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: âBlastProgramâ has not been declared [-Wtemplate-body] 185 | case BlastProgram::TBLASTN: | ^~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:188:57: error: expected primary-expression before â)â token [-Wtemplate-body] 188 | BlastTabularSpecSelector<h>(), | ^ /<<PKGBUILDDIR>>/src/lambda.cpp:189:50: error: âBlastProgramâ has not been declared [-Wtemplate-body] 189 | BlastProgramSelector<BlastProgram::TBLASTN>()); | ^~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:189:73: error: expected primary-expression before â)â token [-Wtemplate-body] 189 | BlastProgramSelector<BlastProgram::TBLASTN>()); | ^ /<<PKGBUILDDIR>>/src/lambda.cpp:190:14: error: âBlastProgramâ has not been declared [-Wtemplate-body] 190 | case BlastProgram::TBLASTX: | ^~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:193:57: error: expected primary-expression before â)â token [-Wtemplate-body] 193 | BlastTabularSpecSelector<h>(), | ^ /<<PKGBUILDDIR>>/src/lambda.cpp:194:50: error: âBlastProgramâ has not been declared [-Wtemplate-body] 194 | BlastProgramSelector<BlastProgram::TBLASTX>()); | ^~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:194:73: error: expected primary-expression before â)â token [-Wtemplate-body] 194 | BlastProgramSelector<BlastProgram::TBLASTX>()); | ^ /<<PKGBUILDDIR>>/src/lambda.cpp: At global scope: /<<PKGBUILDDIR>>/src/lambda.cpp:206:11: error: âBlastTabularSpecâ has not been declared 206 | BlastTabularSpec h, | ^~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:207:11: error: âBlastProgramâ has not been declared 207 | BlastProgram p> | ^~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:211:10: error: âBlastTabularSpecSelectorâ has not been declared 211 | BlastTabularSpecSelector<h> const &, | ^~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:211:34: error: expected â,â or â...â before â<â token 211 | BlastTabularSpecSelector<h> const &, | ^ /<<PKGBUILDDIR>>/src/lambda.cpp: In function âint argConv2(const LambdaOptions&, const TOutFormat&, int)â: /<<PKGBUILDDIR>>/src/lambda.cpp:214:16: error: âBlastTabularSpecSelectorâ does not name a type [-Wtemplate-body] 214 | using Th = BlastTabularSpecSelector<h>; | ^~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:215:16: error: âBlastProgramSelectorâ does not name a type [-Wtemplate-body] 215 | using Tp = BlastProgramSelector<p>; | ^~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:219:52: error: there are no arguments to âThâ that depend on a template parameter, so a declaration of âThâ 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 âTpâ that depend on a template parameter, so a declaration of âTpâ 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 âAminoAcidâ that depend on a template parameter, so a declaration of âAminoAcidâ 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 âThâ that depend on a template parameter, so a declaration of âThâ 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 âTpâ that depend on a template parameter, so a declaration of âTpâ must be available [-Wtemplate-body] 221 | return argConv3(options, TOutFormat(), Th(), Tp(), ReducedAminoAcid<Murphy10>()); | ^~ /<<PKGBUILDDIR>>/src/lambda.cpp:221:64: error: âReducedAminoAcidâ was not declared in this scope; did you mean âseqan2::ReducedAminoAcidâ? [-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: âseqan2::ReducedAminoAcidâ declared here 79 | using ReducedAminoAcid = SimpleType<unsigned char, ReducedAminoAcid_<TRedSpec> >; | ^~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:221:81: error: âMurphy10â was not declared in this scope; did you mean âseqan2::Murphy10â? [-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: âseqan2::Murphy10â declared here 85 | typedef Tag<Murphy10_> Murphy10; | ^~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:221:91: error: expected primary-expression before â)â 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: âBlastTabularSpecâ has not been declared 242 | BlastTabularSpec h, | ^~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:243:11: error: âBlastProgramâ has not been declared 243 | BlastProgram p> | ^~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:247:10: error: âBlastTabularSpecSelectorâ has not been declared 247 | BlastTabularSpecSelector<h> const &, | ^~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:247:34: error: expected â,â or â...