[med-svn] [abyss] 07/10: Adapted patches (including deactivating gtest patch since it needs severe changes
Andreas Tille
tille at debian.org
Thu Jul 16 09:42:33 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository abyss.
commit 852531c68a9072dcb500136a50ccca82a016e61a
Author: Andreas Tille <tille at debian.org>
Date: Thu Jul 16 10:48:18 2015 +0200
Adapted patches (including deactivating gtest patch since it needs severe changes
Signed-off-by: Andreas Tille <tille at debian.org>
---
debian/changelog | 3 +-
debian/patches/abyss-32-bit.patch | 64 ++---------------------------
debian/patches/{abyss-pe => abyss-pe.patch} | 3 ++
debian/patches/gtest.patch | 2 +
debian/patches/privacy-breach.patch | 2 +-
debian/patches/series | 4 +-
6 files changed, 13 insertions(+), 65 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 0583a6e..dd282e2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,11 +1,12 @@
abyss (1.9.0-1) UNRELEASED; urgency=medium
* New upstream version
+ Adapted patches
* Took over COPYRIGHT from upstream as debian/copyright
* Dropped Shaun Jackman from Uploaders since he confirmed that he will not
be able to maintain the package
- -- Andreas Tille <tille at debian.org> Tue, 14 Jul 2015 22:30:15 +0200
+ -- Andreas Tille <tille at debian.org> Thu, 16 Jul 2015 07:41:30 +0200
abyss (1.5.2-2) unstable; urgency=medium
diff --git a/debian/patches/abyss-32-bit.patch b/debian/patches/abyss-32-bit.patch
index ab18c77..f737767 100644
--- a/debian/patches/abyss-32-bit.patch
+++ b/debian/patches/abyss-32-bit.patch
@@ -1,5 +1,5 @@
Author: Graham Inggs <graham at nerve.org.za>
-Last-Update: Fri, 13 Mar 2015 16:41:09 +0200
+Last-Update: Thu, 16 Jul 2015 10:44:56 +0200
Bug-Debian: http://bugs.debian.org/780409
Description: Fix FTBFS on 32-bit architectures
Version 1.5.2-1 of abyss FTBFS on 32-bit architectures (armhf, i386 and
@@ -13,7 +13,7 @@ Description: Fix FTBFS on 32-bit architectures
--- a/Common/StringUtil.h
+++ b/Common/StringUtil.h
-@@ -106,7 +106,7 @@ bool isReadNamePair(const std::string& n
+@@ -178,7 +178,7 @@ bool isReadNamePair(const std::string& n
return false;
}
@@ -22,7 +22,7 @@ Description: Fix FTBFS on 32-bit architectures
{
double size;
std::string units;
-@@ -122,7 +122,7 @@ static inline size_t SIToBytes(std::istr
+@@ -194,7 +194,7 @@ static inline size_t SIToBytes(std::istr
// no units given; clear fail flag
// and assume bytes
iss.clear(std::ios::eofbit);
@@ -31,61 +31,3 @@ Description: Fix FTBFS on 32-bit architectures
}
if (units.size() > 1) {
-@@ -133,22 +133,22 @@ static inline size_t SIToBytes(std::istr
-
- switch(tolower(units[0])) {
- case 'k':
-- size *= (size_t)1<<10; break;
-+ size *= (unsigned long long)1<<10; break;
- case 'm':
-- size *= (size_t)1<<20; break;
-+ size *= (unsigned long long)1<<20; break;
- case 'g':
-- size *= (size_t)1<<30; break;
-+ size *= (unsigned long long)1<<30; break;
- case 't':
-- size *= (size_t)1<<40; break;
-+ size *= (unsigned long long)1<<40; break;
- default:
- iss.setstate(std::ios::failbit);
- return 0;
- }
-
