[med-svn] [Git][med-team/quorum][master] 8 commits: initialise changelog
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Wed Jun 14 21:30:44 BST 2023
Étienne Mollier pushed to branch master at Debian Med / quorum
Commits:
ef705bff by Étienne Mollier at 2023-06-14T22:14:44+02:00
initialise changelog
- - - - -
71bb14ab by Étienne Mollier at 2023-06-14T22:15:24+02:00
New upstream version 1.1.2
- - - - -
a0fd9724 by Étienne Mollier at 2023-06-14T22:15:24+02:00
routine-update: New upstream version
- - - - -
902d85d0 by Étienne Mollier at 2023-06-14T22:15:29+02:00
Update upstream source from tag 'upstream/1.1.2'
Update to upstream version '1.1.2'
with Debian dir 749977af21cf0296e9f8c33307bf7239baeb8ee9
- - - - -
e1f1515a by Étienne Mollier at 2023-06-14T22:15:29+02:00
routine-update: Standards-Version: 4.6.2
- - - - -
b0cf7233 by Étienne Mollier at 2023-06-14T22:18:46+02:00
gcc-12.patch: delete; applied upstream.
- - - - -
ec021a6d by Étienne Mollier at 2023-06-14T22:28:37+02:00
remove spurious d/p/series
Gbp-Dch: ignore
- - - - -
d958e13b by Étienne Mollier at 2023-06-14T22:29:12+02:00
ready to upload to unstable
- - - - -
8 changed files:
- configure.ac
- debian/changelog
- debian/control
- − debian/patches/gcc-12.patch
- − debian/patches/series
- src/create_database.cc
- src/err_log.hpp
- src/error_correct_reads.cc
Changes:
=====================================
configure.ac
=====================================
@@ -1,4 +1,4 @@
-AC_INIT([quorum], [1.1.1], [gmarcais at cs.cmu.edu])
+AC_INIT([quorum], [1.1.2], [gmarcais at cs.cmu.edu])
AC_CONFIG_AUX_DIR([build-aux])
AC_CONFIG_SRCDIR([src/error_correct_reads.hpp])
AC_CONFIG_HEADERS([config.h])
@@ -55,6 +55,21 @@ AM_CONDITIONAL([HAVE_RELATIVE_JF_PATH], [test x$with_relative_jf_path != x])
AC_CHECK_TYPE([__int128],
[AC_DEFINE([HAVE_INT128], [1], [Define if type __int128 is supported])])
+# Check that type __int128 is supported and if the
+# std::numeric_limits<__int128> specialization exists
+AC_ARG_WITH([int128],
+ [AS_HELP_STRING([--with-int128], [enable int128])],
+ [], [with_int128=yes])
+AS_IF([test "x$with_int128" != xno],
+ [AC_CHECK_TYPE([__int128],
+ [AC_DEFINE([HAVE_INT128], [1], [Define if type __int128 is supported])])
+ AC_MSG_CHECKING([for std::numeric_limits<__int128>])
+ AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[#include <limits>
+ template<bool> struct StaticAssert; template<> struct StaticAssert<true> { static void assert() { } };]],
+ [[StaticAssert<std::numeric_limits<__int128>::is_specialized>::assert();]])],
+ [AC_MSG_RESULT([yes])]
+ [AC_DEFINE([HAVE_NUMERIC_LIMITS128], [1], [Define if numeric limits specialization exists for __int128])],
+ [AC_MSG_RESULT([no])])])
# Check the version of strerror_r
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+quorum (1.1.2-1) unstable; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.6.2 (routine-update)
+ * gcc-12.patch: delete; applied upstream.
