[med-svn] [Git][med-team/sra-sdk][master] 14 commits: Help validate-names4.c find internal ncbi-vdb headers (#961049).
Aaron M. Ucko
gitlab at salsa.debian.org
Thu May 21 03:18:40 BST 2020
Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits:
8ef4c86e by Aaron M. Ucko at 2020-05-20T22:08:59-04:00
Help validate-names4.c find internal ncbi-vdb headers (#961049).
Build-depend on libncbi-vdb-dev (>= 2.10.6+dfsg-2~) to ensure these
headers are installed sanely, and patch validate-names4.c accordingly
in a new patch use_exposed_headers.patch. In conjunction with taking
the latest upstream, closes: #961049.
- - - - -
67fe59bb by Aaron M. Ucko at 2020-05-20T22:10:21-04:00
Specify configuration location by passing KONFIG_DIR.
The makefile patch previously in use relied on [fake]root.
- - - - -
fba11deb by Aaron M. Ucko at 2020-05-20T22:10:29-04:00
Fix usage of default Debian build flags.
Use buildflags.mk with appropriate _APPEND settings, and tweak
hardening.patch to add DEB_*FLAGS to the front rather than the end (so
as to keep upstream's preferred optimization level).
- - - - -
53d898b1 by Aaron M. Ucko at 2020-05-20T22:10:29-04:00
Preclean more fully to allow for consecutive builds.
- - - - -
6f94c85c by Aaron M. Ucko at 2020-05-20T22:10:29-04:00
List (wildcard) currently uninstalled files in debian/not-installed.
- - - - -
fef34699 by Aaron M. Ucko at 2020-05-20T22:10:29-04:00
Correct logic for identifying all failing tests when there are any.
- - - - -
b7a7d87e by Aaron M. Ucko at 2020-05-20T22:10:29-04:00
routine-update: Secure URI in copyright format
- - - - -
9dc8d6da by Aaron M. Ucko at 2020-05-20T22:10:29-04:00
routine-update: DEB_BUILD_OPTIONS allow override_dh_auto_test
- - - - -
85d27187 by Aaron M. Ucko at 2020-05-20T22:10:29-04:00
R-U: Trailing whitespace in debian/changelog
- - - - -
13a88a46 by Aaron M. Ucko at 2020-05-20T22:10:29-04:00
R-U: Trailing whitespace in debian/rules
- - - - -
5bff2122 by Aaron M. Ucko at 2020-05-20T22:10:29-04:00
routine-update: Add salsa-ci file
- - - - -
3cca3f01 by Aaron M. Ucko at 2020-05-20T22:10:29-04:00
routine-update: Rules-Requires-Root: no
- - - - -
7a7df042 by Aaron M. Ucko at 2020-05-20T22:11:27-04:00
Add myself (A. Ucko) to uploaders.
- - - - -
3298b962 by Aaron M. Ucko at 2020-05-20T22:15:20-04:00
Finalize sra-sdk 2.10.6+dfsg-1 for release to unstable.
- - - - -
10 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/not-installed
- debian/patches/certs.kfg.patch
- debian/patches/hardening.patch
- debian/patches/series
- + debian/patches/use_exposed_headers.patch
- debian/rules
- + debian/salsa-ci.yml
Changes:
=====================================
debian/changelog
=====================================
@@ -1,7 +1,6 @@
-sra-sdk (2.10.6+dfsg-1) UNRELEASED; urgency=medium
+sra-sdk (2.10.6+dfsg-1) unstable; urgency=medium
[ Steffen Moeller ]
- * Team upload.
* New upstream version
* debhelper-compat 12
* Standards-Version: 4.4.1
@@ -10,7 +9,7 @@ sra-sdk (2.10.6+dfsg-1) UNRELEASED; urgency=medium
fixed to avoid a link error in this package.
[ Michael R. Crusoe ]
- * Convert to Python3. Closes: #943231
+ * Convert to Python3. Closes: #943231
* Standards-Version: 4.5.0 (routine-update)
[ Aaron M. Ucko ]
@@ -21,8 +20,30 @@ sra-sdk (2.10.6+dfsg-1) UNRELEASED; urgency=medium
- Generally standardize on -pab format.
- hardening.patch: Rebase C(P)FLAGS, which no longer request extensions.
- python3: Drop makefile tweaks obsoleted by new PYTHON abstraction.
-
- -- Aaron M. Ucko <ucko at debian.org> Mon, 18 May 2020 21:47:54 -0400
+ * Help validate-names4.c find ncbi-vdb headers that are normally internal.
