[Debian-med-packaging] Bug#1150426: sift: ships prebuilt x86-64 binaries from bin/web, FTBFS on other architectures

[Sebastien Bacher]

Source: sift
Version: 6.2.1-2
Severity: important
Tags: patch ftbfs
X-Debbugs-Cc: seb128 at ubuntu.com
User: ubuntu-devel at lists.ubuntu.com
Usertags: origin-ubuntu stonking ubuntu-patch

Hi,

The sift 6.2.1 upstream tarball contains a bin/web/ directory with five
prebuilt x86-64 executables:

  bin/web/allowed_subst_html
  bin/web/process_alignment
  bin/web/seqs_to_matrixweb
  bin/web/seqs_to_msf
  bin/web/seqs_to_msf_web

src/Makefile doesn't build them (their sources are in src/, but they are not
in BIN), and debian/rules installs the whole bin/ tree with
"dh_install ... -Xlinux -Xsolaris bin", so these upstream binaries end up in
/usr/lib/sift/bin/web/ in the amd64 package rather than being built from
source. Nothing in the package uses them (they are web-server helpers).

Since sift is in non-free and only built on amd64 in Debian (#987606), this
goes unnoticed there, but on every other architecture the build fails in
dh_strip:

  objcopy: Unable to recognise the architecture of the input file
  `debian/sift/usr/lib/sift/bin/web/seqs_to_msf_web'

Ubuntu builds sift on all architectures, so we hit this; the previous
version (4.0.3b) didn't have bin/web.

The attached change excludes bin/web from the installation, which fixes the
build on other architectures and stops shipping binaries that weren't built
from source. The only change in the amd64 package is that /usr/lib/sift/bin/web/
is gone. (An alternative would be to build those tools from src/, if they are
considered useful, or to repack the tarball without them.)

Ubuntu upload: sift 6.2.1-2ubuntu1.

Thanks,
Sebastien Bacher



-- System Information:
Debian Release: forky/sid
  APT prefers resolute-updates
  APT policy: (500, 'resolute-updates'), (500, 'resolute-security'), (500, 'resolute'), (100, 'resolute-backports')
Architecture: amd64 (x86_64)

Kernel: Linux 7.0.0-38-generic (SMP w/16 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_WARN, TAINT_OOT_MODULE
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
-------------- next part --------------
--- a/debian/rules
+++ b/debian/rules
@@ -61,7 +61,8 @@
 
 override_dh_install:
 	# lkajan: fastaseqs comes from the blimps package, this source does not have rules for creating it
-	dh_install -X.svn -X.swp -XIntersectFeatures.jar -XManuals -Xfastaseqs -Xlinux -Xsolaris bin $(prefix)/lib/sift/
+	# bin/web contains prebuilt x86-64 binaries, not built from source here
+	dh_install -X.svn -X.swp -XIntersectFeatures.jar -XManuals -Xfastaseqs -Xlinux -Xsolaris -Xbin/web bin $(prefix)/lib/sift/
 	#dh_install bin/IntersectFeatures.jar $(pkgdatadir)/
 	dh_install -X.svn -X.swp blimps/docs $(prefix)/share/sift/blimps/