New Upstream Snapshot - bio-eagle
Ready changes
Summary
Merged new upstream version: 2.4.1+git20190330.1.10fe822 (was: 2.4.1).
Resulting package
Built on 2022-12-20T06:58 (took 14m29s)
The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:
apt install -t fresh-snapshots bio-eagle-dbgsymapt install -t fresh-snapshots bio-eagle-examplesapt install -t fresh-snapshots bio-eagle
Lintian Result
- bio-eagle-dbgsym_2.4.1+git20190330.1.10fe822-1~jan+nus2_amd64.deb
- bio-eagle-examples_2.4.1+git20190330.1.10fe822-1~jan+nus2_all.deb
- bio-eagle_2.4.1+git20190330.1.10fe822-1~jan+nus2.dsc
- bio-eagle_2.4.1+git20190330.1.10fe822-1~jan+nus2_amd64.buildinfo
- bio-eagle_2.4.1+git20190330.1.10fe822-1~jan+nus2_amd64.deb
- bio-eagle_2.4.1+git20190330.1.10fe822-1~jan+nus2_amd64.changes
Diff
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index e31a722..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-*.o
-src/eagle
diff --git a/debian/changelog b/debian/changelog
index 4050feb..0a6f34f 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+bio-eagle (2.4.1+git20190330.1.10fe822-1) UNRELEASED; urgency=low
+
+ * New upstream snapshot.
+
+ -- Debian Janitor <janitor@jelmer.uk> Tue, 20 Dec 2022 06:45:26 -0000
+
bio-eagle (2.4.1-3) unstable; urgency=medium
[ Andreas Tille ]
diff --git a/debian/patches/Makefile_config.patch b/debian/patches/Makefile_config.patch
index ff49284..3fd383f 100644
--- a/debian/patches/Makefile_config.patch
+++ b/debian/patches/Makefile_config.patch
@@ -3,8 +3,10 @@ Description: Configure the makefile for Debian packaging.
Last-Update: 2018-11-28
Forwarded: not-needed
---- a/src/Makefile
-+++ b/src/Makefile
+Index: bio-eagle.git/src/Makefile
+===================================================================
+--- bio-eagle.git.orig/src/Makefile
++++ bio-eagle.git/src/Makefile
@@ -9,20 +9,20 @@
### modify these paths to local BLAS, Boost and htslib install directories
@@ -32,7 +34,7 @@ Forwarded: not-needed
ifeq ($(strip ${linking}),)
-@@ -41,7 +41,7 @@
+@@ -41,7 +41,7 @@ ifeq (${prof},true)
LFLAGS += -pg
endif
@@ -41,7 +43,7 @@ Forwarded: not-needed
LFLAGS += -fopenmp
-@@ -96,16 +96,16 @@
+@@ -96,16 +96,16 @@ endif
T = eagle
diff --git a/debian/patches/non_x86_malloc b/debian/patches/non_x86_malloc
index 860eae1..099f13a 100644
--- a/debian/patches/non_x86_malloc
+++ b/debian/patches/non_x86_malloc
@@ -1,7 +1,9 @@
From: Michael R. Crusoe <crusoe@debian.org>
Subject: allow compilation on non-x86
---- bio-eagle.orig/src/MemoryUtils.cpp
-+++ bio-eagle/src/MemoryUtils.cpp
+Index: bio-eagle.git/src/MemoryUtils.cpp
+===================================================================
+--- bio-eagle.git.orig/src/MemoryUtils.cpp
++++ bio-eagle.git/src/MemoryUtils.cpp
@@ -25,8 +25,11 @@
void *ALIGNED_MALLOC(uint64 size) {
#ifdef USE_MKL_MALLOC
@@ -15,9 +17,11 @@ Subject: allow compilation on non-x86
#endif
// TODO: change to assert() or dispense with altogether and change ALIGNED_MALLOC to macro?
if (p == NULL) {
---- bio-eagle.orig/src/MemoryUtils.hpp
-+++ bio-eagle/src/MemoryUtils.hpp
-@@ -30,9 +30,11 @@
+Index: bio-eagle.git/src/MemoryUtils.hpp
+===================================================================
+--- bio-eagle.git.orig/src/MemoryUtils.hpp
++++ bio-eagle.git/src/MemoryUtils.hpp
+@@ -30,9 +30,11 @@ void *ALIGNED_MALLOC(uint64 size);
#ifdef USE_MKL_MALLOC
#include <mkl.h>
#define ALIGNED_FREE mkl_free
diff --git a/src/memcpy.cpp b/src/memcpy.cpp
new file mode 100644
index 0000000..ef37e76
--- /dev/null
+++ b/src/memcpy.cpp
@@ -0,0 +1,9 @@
+#include <cstring>
+
+/* some systems do not have newest memcpy@@GLIBC_2.14 - stay with old good one */
+asm (".symver memcpy, memcpy@GLIBC_2.2.5");
+
+extern "C" void *__wrap_memcpy(void *dest, const void *src, size_t n)
+{
+ return memcpy(dest, src, n);
+}
Debdiff
[The following lists of changes regard files as different if they have different names, permissions or owners.]
Files in second set of .debs but not in first
-rw-r--r-- root/root /usr/lib/debug/.build-id/28/1eeec8b111893c199fea6cdd541214f9d5423e.debug
Files in first set of .debs but not in second
-rw-r--r-- root/root /usr/lib/debug/.build-id/6e/894b7dc24d188ed7eb90412a4906174e14a08e.debug
Control files of package bio-eagle: lines which differ (wdiff format)
Depends: libboost-iostreams1.74.0 (>= 1.74.0+ds1), 1.74.0), libboost-program-options1.74.0 (>= 1.74.0+ds1), 1.74.0), libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libhts3 (>= 1.10), libopenblas0, libstdc++6 (>= 11)
Control files of package bio-eagle-dbgsym: lines which differ (wdiff format)
Build-Ids: 6e894b7dc24d188ed7eb90412a4906174e14a08e 281eeec8b111893c199fea6cdd541214f9d5423e
No differences were encountered between the control files of package bio-eagle-examples