+
+ -- Étienne Mollier <emollier at debian.org> Wed, 14 Jun 2023 22:21:18 +0200
+
quorum (1.1.1-7) unstable; urgency=medium
* Fix build with gcc-12
=====================================
debian/control
=====================================
@@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 13),
jellyfish,
yaggo,
pkg-config
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/quorum
Vcs-Git: https://salsa.debian.org/med-team/quorum.git
Homepage: https://github.com/gmarcais/Quorum
=====================================
debian/patches/gcc-12.patch deleted
=====================================
@@ -1,17 +0,0 @@
-Description: Fix build with gcc-12
-Bug-Debian: https://bugs.debian.org/1013026
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 25 Jul 2022 09:34:19 +0200
-Forwarded: https://github.com/gmarcais/Quorum/issues/7
-
---- a/src/err_log.hpp
-+++ b/src/err_log.hpp
-@@ -39,7 +39,7 @@ private:
- entry(type_t t, T p) : type(t), pos(p) {}
- };
-
-- struct greater_than_pos : std::unary_function<entry, bool> {
-+ struct greater_than_pos {
- T pos;
- bool operator()(entry& e) { return e.pos >= *pos; } // Compare the raw value of pos, not using the operator>=
- greater_than_pos(T& pos_) : pos(pos_) { }
=====================================
debian/patches/series deleted
=====================================
@@ -1 +0,0 @@
-gcc-12.patch
=====================================
src/create_database.cc
=====================================
@@ -55,7 +55,6 @@ public:
virtual void start(int thid) {
mer_dna m, rm;
- size_t counted_high = 0, counted_low = 0;
while(true) {
read_parser::job job(parser_);
@@ -85,8 +84,6 @@ public:
if(low_len >= mer_dna::k()) {
if(!ary_.add(m < rm ? m : rm, high_len >= mer_dna::k()))
throw std::runtime_error(err::msg() << "Hash is full");
- counted_high += high_len >= mer_dna::k();
- ++counted_low;
}
}
}
=====================================
src/err_log.hpp
=====================================
@@ -39,7 +39,7 @@ private:
entry(type_t t, T p) : type(t), pos(p) {}
};
- struct greater_than_pos : std::unary_function<entry, bool> {
+ struct greater_than_pos {
T pos;
bool operator()(entry& e) { return e.pos >= *pos; } // Compare the raw value of pos, not using the operator>=
greater_than_pos(T& pos_) : pos(pos_) { }
=====================================
src/error_correct_reads.cc
=====================================
@@ -161,9 +161,9 @@ public:
std::unique_ptr<std::ostream> output(open_file(_prefix, ".fa", "/dev/fd/1"));
// Multiplexers, same thing
std::unique_ptr<jflib::o_multiplexer>
- log_m(new jflib::o_multiplexer(details.get(), 3 * nb_threads, 1024));
+ log_m(new jflib::o_multiplexer(details.get(), 3 * (size_t)nb_threads, 1024));
std::unique_ptr<jflib::o_multiplexer>
- output_m(new jflib::o_multiplexer(output.get(), 3 * nb_threads, 1024));
+ output_m(new jflib::o_multiplexer(output.get(), 3 * (size_t)nb_threads, 1024));
_log = log_m.get();
_output = output_m.get();
@@ -248,7 +248,6 @@ public:
jflib::omstream details(_ec.log());
kmer_t mer, tmer;
- uint64_t nb_reads = 0;
while(true) {
read_parser::job job(_ec.parser());
if(job.is_empty()) break;
@@ -261,7 +260,6 @@ public:
const char* const seq_e = seq_s + sequence.size();
const char* const qual_s = job->data[i].qual.c_str();
- nb_reads++;
insure_length_buffer(sequence.size());
const char* error = "";
View it on GitLab: https://salsa.debian.org/med-team/quorum/-/compare/4db8ca6a606fcf97287b8a68d46905a7eff5e229...d958e13b88af3e4506e09b04be728c493268cab3
--
View it on GitLab: https://salsa.debian.org/med-team/quorum/-/compare/4db8ca6a606fcf97287b8a68d46905a7eff5e229...d958e13b88af3e4506e09b04be728c493268cab3
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