Your message dated Mon, 27 Oct 2025 10:34:43 +0000
with message-id <[email protected]>
and subject line Bug#1117743: fixed in coot 1.1.18+dfsg-2
has caused the Debian Bug report #1117743,
regarding coot: FTBFS:
/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h:66:27: error: 'span' is
not a member of 'std'
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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--
1117743: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1117743
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:coot
Version: 1.1.15+dfsg-1
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, this package failed to build.
Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:
https://people.debian.org/~sanvila/build-logs/202510/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:coot, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TAR
[too-long-redacted] fPIC -DPIC -o .libs/lig-build.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DPACKA
[too-long-redacted] interface.lo rdkit-interface.cc
libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TAR
[too-long-redacted] DPIC -o .libs/rdkit-interface.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DPACKA
[too-long-redacted] -c -o cod-types.lo cod-types.cc
libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TAR
[too-long-redacted] fPIC -DPIC -o .libs/cod-types.o
In file included from use-rdkit.hh:44,
from rdkit-interface.hh:25,
from rdkit-interface.cc:27:
/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h:66:27: error: 'span' is
not a member of 'std'
66 | std::span<const unsigned int> match)>
| ^~~~
/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h:66:27: note: 'std::span'
is only available from C++20 onwards
/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h:66:57: error: expression
list treated as compound expression in functional cast [-fpermissive]
66 | std::span<const unsigned int> match)>
| ^
/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h:66:58: error: template
argument 1 is invalid
66 | std::span<const unsigned int> match)>
| ^
rdkit-interface.cc: In function 'void
coot::delete_excessive_hydrogens(RDKit::RWMol*)':
rdkit-interface.cc:2234:50: warning: 'int RDKit::Atom::getExplicitValence()
const' is deprecated: please use getValence(true) [-Wdeprecated-declarations]
2234 | int e_valence = at_p->getExplicitValence();
| ~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from /usr/include/rdkit/GraphMol/RDKitBase.h:23,
from use-rdkit.hh:41:
/usr/include/rdkit/GraphMol/Atom.h:194:53: note: declared here
194 | [[deprecated("please use getValence(true)")]] int
getExplicitValence() const;
| ^~~~~~~~~~~~~~~~~~
rdkit-interface.cc: In function 'void
coot::assign_formal_charges(RDKit::RWMol*)':
rdkit-interface.cc:2286:67: warning: 'int RDKit::Atom::getExplicitValence()
const' is deprecated: please use getValence(true) [-Wdeprecated-declarations]
2286 | << " with valence " << at_p->getExplicitValence()
| ~~~~~~~~~~~~~~~~~~~~~~~~^~
/usr/include/rdkit/GraphMol/Atom.h:194:53: note: declared here
194 | [[deprecated("please use getValence(true)")]] int
getExplicitValence() const;
| ^~~~~~~~~~~~~~~~~~
rdkit-interface.cc:2291:50: warning: 'int RDKit::Atom::getExplicitValence()
const' is deprecated: please use getValence(true) [-Wdeprecated-declarations]
2291 | int e_valence = at_p->getExplicitValence();
| ~~~~~~~~~~~~~~~~~~~~~~~~^~
/usr/include/rdkit/GraphMol/Atom.h:194:53: note: declared here
194 | [[deprecated("please use getValence(true)")]] int
getExplicitValence() const;
| ^~~~~~~~~~~~~~~~~~
In file included from use-rdkit.hh:44,
from rdkit-interface.hh:25,
from cod-types.cc:27:
/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h:66:27: error: 'span' is
not a member of 'std'
66 | std::span<const unsigned int> match)>
| ^~~~
/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h:66:27: note: 'std::span'
is only available from C++20 onwards
/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h:66:57: error: expression
list treated as compound expression in functional cast [-fpermissive]
66 | std::span<const unsigned int> match)>
| ^
/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h:66:58: error: template
argument 1 is invalid
66 | std::span<const unsigned int> match)>
| ^
make[2]: *** [Makefile:672: rdkit-interface.lo] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: *** [Makefile:672: cod-types.lo] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/lidia-core'
make[1]: *** [Makefile:715: all-recursive] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j2 returned exit code 2
make: *** [debian/rules:93: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: coot
Source-Version: 1.1.18+dfsg-2
Done: Andrius Merkys <[email protected]>
We believe that the bug you reported is fixed in the latest version of
coot, 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.
Andrius Merkys <[email protected]> (supplier of updated coot 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: Mon, 27 Oct 2025 06:06:01 -0400
Source: coot
Architecture: source
Version: 1.1.18+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers
<[email protected]>
Changed-By: Andrius Merkys <[email protected]>
Closes: 1117743
Changes:
coot (1.1.18+dfsg-2) unstable; urgency=medium
.
* Upload to unstable (Closes: #1117743)
* Update debian/copyright.
* Refresh patches, bring back system-fonts.patch, remove alternative
patches fonts-gone and without-fonts.
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