[med-svn] [Git][med-team/ncbi-blastplus][master] 8 commits: Start work on ncbi-blast2+ 2.12.0+ds-4 to downgrade #891197.
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Tue Sep 5 03:43:47 BST 2023
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-blastplus
Commits:
ad472d06 by Aaron M. Ucko at 2023-09-04T22:32:21-04:00
Start work on ncbi-blast2+ 2.12.0+ds-4 to downgrade #891197.
- - - - -
d41ab8a0 by Aaron M. Ucko at 2023-09-04T22:32:48-04:00
debian/control: Drop build dependency on libpcre3-dev (#891197).
PCRE2 support isn't ready yet, but there's a convenience copy of
classic PCRE that will suffice for now. (Partly addresses #891197.)
- - - - -
f6feb225 by Aaron M. Ucko at 2023-09-04T22:35:34-04:00
debian/source/lintian-overrides: Accommodate bracketed paths.
- - - - -
d7eeaa54 by Aaron M. Ucko at 2023-09-04T22:36:10-04:00
routine-update: Standards-Version: 4.6.2
- - - - -
b6a87ef6 by Aaron M. Ucko at 2023-09-04T22:36:14-04:00
routine-update: Remove trailing whitespace in debian/changelog
- - - - -
9a9542de by Aaron M. Ucko at 2023-09-04T22:39:41-04:00
Refer to common license file for Apache-2.0.
Changes-By: lintian-brush
Fixes: lintian: copyright-does-not-refer-to-common-license-file
See-also: https://lintian.debian.org/tags/copyright-does-not-refer-to-common-license-file.html
Fixes: lintian: copyright-not-using-common-license-for-apache2
See-also: https://lintian.debian.org/tags/copyright-not-using-common-license-for-apache2.html
- - - - -
2dec42c5 by Aaron M. Ucko at 2023-09-04T22:39:43-04:00
Avoid explicitly specifying -Wl,--as-needed linker flag.
Changes-By: lintian-brush
Fixes: lintian: debian-rules-uses-as-needed-linker-flag
See-also: https://lintian.debian.org/tags/debian-rules-uses-as-needed-linker-flag.html
- - - - -
77519dae by Aaron M. Ucko at 2023-09-04T22:40:43-04:00
Finalize ncbi-blast+ 2.12.0+ds-4 for unstable.
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/rules
- debian/source/lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
@@ -1,7 +1,20 @@
+ncbi-blast+ (2.12.0+ds-4) unstable; urgency=medium
+
+ * debian/control: Drop build dependency on libpcre3-dev; PCRE2 support
+ isn't ready yet, but there's a convenience copy of classic PCRE that
+ will suffice for now. (Partly addresses #891197.)
+ * debian/source/lintian-overrides: Accommodate bracketed paths.
+ * Standards-Version: 4.6.2 (routine-update)
+ * Remove trailing whitespace in debian/changelog (routine-update)
+ * Refer to common license file for Apache-2.0.
+ * Avoid explicitly specifying -Wl,--as-needed linker flag.
+
+ -- Aaron M. Ucko <ucko at debian.org> Mon, 04 Sep 2023 22:40:42 -0400
+
ncbi-blast+ (2.12.0+ds-3) unstable; urgency=medium
* d/patches/optin_usage_report change usage reports sending over
- internet strategy to optin (disabled by default unless specified)
+ internet strategy to optin (disabled by default unless specified)
(Closes # 1005279).
-- Olivier Sallou <osallou at debian.org> Thu, 10 Feb 2022 12:17:56 +0000
@@ -11,7 +24,7 @@ ncbi-blast+ (2.12.0+ds-2) unstable; urgency=medium
* Clean up spurious release-status comment from 2.12.0+ds-1.
* debian/patches/system_mbedtls_only: Patch out use of local mbed TLS
headers, which formally rename all symbols.
-
+
-- Aaron M. Ucko <ucko at debian.org> Wed, 01 Dec 2021 23:36:32 -0500
ncbi-blast+ (2.12.0+ds-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -13,11 +13,10 @@ Build-Depends-Arch: 2to3,
libgnutls28-dev,
liblmdb-dev,
libmbedtls-dev,
- libpcre3-dev,
time,
zlib1g-dev,
procps
-Standards-Version: 4.6.0
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/ncbi-blastplus
Vcs-Git: https://salsa.debian.org/med-team/ncbi-blastplus.git
Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
=====================================
debian/copyright
=====================================
@@ -40,6 +40,9 @@ License: Apache-2.0
WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
+ .
+ On Debian systems, the full text of the Apache License, Version 2.0 can be
+ found in the file `/usr/share/common-licenses/Apache-2.0'.
Files: c++/src/html/ncbi_menu.js
c++/src/html/ncbi_menu_dnd.js
=====================================
debian/rules
=====================================
@@ -26,8 +26,6 @@ DEB_CONFIGURE_EXTRA_FLAGS += --with-symbols
#export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie
export DEB_BUILD_MAINT_OPTIONS=hardening=+all,-pie
export DEB_CFLAGS_MAINT_APPEND=-Wall -pedantic
-# Kept for the sake of backports, which can't rely on GCC 9+.
-export DEB_LDFLAGS_MAINT_APPEND=-Wl,--as-needed
include /usr/share/dpkg/architecture.mk
include /usr/share/dpkg/buildflags.mk
=====================================
debian/source/lintian-overrides
=====================================
@@ -1,7 +1,7 @@
# Line length detection, nothing missing in source js files
-ncbi-blast+ source: source-is-missing c++/src/html/ncbi_menu.js
-ncbi-blast+ source: source-is-missing c++/src/html/ncbi_menu_dnd.js
-ncbi-blast+ source: source-is-missing c++/src/html/ncbi_menu_dyn.js
+ncbi-blast+ source: source-is-missing *c++/src/html/ncbi_menu.js*
+ncbi-blast+ source: source-is-missing *c++/src/html/ncbi_menu_dnd.js*
+ncbi-blast+ source: source-is-missing *c++/src/html/ncbi_menu_dyn.js*
# JSON not evil license, related code is not present
-ncbi-blast+ source: license-problem-json-evil c++/include/misc/jsonwrapp/rapidjson10/license.txt
-ncbi-blast+ source: license-problem-json-evil c++/include/misc/jsonwrapp/rapidjson11/license.txt
+ncbi-blast+ source: license-problem-json-evil *c++/include/misc/jsonwrapp/rapidjson10/license.txt*
+ncbi-blast+ source: license-problem-json-evil *c++/include/misc/jsonwrapp/rapidjson11/license.txt*
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/84e9a187b0f9a95f292c9a640ec20509e02d4c14...77519daef0c13c73c6ad8b1d9a4a7dfe48cc97d1
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-blastplus/-/compare/84e9a187b0f9a95f292c9a640ec20509e02d4c14...77519daef0c13c73c6ad8b1d9a4a7dfe48cc97d1
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