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commit 9b1eca7c5560161e1ebd78b2dde6f92adff4e087 Author: Andreas Tille <[email protected]> Date: Wed Jan 18 16:52:25 2017 +0100 Specify correct format in printf statement --- debian/changelog | 8 +++++++ debian/patches/fix_type_mismatch_in_printf.patch | 30 ++++++++++++++++++++++++ debian/patches/series | 1 + 3 files changed, 39 insertions(+) diff --git a/debian/changelog b/debian/changelog index 3e0ff88..c7ab302 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,11 @@ +hhsuite (3.0~beta2+dfsg-3) unstable; urgency=medium + + * Specify correct format in printf statement (Thanks for the patch to + Daniel Shahaf <[email protected]>) + Closes: #851764 + + -- Andreas Tille <[email protected]> Wed, 18 Jan 2017 16:52:21 +0100 + hhsuite (3.0~beta2+dfsg-2) unstable; urgency=medium * Really fix watch file to fetch latest version diff --git a/debian/patches/fix_type_mismatch_in_printf.patch b/debian/patches/fix_type_mismatch_in_printf.patch new file mode 100644 index 0000000..ab2d5df --- /dev/null +++ b/debian/patches/fix_type_mismatch_in_printf.patch @@ -0,0 +1,30 @@ +Author: Daniel Shahaf <[email protected]> +Last-Update: Wed, Jan 18, 2017 at 15:22:26 +0000 +Bug-Debian: https://bugs.debian.org/851764 +Description: hhblits.cpp uses the %i printf(3) conversion to format a 'double' value + Thats undefined and prints garbage - the patch inserts the correct format + (and also fixes the doc about the correct default value + +--- a/doc/hhsuite-userguide.tex ++++ b/doc/hhsuite-userguide.tex +@@ -1466,7 +1466,7 @@ + -maxfilt max number of hits allowed to pass 2nd prefilter (default=20000) + -min_prefilter_hits min number of hits to pass prefilter (default=100) + -prepre_smax_thresh min score threshold of ungapped prefilter (default=10) +- -pre_evalue_thresh max E-value threshold of Smith-Waterman prefilter score (default=0) ++ -pre_evalue_thresh max E-value threshold of Smith-Waterman prefilter score (default=1000.0) + -pre_bitfactor prefilter scores are in units of 1 bit / pre_bitfactor (default=4) + -pre_gap_open gap open penalty in prefilter Smith-Waterman alignment (default=20) + -pre_gap_extend gap extend penalty in prefilter Smith-Waterman alignment (default=4) +--- a/src/hhblits.cpp ++++ b/src/hhblits.cpp +@@ -330,7 +330,7 @@ + printf(" -maxfilt max number of hits allowed to pass 2nd prefilter (default=%i) \n", par.maxnumdb); + printf(" -min_prefilter_hits min number of hits to pass prefilter (default=%i) \n", par.min_prefilter_hits); + printf(" -prepre_smax_thresh min score threshold of ungapped prefilter (default=%i) \n", par.preprefilter_smax_thresh); +- printf(" -pre_evalue_thresh max E-value threshold of Smith-Waterman prefilter score (default=%i)\n", par.prefilter_evalue_thresh); ++ printf(" -pre_evalue_thresh max E-value threshold of Smith-Waterman prefilter score (default=%.1f)\n", par.prefilter_evalue_thresh); + printf(" -pre_bitfactor prefilter scores are in units of 1 bit / pre_bitfactor (default=%i)\n", par.prefilter_bit_factor); + printf(" -pre_gap_open gap open penalty in prefilter Smith-Waterman alignment (default=%i)\n", par.prefilter_gap_open); + printf(" -pre_gap_extend gap extend penalty in prefilter Smith-Waterman alignment (default=%i)\n", par.prefilter_gap_extend); + diff --git a/debian/patches/series b/debian/patches/series index ae933a6..1a22412 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -8,3 +8,4 @@ drop-fmemopen.h.patch build-own-manual-PDF.patch set-default-HHLIB-dir.patch disable-AVX-SSE.patch +fix_type_mismatch_in_printf.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/hhsuite.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
