc/file.c | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/mfhdf/libsrc/file.c b/mfhdf/libsrc/file.c
+index a53301f..df73212 100644
+--- a/mfhdf/libsrc/file.c
++++ b/mfhdf/libsrc/file.c
+@@ -20,6 +20,7 @@
+ #include <assert.h>
+ #endif /* DEBUG */
+ 
++#include <unistd.h>
+ #include    <string.h>
+ #include    <errno.h>
+ #include    "local_nc.h"
+-- 
+2.43.2
+
+
+From 2b4772cf958a1af0fff6117d4f7127607d3f1a50 Mon Sep 17 00:00:00 2001
+From: Eli Schwartz <eschwartz93@gmail.com>
+Date: Sun, 7 Apr 2024 20:48:56 -0400
+Subject: [PATCH 04/11] add brand new definition of function no one bothered to
+ define at all
+
+Added upstream in https://github.com/HDFGroup/hdf4/commit/8a4137d60e2d932703fc6ee91501ad374ccba885
+---
+ mfhdf/test/hdftest.h | 6 ++++++
+ 1 file changed, 6 insertions(+)
+
+diff --git a/mfhdf/test/hdftest.h b/mfhdf/test/hdftest.h
+index a211c49..a946e5c 100644
+--- a/mfhdf/test/hdftest.h
++++ b/mfhdf/test/hdftest.h
+@@ -52,6 +52,9 @@
+ 
+ /*************************** Utility Functions ***************************/
+ 
++/* Generates the correct name for the test file */
++intn make_datafilename(char* basename, char* testfile, unsigned int size);
++
+ /* Calls SDcreate, SDwritedata, and SDendaccess */
+ int32 make_SDS(int32 sd_id, char* sds_name, int32 type, int32 rank,
+ 			  int32* dim_sizes, int32 unlim_dim, VOIDP written_data);
+@@ -65,6 +68,9 @@ int32 make_Ext3D_SDS(int32 sd_id, char* sds_name, int32 type, int32 rank,
+ 		     int32* dim_sizes, VOIDP written_data,
+ 		     int32 offset, char* ext_file_name);
+ 
++/* Verifies the unlimited dimension's size and the variable's data. */
++int verify_info_data(int32 sds_id, int32 expected_dimsize, int16 *result);
++
+ /* Calls SDnametoindex and SDselect */
+ int32 get_SDSbyName(int32 sd_id, char* sds_name);
+ 
+-- 
+2.43.2
+
+
+From 1be129c91ec9db6991daebddfe5124cc8180f0ea Mon Sep 17 00:00:00 2001
+From: Eli Schwartz <eschwartz93@gmail.com>
+Date: Sun, 7 Apr 2024 20:58:13 -0400
+Subject: [PATCH 05/11] fix typoed function definition
+
+https://github.com/HDFGroup/hdf4/commit/490abfc71219657ecfa81cd90413b623f73603fd
+---
+ mfhdf/test/hdftest.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/mfhdf/test/hdftest.c b/mfhdf/test/hdftest.c
+index da9a36b..04f8641 100644
+--- a/mfhdf/test/hdftest.c
++++ b/mfhdf/test/hdftest.c
+@@ -59,7 +59,7 @@ extern int test_SDSprops();
+ extern int test_coordvar();
+ extern int test_chunk();
+ extern int test_compression();
+-extern int test_dimension();
++extern int test_dimensions();
+ extern int test_attributes();
+ extern int test_datasizes();
+ extern int test_datainfo();
+-- 
+2.43.2
+
+
+From 60fcf1802bd015b01095c6a0463200f09c47f677 Mon Sep 17 00:00:00 2001
+From: Eli Schwartz <eschwartz93@gmail.com>
+Date: Sun, 7 Apr 2024 21:53:59 -0400
+Subject: [PATCH 06/11] make defines actually do anything whatsoever
+
+Rendered obsolete by https://github.com/HDFGroup/hdf4/commit/218c8da49eda25799577ac905209c1e972a77771
