CVS commit: pkgsrc/biology/stacks

["Tobias Nygren" <tnn%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   tnn
Date:           Mon Apr 25 14:34:06 UTC 2022

Modified Files:
        pkgsrc/biology/stacks: distinfo
Added Files:
        pkgsrc/biology/stacks/patches: patch-src_Hwp.cc patch-src_PopSum.cc
            patch-src_Vcf.cc patch-src_kmers.cc patch-src_smoothing__utils.h
            patch-src_utils.cc

Log Message:
stacks: avoid ambiguous math functions


To generate a diff of this commit:
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/stacks/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/stacks/patches/patch-src_Hwp.cc \
    pkgsrc/biology/stacks/patches/patch-src_PopSum.cc \
    pkgsrc/biology/stacks/patches/patch-src_Vcf.cc \
    pkgsrc/biology/stacks/patches/patch-src_kmers.cc \
    pkgsrc/biology/stacks/patches/patch-src_smoothing__utils.h \
    pkgsrc/biology/stacks/patches/patch-src_utils.cc

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

Modified files:

Index: pkgsrc/biology/stacks/distinfo
diff -u pkgsrc/biology/stacks/distinfo:1.4 pkgsrc/biology/stacks/distinfo:1.5
--- pkgsrc/biology/stacks/distinfo:1.4  Thu Mar 17 23:49:08 2022
+++ pkgsrc/biology/stacks/distinfo      Mon Apr 25 14:34:06 2022
@@ -1,5 +1,11 @@
-$NetBSD: distinfo,v 1.4 2022/03/17 23:49:08 bacon Exp $
+$NetBSD: distinfo,v 1.5 2022/04/25 14:34:06 tnn Exp $
 
 BLAKE2s (stacks-2.60.tar.gz) = 10dc694d464172fdfadec6dadd973d5e44bba83150d564e964479166f87192a5
 SHA512 (stacks-2.60.tar.gz) = 9bb2bf730ab5a35cb732107b989ca5068c1e2a8d7a647423d62195ab2049f61409e5ad5b9f16444c10791196f322d677aa7f0e0e73bcfccb9b7c4c00ec40ad32
 Size (stacks-2.60.tar.gz) = 12135281 bytes
+SHA1 (patch-src_Hwp.cc) = 15b1872fd0199a13020cecf7ff34478cf83007fd
+SHA1 (patch-src_PopSum.cc) = fbf56bbdb3f8e0cc146ca19c75c910fbc00ae36b
+SHA1 (patch-src_Vcf.cc) = 26f04decced076cd189fe3162c4641809d070060
+SHA1 (patch-src_kmers.cc) = 8fbe6c7be1d35f4dc17f2f250538c9b5f136e524
+SHA1 (patch-src_smoothing__utils.h) = be331ef1d89998b946cf923d95f9eda676a245ab
+SHA1 (patch-src_utils.cc) = 3474a1d0dcc395892e362c877df0daa33050b500

Added files:

