CVS commit: pkgsrc/biology/sra-tools

["Thomas Klausner" <wiz%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   wiz
Date:           Fri Apr 25 07:37:15 UTC 2025

Modified Files:
        pkgsrc/biology/sra-tools: distinfo
Added Files:
        pkgsrc/biology/sra-tools/patches: patch-libs_kxml_xml.c

Log Message:
sra-tools: fix build with libxml2


To generate a diff of this commit:
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/sra-tools/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/sra-tools/patches/patch-libs_kxml_xml.c

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/sra-tools/distinfo
diff -u pkgsrc/biology/sra-tools/distinfo:1.3 pkgsrc/biology/sra-tools/distinfo:1.4
--- pkgsrc/biology/sra-tools/distinfo:1.3       Sun Feb  2 14:25:34 2025
+++ pkgsrc/biology/sra-tools/distinfo   Fri Apr 25 07:37:15 2025
@@ -1,4 +1,4 @@
-$NetBSD: distinfo,v 1.3 2025/02/02 14:25:34 bacon Exp $
+$NetBSD: distinfo,v 1.4 2025/04/25 07:37:15 wiz Exp $
 
 BLAKE2s (ncbi-ncbi-vdb-3.2.0.tar.gz) = eb3a98cb754ea78869adfc3651afce3f8e961e1f512e1f77427e9de85924ace2
 SHA512 (ncbi-ncbi-vdb-3.2.0.tar.gz) = badd63525eaaaeedb4de8bb0ab88b40cbeb388e0a0f93ac934c1af716da6f0fb2425eb2e1e95c198496a32fd9c04dfb8badf43b9b6f686b970411b18afec9ea2
@@ -7,6 +7,7 @@ BLAKE2s (sra-tools-3.2.0.tar.gz) = 6afcc
 SHA512 (sra-tools-3.2.0.tar.gz) = ceddc5a2fd97c16ad56d130dc4469c6c8dd0f550825718b4fdd4c50d19e182bc42bc4c1681790ab3ea8912812fddb11dff03aca254999fc5b9e2c3fd39d42402
 Size (sra-tools-3.2.0.tar.gz) = 60313243 bytes
 SHA1 (patch-build_env.cmake) = 7c95dbe65c818ac638754ba6165eab1e613fe0eb
+SHA1 (patch-libs_kxml_xml.c) = f9360408a6da8430c9cef628df82335c6d5b16ca
 SHA1 (patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c) = f49eb28f8bfeb528c1d7c2e9d184502b9eba273c
 SHA1 (patch-ngs_ngs-java_CMakeLists.txt) = 44b822381fd564d045406cc926f807adae9fbe59
 SHA1 (patch-ngs_ngs-python_examples_CMakeLists.txt) = a8a01d17a27c060c08311ab8571ae10af265781d

Added files:

Index: pkgsrc/biology/sra-tools/patches/patch-libs_kxml_xml.c
diff -u /dev/null pkgsrc/biology/sra-tools/patches/patch-libs_kxml_xml.c:1.1
--- /dev/null   Fri Apr 25 07:37:15 2025
+++ pkgsrc/biology/sra-tools/patches/patch-libs_kxml_xml.c      Fri Apr 25 07:37:15 2025
@@ -0,0 +1,15 @@
+$NetBSD: patch-libs_kxml_xml.c,v 1.1 2025/04/25 07:37:15 wiz Exp $
+
+libxml2 2.14 compatibility.
+
+--- libs/kxml/xml.c.orig       2025-04-25 07:35:01.143677606 +0000
++++ libs/kxml/xml.c
+@@ -171,7 +171,7 @@ rc_t KXMLMgrSchemaValidate ( const KXMLM
+ }
+ #endif
+ 
+-static void s_xmlGenericErrorDefaultFunc(void *ctx ATTRIBUTE_UNUSED,
++static void s_xmlGenericErrorDefaultFunc(void *ctx,
+     const char *msg,
+     ...)
+ {