Your message dated Thu, 11 Jun 2026 19:33:41 +0000
with message-id <[email protected]>
and subject line Bug#1136251: fixed in nanopolish 0.14.0-3
has caused the Debian Bug report #1136251,
regarding nanopolish: FTBFS with libeigen3-dev 5.0 (major version transition)
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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--
1136251: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1136251
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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Hash: SHA512
Package: src:nanopolish
Version: 0.14.0-2
Severity: important
Tags: sid forky ftbfs
User: [email protected]
Usertags: eigen3-5.0
Dear Maintainer,
your package depends on libeigen3-dev. The upstream released a
new major version of this mathematical library, 5.0.0. Some
basic information about new features and changes in this version
can be found here:
https://libeigen.gitlab.io/releases/5.0/
This is a major version change and may require code changes in packages
depending on eigen3. The key breaking changes include:
- Minimum required C++ standard is now C++14
- Changes in the build system integration
- Some API name changes
nanopolish FTBFS with libeigen3-dev 5.0.1. The full build log is available at:
https://debusine.debian.net/debian/developers-gladk-eigen3/artifact/3759200/
Here is the most probably relevant part of the failing build log:
===========================================
g++ -o src/common/nanopolish_variant.o -c -g -O2
-ffile-prefix-map=/build/reproducible-path/nanopolish-0.14.0=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -O3 -flto -std=c++11 -fopenmp
-fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2
-I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2
-I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty
-I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model
-I./src/io -I./src/basemods -fPIC src/common/nanopolish_variant.cpp
In file included from /usr/include/eigen3/Eigen/Core:22,
from /usr/include/eigen3/Eigen/Dense:1,
from src/nanopolish_methyltrain.cpp:48:
/usr/include/eigen3/Eigen/src/Core/util/Macros.h:749:2: error: #error Eigen
requires at least c++14 support.
749 | #error Eigen requires at least c++14 support.
| ^~~~~
===========================================
libeigen3-dev_5.0.1-1 is available in experimental.
When this package version lands into unstable (probably at the beginning
of June 2026), this bug will be increased in severity to serious.
Thanks,
Anton
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--- Begin Message ---
Source: nanopolish
Source-Version: 0.14.0-3
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
nanopolish, 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 nanopolish 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])
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Format: 1.8
Date: Thu, 11 Jun 2026 21:17:19 +0200
Source: nanopolish
Architecture: source
Version: 0.14.0-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1136251
Changes:
nanopolish (0.14.0-3) unstable; urgency=medium
.
* d/watch: version=5
* libeigen 5.0 requires minimum -std=c++14
Closes: #1136251
* Standards-Version: 4.7.4 (routine-update)
* Reflow Uploaders field (cme)
* Remove Priority field (cme)
* Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
* Drop 'Rules-Requires-Root: no' from d/control (routine-update)
* Reformat the Last-Update date as ISO YYYY-MM-DD.
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