-- return (size_t)ceil(size);
-+ return (unsigned long long)ceil(size);
- }
-
--static inline size_t SIToBytes(const std::string& str)
-+static inline unsigned long long SIToBytes(const std::string& str)
- {
- std::istringstream iss(str);
- return SIToBytes(iss);
---- a/Bloom/Bloom.h
-+++ b/Bloom/Bloom.h
-@@ -165,10 +165,10 @@ namespace Bloom {
- // bloom filter bits
-
- size_t bits = endBitPos - startBitPos + 1;
-- size_t bytes = (bits + 7) / 8;
-+ unsigned long bytes = (bits + 7) / 8;
- char buf[IO_BUFFER_SIZE];
- for (size_t i = 0, j = 0; i < bytes;) {
-- size_t writeSize = std::min(IO_BUFFER_SIZE, bytes - i);
-+ unsigned long writeSize = std::min(IO_BUFFER_SIZE, bytes - i);
- for (size_t k = 0; k < writeSize; k++) {
- buf[k] = 0;
- for (unsigned l = 0; l < 8; l++, j++) {
-@@ -270,11 +270,11 @@ namespace Bloom {
-
- size_t offset = header.startBitPos;
- size_t bits = header.endBitPos - header.startBitPos + 1;
-- size_t bytes = (bits + 7) / 8;
-+ unsigned long bytes = (bits + 7) / 8;
-
- char buf[IO_BUFFER_SIZE];
- for (size_t i = 0, j = offset; i < bytes; ) {
-- size_t readSize = std::min(IO_BUFFER_SIZE, bytes - i);
-+ unsigned long readSize = std::min(IO_BUFFER_SIZE, bytes - i);
- in.read(buf, readSize);
- assert(in);
- for (size_t k = 0; k < readSize; k++) {
diff --git a/debian/patches/abyss-pe b/debian/patches/abyss-pe.patch
similarity index 74%
rename from debian/patches/abyss-pe
rename to debian/patches/abyss-pe.patch
index eb0d912..bfb7872 100644
--- a/debian/patches/abyss-pe
+++ b/debian/patches/abyss-pe.patch
@@ -1,3 +1,6 @@
+Author: Shaun Jackman <sjackman at debian.org>
+Description: Add internal PATH to find abyss tools
+
--- a/bin/abyss-pe
+++ b/bin/abyss-pe
@@ -3,6 +3,8 @@
diff --git a/debian/patches/gtest.patch b/debian/patches/gtest.patch
index 1bf6580..16ea66c 100644
--- a/debian/patches/gtest.patch
+++ b/debian/patches/gtest.patch
@@ -3,6 +3,8 @@ Last-Updated: Wed, 17 Sep 2014 12:17:23 -0700
Description: Make sure gtest works properly
I had to follow the instructions on this post to build libgtest.a and libgtest_main.a:
http://askubuntu.com/questions/145887/why-no-library-files-installed-for-google-test
+ .
+ Attention: This patch needs heave adaption and is deactivated for the moment
--- a/Unittest/Makefile.am
+++ b/Unittest/Makefile.am
diff --git a/debian/patches/privacy-breach.patch b/debian/patches/privacy-breach.patch
index ba4ed03..8a2cf64 100644
--- a/debian/patches/privacy-breach.patch
+++ b/debian/patches/privacy-breach.patch
@@ -4,7 +4,7 @@ Description: Prevent privacy breach
--- a/README.md
+++ b/README.md
-@@ -427,4 +427,3 @@ Supervised by [**Dr. İnanç Birol**](ht
+@@ -512,4 +512,3 @@ Supervised by [**Dr. İnanç Birol**](ht
Copyright 2014 Canada's Michael Smith Genome Sciences Centre
diff --git a/debian/patches/series b/debian/patches/series
index fe386b7..777c476 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,4 @@
-abyss-pe
-gtest.patch
+abyss-pe.patch
+# gtest.patch
privacy-breach.patch
abyss-32-bit.patch
--
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