[med-svn] [nanopolish] 03/03: Proceeded to version 0.8.1
Steffen Möller
moeller at moszumanska.debian.org
Sat Sep 16 00:14:56 UTC 2017
This is an automated email from the git hooks/post-receive script.
moeller pushed a commit to branch master
in repository nanopolish.
commit 79cea4f1be151a146a9815bd2da60823855cf8ad
Author: Steffen Moeller <moeller at debian.org>
Date: Sat Sep 16 02:14:07 2017 +0200
Proceeded to version 0.8.1
---
debian/changelog | 12 +++++++++++
debian/control | 2 +-
debian/patches/dontinstalleigen.patch | 13 ++++++++++++
debian/patches/fprintf_sizet.patch | 26 ++++++++++++++++++++++++
debian/patches/gcc7.patch | 12 +++++++++++
debian/patches/series | 4 ++++
debian/patches/write_return_values_ignored.patch | 22 ++++++++++++++++++++
debian/rules | 3 +++
8 files changed, 93 insertions(+), 1 deletion(-)
diff --git a/debian/changelog b/debian/changelog
index 2b1d51f..212feb9 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,15 @@
+nanopolish (0.8.1-1) unstable; urgency=medium
+
+ * Team upload
+ * New upstream version
+ - bumped dependency on fast5 to 0.6.2
+ - established compatibility with gcc/g++ 7
+ - needed some extra persuasion to not download
+ eigen library.
+ - added link-time optimisation
+
+ -- Steffen Moeller <moeller at debian.org> Thu, 14 Sep 2017 16:59:29 +0200
+
nanopolish (0.7.2-1) UNRELEASED; urgency=medium
* Team upload
diff --git a/debian/control b/debian/control
index da512b1..3b72655 100644
--- a/debian/control
+++ b/debian/control
@@ -6,7 +6,7 @@ Uploaders: Afif Elghraoui <afif at debian.org>
Build-Depends:
debhelper (>= 10),
zlib1g-dev,
- libfast5-dev,
+ libfast5-dev (>= 0.6.2-3),
libhts-dev,
libeigen3-dev,
Standards-Version: 4.1.0
diff --git a/debian/patches/dontinstalleigen.patch b/debian/patches/dontinstalleigen.patch
new file mode 100644
index 0000000..3241833
--- /dev/null
+++ b/debian/patches/dontinstalleigen.patch
@@ -0,0 +1,13 @@
+Index: nanopolish/Makefile
+===================================================================
+--- nanopolish.orig/Makefile
++++ nanopolish/Makefile
+@@ -16,7 +16,7 @@ CXX ?= g++
+ CC ?= gcc
+
+ # Change the value of HDF5 or EIGEN below to any value to disable compilation of bundled HDF5 code
+-EIGEN=install
++#EIGEN=install
+
+ # Check operating system, OSX doesn't have -lrt
+ UNAME_S := $(shell uname -s)
diff --git a/debian/patches/fprintf_sizet.patch b/debian/patches/fprintf_sizet.patch
new file mode 100644
index 0000000..869707e
--- /dev/null
+++ b/debian/patches/fprintf_sizet.patch
@@ -0,0 +1,26 @@
+Index: nanopolish/src/common/nanopolish_variant.cpp
+===================================================================
+--- nanopolish.orig/src/common/nanopolish_variant.cpp
++++ nanopolish/src/common/nanopolish_variant.cpp
+@@ -175,7 +175,7 @@ void score_variant_group(VariantGroup& v
+ max_r -= 1;
+
+ if(max_r != num_variants) {
+- fprintf(stderr, "Number of variants in span (%d) would exceed max-haplotypes. Variants may be missed. Consider running with a higher value of max-haplotypes!\n", num_variants);
++ fprintf(stderr, "Number of variants in span (%lu) would exceed max-haplotypes. Variants may be missed. Consider running with a higher value of max-haplotypes!\n", num_variants);
+ }
+
