Your message dated Wed, 21 Oct 2026 09:00:19 +0000
with message-id <[email protected]>
and subject line Bug#1105470: fixed in ltrsift 1.0.2-12
has caused the Debian Bug report #1105470,
regarding ltrsift: FTBFS with make --shuffle=reverse: Fatal error: can't create
obj/src/ltrsift_encode.o: No such file or directory
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.
(NB: If you are a system administrator and have no idea what this
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--
1105470: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1105470
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: ltrsift
Version: 1.0.2-10
Severity: minor
Tags: trixie sid ftbfs
User: [email protected]
Usertags: ftbfs-shuffle
Hi,
GNU Make now has a --shuffle option that simulates non-deterministic ordering
of target prerequisites. See
https://trofi.github.io/posts/238-new-make-shuffle-mode.html and also previous
work in Debian by Santiago Vila:
https://people.debian.org/~sanvila/make-shuffle/
This package fails to build with make --shuffle=reverse.
This is likely to be caused by a missing dependency in
debian/rules or an upstream Makefile.
More information about this mass bug filing is available at
https://wiki.debian.org/qa.debian.org/FTBFS/Shuffle
Relevant part (hopefully):
> make[2]: Entering directory '/build/reproducible-path/ltrsift-1.0.2'
> Makefile:46: update target 'obj/src/ltrsift_encode.o' due to: target does not
> exist
> echo "[compile obj/src/ltrsift_encode.o]"
> Makefile:46: update target 'obj/src/ltrsift.o' due to: target does not exist
> echo "[compile obj/src/ltrsift.o]"
> [compile obj/src/ltrsift_encode.o]
> [compile obj/src/ltrsift.o]
> cc -c -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/build/reproducible-path/ltrsift-1.0.2=.
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -g -Wall -Wunused-parameter -O3
> -Wdate-time -D_FORTIFY_SOURCE=2 `pkg-config --cflags --libs gtk+-2.0
> gthread-2.0` -I/usr/include/genometools -I/usr/include/genometools -I/src
> -lgenometools -L/usr/lib -Wl,-z,relro -Wl,-z,now src/ltrsift_encode.c -o
> obj/src/ltrsift_encode.o
> cc -c -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/build/reproducible-path/ltrsift-1.0.2=.
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -g -Wall -Wunused-parameter -O3
> -Wdate-time -D_FORTIFY_SOURCE=2 `pkg-config --cflags --libs gtk+-2.0
> gthread-2.0` -I/usr/include/genometools -I/usr/include/genometools -I/src
> -lgenometools -L/usr/lib -Wl,-z,relro -Wl,-z,now src/ltrsift.c -o
> obj/src/ltrsift.o
> Makefile:46: update target 'obj/src/support.o' due to: target does not exist
> echo "[compile obj/src/support.o]"
> Makefile:46: update target 'obj/src/statusbar.o' due to: target does not exist
> echo "[compile obj/src/statusbar.o]"
> [compile obj/src/support.o]
> [compile obj/src/statusbar.o]
> cc -c -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/build/reproducible-path/ltrsift-1.0.2=.
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -g -Wall -Wunused-parameter -O3
> -Wdate-time -D_FORTIFY_SOURCE=2 `pkg-config --cflags --libs gtk+-2.0
> gthread-2.0` -I/usr/include/genometools -I/usr/include/genometools -I/src
> -lgenometools -L/usr/lib -Wl,-z,relro -Wl,-z,now src/support.c -o
> obj/src/support.o
> cc -c -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/build/reproducible-path/ltrsift-1.0.2=.
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -g -Wall -Wunused-parameter -O3
> -Wdate-time -D_FORTIFY_SOURCE=2 `pkg-config --cflags --libs gtk+-2.0
> gthread-2.0` -I/usr/include/genometools -I/usr/include/genometools -I/src
> -lgenometools -L/usr/lib -Wl,-z,relro -Wl,-z,now src/statusbar.c -o
> obj/src/statusbar.o
> Makefile:46: update target 'obj/src/script_filter_stream.o' due to: target
> does not exist
> echo "[compile obj/src/script_filter_stream.o]"
> Makefile:46: update target 'obj/src/project_wizard.o' due to: target does not
> exist
> echo "[compile obj/src/project_wizard.o]"
> [compile obj/src/script_filter_stream.o]
> cc -c -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/build/reproducible-path/ltrsift-1.0.2=.
