[med-svn] [sra-sdk] 06/06: TODO: package ngs-sdk (https://github.com/ncbi/ngs)
Andreas Tille
tille at debian.org
Fri Oct 24 12:53:57 UTC 2014
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tille pushed a commit to branch master
in repository sra-sdk.
commit 4dd6daca67b2bab1b53e9b7971bbb18ce011cd87
Author: Andreas Tille <tille at debian.org>
Date: Fri Oct 24 14:53:18 2014 +0200
TODO: package ngs-sdk (https://github.com/ncbi/ngs)
---
debian/changelog | 2 +
debian/control | 3 +-
debian/patches/build-with-system-libbz2-libz.patch | 34 -----------------
debian/patches/do_not_build_external_libs.patch | 14 -------
debian/patches/hardening-format-security.patch | 43 ----------------------
debian/patches/series | 1 -
debian/rules | 1 -
7 files changed, 4 insertions(+), 94 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index c02941d..49f373b 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,6 +4,8 @@ sra-sdk (2.4.2-1-1) UNRELEASED; urgency=medium
* d/watch points to github
* d/copyright: no need to exclude any files any more
* cme fix dpkg-control
+ * New Build-Depends: libhdf5-dev
+ TODO: package ngs-sdk (https://github.com/ncbi/ngs)
-- Andreas Tille <tille at debian.org> Fri, 24 Oct 2014 14:26:24 +0200
diff --git a/debian/control b/debian/control
index 91437f2..87dcc30 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,8 @@ Priority: optional
Build-Depends: debhelper (>= 9),
libbz2-dev,
zlib1g-dev,
- libxml2-dev
+ libxml2-dev,
+ libhdf5-dev
Standards-Version: 3.9.6
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/sra-sdk.git
Vcs-Git: git://anonscm.debian.org/debian-med/sra-sdk.git
diff --git a/debian/patches/build-with-system-libbz2-libz.patch b/debian/patches/build-with-system-libbz2-libz.patch
deleted file mode 100644
index 1c8359a..0000000
--- a/debian/patches/build-with-system-libbz2-libz.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-Author: Gert Wollny <gw.fossdev at gmail.com>
-LastChanged: Tue, 22 Oct 2013 00:15:19 +0200
-Description: Fix issue when trying to build against Debian packaged
- libbz2
-
---- a/libs/ncbi-vdb/Makefile
-+++ b/libs/ncbi-vdb/Makefile
-@@ -87,7 +87,6 @@ endif
- VDB_LIB_CMN = \
- align-access \
- ncbi-bam \
-- bz2 \
- kfg \
- kfs \
- klib \
-@@ -97,8 +96,7 @@ VDB_LIB_CMN = \
- ksrch \
- $(LIBKXML) \
- kns \
-- vfs \
-- z
-+ vfs
-
- VDB_LIB_RD = \
- $(VDB_LIB_CMN) \
-@@ -115,7 +113,7 @@ VDB_OBJ = \
- $(addprefix $(ILIBDIR)/lib,$(addsuffix .a,$(VDB_LIB_RD)))
-
- VDB_LIB = \
-- $(addprefix -s,$(VDB_LIB_RD))
-+ $(addprefix -s,$(VDB_LIB_RD)) -lbz2 -lz
-
- $(LIBDIR)/libncbi-vdb.$(SHLX): $(VDB_OBJ)
- $(LD) --dlib --vers $(SRCDIR) -o $@ $(VDB_LIB)
diff --git a/debian/patches/do_not_build_external_libs.patch b/debian/patches/do_not_build_external_libs.patch
deleted file mode 100644
index 752806a..0000000
--- a/debian/patches/do_not_build_external_libs.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Author: Charles Plessy <plessy at debian.org>
-Description: Do not use third party libs but use Debian packaged
- libraries instead
-
---- a/libs/Makefile
-+++ b/libs/Makefile
-@@ -32,7 +32,6 @@ include $(TOP)/build/Makefile.shell
- # default
- #
- SUBDIRS = \
-- ext \
- klib \
- kproc \
- kfs \
diff --git a/debian/patches/hardening-format-security.patch b/debian/patches/hardening-format-security.patch
deleted file mode 100644
index 6457902..0000000
--- a/debian/patches/hardening-format-security.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-LastChanged: Wed, 23 Oct 2013 10:43:20 +0200
-Description: Fix format strings in snprintf() calls
- When using hardening options, specifically -Werror=format-security
- some errors of kind:
- format not a string literal and no format arguments
- appeared in some snprintf() calls. This is fixed by providing
- the expected format string
-
-
---- a/libs/kdb/database.c
-+++ b/libs/kdb/database.c
-@@ -216,7 +216,7 @@ rc_t KDBManagerVOpenDBReadInt ( const KD
- is that of stdc library's printf, not vdb printf */
- char dbpath [ 4096 ];
- int z = ( args == NULL ) ?
-- snprintf ( dbpath, sizeof dbpath, path ):
-+ snprintf ( dbpath, sizeof dbpath, "%s", path ):
- vsnprintf ( dbpath, sizeof dbpath, path, args );
- if ( z < 0 || ( size_t ) z >= sizeof dbpath )
- rc = RC ( rcDB, rcMgr, rcOpening, rcPath, rcExcessive );
---- a/libs/kdb/table.c
-+++ b/libs/kdb/table.c
-@@ -216,7 +216,7 @@ rc_t KDBManagerVOpenTableReadInt ( const
-
- char tblpath [ 4096 ];
- int z = ( args == NULL ) ?
-- snprintf ( tblpath, sizeof tblpath, path ):
-+ snprintf ( tblpath, sizeof tblpath, "%s", path ):
- vsnprintf ( tblpath, sizeof tblpath, path, args );
- if ( z < 0 || ( size_t ) z >= sizeof tblpath )
- rc = RC ( rcDB, rcMgr, rcOpening, rcPath, rcExcessive );
---- a/libs/kdb/index.c
-+++ b/libs/kdb/index.c
-@@ -492,7 +492,7 @@ LIB_EXPORT rc_t CC KTableVOpenIndexRead
- {
- int len;
- if ( args == 0 )
-- len = snprintf ( path, sizeof path, name );
-+ len = snprintf ( path, sizeof path, "%s", name );
- else
- len = vsnprintf ( path, sizeof path, name, args );
- if ( len < 0 || ( size_t ) len >= sizeof path )
diff --git a/debian/patches/series b/debian/patches/series
index dd39ee3..523daa0 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
10_portability.patch
hardening.patch
-# hardening-format-security.patch
diff --git a/debian/rules b/debian/rules
index 66ef1bf..55bd55e 100755
--- a/debian/rules
+++ b/debian/rules
@@ -8,7 +8,6 @@ override_dh_auto_clean:
override_dh_clean:
dh_clean
- find libs/krypto -name "*.pic.o.list" -delete
rm -f build/OUTDIR.linux
override_dh_auto_configure:
--
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