[Debian-med-packaging] Bug#1125646: lambda-align: FTBFS: /<<PKGBUILDDIR>>/src/output.hpp:28:17: error: 'seqan' is not a namespace-name
Santiago Vila
sanvila at debian.org
Thu Jan 15 16:54:14 GMT 2026
Package: src:lambda-align
Version: 1.0.3-8
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/202601/
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:lambda-align, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --builddirectory=build
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f *.1
dh_auto_clean --
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf_clean -O--builddirectory=build
dh_clean -O--builddirectory=build
debian/rules binary
dh binary --builddirectory=build
dh_update_autotools_config -O--builddirectory=build
dh_autoreconf -O--builddirectory=build
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
[... snipped ...]
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:185:14: error: ‘BlastProgram’ has not been declared [-Wtemplate-body]
185 | case BlastProgram::TBLASTN:
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:188:57: error: expected primary-expression before ‘)’ token [-Wtemplate-body]
188 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:189:50: error: ‘BlastProgram’ has not been declared [-Wtemplate-body]
189 | BlastProgramSelector<BlastProgram::TBLASTN>());
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:189:73: error: expected primary-expression before ‘)’ token [-Wtemplate-body]
189 | BlastProgramSelector<BlastProgram::TBLASTN>());
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:190:14: error: ‘BlastProgram’ has not been declared [-Wtemplate-body]
190 | case BlastProgram::TBLASTX:
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:193:57: error: expected primary-expression before ‘)’ token [-Wtemplate-body]
193 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:194:50: error: ‘BlastProgram’ has not been declared [-Wtemplate-body]
194 | BlastProgramSelector<BlastProgram::TBLASTX>());
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:194:73: error: expected primary-expression before ‘)’ token [-Wtemplate-body]
194 | BlastProgramSelector<BlastProgram::TBLASTX>());
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda.cpp:206:11: error: ‘BlastTabularSpec’ has not been declared
206 | BlastTabularSpec h,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:207:11: error: ‘BlastProgram’ has not been declared
207 | BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:211:10: error: ‘BlastTabularSpecSelector’ has not been declared
211 | BlastTabularSpecSelector<h> const &,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:211:34: error: expected ‘,’ or ‘...’ before ‘<’ token
211 | BlastTabularSpecSelector<h> const &,
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp: In function ‘int argConv2(const LambdaOptions&, const TOutFormat&, int)’:
/<<PKGBUILDDIR>>/src/lambda.cpp:214:16: error: ‘BlastTabularSpecSelector’ does not name a type [-Wtemplate-body]
214 | using Th = BlastTabularSpecSelector<h>;
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:215:16: error: ‘BlastProgramSelector’ does not name a type [-Wtemplate-body]
215 | using Tp = BlastProgramSelector<p>;
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:219:52: error: there are no arguments to ‘Th’ that depend on a template parameter, so a declaration of ‘Th’ must be available [-Wtemplate-body]
219 | return argConv3(options, TOutFormat(), Th(), Tp(), AminoAcid());
| ^~
/<<PKGBUILDDIR>>/src/lambda.cpp:219:58: error: there are no arguments to ‘Tp’ that depend on a template parameter, so a declaration of ‘Tp’ must be available [-Wtemplate-body]
219 | return argConv3(options, TOutFormat(), Th(), Tp(), AminoAcid());
| ^~
/<<PKGBUILDDIR>>/src/lambda.cpp:219:64: error: there are no arguments to ‘AminoAcid’ that depend on a template parameter, so a declaration of ‘AminoAcid’ must be available [-Wtemplate-body]
219 | return argConv3(options, TOutFormat(), Th(), Tp(), AminoAcid());
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:221:52: error: there are no arguments to ‘Th’ that depend on a template parameter, so a declaration of ‘Th’ must be available [-Wtemplate-body]