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -g -Wall -Wunused-parameter -O3
> -Wdate-time -D_FORTIFY_SOURCE=2 `pkg-config --cflags --libs gtk+-2.0
> gthread-2.0` -I/usr/include/genometools -I/usr/include/genometools -I/src
> -lgenometools -L/usr/lib -Wl,-z,relro -Wl,-z,now src/script_filter_stream.c
> -o obj/src/script_filter_stream.o
> [compile obj/src/project_wizard.o]
> cc -c -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/build/reproducible-path/ltrsift-1.0.2=.
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -g -Wall -Wunused-parameter -O3
> -Wdate-time -D_FORTIFY_SOURCE=2 `pkg-config --cflags --libs gtk+-2.0
> gthread-2.0` -I/usr/include/genometools -I/usr/include/genometools -I/src
> -lgenometools -L/usr/lib -Wl,-z,relro -Wl,-z,now src/project_wizard.c -o
> obj/src/project_wizard.o
> Makefile:46: update target 'obj/src/preprocess_visitor.o' due to: target does
> not exist
> echo "[compile obj/src/preprocess_visitor.o]"
> [compile obj/src/preprocess_visitor.o]
> cc -c -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/build/reproducible-path/ltrsift-1.0.2=.
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -g -Wall -Wunused-parameter -O3
> -Wdate-time -D_FORTIFY_SOURCE=2 `pkg-config --cflags --libs gtk+-2.0
> gthread-2.0` -I/usr/include/genometools -I/usr/include/genometools -I/src
> -lgenometools -L/usr/lib -Wl,-z,relro -Wl,-z,now src/preprocess_visitor.c -o
> obj/src/preprocess_visitor.o
> Makefile:46: update target 'obj/src/preprocess_stream.o' due to: target does
> not exist
> echo "[compile obj/src/preprocess_stream.o]"
> [compile obj/src/preprocess_stream.o]
> cc -c -g -O2 -Werror=implicit-function-declaration
> -ffile-prefix-map=/build/reproducible-path/ltrsift-1.0.2=.
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -g -Wall -Wunused-parameter -O3
> -Wdate-time -D_FORTIFY_SOURCE=2 `pkg-config --cflags --libs gtk+-2.0
> gthread-2.0` -I/usr/include/genometools -I/usr/include/genometools -I/src
> -lgenometools -L/usr/lib -Wl,-z,relro -Wl,-z,now src/preprocess_stream.c -o
> obj/src/preprocess_stream.o
> Assembler messages:
> Fatal error: can't create obj/src/ltrsift_encode.o: No such file or directory
> make[2]: *** [Makefile:47: obj/src/ltrsift_encode.o] Error 1 shuffle=reverse
The full build log is available from:
http://qa-logs.debian.net/2025/05/05/shuffle/reverse/ltrsift_1.0.2-10_unstable_reverse.log
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
--- End Message ---
--- Begin Message ---
Source: ltrsift
Source-Version: 1.0.2-12
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
ltrsift, 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.
Andreas Tille <[email protected]> (supplier of updated ltrsift 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: Tue, 20 Oct 2026 20:25:55 +0200
Source: ltrsift
Binary: ltrsift ltrsift-dbgsym ltrsift-sample
Architecture: source amd64 all
Version: 1.0.2-12
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
ltrsift - postprocessing and classification of LTR retrotransposons
ltrsift-sample - postprocessing and classification of LTR retrotransposons
(sample
Closes: 967603 1105470 1126708
Changes:
ltrsift (1.0.2-12) unstable; urgency=medium
.
* Team upload.
* d/watch: version=5
* Standards-Version: 4.7.4 (routine-update)
* Reflow Uploaders field (cme)
* Port from GTK+ 2 to GTK+ 3. Closes: #967603
* Add autopkgtest checking the GTK+ 3 port.
* Create ltrsift-sample package containing upstream sample data to enable
running more decent autopkgtest and enable users verifying functionality
easily
* Fix use-after-free when creating a project. Closes: #1126708
* Add autopkgtest reproducing the project creation crash.
* Fix build failure with make --shuffle=reverse by creating output
directories before compiling and linking. Closes: #1105470
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