Pranav Ballaney pushed to branch master at Debian Med / kallisto
Commits: 801c272b by Pranav Ballaney at 2020-05-16T04:47:02+05:30 Patch to avoid segfault - exit with an error - - - - - 547fd1b6 by Pranav Ballaney at 2020-05-16T04:47:43+05:30 Update changelog - - - - - 2 changed files: - debian/changelog - debian/patches/Check_busOptions.seq_length_before_accessing.patch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,9 @@ +kallisto (0.46.2+dfsg-2) UNRELEASED; urgency=medium + + * Patch to avoid segfault (Closes: #960368) + + -- Pranav Ballaney <[email protected]> Sat, 16 May 2020 04:47:12 +0530 + kallisto (0.46.2+dfsg-1) unstable; urgency=medium * Team upload. ===================================== debian/patches/Check_busOptions.seq_length_before_accessing.patch ===================================== @@ -2,13 +2,13 @@ Description: Check busOptions.seq.empty() before trying to access it, to avoid a segfault. More details can be found at the upstream bug. Author: Pranav Ballaney <[email protected]> Bug: https://github.com/pachterlab/kallisto/issues/254 -Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=960368#15 +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=960368 Last-Update: 2020-05-16 --- This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ --- a/src/ProcessReads.cpp +++ b/src/ProcessReads.cpp -@@ -1408,6 +1408,12 @@ void BUSProcessor::processBuffer() { +@@ -1408,6 +1408,13 @@ void BUSProcessor::processBuffer() { std::vector<int> l(jmax,0); bool singleSeq = busopt.seq.size() ==1 ; @@ -17,11 +17,12 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ + std::cerr << "No seq technology specified.\n"; + std::cerr << "If you believe this is a bug, please report using reportbug."; + std::cerr.flush(); ++ exit(1); + } const BUSOptionSubstr seqopt = busopt.seq.front(); -@@ -2145,7 +2151,7 @@ void AlnProcessor::processBufferGenome() +@@ -2145,7 +2152,7 @@ void AlnProcessor::processBufferGenome() rlen2 = seqs[si2].second; } View it on GitLab: https://salsa.debian.org/med-team/kallisto/-/compare/9af9aec0b4000395bdd9bdfa0e97aa9551bce9a3...547fd1b6a0fade81dea21e8f1093b1ef2c6961c6 -- View it on GitLab: https://salsa.debian.org/med-team/kallisto/-/compare/9af9aec0b4000395bdd9bdfa0e97aa9551bce9a3...547fd1b6a0fade81dea21e8f1093b1ef2c6961c6 You're receiving this email because of your account on salsa.debian.org.
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