221 | return argConv3(options, TOutFormat(), Th(), Tp(), ReducedAminoAcid<Murphy10>());
| ^~
/<<PKGBUILDDIR>>/src/lambda.cpp:221:58: error: there are no arguments to ‘Tp’ that depend on a template parameter, so a declaration of ‘Tp’ must be available [-Wtemplate-body]
221 | return argConv3(options, TOutFormat(), Th(), Tp(), ReducedAminoAcid<Murphy10>());
| ^~
/<<PKGBUILDDIR>>/src/lambda.cpp:221:64: error: ‘ReducedAminoAcid’ was not declared in this scope; did you mean ‘seqan2::ReducedAminoAcid’? [-Wtemplate-body]
221 | return argConv3(options, TOutFormat(), Th(), Tp(), ReducedAminoAcid<Murphy10>());
| ^~~~~~~~~~~~~~~~
| seqan2::ReducedAminoAcid
/usr/include/seqan/reduced_aminoacid/reduced_aminoacid_base.h:79:7: note: ‘seqan2::ReducedAminoAcid’ declared here
79 | using ReducedAminoAcid = SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >;
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:221:81: error: ‘Murphy10’ was not declared in this scope; did you mean ‘seqan2::Murphy10’? [-Wtemplate-body]
221 | return argConv3(options, TOutFormat(), Th(), Tp(), ReducedAminoAcid<Murphy10>());
| ^~~~~~~~
| seqan2::Murphy10
/usr/include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h:85:24: note: ‘seqan2::Murphy10’ declared here
85 | typedef Tag<Murphy10_> Murphy10;
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:221:91: error: expected primary-expression before ‘)’ token [-Wtemplate-body]
221 | return argConv3(options, TOutFormat(), Th(), Tp(), ReducedAminoAcid<Murphy10>());
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda.cpp:242:11: error: ‘BlastTabularSpec’ has not been declared
242 | BlastTabularSpec h,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:243:11: error: ‘BlastProgram’ has not been declared
243 | BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:247:10: error: ‘BlastTabularSpecSelector’ has not been declared
247 | BlastTabularSpecSelector<h> const &,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:247:34: error: expected ‘,’ or ‘...’ before ‘<’ token
247 | BlastTabularSpecSelector<h> const &,
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp: In function ‘int argConv3(const LambdaOptions&, const TOutFormat&, int)’:
/<<PKGBUILDDIR>>/src/lambda.cpp:268:25: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’? [-Wtemplate-body]
268 | BlastTabularSpecSelector<h>(),
| ^~~~~~~~~~~~~~~~~~~~~~~~
| seqan2::BlastTabularSpecSelector
/usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here
156 | struct BlastTabularSpecSelector
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:268:50: error: ‘h’ was not declared in this scope [-Wtemplate-body]
268 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:268:53: error: expected primary-expression before ‘)’ token [-Wtemplate-body]
268 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:269:25: error: ‘BlastProgramSelector’ was not declared in this scope; did you mean ‘seqan2::BlastProgramSelector’? [-Wtemplate-body]
269 | BlastProgramSelector<p>(),
| ^~~~~~~~~~~~~~~~~~~~
| seqan2::BlastProgramSelector
/usr/include/seqan/blast/blast_base.h:133:8: note: ‘seqan2::BlastProgramSelector’ declared here
133 | struct BlastProgramSelector
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:269:46: error: ‘p’ was not declared in this scope [-Wtemplate-body]
269 | BlastProgramSelector<p>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:269:49: error: expected primary-expression before ‘)’ token [-Wtemplate-body]
269 | BlastProgramSelector<p>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:271:25: error: there are no arguments to ‘AffineGaps’ that depend on a template parameter, so a declaration of ‘AffineGaps’ must be available [-Wtemplate-body]
271 | AffineGaps());
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda.cpp:277:11: error: ‘BlastTabularSpec’ has not been declared
277 | BlastTabularSpec h,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:278:11: error: ‘BlastProgram’ has not been declared
278 | BlastProgram p>
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:282:10: error: ‘BlastTabularSpecSelector’ has not been declared
282 | BlastTabularSpecSelector<h> const &,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:282:34: error: expected ‘,’ or ‘...’ before ‘<’ token
