commit: cd124fce591dc879a82805175313c4b2e0ef18a6 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Dec 24 17:11:30 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Dec 24 18:00:22 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=cd124fce
sci-biology/allpathslg: Fix building with GCC 7 Closes: https://bugs.gentoo.org/638724 Package-Manager: Portage-2.3.19, Repoman-2.3.6 sci-biology/allpathslg/allpathslg-52488-r2.ebuild | 5 +++-- 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 e68430e2462..391575f4f05 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 00000000000..7c5e1267e4e --- /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)
