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| author |   David Seifert <soap@gentoo.org> | 2017-12-24 18:11:30 +0100 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2017-12-24 19:00:22 +0100 |
| commit | cd124fce591dc879a82805175313c4b2e0ef18a6 (patch) | |
| tree | 74c0b887faca05bcde23377a8c376e568555b805 /sci-biology | |
| parent | sci-biology/mosaik: Fix building with GCC 7 (diff) | |
| download | gentoo-cd124fce591dc879a82805175313c4b2e0ef18a6.tar.gz gentoo-cd124fce591dc879a82805175313c4b2e0ef18a6.tar.bz2 gentoo-cd124fce591dc879a82805175313c4b2e0ef18a6.zip | |
sci-biology/allpathslg: Fix building with GCC 7
Closes: https://bugs.gentoo.org/638724
Package-Manager: Portage-2.3.19, Repoman-2.3.6
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/allpathslg/allpathslg-52488-r2.ebuild | 5 | ||||
| -rw-r--r-- | sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch | 13 |
2 files changed, 16 insertions, 2 deletions
diff --git a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild index e68430e2462d..391575f4f057 100644 --- a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild +++ b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild @@ -23,8 +23,9 @@ DEPEND=" dev-libs/boost:=" PATCHES=( - "${WORKDIR}/${P}-patchset/${P}_fix-buildsystem.patch" - "${WORKDIR}/${P}-patchset/${P}_remove-namespace-std.patch" + "${WORKDIR}"/${P}-patchset/${P}_fix-buildsystem.patch + "${WORKDIR}"/${P}-patchset/${P}_remove-namespace-std.patch + "${FILESDIR}"/${P}-gcc7.patch ) pkg_pretend() { diff --git a/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch b/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch new file mode 100644 index 000000000000..7c5e1267e4e9 --- /dev/null +++ b/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch @@ -0,0 +1,13 @@ +--- a/src/paths/long/VariantCallTools.cc ++++ b/src/paths/long/VariantCallTools.cc +@@ -1870,8 +1870,8 @@ + bool i_is_indel = (change[i].first.size() != change[i].second.size()); + if (i_is_indel) inserted_base += change[i].second.size()-1; + size_t j = i + 1; +- while (j < edits.size() && abs(edits[j].second - edits[j-1].second +- - change[j-1].first.size()) < MinClumpSep) { ++ while (j < edits.size() && std::abs(edits[j].second - edits[j-1].second ++ - static_cast<int>(change[j-1].first.size())) < MinClumpSep) { + nmatch += edits[j].second - edits[j-1].second - change[j-1].first.size(); + bool j_is_indel = (change[j].first.size() != change[j].second.size()); + if (j_is_indel) |