[pkgsrc/trunk]: pkgsrc/biology/stacks stacks: avoid ambiguous math functions

[tnn <tnn%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/426d114c725a
branches:  trunk
changeset: 377938:426d114c725a
user:      tnn <tnn%pkgsrc.org@localhost>
date:      Mon Apr 25 14:34:06 2022 +0000

description:
stacks: avoid ambiguous math functions

diffstat:

 biology/stacks/distinfo                             |   8 +++++++-
 biology/stacks/patches/patch-src_Hwp.cc             |  16 ++++++++++++++++
 biology/stacks/patches/patch-src_PopSum.cc          |  15 +++++++++++++++
 biology/stacks/patches/patch-src_Vcf.cc             |  15 +++++++++++++++
 biology/stacks/patches/patch-src_kmers.cc           |  16 ++++++++++++++++
 biology/stacks/patches/patch-src_smoothing__utils.h |  15 +++++++++++++++
 biology/stacks/patches/patch-src_utils.cc           |  16 ++++++++++++++++
 7 files changed, 100 insertions(+), 1 deletions(-)

diffs (133 lines):

diff -r 61de5d5d72b9 -r 426d114c725a biology/stacks/distinfo
--- a/biology/stacks/distinfo   Mon Apr 25 13:58:46 2022 +0000
+++ b/biology/stacks/distinfo   Mon Apr 25 14:34:06 2022 +0000
@@ -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
diff -r 61de5d5d72b9 -r 426d114c725a biology/stacks/patches/patch-src_Hwp.cc
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/stacks/patches/patch-src_Hwp.cc   Mon Apr 25 14:34:06 2022 +0000
@@ -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)
+ {
diff -r 61de5d5d72b9 -r 426d114c725a biology/stacks/patches/patch-src_PopSum.cc
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/stacks/patches/patch-src_PopSum.cc        Mon Apr 25 14:34:06 2022 +0000
@@ -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();
diff -r 61de5d5d72b9 -r 426d114c725a biology/stacks/patches/patch-src_Vcf.cc
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/stacks/patches/patch-src_Vcf.cc   Mon Apr 25 14:34:06 2022 +0000
@@ -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\">");
diff -r 61de5d5d72b9 -r 426d114c725a biology/stacks/patches/patch-src_kmers.cc
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/stacks/patches/patch-src_kmers.cc Mon Apr 25 14:34:06 2022 +0000
@@ -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;
+ 
diff -r 61de5d5d72b9 -r 426d114c725a biology/stacks/patches/patch-src_smoothing__utils.h
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/stacks/patches/patch-src_smoothing__utils.h       Mon Apr 25 14:34:06 2022 +0000
@@ -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
diff -r 61de5d5d72b9 -r 426d114c725a biology/stacks/patches/patch-src_utils.cc
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/stacks/patches/patch-src_utils.cc Mon Apr 25 14:34:06 2022 +0000
@@ -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.