+ To wit, build-depend on libncbi-vdb-dev (>= 2.10.6+dfsg-2~) to ensure
+ these headers are installed sanely, and patch validate-names4.c
+ accordingly in a new patch use_exposed_headers.patch. In conjunction
+ with taking the latest upstream, closes: #961049.
+ * Specify configuration location by passing KONFIG_DIR. (The makefile
+ patch previously in use relied on [fake]root.)
+ * Fix usage of default Debian build flags: Use buildflags.mk with
+ appropriate _APPEND settings, and tweak hardening.patch to add
+ DEB_*FLAGS to the front rather than the end (so as to keep upstream's
+ preferred optimization level).
+ * Preclean more fully to allow for consecutive builds.
+ * List (wildcard) currently uninstalled files in debian/not-installed.
+ * Correct logic for identifying all failing tests when there are any.
+ * Secure URI in copyright format (routine-update)
+ * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine-
+ update)
+ * Remove trailing whitespace in debian/changelog (routine-update)
+ * Remove trailing whitespace in debian/rules (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Add myself to uploaders.
+
+ -- Aaron M. Ucko <ucko at debian.org> Wed, 20 May 2020 22:15:19 -0400
sra-sdk (2.9.4+dfsg-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -1,12 +1,13 @@
Source: sra-sdk
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>
+ Andreas Tille <tille at debian.org>,
+ Aaron M. Ucko <ucko at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
libngs-sdk-dev (>= 2.9.0),
- libncbi-vdb-dev (>= 2.9.1),
+ libncbi-vdb-dev (>= 2.10.6+dfsg-2~),
libvdb-sqlite-dev,
libfuse-dev,
libhdf5-dev,
@@ -17,6 +18,7 @@ Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/sra-sdk
Vcs-Git: https://salsa.debian.org/med-team/sra-sdk.git
Homepage: https://github.com/ncbi/sra-tools/
+Rules-Requires-Root: no
Package: sra-toolkit
Architecture: amd64
=====================================
debian/copyright
=====================================
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: https://github.com/ncbi/sra-tools/
Files-Excluded: */libs/ext
*/MSVC
=====================================
debian/not-installed
=====================================
@@ -0,0 +1,7 @@
+usr/lib/x86_64-linux-gnu
+usr/sra-tools/linux/gcc/x86_64/rel/bin/*
+usr/sra-tools/linux/gcc/x86_64/rel/ilib/*
+usr/sra-tools/linux/gcc/x86_64/rel/obj/shared/*
+usr/sra-tools/linux/gcc/x86_64/rel/obj/test/*/*
+usr/sra-tools/linux/gcc/x86_64/rel/obj/tools/*/*
+usr/sra-tools/linux/gcc/x86_64/rel/test-bin/*
=====================================
debian/patches/certs.kfg.patch
=====================================
@@ -15,13 +15,3 @@ Description: Point to correct location of kfg config files in libncbi-vdb2 packa
# make reissue command
MAKE_CMD = $(MAKE) BUILD=$(BUILD) TOOLSET=$(TOOLSET) COMP=$(COMP) LNKG=$(LNKG) \
---- a/build/Makefile.install
-+++ b/build/Makefile.install
-@@ -50,6 +50,7 @@ LINUX_ROOT =
- #fake root for debugging
- #uncomment this line and change the test for root ( see under install: ) to succeed:
- #ROOT = ~/root
-+ROOT=$(CURDIR)/debian/sra-toolkit
- ifeq (linux, $(OS))
- ifeq (0, $(shell id -u))
- LINUX_ROOT = true
=====================================
debian/patches/hardening.patch
=====================================
@@ -32,9 +32,9 @@ Description: Propagate Debian hardening options into build system
-CFLAGS = -std=c11 $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
-CPFLAGS = -std=c++11 $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
-LDFLAGS = $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS)
-+CFLAGS = -std=c11 $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS) $(DEB_CFLAGS)
-+CPFLAGS = -std=c++11 $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS) $(DEB_CXXFLAGS)
