Your message dated Mon, 30 Sep 2019 02:41:24 +0000
with message-id <[email protected]>
and subject line Bug#930240: fixed in ncbi-blast+ 2.9.0-2
has caused the Debian Bug report #930240,
regarding ncbi-blast+ FTCBFS: configures for the build architecture
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
930240: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=930240
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: ncbi-blast+
Version: 2.8.1-1
Tags: patch
User: [email protected]
Usertags: ftcbfs
ncbi-blast+ fails to cross build from source, because it does not pass
--host to ./configure. The easiest way of fixing that - using
dh_auto_configure - does not work here, because it passes a
--runstatedir flag that is not understood. Thus, the --host flag must be
added manually.
I also noticed that ncbi-blast+ runs tests in the presence of
DEB_BUILD_OPTIONS=nocheck. Doing so typically breaks cross compilation.
The attached patch fixes the issues above, but does not make ncbi-blast+
cross buildable. It seems to build a project_tree_builder with the host
compiler and then fails running it. I didn't figure out how to fix this.
Please consider applying the attached patch as an incremental
improvement and close this bug when doing so.
Helmut
diff --minimal -Nru ncbi-blast+-2.8.1/debian/changelog
ncbi-blast+-2.8.1/debian/changelog
--- ncbi-blast+-2.8.1/debian/changelog 2019-02-04 04:47:45.000000000 +0100
+++ ncbi-blast+-2.8.1/debian/changelog 2019-06-09 07:21:54.000000000 +0200
@@ -1,3 +1,12 @@
+ncbi-blast+ (2.8.1-1.1) UNRELEASED; urgency=medium
+
+ * Non-maintainer upload.
+ * Improve cross building: (Closes: #-1)
+ + Pass --host to the configure script.
+ + Honour DEB_BUILD_OPTIONS=nocheck.
+
+ -- Helmut Grohne <[email protected]> Sun, 09 Jun 2019 07:21:54 +0200
+
ncbi-blast+ (2.8.1-1) unstable; urgency=medium
* New upstream release.
diff --minimal -Nru ncbi-blast+-2.8.1/debian/rules
ncbi-blast+-2.8.1/debian/rules
--- ncbi-blast+-2.8.1/debian/rules 2019-02-04 03:52:00.000000000 +0100
+++ ncbi-blast+-2.8.1/debian/rules 2019-06-09 07:21:54.000000000 +0200
@@ -26,7 +26,11 @@
export DEB_CFLAGS_MAINT_APPEND=-Wall -pedantic
export DEB_LDFLAGS_MAINT_APPEND=-Wl,--as-needed
-DEB_HOST_ARCH := $(shell dpkg-architecture -qDEB_HOST_ARCH)
+include /usr/share/dpkg/architecture.mk
+
+ifneq ($(DEB_BUILD_ARCH),$(DEB_HOST_ARCH))
+DEB_CONFIGURE_EXTRA_FLAGS += --build=$(DEB_BUILD_GNU_TYPE)
--host=$(DEB_HOST_GNU_TYPE)
+endif
CFLAGS := $(shell dpkg-buildflags --get CFLAGS)
CPPFLAGS := $(shell dpkg-buildflags --get CPPFLAGS)
@@ -62,9 +66,11 @@
echo "Save time and do nothing for architecture independent builds"
override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-dh_auto_test
-c++/BUILD/build/check.sh concat_err
-cat c++/BUILD/build/check.sh.out_err
+endif
instroot = debian/ncbi-blast+/usr
leg_bin = debian/ncbi-blast+-legacy/usr/bin
--- End Message ---
--- Begin Message ---
Source: ncbi-blast+
Source-Version: 2.9.0-2
We believe that the bug you reported is fixed in the latest version of
ncbi-blast+, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Aaron M. Ucko <[email protected]> (supplier of updated ncbi-blast+ package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Sun, 29 Sep 2019 21:57:31 -0400
Source: ncbi-blast+
Architecture: source
Version: 2.9.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Aaron M. Ucko <[email protected]>
Closes: 930240
Changes:
ncbi-blast+ (2.9.0-2) unstable; urgency=medium
.
* debian/control: Standards-Version: 4.4.1 (already compliant).
* debian/copyright: Remove redundant ncbi_menu_*.js stanza.
* debian/rules:
- Delegate dpkg-{architecture,buildflags} calls to
/usr/share/dpkg/{architecture,buildflags}.mk respectively.
- Allow for cross-building (Closes: #930240):
-- Factor a DEB_CONFIGURE_COMMON_FLAGS macro out of
DEB_CONFIGURE_EXTRA_FLAGS for flags that also make sense for native
builds of internal helpers.
-- Conditionally supply --build=... and --host= to the main
(historically, only) configure run per Helmut Grohne's suggestion.
(dh_auto_configure would take care of this, but insists on passing
a --runstatedir=... flag this configure script doesn't accept.)
-- Conditionally add a rule for building native datatool and
project_tree_builder binaries (in a parallel build tree established
via another configure invocation), make it a dependency of
override_dh_auto_configure-arch, and arrange for everything else to
use these binaries as needed.
-- Honor DEB_BUILD_OPTIONS="... nocheck ...", also per Helmut.
-- Rework logic to install (possibly indirect) local library
dependencies to use readelf rather than ldd, making as many passes
as necessary (four at present, but no hardcoded count).
- Install get_species_taxids without the .sh suffix.
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