[med-svn] [Git][med-team/nanopolish][master] 3 commits: Bump minimum required fast5 version

[Afif Elghraoui]

Afif Elghraoui pushed to branch master at Debian Med / nanopolish


Commits:
cccda957 by Afif Elghraoui at 2018-02-17T20:46:45-05:00
Bump minimum required fast5 version

- - - - -
5844c060 by Afif Elghraoui at 2018-02-17T22:01:39-05:00
Include upstream patch to fix HDF5 errors appearing in autopkgtest

See https://github.com/jts/nanopolish/issues/335

- - - - -
34ec40c2 by Afif Elghraoui at 2018-02-17T22:02:38-05:00
releasing package nanopolish version 0.9.0-1

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/hdf5-groupcheck.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,10 +1,12 @@
-nanopolish (0.9.0-1) UNRELEASED; urgency=medium
+nanopolish (0.9.0-1) unstable; urgency=medium
 
-  * New upstream version 0.9.0
+  * New upstream version
   * Refresh patches
   * Bump upstream copyright year
+  * Bump minimum required fast5 version
+  * Include upstream patch to fix HDF5 errors appearing in autopkgtest
 
- -- Afif Elghraoui <afif at debian.org>  Sat, 17 Feb 2018 18:06:03 -0500
+ -- Afif Elghraoui <afif at debian.org>  Sat, 17 Feb 2018 22:02:10 -0500
 
 nanopolish (0.8.5-2) unstable; urgency=low
 


=====================================
debian/control
=====================================
--- 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 (>= 0.6.4),
+	libfast5-dev (>= 0.6.5),
 	libhts-dev,
 	libeigen3-dev,
 Standards-Version: 4.1.3


=====================================
debian/patches/hdf5-groupcheck.patch
=====================================
--- /dev/null
+++ b/debian/patches/hdf5-groupcheck.patch
@@ -0,0 +1,27 @@
+From 303971c245d507988132ad8404f840461ff4d87d Mon Sep 17 00:00:00 2001
+From: Jared Simpson <jared.simpson at gmail.com>
+Date: Sat, 17 Feb 2018 21:48:45 -0500
+Subject: [PATCH] check for existence of group before opening it (#335)
+
+---
+ src/common/nanopolish_fast5_io.cpp | 7 +++++++
+ 1 file changed, 7 insertions(+)
+
+diff --git a/src/common/nanopolish_fast5_io.cpp b/src/common/nanopolish_fast5_io.cpp
+index 0144062..7f38719 100644
+--- a/src/common/nanopolish_fast5_io.cpp
++++ b/src/common/nanopolish_fast5_io.cpp
+@@ -208,6 +208,13 @@ std::string fast5_get_fixed_string_attribute(hid_t hdf5_file, const std::string&
+     int ret;
+     std::string out;
+ 
++    // according to http://hdf-forum.184993.n3.nabble.com/check-if-dataset-exists-td194725.html
++    // we should use H5Lexists to check for the existence of a group/dataset using an arbitrary path
++    ret = H5Lexists(hdf5_file, group_name.c_str(), H5P_DEFAULT);
++    if(ret <= 0) {
++        return "";
++    }
++
+     // Open the group /Raw/Reads/Read_nnn
+     group = H5Gopen(hdf5_file, group_name.c_str(), H5P_DEFAULT);
+     if(group < 0) {


=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 add-shebang-to-script.patch
 reproducible.patch
+hdf5-groupcheck.patch



View it on GitLab: https://salsa.debian.org/med-team/nanopolish/compare/326887cec4e0a418b5b9089c13910c75334d181b...34ec40c2564b5e7fa2abeb244259b52bb47d8b00

---
View it on GitLab: https://salsa.debian.org/med-team/nanopolish/compare/326887cec4e0a418b5b9089c13910c75334d181b...34ec40c2564b5e7fa2abeb244259b52bb47d8b00
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.alioth.debian.org/pipermail/debian-med-commit/attachments/20180218/f91dfd53/attachment-0001.html>