[Debian-med-packaging] Bug#1008402: khmer: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.10 3.9" returned exit code 13
Lucas Nussbaum
lucas at debian.org
Sat Mar 26 21:21:07 GMT 2022
Source: khmer
Version: 2.1.2+dfsg-10
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20220326 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_install
> install -d /<<BUILDDIR>>/khmer-2.1.2\+dfsg/debian/tmp
> pybuild --install -i python{version} -p "3.10 3.9" --dest-dir /<<BUILDDIR>>/khmer-2.1.2\+dfsg/debian/tmp
> I: pybuild base:237: /usr/bin/python3.10 setup.py install --root /<<PKGBUILDDIR>>/debian/khmer '--install-scripts=/usr/lib/khmer/bin'
> /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead
> warnings.warn(
> running install
> /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
> warnings.warn(
> running build
> running build_py
> running egg_info
> writing khmer.egg-info/PKG-INFO
> writing dependency_links to khmer.egg-info/dependency_links.txt
> writing requirements to khmer.egg-info/requires.txt
> writing top-level names to khmer.egg-info/top_level.txt
> reading manifest file 'khmer.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> warning: no files found matching 'ChangeLog'
> warning: no files found matching 'ez_setup.py'
> warning: no files found matching 'IDEAS'
> warning: no files found matching 'README.md'
> warning: no files found matching 'TODO'
> warning: no files found matching '.ycm_extra_conf.py'
> warning: no files found matching '*.hh' under directory 'lib'
> warning: no files found matching '*.cc' under directory 'lib'
> warning: no files found matching '[Mm]akefile*' under directory 'lib'
> warning: no files found matching 'get_version.py' under directory 'lib'
> warning: no files found matching '*.hh' under directory 'khmer'
> warning: no files found matching '*.1' under directory 'third-party'
> warning: no files found matching '*.xsl' under directory 'third-party'
> warning: no files found matching 'sample*' under directory 'third-party'
> warning: no files found matching 'words*' under directory 'third-party'
> warning: no files found matching '*.sh' under directory 'third-party'
> warning: no files found matching '*.c' under directory 'third-party'
> warning: no files found matching 'manual*' under directory 'third-party'
> warning: no files found matching '[Mm]akefile*' under directory 'third-party'
> warning: no files found matching '*.pl' under directory 'third-party'
> warning: no files found matching '*.dsp' under directory 'third-party'
> warning: no files found matching 'CHANGES' under directory 'third-party'
> warning: no files found matching '*.txt' under directory 'third-party'
> warning: no files found matching 'FAQ' under directory 'third-party'
> warning: no files found matching 'INDEX' under directory 'third-party'
> warning: no files found matching 'configure' under directory 'third-party'
> warning: no files found matching '*.xsl' under directory 'third-party'
> warning: no files found matching 'bzip.css' under directory 'third-party/bzip2'
> warning: no files found matching 'entities.xml' under directory 'third-party/bzip2'
> warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2'
> warning: no files found matching 'LICENSE' under directory 'third-party/bzip2'
> warning: no files found matching 'third-party/zlib/zconf.h.in'
> warning: no files found matching 'third-party/zlib/zlib.pc.in'
> warning: no previously-included files found matching 'third-party/zlib/Makefile'
> warning: no previously-included files found matching 'third-party/zlib/zconf.h'
> warning: no files found matching 'README.txt' under directory 'scripts'
> warning: no previously-included files matching '*.orig' found anywhere in distribution
> warning: no previously-included files matching '*.pyc' found anywhere in distribution
> adding license file 'LICENSE'
> writing manifest file 'khmer.egg-info/SOURCES.txt'
> copying khmer/_oxli/assembly.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli
> copying khmer/_oxli/graphs.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli
> copying khmer/_oxli/hashing.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli
> copying khmer/_oxli/parsing.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli
> copying khmer/_oxli/utils.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli
> UPDATING /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_version.py
> set /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_version.py to '2.1.2'
> running build_ext
> skipping 'khmer/_oxli/hashing.cpp' Cython extension (up-to-date)
> skipping 'khmer/_oxli/assembly.cpp' Cython extension (up-to-date)
> skipping 'khmer/_oxli/parsing.cpp' Cython extension (up-to-date)
> skipping 'khmer/_oxli/utils.cpp' Cython extension (up-to-date)
> skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date)
> building 'khmer._khmer' extension
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_counttable.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashset.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-3.10/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp
> In file included from src/oxli/assembler.cc:38:
> include/oxli/assembler.hh: In constructor ‘oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)’:
> include/oxli/assembler.hh:80:23: warning: ‘oxli::LinearAssembler::graph’ will be initialized after [-Wreorder]
> 80 | const Hashgraph * graph;
> | ^~~~~
> include/oxli/assembler.hh:79:16: warning: ‘oxli::WordLength oxli::LinearAssembler::_ksize’ [-Wreorder]
> 79 | WordLength _ksize;
> | ^~~~~~
> src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder]
> 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) :
> | ^~~~~~~~~~~~~~~
> src/oxli/assembler.cc: In destructor ‘oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()’:
> src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type ‘oxli::LinearAssembler’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
> 189 | delete this->linear_asm;
> | ^~~~~~~~~~~~~~~~~~~~~~~
> In file included from src/oxli/assembler.cc:38:
> include/oxli/assembler.hh: In constructor ‘oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)’:
> include/oxli/assembler.hh:158:16: warning: ‘oxli::JunctionCountAssembler::_ksize’ will be initialized after [-Wreorder]
> 158 | WordLength _ksize;
> | ^~~~~~
> include/oxli/assembler.hh:153:15: warning: ‘oxli::Traverser oxli::JunctionCountAssembler::traverser’ [-Wreorder]
> 153 | Traverser traverser;
> | ^~~~~~~~~
> src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder]
> 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) :
> | ^~~~~~~~~~~~~~~~~~~~~~
> In file included from src/oxli/assembler.cc:38:
> include/oxli/assembler.hh:153:15: warning: ‘oxli::JunctionCountAssembler::traverser’ will be initialized after [-Wreorder]
> 153 | Traverser traverser;