â before â<â token 247 | BlastTabularSpecSelector<h> const &, | ^ /<<PKGBUILDDIR>>/src/lambda.cpp: In function âint argConv3(const LambdaOptions&, const TOutFormat&, int)â: /<<PKGBUILDDIR>>/src/lambda.cpp:268:25: error: âBlastTabularSpecSelectorâ was not declared in this scope; did you mean âseqan2::BlastTabularSpecSelectorâ? [-Wtemplate-body] 268 | BlastTabularSpecSelector<h>(), | ^~~~~~~~~~~~~~~~~~~~~~~~ | seqan2::BlastTabularSpecSelector /usr/include/seqan/blast/blast_tabular.h:156:8: note: âseqan2::BlastTabularSpecSelectorâ declared here 156 | struct BlastTabularSpecSelector | ^~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:268:50: error: âhâ was not declared in this scope [-Wtemplate-body] 268 | BlastTabularSpecSelector<h>(), | ^ /<<PKGBUILDDIR>>/src/lambda.cpp:268:53: error: expected primary-expression before â)â token [-Wtemplate-body] 268 | BlastTabularSpecSelector<h>(), | ^ /<<PKGBUILDDIR>>/src/lambda.cpp:269:25: error: âBlastProgramSelectorâ was not declared in this scope; did you mean âseqan2::BlastProgramSelectorâ? [-Wtemplate-body] 269 | BlastProgramSelector<p>(), | ^~~~~~~~~~~~~~~~~~~~ | seqan2::BlastProgramSelector /usr/include/seqan/blast/blast_base.h:133:8: note: âseqan2::BlastProgramSelectorâ declared here 133 | struct BlastProgramSelector | ^~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:269:46: error: âpâ was not declared in this scope [-Wtemplate-body] 269 | BlastProgramSelector<p>(), | ^ /<<PKGBUILDDIR>>/src/lambda.cpp:269:49: error: expected primary-expression before â)â token [-Wtemplate-body] 269 | BlastProgramSelector<p>(), | ^ /<<PKGBUILDDIR>>/src/lambda.cpp:271:25: error: there are no arguments to âAffineGapsâ that depend on a template parameter, so a declaration of âAffineGapsâ must be available [-Wtemplate-body] 271 | AffineGaps()); | ^~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp: At global scope: /<<PKGBUILDDIR>>/src/lambda.cpp:277:11: error: âBlastTabularSpecâ has not been declared 277 | BlastTabularSpec h, | ^~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:278:11: error: âBlastProgramâ has not been declared 278 | BlastProgram p> | ^~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:282:10: error: âBlastTabularSpecSelectorâ has not been declared 282 | BlastTabularSpecSelector<h> const &, | ^~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:282:34: error: expected â,â or â...â before â<â token 282 | BlastTabularSpecSelector<h> const &, | ^ /<<PKGBUILDDIR>>/src/lambda.cpp: In function âint argConv4(const LambdaOptions&, const TOutFormat&, int)â: /<<PKGBUILDDIR>>/src/lambda.cpp:316:25: error: âIndexSaâ was not declared in this scope; did you mean âseqan2::IndexSaâ? [-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: âseqan2::IndexSaâ 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: âBlastTabularSpecSelectorâ was not declared in this scope; did you mean âseqan2::BlastTabularSpecSelectorâ? [-Wtemplate-body] 318 | BlastTabularSpecSelector<h>(), | ^~~~~~~~~~~~~~~~~~~~~~~~ | seqan2::BlastTabularSpecSelector /usr/include/seqan/blast/blast_tabular.h:156:8: note: âseqan2::BlastTabularSpecSelectorâ declared here 156 | struct BlastTabularSpecSelector | ^~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:318:61: error: âhâ was not declared in this scope [-Wtemplate-body] 318 | BlastTabularSpecSelector<h>(), | ^ /<<PKGBUILDDIR>>/src/lambda.cpp:318:64: error: expected primary-expression before â)â token [-Wtemplate-body] 318 | BlastTabularSpecSelector<h>(), | ^ /<<PKGBUILDDIR>>/src/lambda.cpp:319:36: error: âBlastProgramSelectorâ was not declared in this scope; did you mean âseqan2::BlastProgramSelectorâ? [-Wtemplate-body] 319 | BlastProgramSelector<p>(), | ^~~~~~~~~~~~~~~~~~~~ | seqan2::BlastProgramSelector /usr/include/seqan/blast/blast_base.h:133:8: note: âseqan2::BlastProgramSelectorâ declared here 133 | struct BlastProgramSelector | ^~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:319:57: error: âpâ was not declared in this scope [-Wtemplate-body] 319 | BlastProgramSelector<p>(), | ^ /<<PKGBUILDDIR>>/src/lambda.cpp:319:60: error: expected primary-expression before â)â token [-Wtemplate-body] 319 | BlastProgramSelector<p>(), | ^ /<<PKGBUILDDIR>>/src/lambda.cpp:323:25: error: âTFMIndexâ 