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 <[email protected]> Sat, 17 Feb 2018 18:06:03 -0500 + -- Afif Elghraoui <[email protected]> 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 <[email protected]> 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 <[email protected]> +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.
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