+---
+ mfhdf/test/tdatainfo.c | 7 +++----
+ 1 file changed, 3 insertions(+), 4 deletions(-)
+
+diff --git a/mfhdf/test/tdatainfo.c b/mfhdf/test/tdatainfo.c
+index df2539b..ab36044 100644
+--- a/mfhdf/test/tdatainfo.c
++++ b/mfhdf/test/tdatainfo.c
+@@ -23,6 +23,9 @@
+  * -BMR, Jul 2010
+  ****************************************************************************/
+ 
++#ifndef DATAINFO_TESTER
++#define DATAINFO_TESTER /* to include mfdatainfo.h */
++#endif
+ #include "mfhdf.h"
+ 
+ #ifdef H4_HAVE_SYS_TYPES_H
+@@ -44,10 +47,6 @@
+ #define ssize_t int32
+ #endif
+ 
+-#ifndef DATAINFO_TESTER
+-#define DATAINFO_TESTER /* to include mfdatainfo.h */
+-#endif
+-
+ #ifdef H4_HAVE_LIBSZ
+ #include "szlib.h"
+ #endif
+-- 
+2.43.2
+
+
+From e967cb577fa0ba39cee7d5a128672c61adbb839e Mon Sep 17 00:00:00 2001
+From: Eli Schwartz <eschwartz93@gmail.com>
+Date: Sun, 7 Apr 2024 22:01:14 -0400
+Subject: [PATCH 07/11] Include correct header
+
+https://github.com/HDFGroup/hdf4/commit/3f61fb461d2d19cc1d9da41f29e5cbb2ce0c4365
+---
+ mfhdf/test/tfile.c | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/mfhdf/test/tfile.c b/mfhdf/test/tfile.c
+index a90fc02..b0ea001 100644
+--- a/mfhdf/test/tfile.c
++++ b/mfhdf/test/tfile.c
+@@ -13,6 +13,7 @@
+ 
+ /* $Id: tfile.c 5218 2009-08-29 04:21:49Z bmribler $ */
+ 
++#include "local_nc.h"
+ #include "mfhdf.h"
+ 
+ #ifdef HDF
+-- 
+2.43.2
+
+
+From fda204abcb83516177d6c81a23261e1c641bcdcf Mon Sep 17 00:00:00 2001
+From: Eli Schwartz <eschwartz93@gmail.com>
+Date: Sun, 7 Apr 2024 22:03:18 -0400
+Subject: [PATCH 08/11] include header needed for unlink()
+
+Upstream in https://github.com/HDFGroup/hdf4/commit/9055b673990b2dc3c9248f720f3e8a03f8d86434
+
+It is unclear why they think it was only needed then...
+---
+ mfhdf/test/tsd.c | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/mfhdf/test/tsd.c b/mfhdf/test/tsd.c
+index 397aeba..a6e9b6c 100644
+--- a/mfhdf/test/tsd.c
++++ b/mfhdf/test/tsd.c
+@@ -15,6 +15,8 @@
+  * tsd.c - tests SDstart for file with no write permission
+ ****************************************************************************/
+ 
++#include <unistd.h>
++
+ #include "mfhdf.h"
+ 
+ #ifdef HDF
+-- 
+2.43.2
+
+
+From 572ef6889599b58535bd2285d98ac63c7fdf870d Mon Sep 17 00:00:00 2001
+From: Eli Schwartz <eschwartz93@gmail.com>
+Date: Sun, 7 Apr 2024 22:49:39 -0400
+Subject: [PATCH 09/11] include the getopt() header
+
+Which isn't getopt.h, though upstream helpfully added one in
+https://github.com/HDFGroup/hdf4/commit/9be7f29942d286873d0b4fa125be11b3f79f6916
+
+They then went a bit further and stopped using getopt at all:
+https://github.com/HDFGroup/hdf4/commit/0b3ad421b3ba8045d078196edd0492067f1ea576
+
+Helpful rationale:
+>  Instead of relying on the system getopt(), HDF4 includes its own
+
+Intriguing.
+
+"Fortunately" this is a patch for an old version of hdf4. All we want to
+do is get the POSIX prototype which we intend to link to.