+ // Construct haplotypes (including the base haplotype with no variants)
+Index: nanopolish/src/nanopolish_haplotype.cpp
+===================================================================
+--- nanopolish.orig/src/nanopolish_haplotype.cpp
++++ nanopolish/src/nanopolish_haplotype.cpp
+@@ -169,7 +169,7 @@ size_t Haplotype::_find_derived_index_by
+
+ void Haplotype::print_debug_info() const
+ {
+- fprintf(stderr, "[haplotype-debug] ctg: %s, position: %d\n", m_ref_name.c_str(), m_ref_position);
++ fprintf(stderr, "[haplotype-debug] ctg: %s, position: %lu\n", m_ref_name.c_str(), m_ref_position);
+ fprintf(stderr, "[haplotype-debug] r-sequence: %s\n", m_reference.c_str());
+ fprintf(stderr, "[haplotype-debug] h-sequence: %s\n", m_sequence.c_str());
+ for(size_t i = 0; i < m_variants.size(); ++i) {
diff --git a/debian/patches/gcc7.patch b/debian/patches/gcc7.patch
new file mode 100644
index 0000000..104ca19
--- /dev/null
+++ b/debian/patches/gcc7.patch
@@ -0,0 +1,12 @@
+Index: nanopolish/src/common/logger.hpp
+===================================================================
+--- nanopolish.orig/src/common/logger.hpp
++++ nanopolish/src/common/logger.hpp
+@@ -72,6 +72,7 @@
+ #include <iostream>
+ #include <mutex>
+ #include <stdexcept>
++#include <functional>
+
+ namespace logger
+ {
diff --git a/debian/patches/series b/debian/patches/series
index dacdb9f..851fdbe 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,7 @@ compiler-flags.patch
external-libs.patch
add-shebang-to-script.patch
reproducible.patch
+dontinstalleigen.patch
+write_return_values_ignored.patch
+gcc7.patch
+fprintf_sizet.patch
diff --git a/debian/patches/write_return_values_ignored.patch b/debian/patches/write_return_values_ignored.patch
new file mode 100644
index 0000000..be1b66f
--- /dev/null
+++ b/debian/patches/write_return_values_ignored.patch
@@ -0,0 +1,22 @@
+Index: nanopolish/src/alignment/nanopolish_eventalign.cpp
+===================================================================
+--- nanopolish.orig/src/alignment/nanopolish_eventalign.cpp
++++ nanopolish/src/alignment/nanopolish_eventalign.cpp
+@@ -221,7 +221,7 @@ void emit_tsv_header(FILE* fp)
+
+ void emit_sam_header(samFile* fp, const bam_hdr_t* hdr)
+ {
+- sam_hdr_write(fp, hdr);
++ int r = sam_hdr_write(fp, hdr);
+ }
+
+ std::string cigar_ops_to_string(const std::vector<uint32_t>& ops)
+@@ -360,7 +360,7 @@ void emit_event_alignment_sam(htsFile* f
+ int stride = alignments.front().event_idx < alignments.back().event_idx ? 1 : -1;
+ bam_aux_append(event_record, "ES", 'i', 4, reinterpret_cast<uint8_t*>(&stride));
+
+- sam_write1(fp, base_hdr, event_record);
++ int r = sam_write1(fp, base_hdr, event_record);
+ bam_destroy1(event_record); // automatically frees malloc'd segment
+ }
+
diff --git a/debian/rules b/debian/rules
index d946546..14e94da 100755
--- a/debian/rules
+++ b/debian/rules
@@ -7,6 +7,9 @@ export DEB_CPPFLAGS_MAINT_APPEND = -I/usr/include/hdf5/serial
export DEB_LDFLAGS_MAINT_APPEND = -L/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export CXXFLAGS += -flto
+export LDFLAGS += $(CXXFLAGS) $(CPPFLAGS) -L/usr/lib/$(shell dpkg-architecture -qDEB_TARGET_GNU_TYPE)/hdf5/serial
+
%:
dh $@
--
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