> | ^~~~~~~~~
> include/oxli/assembler.hh:151:21: warning: ‘oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm’ [-Wreorder]
> 151 | LinearAssembler linear_asm;
> | ^~~~~~~~~~
> src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder]
> 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) :
> | ^~~~~~~~~~~~~~~~~~~~~~
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp
> src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr<SeqIO>&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr<SeqIO> = std::unique_ptr<oxli::read_parsers::ReadParser<oxli::read_parsers::FastxReader> >]’:
> src/oxli/hashtable.cc:512:1: required from here
> src/oxli/hashtable.cc:103:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=]
> 103 | } catch (NoMoreReadsAvailable) {
> | ^~~~~~~~~~~~~~~~~~~~
> src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr<SeqIO>&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr<SeqIO> = std::unique_ptr<oxli::read_parsers::ReadParser<oxli::read_parsers::FastxReader> >]’:
> src/oxli/hashtable.cc:529:1: required from here
> src/oxli/hashtable.cc:133:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=]
> 133 | } catch (NoMoreReadsAvailable) {
> | ^~~~~~~~~~~~~~~~~~~~
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp
> src/oxli/hllcounter.cc: In instantiation of ‘void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr<SeqIO>&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr<SeqIO> = std::unique_ptr<oxli::read_parsers::ReadParser<oxli::read_parsers::FastxReader> >]’:
> src/oxli/hllcounter.cc:524:1: required from here
> src/oxli/hllcounter.cc:428:40: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=]
> 428 | } catch (read_parsers::NoMoreReadsAvailable) {
> | ^~~~~~~~~~~~~~~~~~~~
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp
> In file included from third-party/seqan/core/include/seqan/basic.h:62,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 92 | std::auto_ptr<Test> instance;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 105 | std::auto_ptr<Stream<GZFile> > _gzStream;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 108 | std::auto_ptr<Stream<BZ2File> > _bz2Stream;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 110 | std::auto_ptr<String<char, MMap<> > > _mmapString;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 111 | std::auto_ptr<std::ifstream> _plainStream;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 116 | std::auto_ptr<RecordReader<Stream<GZFile>, SinglePass<> > > _gzReader;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 119 | std::auto_ptr<RecordReader<Stream<BZ2File>, SinglePass<> > > _bz2Reader;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 121 | std::auto_ptr<RecordReader<String<char, MMap<> >, SinglePass<StringReader> > > _mmapReaderSinglePass;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 122 | std::auto_ptr<RecordReader<String<char, MMap<> >, DoublePass<StringReader> > > _mmapReaderDoublePass;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 123 | std::auto_ptr<RecordReader<std::istream, SinglePass<> > > _istreamReader;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 124 | std::auto_ptr<RecordReader<std::ifstream, SinglePass<> > > _ifstreamReader;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/align.h:116,
> from third-party/seqan/core/include/seqan/store.h:38,
> from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40,
> from third-party/seqan/core/include/seqan/seq_io.h:83,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function ‘seqan::DPCell_<TScoreValue, seqan::Tag<seqan::AffineGaps_> >& seqan::DPCell_<TScoreValue, seqan::Tag<seqan::AffineGaps_> >::operator=(const seqan::DPCell_<TScoreValue, seqan::Tag<seqan::AffineGaps_> >&)’:
> third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
> 84 | if (this != &other)
> | ^~
> third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
> 86 | _horizontalScore = other._horizontalScore;
> | ^~~~~~~~~~~~~~~~
> In file included from third-party/seqan/core/include/seqan/align.h:166,
> from third-party/seqan/core/include/seqan/store.h:38,
> from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40,
> from third-party/seqan/core/include/seqan/seq_io.h:83,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const seqan::String<TValue, TSpec>&, const seqan::String<TValue2, TSpec2>&, const MyersBitVector&)’:
> third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
> 70 | if (length(seqH) < length(seqV))
> | ^~
> third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
> 74 | const unsigned int BLOCK_SIZE = BitsPerValue<unsigned int>::VALUE;
> | ^~~~~
> In file included from third-party/seqan/core/include/seqan/align.h:174,
> from third-party/seqan/core/include/seqan/store.h:38,
> from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40,
> from third-party/seqan/core/include/seqan/seq_io.h:83,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair<seqan::Pair<TDiagonal> > seqan::_alignBandedSmithWatermanTrace(seqan::LocalAlignmentFinder<TScoreValue>&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’:
> third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
> 409 | if ((actualCol == 0) || (actualRow == 0))
> | ^~
> third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
> 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal);
> | ^~
> In file included from third-party/seqan/core/include/seqan/bam_io.h:107,
> from third-party/seqan/core/include/seqan/store.h:41,
> from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40,
> from third-party/seqan/core/include/seqan/seq_io.h:83,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope:
> third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 180 | std::auto_ptr<XamWriter_> _writer;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/bam_io.h:107,
> from third-party/seqan/core/include/seqan/store.h:41,
> from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40,
> from third-party/seqan/core/include/seqan/seq_io.h:83,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 182 | std::auto_ptr<XamReader_> _reader;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/store.h:61,
> from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40,
> from third-party/seqan/core/include/seqan/seq_io.h:83,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(seqan::FragmentStore<TSpec, TConfig>&, const TScore&, const TShrinkMatches&)’:
> third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
> 1733 | if (alignQualityStoreLengthPre == 0u)
> | ^~
> third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
> 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos());
> | ^~~~~~~~~~~~~~~~
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/storage.cc -o build/temp.linux-x86_64-3.10/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/subset.cc -o build/temp.linux-x86_64-3.10/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp
> src/oxli/subset.cc: In member function ‘size_t oxli::SubsetPartition::output_partitioned_file(const string&, const string&, bool, oxli::CallbackFn, void*)’:
> src/oxli/subset.cc:136:24: warning: unused variable ‘ksize’ [-Wunused-variable]
> 136 | const unsigned int ksize = _ht->ksize();
> | ^~~~~
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-3.10/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp
> In file included from src/oxli/traversal.cc:39:
> src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer<direction>::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list<std::function<bool(const oxli::Kmer&)> >]’:
> src/oxli/traversal.cc:202:5: required from here
> include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer<false>::graph’ will be initialized after [-Wreorder]
> 79 | const Hashgraph * graph;
> | ^~~~~
> include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer<false>::filters’ [-Wreorder]
> 76 | KmerFilterList filters;
> | ^~~~~~~
> src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder]
> 53 | NodeGatherer<direction>::NodeGatherer(const Hashgraph * ht,
> | ^~~~~~~~~~~~~~~~~~~~~~~
> In file included from src/oxli/traversal.cc:39:
> src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer<direction>::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list<std::function<bool(const oxli::Kmer&)> >]’:
> src/oxli/traversal.cc:203:5: required from here
> include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer<true>::graph’ will be initialized after [-Wreorder]
> 79 | const Hashgraph * graph;
> | ^~~~~
> include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer<true>::filters’ [-Wreorder]
> 76 | KmerFilterList filters;
> | ^~~~~~~
> src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder]
> 53 | NodeGatherer<direction>::NodeGatherer(const Hashgraph * ht,
> | ^~~~~~~~~~~~~~~~~~~~~~~
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_khmer.cpython-310-x86_64-linux-gnu.so -fopenmp
> running build_scripts
> running install_lib
> creating /<<PKGBUILDDIR>>/debian/khmer
> creating /<<PKGBUILDDIR>>/debian/khmer/usr
> creating /<<PKGBUILDDIR>>/debian/khmer/usr/lib
> creating /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10
> creating /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages
> creating /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/oxli/__init__.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/oxli/build_graph.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/oxli/functions.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/oxli/partition.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/oxli
> creating /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/__init__.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/khmer_args.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/kfile.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/trimming.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer
> creating /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/__init__.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/oxli_types.pxd -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.cpp -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.cpp -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.pxd -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.cpp -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.cpp -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.pxd -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hllcounter.pxd -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.pxd -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.pxd -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.pyx -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.pyx -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/traversal.pxd -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.pyx -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.cpython-310-x86_64-linux-gnu.so -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.pxd -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.cpp -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.pyx -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.cpython-310-x86_64-linux-gnu.so -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.pyx -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/thread_utils.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_khmer.cpython-310-x86_64-linux-gnu.so -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer
> creating /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__init__.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_script_output.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_normalize_by_median.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_read_aligner.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_tabletype.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_functions.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_sandbox_scripts.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_subset_graph.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_nodegraph.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_oxli_functions.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_filter_abund.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_hll.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/graph_features.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_labelhash.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_sequence_validation.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_read_handling.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_threaded_sequence_processor.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_counting_single.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_cython_assembly.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_nibblestorage.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/khmer_tst_utils.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_cython_parsing.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_counttable.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_banding.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_read_parsers.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_lump.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/.gitignore -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_hashset.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_streaming_io.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> creating /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.gz -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-transcript.