282 | BlastTabularSpecSelector<h> const &,
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp: In function ‘int argConv4(const LambdaOptions&, const TOutFormat&, int)’:
/<<PKGBUILDDIR>>/src/lambda.cpp:316:25: error: ‘IndexSa’ was not declared in this scope; did you mean ‘seqan2::IndexSa’? [-Wtemplate-body]
316 | return realMain<IndexSa<>>(options,
| ^~~~~~~
| seqan2::IndexSa
In file included from /usr/include/seqan/index.h:142:
/usr/include/seqan/index/index_sa_stree.h:58:8: note: ‘seqan2::IndexSa’ declared here
58 | struct IndexSa {};
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:316:16: error: parse error in template argument list [-Wtemplate-body]
316 | return realMain<IndexSa<>>(options,
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:318:36: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’? [-Wtemplate-body]
318 | BlastTabularSpecSelector<h>(),
| ^~~~~~~~~~~~~~~~~~~~~~~~
| seqan2::BlastTabularSpecSelector
/usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here
156 | struct BlastTabularSpecSelector
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:318:61: error: ‘h’ was not declared in this scope [-Wtemplate-body]
318 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:318:64: error: expected primary-expression before ‘)’ token [-Wtemplate-body]
318 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:319:36: error: ‘BlastProgramSelector’ was not declared in this scope; did you mean ‘seqan2::BlastProgramSelector’? [-Wtemplate-body]
319 | BlastProgramSelector<p>(),
| ^~~~~~~~~~~~~~~~~~~~
| seqan2::BlastProgramSelector
/usr/include/seqan/blast/blast_base.h:133:8: note: ‘seqan2::BlastProgramSelector’ declared here
133 | struct BlastProgramSelector
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:319:57: error: ‘p’ was not declared in this scope [-Wtemplate-body]
319 | BlastProgramSelector<p>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:319:60: error: expected primary-expression before ‘)’ token [-Wtemplate-body]
319 | BlastProgramSelector<p>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:323:25: error: ‘TFMIndex’ was not declared in this scope [-Wtemplate-body]
323 | return realMain<TFMIndex<>>(options,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:323:16: error: parse error in template argument list [-Wtemplate-body]
323 | return realMain<TFMIndex<>>(options,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:325:36: error: ‘BlastTabularSpecSelector’ was not declared in this scope; did you mean ‘seqan2::BlastTabularSpecSelector’? [-Wtemplate-body]
325 | BlastTabularSpecSelector<h>(),
| ^~~~~~~~~~~~~~~~~~~~~~~~
| seqan2::BlastTabularSpecSelector
/usr/include/seqan/blast/blast_tabular.h:156:8: note: ‘seqan2::BlastTabularSpecSelector’ declared here
156 | struct BlastTabularSpecSelector
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:325:61: error: ‘h’ was not declared in this scope [-Wtemplate-body]
325 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:325:64: error: expected primary-expression before ‘)’ token [-Wtemplate-body]
325 | BlastTabularSpecSelector<h>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:326:36: error: ‘BlastProgramSelector’ was not declared in this scope; did you mean ‘seqan2::BlastProgramSelector’? [-Wtemplate-body]
326 | BlastProgramSelector<p>(),
| ^~~~~~~~~~~~~~~~~~~~
| seqan2::BlastProgramSelector
/usr/include/seqan/blast/blast_base.h:133:8: note: ‘seqan2::BlastProgramSelector’ declared here
133 | struct BlastProgramSelector
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:326:57: error: ‘p’ was not declared in this scope [-Wtemplate-body]
326 | BlastProgramSelector<p>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:326:60: error: expected primary-expression before ‘)’ token [-Wtemplate-body]
326 | BlastProgramSelector<p>(),
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp: At global scope:
/<<PKGBUILDDIR>>/src/lambda.cpp:341:11: error: ‘BlastProgram’ has not been declared
341 | BlastProgram p,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:342:11: error: ‘BlastTabularSpec’ has not been declared
342 | BlastTabularSpec h>
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:346:10: error: ‘BlastTabularSpecSelector’ has not been declared
