[med-svn] [bedtools] 01/01: Fix MIPS build issue
Andreas Tille
tille at debian.org
Thu Jul 16 12:45:53 UTC 2015
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tille pushed a commit to branch debian/unstable
in repository bedtools.
commit 9213f1bcf891173c6643d0f4a6a6dda09877350b
Author: Andreas Tille <tille at debian.org>
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 <arturo.borrero.glez at gmail.com>)
+ Closes: #791830
-- Andreas Tille <tille at debian.org> 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 <arq5x at virginia.edu>
+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
--
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