Your message dated Wed, 07 Jan 2026 20:33:41 +0000
with message-id <[email protected]>
and subject line Bug#1124857: fixed in gatk-fermilite 1.2.1+dfsg-3
has caused the Debian Bug report #1124857,
regarding gatk-fermilite: please build using the default build flags
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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--
1124857: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1124857
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: gatk-fermilite
Version: 1.2.1+dfsg-2
User: [email protected]
Usertags: hardening-buildflags
gatk-fermilite is not currently using the default build flags set by
dpkg-buildflags(1).
The default flags are chosen for multiple reasons including security,
performance, reproducibility, adherence to standards, and error handling.
Please make sure that gatk-fermilite builds using the default build flags.
blhc(1p)
and hardening-check(1) can be used to confirm that the issue is fixed.
In the general case, packages honoring CFLAGS, LDFLAGS, and other
similar environment variables get the default build flags for free
without the need for any work on the maintainer side. In the case of
gatk-fermilite, the flags are either ignored or overridden.
The most common reasons for this are:
Hand-written Makefiles
----------------------
Some upstream Makefiles either override the values of variables such as
CFLAGS and similar or do not use them at all. See:
https://wiki.debian.org/HardeningWalkthrough#Handwritten_Makefiles
Misconfigured build systems
---------------------------
If the upstream code uses autotools, CMake, or other popular build
systems, it usually requires no further modifications. If might however
be that some variables are hardcoded in some way.
In this CMake snippet, the value of CXXFLAGS is overwritten with "-O2":
set(CMAKE_CXX_FLAGS "-O2")
If the intention is to append to CXXFLAGS, one should use the following
instead:
set(CMAKE_CXX_FLAGS "-O2 ${CMAKE_CXX_FLAGS}")
See #655870 for a similar autotools example.
Very old debhelper usage
------------------------
Packages not using dh(1), or those using a debhelper compatibility level
less than 9, need to manually include /usr/share/dpkg/buildflags.mk in
order for the dpkg-buildflags variables to be set:
https://wiki.debian.org/Hardening#dpkg-buildflags
Flags hardcoded in debian/rules (either voluntarily or not)
-----------------------------------------------------------
Some packages voluntarily hardcode the values of CFLAGS and friends in
debian/rules, ignoring the defaults set by dpkg-buildflags(1).
Others attempt to append to the variables, but end up accidentally
overriding the defaults:
#!/usr/bin/make -f
export CFLAGS += -pipe -fPIC -Wall
%:
dh $@
Debhelper only sets CFLAGS if it is not set yet. In the example above,
when dh is invoked the value of CFLAGS is "-pipe -fPIC -Wall", hence the
hardened defaults are not used. The right way to append to CFLAGS is
using DEB_CFLAGS_MAINT_APPEND instead, as documented in
dpkg-buildflags(1).
For a detailed analysis of this issue, see https://hal.science/hal-05334704/
--- End Message ---
--- Begin Message ---
Source: gatk-fermilite
Source-Version: 1.2.1+dfsg-3
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
gatk-fermilite, 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.
Étienne Mollier <[email protected]> (supplier of updated gatk-fermilite
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: SHA512
Format: 1.8
Date: Wed, 07 Jan 2026 20:45:55 +0100
Source: gatk-fermilite
Architecture: source
Version: 1.2.1+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1124857
Changes:
gatk-fermilite (1.2.1+dfsg-3) unstable; urgency=medium
.
* Team upload.
* buildflags.patch: new: forward build flags. (Closes: #1124857)
* d/rules: flag false positive blhc non-verbose builds.
* d/watch: convert to v5 Github template.
* d/control: drop redundant Rules-Requires-Root: no.
* d/control: drop redundant Priority: optional.
* d/control: declare compliance to standards version 4.7.3.
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gatk-fermilite_1.2.1+dfsg-3.debian.tar.xz
Checksums-Sha256:
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gatk-fermilite_1.2.1+dfsg-3.debian.tar.xz
Files:
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gatk-fermilite_1.2.1+dfsg-3.dsc
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