346 | BlastTabularSpecSelector<h> const &,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:346:34: error: expected ‘,’ or ‘...’ before ‘<’ token
346 | BlastTabularSpecSelector<h> const &,
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp: In function ‘int realMain(const LambdaOptions&, const TOutFormat&, int)’:
/<<PKGBUILDDIR>>/src/lambda.cpp:351:78: error: ‘p’ was not declared in this scope [-Wtemplate-body]
351 | using TGlobalHolder = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>;
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:351:81: error: ‘h’ was not declared in this scope [-Wtemplate-body]
351 | using TGlobalHolder = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>;
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:351:82: error: template argument 4 is invalid [-Wtemplate-body]
351 | using TGlobalHolder = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>;
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:351:82: error: template argument 5 is invalid [-Wtemplate-body]
/<<PKGBUILDDIR>>/src/lambda.cpp:352:42: error: ‘TGlobalHolder’ was not declared in this scope; did you mean ‘GlobalDataHolder’? [-Wtemplate-body]
352 | using TLocalHolder = LocalDataHolder<TGlobalHolder, TScoreExtension>;
| ^~~~~~~~~~~~~
| GlobalDataHolder
/<<PKGBUILDDIR>>/src/lambda.cpp:352:72: error: template argument 1 is invalid [-Wtemplate-body]
352 | using TLocalHolder = LocalDataHolder<TGlobalHolder, TScoreExtension>;
| ^
/<<PKGBUILDDIR>>/src/lambda.cpp:359:22: error: ‘TLocalHolder’ was not declared in this scope; did you mean ‘totalorder’? [-Wtemplate-body]
359 | printOptions<TLocalHolder>(options);
| ^~~~~~~~~~~~
| totalorder
/<<PKGBUILDDIR>>/src/lambda.cpp:361:18: error: expected ‘;’ before ‘globalHolder’ [-Wtemplate-body]
361 | TGlobalHolder globalHolder;
| ^~~~~~~~~~~~~
| ;
/<<PKGBUILDDIR>>/src/lambda.cpp:364:30: error: ‘globalHolder’ was not declared in this scope; did you mean ‘GlobalDataHolder’? [-Wtemplate-body]
364 | int ret = prepareScoring(globalHolder, options);
| ^~~~~~~~~~~~
| GlobalDataHolder
/<<PKGBUILDDIR>>/src/lambda.cpp:421:20: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body]
421 | double start = sysTime();
| ^~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:428:27: error: there are no arguments to ‘length’ that depend on a template parameter, so a declaration of ‘length’ must be available [-Wtemplate-body]
428 | : length(globalHolder.qryIds));
| ^~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:434:9: error: ‘TLocalHolder’ was not declared in this scope; did you mean ‘totalorder’? [-Wtemplate-body]
434 | TLocalHolder localHolder(options, globalHolder);
| ^~~~~~~~~~~~
| totalorder
/<<PKGBUILDDIR>>/src/lambda.cpp:441:13: error: ‘localHolder’ was not declared in this scope [-Wtemplate-body]
441 | localHolder.init(t);
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:481:35: error: ‘localHolder’ was not declared in this scope [-Wtemplate-body]
481 | globalHolder.stats += localHolder.stats;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/lambda.cpp:492:42: error: there are no arguments to ‘sysTime’ that depend on a template parameter, so a declaration of ‘sysTime’ must be available [-Wtemplate-body]
492 | myPrint(options, 2, "Runtime: ", sysTime() - start, "s.\n\n");
| ^~~~~~~
make[3]: *** [src/CMakeFiles/lambda_indexer.dir/build.make:82: src/CMakeFiles/lambda_indexer.dir/lambda_indexer.cpp.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build'
make[2]: *** [CMakeFiles/Makefile2:194: src/CMakeFiles/lambda_indexer.dir/all] Error 2
make[2]: *** Waiting for unfinished jobs....
make[3]: *** [src/CMakeFiles/lambda.dir/build.make:82: src/CMakeFiles/lambda.dir/lambda.cpp.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build'
make[2]: *** [CMakeFiles/Makefile2:162: src/CMakeFiles/lambda.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build'
make[1]: *** [Makefile:159: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build'
dh_auto_build: error: cd build && make -j2 INSTALL="install --strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
--------------------------------------------------------------------------------
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