-+LDFLAGS = $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS) $(DEB_LDFLAGS)
++CFLAGS = $(DEB_CFLAGS) -std=c11 $(DEBUG) $(DBG) $(CARCH) $(PROF) $(PED) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
++CPFLAGS = $(DEB_CXXFLAGS) -std=c++11 $(DEBUG) $(DBG) $(CARCH) $(PROF) $(DEFINES) $(ARCHDEFS) $(MIN_DEPLOY_OS_OPT) $(INCDIRS)
++LDFLAGS = $(DEB_LDFLAGS) $(DBG) $(PROF) $(CARCH) $(MIN_DEPLOY_OS_OPT) $(LDPATHS)
#-------------------------------------------------------------------------------
# runtests
=====================================
debian/patches/series
=====================================
@@ -17,3 +17,4 @@ certs.kfg.patch
drop_tests.patch
ignore_failing_test_for_the_moment_FIXME.patch
python3
+use_exposed_headers.patch
=====================================
debian/patches/use_exposed_headers.patch
=====================================
@@ -0,0 +1,13 @@
+--- a/tools/util/validate-names4.c
++++ b/tools/util/validate-names4.c
+@@ -30,8 +30,8 @@
+ #include <klib/rc.h> /* RC */
+ #include <vfs/path.h> /* VPath */
+
+-#include "../../../ncbi-vdb/libs/vfs/json-response.h" /* Response4Make4 */
+-#include "../../../ncbi-vdb/libs/vfs/services-priv.h"/*KServiceGetKSrvResponse*/
++#include <vfs/json-response.h> /* Response4Make4 */
++#include <vfs/services-priv-internal.h> /*KServiceGetKSrvResponse*/
+
+ #define RELEASE(type, obj) do { rc_t rc2 = type##Release(obj); \
+ if (rc2 && !rc) { rc = rc2; } obj = NULL; } while (false)
=====================================
debian/rules
=====================================
@@ -5,8 +5,9 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
pkg := sra-toolkit
-export CFLAGS += -I/usr/include/ncbi-vdb
-export CXXFLAGS += -I/usr/include/ncbi-vdb
+export DEB_CFLAGS_MAINT_APPEND = -I/usr/include/ncbi-vdb
+export DEB_CXXFLAGS_MAINT_APPEND = -I/usr/include/ncbi-vdb
+include /usr/share/dpkg/buildflags.mk
%:
dh $@ --no-parallel
@@ -15,12 +16,12 @@ OUTDIR=$(CURDIR)/debian/tmp
MULTIARCH := $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
override_dh_auto_clean:
+ -dh_auto_clean
override_dh_clean:
dh_clean
- rm -f build/OUTDIR.linux
rm -f reconfigure build/ld.linux.exe_cmd.sh build/Makefile.config build/Makefile.config.linux.x86_64
-
+ rm -rf test/*/actual test/*/tmp.kfg tools/kqsh/kqsh-sra.[ch]
override_dh_update_autotools_config:
echo "do nothing"
@@ -38,7 +39,10 @@ override_dh_auto_configure:
./configure --build=$(MULTIARCH) --prefix=$(CURDIR)/debian/tmp/usr --build-prefix=$(CURDIR)/debian/tmp/usr --with-ngs-sdk-prefix=/usr
override_dh_auto_build:
- export LD_LIBRARY_PATH="$$LD_LIBRARY_PATH:$(OUTDIR)/lib"; export OUTDIR=$(OUTDIR) ; make DEB_CFLAGS="$(CFLAGS)" DEB_CXXFLAGS="$(CXXFLAGS)" DEB_LDFLAGS="$(LDFLAGS)"
+ export LD_LIBRARY_PATH="$$LD_LIBRARY_PATH:$(OUTDIR)/lib"; export OUTDIR=$(OUTDIR) ; make DEB_CFLAGS="$(CFLAGS)" DEB_CXXFLAGS="$(CXXFLAGS)" DEB_LDFLAGS="$(LDFLAGS)"
+
+override_dh_auto_install:
+ dh_auto_install -- KONFIG_DIR=$(CURDIR)/debian/sra-toolkit/etc/ncbi
override_dh_install:
# upstream installs versioned *.a libs - we only want a single version
@@ -53,8 +57,9 @@ override_dh_install:
mv debian/$(pkg)/usr/bin/kget debian/$(pkg)/usr/bin/vdb-get
override_dh_auto_test:
- dh_auto_test --no-parallel || true
- dh_auto_test --no-parallel
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+ dh_auto_test --no-parallel -- -k
+endif
override_dh_prep:
dh_prep -X debian/tmp
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/09cb8d787ac24ebaf245f11d7c1ff974d9d86174...3298b962e8293e171eb77d0e600c73f159519551
--
View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/09cb8d787ac24ebaf245f11d7c1ff974d9d86174...3298b962e8293e171eb77d0e600c73f159519551
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