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: âBlastTabularSpecSelectorâ was not declared in this scope; did you mean âseqan2::BlastTabularSpecSelectorâ? [-Wtemplate-body] 325 | BlastTabularSpecSelector<h>(), | ^~~~~~~~~~~~~~~~~~~~~~~~ | seqan2::BlastTabularSpecSelector /usr/include/seqan/blast/blast_tabular.h:156:8: note: âseqan2::BlastTabularSpecSelectorâ declared here 156 | struct BlastTabularSpecSelector | ^~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:325:61: error: âhâ was not declared in this scope [-Wtemplate-body] 325 | BlastTabularSpecSelector<h>(), | ^ /<<PKGBUILDDIR>>/src/lambda.cpp:325:64: error: expected primary-expression before â)â token [-Wtemplate-body] 325 | BlastTabularSpecSelector<h>(), | ^ /<<PKGBUILDDIR>>/src/lambda.cpp:326:36: error: âBlastProgramSelectorâ was not declared in this scope; did you mean âseqan2::BlastProgramSelectorâ? [-Wtemplate-body] 326 | BlastProgramSelector<p>(), | ^~~~~~~~~~~~~~~~~~~~ | seqan2::BlastProgramSelector /usr/include/seqan/blast/blast_base.h:133:8: note: âseqan2::BlastProgramSelectorâ declared here 133 | struct BlastProgramSelector | ^~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:326:57: error: âpâ was not declared in this scope [-Wtemplate-body] 326 | BlastProgramSelector<p>(), | ^ /<<PKGBUILDDIR>>/src/lambda.cpp:326:60: error: expected primary-expression before â)â token [-Wtemplate-body] 326 | BlastProgramSelector<p>(), | ^ /<<PKGBUILDDIR>>/src/lambda.cpp: At global scope: /<<PKGBUILDDIR>>/src/lambda.cpp:341:11: error: âBlastProgramâ has not been declared 341 | BlastProgram p, | ^~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:342:11: error: âBlastTabularSpecâ has not been declared 342 | BlastTabularSpec h> | ^~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:346:10: error: âBlastTabularSpecSelectorâ has not been declared 346 | BlastTabularSpecSelector<h> const &, | ^~~~~~~~~~~~~~~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:346:34: error: expected â,â or â...â before â<â token 346 | BlastTabularSpecSelector<h> const &, | ^ /<<PKGBUILDDIR>>/src/lambda.cpp: In function âint realMain(const LambdaOptions&, const TOutFormat&, int)â: /<<PKGBUILDDIR>>/src/lambda.cpp:351:78: error: âpâ was not declared in this scope [-Wtemplate-body] 351 | using TGlobalHolder = GlobalDataHolder<TRedAlph, TIndexSpec, TOutFormat, p, h>; | ^ /<<PKGBUILDDIR>>/src/lambda.cpp:351:81: error: âhâ 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: âTGlobalHolderâ was not declared in this scope; did you mean âGlobalDataHolderâ? [-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: âTLocalHolderâ was not declared in this scope; did you mean âtotalorderâ? [-Wtemplate-body] 359 | printOptions<TLocalHolder>(options); | ^~~~~~~~~~~~ | totalorder /<<PKGBUILDDIR>>/src/lambda.cpp:361:18: error: expected â;â before âglobalHolderâ [-Wtemplate-body] 361 | TGlobalHolder globalHolder; | ^~~~~~~~~~~~~ | ; /<<PKGBUILDDIR>>/src/lambda.cpp:364:30: error: âglobalHolderâ was not declared in this scope; did you mean âGlobalDataHolderâ? [-Wtemplate-body] 364 | int ret = prepareScoring(globalHolder, options); | ^~~~~~~~~~~~ | GlobalDataHolder /<<PKGBUILDDIR>>/src/lambda.cpp:421:20: error: there are no arguments to âsysTimeâ that depend on a template parameter, so a declaration of âsysTimeâ must be available [-Wtemplate-body] 421 | double start = sysTime(); | ^~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:428:27: error: there are no arguments to âlengthâ that depend on a template parameter, so a declaration of âlengthâ must be available [-Wtemplate-body] 428 | : length(globalHolder.qryIds)); | ^~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:434:9: error: âTLocalHolderâ was not declared in this scope; did you mean âtotalorderâ? [-Wtemplate-body] 434 | TLocalHolder localHolder(options, globalHolder); | ^~~~~~~~~~~~ | totalorder /<<PKGBUILDDIR>>/src/lambda.cpp:441:13: error: âlocalHolderâ was not declared in this scope [-Wtemplate-body] 441 | localHolder.init(t); | ^~~~~~~~~~~ /<<PKGBUILDDIR>>/src/lambda.cpp:481:35: error: âlocalHolderâ 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 âsysTimeâ that depend on a template parameter, so a declaration of âsysTimeâ 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 --------------------------------------------------------------------------------
