This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch debian/unstable in repository bedtools.
commit 9213f1bcf891173c6643d0f4a6a6dda09877350b Author: Andreas Tille <[email protected]> Date: Thu Jul 16 14:33:14 2015 +0200 Fix MIPS build issue --- debian/changelog | 3 + ...int32_t-signature-for-QuickString.-Resolv.patch | 162 +++++++++++++++++++++ debian/patches/series | 1 + 3 files changed, 166 insertions(+) diff --git a/debian/changelog b/debian/changelog index c6196a1..45426ca 100644 --- a/debian/changelog +++ b/debian/changelog @@ -3,6 +3,9 @@ bedtools (2.24.0-2) UNRELEASED; urgency=medium * Tests need bgzip from tabix package * Add missing input files for tests * link to genomes files in autopkgtests to enable more tests passing + * Fix MIPS build issue (Thanks for picking the patch from upstream + Arturo Borrero Gonzalez <[email protected]>) + Closes: #791830 -- Andreas Tille <[email protected]> Tue, 14 Jul 2015 11:01:25 +0200 diff --git a/debian/patches/0001-settle-on-uint32_t-signature-for-QuickString.-Resolv.patch b/debian/patches/0001-settle-on-uint32_t-signature-for-QuickString.-Resolv.patch new file mode 100644 index 0000000..e96f725 --- /dev/null +++ b/debian/patches/0001-settle-on-uint32_t-signature-for-QuickString.-Resolv.patch @@ -0,0 +1,162 @@ +From: arq5x <[email protected]> +Date: Wed, 15 Jul 2015 15:15:23 -0600 +Bug-Debian: http://bugs.debian.org/791830 +Forwarded-Upstream: Patch is from upstream Git +Subject: [PATCH] settle on uint32_t signature for QuickString. Resolves #267 + and #271? + +--- + src/coverageFile/coverageFile.cpp | 24 ++++++++++++------------ + src/utils/general/QuickString.cpp | 27 ++++++++++++++------------- + src/utils/general/QuickString.h | 6 +++--- + 3 files changed, 29 insertions(+), 28 deletions(-) + +--- a/src/coverageFile/coverageFile.cpp ++++ b/src/coverageFile/coverageFile.cpp +@@ -78,11 +78,11 @@ void CoverageFile::giveFinalReport(Recor + float depthPct = (float)basesAtDepth / (float)_totalQueryLen; + + _finalOutput = "all\t"; +- _finalOutput.append(depth); ++ _finalOutput.append(static_cast<uint32_t>(depth)); + _finalOutput.append("\t"); +- _finalOutput.append(basesAtDepth); ++ _finalOutput.append(static_cast<uint32_t>(basesAtDepth)); + _finalOutput.append("\t"); +- _finalOutput.append(_totalQueryLen); ++ _finalOutput.append(static_cast<uint32_t>(_totalQueryLen)); + _finalOutput.append("\t"); + format(depthPct); + +@@ -133,7 +133,7 @@ size_t CoverageFile::countBasesAtDepth(s + + void CoverageFile::doCounts(RecordOutputMgr *outputMgr, RecordKeyVector &hits) + { +- _finalOutput = hits.size(); ++ _finalOutput = static_cast<uint32_t>(hits.size()); + outputMgr->printRecord(hits.getKey(), _finalOutput); + } + +@@ -142,9 +142,9 @@ void CoverageFile::doPerBase(RecordOutpu + //loop through all bases in query, printing full record and metrcis for each + const Record * queryRec = hits.getKey(); + for (size_t i= 0; i < _queryLen; i++) { +- _finalOutput = i +1; ++ _finalOutput = static_cast<uint32_t>(i+1); + _finalOutput.append("\t"); +- _finalOutput.append(_depthArray[i]); ++ _finalOutput.append(static_cast<uint32_t>(_depthArray[i])); + + outputMgr->printRecord(queryRec, _finalOutput); + } +@@ -165,11 +165,11 @@ void CoverageFile::doHist(RecordOutputMg + size_t numBasesAtDepth = iter->second; + float coveredBases = (float)numBasesAtDepth / (float)_queryLen; + +- _finalOutput = depth; ++ _finalOutput = static_cast<uint32_t>(depth); + _finalOutput.append("\t"); +- _finalOutput.append(numBasesAtDepth); ++ _finalOutput.append(static_cast<uint32_t>(numBasesAtDepth)); + _finalOutput.append("\t"); +- _finalOutput.append(_queryLen); ++ _finalOutput.append(static_cast<uint32_t>(_queryLen)); + _finalOutput.append("\t"); + format(coveredBases); + +@@ -183,11 +183,11 @@ void CoverageFile::doDefault(RecordOutpu + size_t nonZeroBases = _queryLen - countBasesAtDepth(0); + float coveredBases = (float)nonZeroBases / (float)_queryLen; + +- _finalOutput = hits.size(); ++ _finalOutput = static_cast<uint32_t>(hits.size()); + _finalOutput.append("\t"); +- _finalOutput.append(nonZeroBases); ++ _finalOutput.append(static_cast<uint32_t>(nonZeroBases)); + _finalOutput.append("\t"); +- _finalOutput.append(_queryLen); ++ _finalOutput.append(static_cast<uint32_t>(_queryLen)); + _finalOutput.append("\t"); + format(coveredBases); + +--- a/src/utils/general/QuickString.cpp ++++ b/src/utils/general/QuickString.cpp +@@ -105,11 +105,11 @@ QuickString &QuickString::operator = (ui + return *this; + } + +-QuickString &QuickString::operator = (size_t val) { +- clear(); +- append(val); +- return *this; +-} ++// QuickString &QuickString::operator = (size_t val) { ++// clear(); ++// append(val); ++// return *this; ++// } + + QuickString &QuickString::operator = (float val) { + clear(); +@@ -158,10 +158,11 @@ QuickString &QuickString::operator += (u + return *this; + } + +-QuickString &QuickString::operator += (size_t num) { +- append(num); +- return *this; +-} ++// QuickString &QuickString::operator += (size_t num) { ++// append(num); ++// return *this; ++// } ++ + QuickString &QuickString::operator += (float num) { + append(num); + return *this; +@@ -261,12 +262,12 @@ void QuickString::append(int num) { + } + + void QuickString::append(uint32_t num) { +- int2str((int)num, *this, true); ++ int2str((int)num, *this, true); + } + +-void QuickString::append(size_t num) { +- int2str((int)num, *this, true); +-} ++// void QuickString::append(size_t num) { ++// int2str((int)num, *this, true); ++// } + + void QuickString::append(float num) { + append(ToString(num)); +--- a/src/utils/general/QuickString.h ++++ b/src/utils/general/QuickString.h +@@ -38,7 +38,7 @@ public: + QuickString &operator = (char); + QuickString &operator = (int); + QuickString &operator = (uint32_t); +- QuickString &operator = (size_t); ++ //QuickString &operator = (size_t); + QuickString &operator = (float); + QuickString &operator = (double); + QuickString &operator += (const QuickString &); +@@ -47,7 +47,7 @@ public: + QuickString &operator += (char); + QuickString &operator += (int); + QuickString &operator += (uint32_t); +- QuickString &operator += (size_t); ++ //QuickString &operator += (size_t); + QuickString &operator += (float); + QuickString &operator += (double); + +@@ -73,7 +73,7 @@ public: + //for better performance. + void append(int num); + void append(uint32_t num); +- void append(size_t num); ++ //void append(size_t num); + void append(float num); + void append(double num); + diff --git a/debian/patches/series b/debian/patches/series index aeb5e3a..de905d3 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,2 +1,3 @@ gzstream.h.patch fix_test_script.patch +0001-settle-on-uint32_t-signature-for-QuickString.-Resolv.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bedtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
