From: sanvila@debian.org
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.
----------------------------------------------------------------
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[...]
libtool: compile: g++ -DPACKAGE_NAME=\\"coot\\" -DPACKAGE_TAR [to
-long-redacted] fPIC -DPIC -o .libs/lig-build.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DPACKA [to
-long-redacted] interface.lo rdkit-interface.cc
libtool: compile: g++ -DPACKAGE_NAME=\\"coot\\" -DPACKAGE_TAR [to
-long-redacted] DPIC -o .libs/rdkit-interface.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DPACKA [to
-long-redacted] -c -o cod-types.lo cod-types.cc
libtool: compile: g++ -DPACKAGE_NAME=\\"coot\\" -DPACKAGE_TAR [to
-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 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 match)>
| ^
/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h:66:58: error:
template
argument 1 is invalid
66 | std::span match)>
| ^
rdkit-interface.cc: In function 'void coot::delete_excessive_hyd
ogens(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 getE
plicitValence() const;
|
^~~~~~~~~~~~~~~~~~
rdkit-interface.cc: In function 'void coot::assign_formal_charge
(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 getE
plicitValence() 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 getE
plicitValence() 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 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 match)>
| ^
/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h:66:58: error:
template
argument 1 is invalid
66 | std::span 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 '/<>/lidia-core'
make[1]: *** [Makefile:715: all-recursive] Error 1
make[1]: Leaving directory '/<>'
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
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--- SoupGate-Win32 v1.05
* Origin: you cannot sedate... all the things you hate (1:229/2)
|