Index: pkgsrc/biology/stacks/patches/patch-src_Hwp.cc
diff -u /dev/null pkgsrc/biology/stacks/patches/patch-src_Hwp.cc:1.1
--- /dev/null   Mon Apr 25 14:34:06 2022
+++ pkgsrc/biology/stacks/patches/patch-src_Hwp.cc      Mon Apr 25 14:34:06 2022
@@ -0,0 +1,16 @@
+$NetBSD: patch-src_Hwp.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $
+
+avoid ambiguous math functions
+
+--- src/Hwp.cc.orig    2020-06-24 17:47:53.000000000 +0000
++++ src/Hwp.cc
+@@ -20,6 +20,9 @@
+ 
+ #include "Hwp.h"
+ 
++using std::log;
++using std::pow;
++
+ double
+ GuoThompson_Hwp::exec_locus(int start, int end, const Datum **d, size_t hap_cnt)
+ {
Index: pkgsrc/biology/stacks/patches/patch-src_PopSum.cc
diff -u /dev/null pkgsrc/biology/stacks/patches/patch-src_PopSum.cc:1.1
--- /dev/null   Mon Apr 25 14:34:06 2022
+++ pkgsrc/biology/stacks/patches/patch-src_PopSum.cc   Mon Apr 25 14:34:06 2022
@@ -0,0 +1,15 @@
+$NetBSD: patch-src_PopSum.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $
+
+avoid ambiguous math functions
+
+--- src/PopSum.cc.orig 2021-10-21 14:47:59.000000000 +0000
++++ src/PopSum.cc
+@@ -20,6 +20,8 @@
+ 
+ #include "PopSum.h"
+ 
++using std::log;
++
+ LocPopSum::LocPopSum(size_t cloc_len, const MetaPopInfo& mpopi)
+ {
+     this->_pop_cnt  = mpopi.pops().size();
Index: pkgsrc/biology/stacks/patches/patch-src_Vcf.cc
diff -u /dev/null pkgsrc/biology/stacks/patches/patch-src_Vcf.cc:1.1
--- /dev/null   Mon Apr 25 14:34:06 2022
+++ pkgsrc/biology/stacks/patches/patch-src_Vcf.cc      Mon Apr 25 14:34:06 2022
@@ -0,0 +1,15 @@
+$NetBSD: patch-src_Vcf.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $
+
+avoid ambiguous math functions
+
+--- src/Vcf.cc.orig    2021-06-28 20:21:30.000000000 +0000
++++ src/Vcf.cc
+@@ -22,6 +22,8 @@
+ 
+ #include "Vcf.h"
+ 
++using std::log;
++
+ const VcfMeta VcfMeta::predefs::info_AD ("INFO","<ID=AD,Number=R,Type=Integer,Description=\"Total Depth for Each Allele\">");
+ const VcfMeta VcfMeta::predefs::info_AF ("INFO","<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency\">");
+ const VcfMeta VcfMeta::predefs::info_DP ("INFO","<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">");
Index: pkgsrc/biology/stacks/patches/patch-src_kmers.cc
diff -u /dev/null pkgsrc/biology/stacks/patches/patch-src_kmers.cc:1.1
--- /dev/null   Mon Apr 25 14:34:06 2022
+++ pkgsrc/biology/stacks/patches/patch-src_kmers.cc    Mon Apr 25 14:34:06 2022
@@ -0,0 +1,16 @@
+$NetBSD: patch-src_kmers.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $
+
+avoid ambiguous math functions
+
+--- src/kmers.cc.orig  2021-06-08 21:08:14.000000000 +0000
++++ src/kmers.cc
+@@ -23,6 +23,9 @@
+ //
+ #include "kmers.h"
+ 
++using std::floor;
++using std::pow;
++
+ int determine_kmer_length(int read_len, int dist) {
+     int kmer_len, span, min_matches;
+ 
Index: pkgsrc/biology/stacks/patches/patch-src_smoothing__utils.h
diff -u /dev/null pkgsrc/biology/stacks/patches/patch-src_smoothing__utils.h:1.1
--- /dev/null   Mon Apr 25 14:34:06 2022
+++ pkgsrc/biology/stacks/patches/patch-src_smoothing__utils.h  Mon Apr 25 14:34:06 2022
@@ -0,0 +1,15 @@
+$NetBSD: patch-src_smoothing__utils.h,v 1.1 2022/04/25 14:34:06 tnn Exp $
+
+avoid ambiguous math functions
+
+--- src/smoothing_utils.h.orig 2020-06-24 17:47:55.000000000 +0000
++++ src/smoothing_utils.h
+@@ -24,6 +24,8 @@
+ #include <cmath>
+ #include <vector>
+ 
++using std::pow;
++
+ extern double sigma;
+ 
+ inline
Index: pkgsrc/biology/stacks/patches/patch-src_utils.cc
diff -u /dev/null pkgsrc/biology/stacks/patches/patch-src_utils.cc:1.1
--- /dev/null   Mon Apr 25 14:34:06 2022
+++ pkgsrc/biology/stacks/patches/patch-src_utils.cc    Mon Apr 25 14:34:06 2022
@@ -0,0 +1,16 @@
+$NetBSD: patch-src_utils.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $
+
+provide fallback declaration for ACCESSPERMS
+
+--- src/utils.cc.orig  2021-10-07 19:33:41.000000000 +0000
++++ src/utils.cc
+@@ -401,6 +401,9 @@ void check_or_mk_dir(const string& path)
+             cerr << "Error: '" << *path_p << "' is not a directory.\n";
+             throw exception();
+         }
++#ifndef ACCESSPERMS
++#define ACCESSPERMS (S_IRWXU|S_IRWXG|S_IRWXO)
++#endif
+     } else if (mkdir(path_p->c_str(), ACCESSPERMS) != 0) {
+         //
+         // Failed to create the directory.