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-reads.fq.gz -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/biglump-random-20-a.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-large.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.1 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/fakelump.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/badversion-k32.tagset -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-sweep-reads.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fq.1 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fq.pe -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-graph.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-overlap1.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/empty-file.gz -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/goodversion-k12.ht.gz -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/simple-genome-reads.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken3.fq.2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-fastq-reads.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.malformat.fq.2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.malformat.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/real-partition-small.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-impaired.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/dn-test-some-paired-all-keep.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-paired.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/single-read.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.paired_bad -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-paired.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/unclean-reads.fastq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-overlap2.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-output-partitions.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-short.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-empty.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken4.fq.1 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed-broken.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/real-partition-tiny.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-reads.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/filter-test-A.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/100-reads.fq.gz -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/100-reads.fq.bz2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/empty-file -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/casava_18-pe.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/dn-test-none-paired.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-fastq-n-reads.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-labels.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-3.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.bz2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-slash1.fq.1 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-X2.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fa.bz2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-sweep-reads.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-graph5.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/goodversion-k32.tagset -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fa.se -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/badversion-k12.ht -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fq.2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/multi-output.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/empty-file.bz2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-b.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.paired2.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired_one.base.dif.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-graph2.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fa.2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/bogus.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.paired.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.bz2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fa.pe -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/valid-read-testing.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/readaligner-k12.json -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken4.fq.2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/goodversion-k12.ht -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fq.gz -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-multi.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken3.fq.1 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.gz -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-slash1.fq.2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.badleft -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/readaligner-default.json -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fa.part -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fa.1 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.badright -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.even.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/filter-test-B.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-31-c.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-filter-abund-Ns.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fq.bz2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-slash1.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/README.rst -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed-2.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-fastq-reads.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/combine_parts_1.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken2.fq.1 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed-witherror.fa.pe -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/normC20k20.ct -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-error-reads.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-empty.fa.bz2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.odd.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/goodversion-k32.stoptags -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/banding-reads.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/single-read.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/truncated.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fq.se -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken2.fq.2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/badversion-k32.stoptags -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fa.gz -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/simple-genome.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/dn-test-all-paired-all-keep.