CVS commit: pkgsrc/biology/canu

["Roland Illig" <rillig%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   rillig
Date:           Sat May 16 19:50:21 UTC 2020

Modified Files:
        pkgsrc/biology/canu: distinfo
Added Files:
        pkgsrc/biology/canu/patches: patch-fastq-utilities_fastqSimulate_C

Log Message:
biology/canu: fix build on NetBSD-8.0-x86_64


To generate a diff of this commit:
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/canu/distinfo
cvs rdiff -u -r0 -r1.1 \
    pkgsrc/biology/canu/patches/patch-fastq-utilities_fastqSimulate_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/canu/distinfo
diff -u pkgsrc/biology/canu/distinfo:1.1 pkgsrc/biology/canu/distinfo:1.2
--- pkgsrc/biology/canu/distinfo:1.1    Mon Jan  7 02:33:17 2019
+++ pkgsrc/biology/canu/distinfo        Sat May 16 19:50:21 2020
@@ -1,10 +1,11 @@
-$NetBSD: distinfo,v 1.1 2019/01/07 02:33:17 bacon Exp $
+$NetBSD: distinfo,v 1.2 2020/05/16 19:50:21 rillig Exp $
 
 SHA1 (canu-1.8.tar.gz) = 7dd79415aa5ecb95f05109f0d8d58f7cbfc336e9
 RMD160 (canu-1.8.tar.gz) = 78d4872b4034f526037ce225c699debd910bd586
 SHA512 (canu-1.8.tar.gz) = 650bc96675f371596f8e7748d4ab2d229f0262bf84cee8fed59af43d534d76095a72e4ba0b4a5ce9f561992268c317964cda2f6c89ee514f4920e2ba47fbc86c
 Size (canu-1.8.tar.gz) = 2465314 bytes
 SHA1 (patch-Makefile) = aa83003677cbb12558e438c776402ec48df0598d
+SHA1 (patch-fastq-utilities_fastqSimulate_C) = 959beef6e42c8158050958964924813b814b5a11
 SHA1 (patch-pipelines_canu_Defaults.pm) = 55a4631d86abb1881b0cc997514d44c536209ea6
 SHA1 (patch-pipelines_canu_Execution.pm) = fbb080c06ea5d2393d1835a61771715d2aef0274
 SHA1 (patch-utility_objectStore.C) = c8407de79abbaf296f027f704080cc7e878b85f4

Added files:

Index: pkgsrc/biology/canu/patches/patch-fastq-utilities_fastqSimulate_C
diff -u /dev/null pkgsrc/biology/canu/patches/patch-fastq-utilities_fastqSimulate_C:1.1
--- /dev/null   Sat May 16 19:50:21 2020
+++ pkgsrc/biology/canu/patches/patch-fastq-utilities_fastqSimulate_C   Sat May 16 19:50:21 2020
@@ -0,0 +1,19 @@
+$NetBSD: patch-fastq-utilities_fastqSimulate_C,v 1.1 2020/05/16 19:50:21 rillig Exp $
+
+fastq-utilities/fastqSimulate.C:796:31: error: 'UINT64_MAX' was not declared in this scope
+   uint64     numReads       = UINT64_MAX;  //  Number of reads to generate, constant
+
+AS_global.h must be included before the headers from the standard library
+to get the UINT64_MAX macro.
+
+--- fastq-utilities/fastqSimulate.C.orig       2018-10-22 16:47:31.000000000 +0000
++++ fastq-utilities/fastqSimulate.C
+@@ -35,6 +35,8 @@
+  *  full conditions and disclaimers for each license.
+  */
+ 
++#include "AS_global.H"
++
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <errno.h>