+---
+ mfhdf/hdiff/hdiff_main.c | 1 +
+ mfhdf/ncdump/ncdump.c    | 1 +
+ mfhdf/ncgen/main.c       | 1 +
+ 3 files changed, 3 insertions(+)
+
+diff --git a/mfhdf/hdiff/hdiff_main.c b/mfhdf/hdiff/hdiff_main.c
+index 2fb2342..e2987be 100644
+--- a/mfhdf/hdiff/hdiff_main.c
++++ b/mfhdf/hdiff/hdiff_main.c
+@@ -12,6 +12,7 @@
+  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+ 
+ 
++#include <unistd.h>
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <string.h>
+diff --git a/mfhdf/ncdump/ncdump.c b/mfhdf/ncdump/ncdump.c
+index bdaa120..8697c0a 100644
+--- a/mfhdf/ncdump/ncdump.c
++++ b/mfhdf/ncdump/ncdump.c
+@@ -4,6 +4,7 @@
+  *   $Id$
+  *********************************************************************/
+ 
++#include <unistd.h>
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <string.h>
+diff --git a/mfhdf/ncgen/main.c b/mfhdf/ncgen/main.c
+index 16c0204..7f6e2c0 100644
+--- a/mfhdf/ncgen/main.c
++++ b/mfhdf/ncgen/main.c
+@@ -4,6 +4,7 @@
+  *   $Id$
+  *********************************************************************/
+ 
++#include <unistd.h>
+ #include <stdio.h>
+ #include <string.h>
+ #include <stdlib.h>
+-- 
+2.43.2
+
+
+From b569c20be9d3c65ba48bd2a81a5daa9ee8a419bc Mon Sep 17 00:00:00 2001
+From: Eli Schwartz <eschwartz93@gmail.com>
+Date: Sun, 7 Apr 2024 22:57:19 -0400
+Subject: [PATCH 10/11] Remove never-defined macros that prevented including a
+ crucial header
+
+Also removed upstream:
+https://github.com/HDFGroup/hdf4/commit/3f61fb461d2d19cc1d9da41f29e5cbb2ce0c4365
+---
+ mfhdf/ncgen/close.c | 2 --
+ 1 file changed, 2 deletions(-)
+
+diff --git a/mfhdf/ncgen/close.c b/mfhdf/ncgen/close.c
+index 036d8f0..3dedbd7 100644
+--- a/mfhdf/ncgen/close.c
++++ b/mfhdf/ncgen/close.c
+@@ -6,9 +6,7 @@
+ 
+ #include <stdio.h>
+ #include "ncgen.h"
+-#ifdef EIP
+ #include "genlib.h"
+-#endif
+ 
+ extern void fline(), cline();
+ extern int netcdf_flag;
+-- 
+2.43.2
+
+
+From 9bce6a7a5ea7095f4a51d38bd7e378670c33fb06 Mon Sep 17 00:00:00 2001
+From: Eli Schwartz <eschwartz93@gmail.com>
+Date: Sun, 7 Apr 2024 23:23:16 -0400
+Subject: [PATCH 11/11] fix blatantly missing type
+
+Upstream applied via:
+https://github.com/HDFGroup/hdf4/commit/38e08e0d12d2ee84917111583a007fdcb5ad1aed
+---
+ mfhdf/hdfimport/gen_sds_floats.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/mfhdf/hdfimport/gen_sds_floats.c b/mfhdf/hdfimport/gen_sds_floats.c
+index 81f62c5..d08576f 100644
+--- a/mfhdf/hdfimport/gen_sds_floats.c
++++ b/mfhdf/hdfimport/gen_sds_floats.c
+@@ -23,7 +23,7 @@
+ #define RANK2          2  /* Number of dimensions of the SDS */
+ #define RANK3          3  /* Number of dimensions of the SDS */
+ 
+-main() 
++int main()
+ {
+     /************************* Variable declaration ************************/
+ 
+-- 
+2.43.2
+
diff --git a/sci-libs/hdf/hdf-4.2.15-r1.ebuild b/sci-libs/hdf/hdf-4.2.15-r2.ebuild
index c809222acf56..02fc69143873 100644
--- a/sci-libs/hdf/hdf-4.2.15-r1.ebuild
+++ b/sci-libs/hdf/hdf-4.2.15-r2.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 FORTRAN_NEEDED=fortran
 
@@ -34,6 +34,12 @@ PATCHES=(
 	# May need to extend these for more arches in future.
 	# bug #664856
 	"${WORKDIR}"/${PN}-4.2.15-arch-patches/
+
+	# backport fix for Modern C
+	"${FILESDIR}"/hdf4-c99.patch
+
+	# These tools were dropped upstream. Get them from netcdf...
+	"${FILESDIR}"/0001-simply-do-not-build-the-mfhdf-tools-ncgen-ncdump.patch
 )
 
 src_prepare() {
@@ -44,6 +50,14 @@ src_prepare() {
 }
 
 src_configure() {
+	# -Werror=strict-aliasing, -Werror=lto-type-mismatch
+	# https://bugs.gentoo.org/862720
+	#
+	# Do not trust with LTO either, just because of strict-aliasing.
+	# But also because it does have blatant LTO errors too.
+	append-flags -fno-strict-aliasing
+	filter-lto
+
 	[[ $(tc-getFC) = *gfortran ]] && append-fflags -fno-range-check
 	# GCC 10 workaround
 	# bug #723014
@@ -75,9 +89,4 @@ src_install() {
 	else
 		rm -r share/hdf4_examples || die
 	fi
-
-	mv bin/ncgen{,-hdf} || die
-	mv bin/ncdump{,-hdf} || die
-	mv share/man/man1/ncgen{,-hdf}.1 || die
-	mv share/man/man1/ncdump{,-hdf}.1 || die
 }