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/fakelump.fa.stoptags.txt -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-sweep-contigs.fp -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/badversion-k12.ct -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-reads.fq.bz2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/old-style-format-w-comments.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/all-A.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_countgraph.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_scripts.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_script_arguments.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_version.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_graph.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_cpython_hierarchy.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/khmer_logger.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_version.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/utils.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/oxli/__init__.py to __init__.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/oxli/build_graph.py to build_graph.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/oxli/functions.py to functions.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/oxli/partition.py to partition.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/__init__.py to __init__.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/khmer_args.py to khmer_args.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/kfile.py to kfile.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/trimming.py to trimming.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli/__init__.py to __init__.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/thread_utils.py to thread_utils.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__init__.py to __init__.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_script_output.py to test_script_output.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_normalize_by_median.py to test_normalize_by_median.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_read_aligner.py to test_read_aligner.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_tabletype.py to test_tabletype.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_functions.py to test_functions.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_sandbox_scripts.py to test_sandbox_scripts.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py to test_subset_graph.cpython-310.pyc
> /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:61: SyntaxWarning: "is" with a literal. Did you mean "=="?
> /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:82: SyntaxWarning: "is" with a literal. Did you mean "=="?
> /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:278: SyntaxWarning: "is" with a literal. Did you mean "=="?
> /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:476: SyntaxWarning: "is" with a literal. Did you mean "=="?
> /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:509: SyntaxWarning: "is" with a literal. Did you mean "=="?
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_nodegraph.py to test_nodegraph.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_oxli_functions.py to test_oxli_functions.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_filter_abund.py to test_filter_abund.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_hll.py to test_hll.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/graph_features.py to graph_features.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_labelhash.py to test_labelhash.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_sequence_validation.py to test_sequence_validation.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_read_handling.py to test_read_handling.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_threaded_sequence_processor.py to test_threaded_sequence_processor.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_counting_single.py to test_counting_single.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_cython_assembly.py to test_cython_assembly.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_nibblestorage.py to test_nibblestorage.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/khmer_tst_utils.py to khmer_tst_utils.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_cython_parsing.py to test_cython_parsing.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_counttable.py to test_counttable.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_banding.py to test_banding.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_read_parsers.py to test_read_parsers.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_lump.py to test_lump.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_hashset.py to test_hashset.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_streaming_io.py to test_streaming_io.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_countgraph.py to test_countgraph.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_scripts.py to test_scripts.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_script_arguments.py to test_script_arguments.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_version.py to test_version.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_graph.py to test_graph.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_cpython_hierarchy.py to test_cpython_hierarchy.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/khmer_logger.py to khmer_logger.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_version.py to _version.cpython-310.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer/utils.py to utils.cpython-310.pyc
> running install_egg_info
> Copying khmer.egg-info to /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.10/dist-packages/khmer-2.1.2.egg-info
> Skipping SOURCES.txt
> running install_scripts
> creating /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer
> creating /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/abundance-dist.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/do-partition.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/extract-paired-reads.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/normalize-by-median.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/make-initial-stoptags.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/interleave-reads.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/count-median.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/extract-partitions.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/load-graph.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/fastq-to-fasta.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/filter-abund.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/extract-long-sequences.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/filter-stoptags.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/load-into-counting.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/readstats.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/partition-graph.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/abundance-dist-single.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/filter-abund-single.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/trim-low-abund.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/annotate-partitions.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/merge-partitions.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/find-knots.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/sample-reads-randomly.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/split-paired-reads.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.10/unique-kmers.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/abundance-dist.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/do-partition.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/extract-paired-reads.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/normalize-by-median.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/make-initial-stoptags.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/interleave-reads.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/count-median.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/extract-partitions.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/load-graph.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/fastq-to-fasta.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/filter-abund.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/extract-long-sequences.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/filter-stoptags.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/load-into-counting.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/readstats.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/partition-graph.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/abundance-dist-single.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/filter-abund-single.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/trim-low-abund.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/annotate-partitions.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/merge-partitions.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/find-knots.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/split-paired-reads.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/unique-kmers.py to 755
> I: pybuild base:237: /usr/bin/python3 setup.py install --root /<<PKGBUILDDIR>>/debian/khmer '--install-scripts=/usr/lib/khmer/bin'
> /usr/lib/python3/dist-packages/setuptools/dist.py:723: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead
> warnings.warn(
> running install
> /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
> warnings.warn(
> running build
> running build_py
> running egg_info
> writing khmer.egg-info/PKG-INFO
> writing dependency_links to khmer.egg-info/dependency_links.txt
> writing requirements to khmer.egg-info/requires.txt
> writing top-level names to khmer.egg-info/top_level.txt
> reading manifest file 'khmer.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> warning: no files found matching 'ChangeLog'
> warning: no files found matching 'ez_setup.py'
> warning: no files found matching 'IDEAS'
> warning: no files found matching 'README.md'
> warning: no files found matching 'TODO'
> warning: no files found matching '.ycm_extra_conf.py'
> warning: no files found matching '*.hh' under directory 'lib'
> warning: no files found matching '*.cc' under directory 'lib'
> warning: no files found matching '[Mm]akefile*' under directory 'lib'
> warning: no files found matching 'get_version.py' under directory 'lib'
> warning: no files found matching '*.hh' under directory 'khmer'
> warning: no files found matching '*.1' under directory 'third-party'
> warning: no files found matching '*.xsl' under directory 'third-party'
> warning: no files found matching 'sample*' under directory 'third-party'
> warning: no files found matching 'words*' under directory 'third-party'
> warning: no files found matching '*.sh' under directory 'third-party'
> warning: no files found matching '*.c' under directory 'third-party'
> warning: no files found matching 'manual*' under directory 'third-party'
> warning: no files found matching '[Mm]akefile*' under directory 'third-party'
> warning: no files found matching '*.pl' under directory 'third-party'
> warning: no files found matching '*.dsp' under directory 'third-party'
> warning: no files found matching 'CHANGES' under directory 'third-party'
> warning: no files found matching '*.txt' under directory 'third-party'
> warning: no files found matching 'FAQ' under directory 'third-party'
> warning: no files found matching 'INDEX' under directory 'third-party'
> warning: no files found matching 'configure' under directory 'third-party'
> warning: no files found matching '*.xsl' under directory 'third-party'
> warning: no files found matching 'bzip.css' under directory 'third-party/bzip2'
> warning: no files found matching 'entities.xml' under directory 'third-party/bzip2'
> warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2'
> warning: no files found matching 'LICENSE' under directory 'third-party/bzip2'
> warning: no files found matching 'third-party/zlib/zconf.h.in'
> warning: no files found matching 'third-party/zlib/zlib.pc.in'
> warning: no previously-included files found matching 'third-party/zlib/Makefile'
> warning: no previously-included files found matching 'third-party/zlib/zconf.h'
> warning: no files found matching 'README.txt' under directory 'scripts'
> warning: no previously-included files matching '*.orig' found anywhere in distribution
> warning: no previously-included files matching '*.pyc' found anywhere in distribution
> adding license file 'LICENSE'
> writing manifest file 'khmer.egg-info/SOURCES.txt'
> UPDATING /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py
> set /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py to '2.1.2'
> running build_ext
> skipping 'khmer/_oxli/hashing.cpp' Cython extension (up-to-date)
> skipping 'khmer/_oxli/assembly.cpp' Cython extension (up-to-date)
> skipping 'khmer/_oxli/parsing.cpp' Cython extension (up-to-date)
> skipping 'khmer/_oxli/utils.cpp' Cython extension (up-to-date)
> skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date)
> building 'khmer._khmer' extension
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_counttable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashset.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-3.9/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp
> In file included from src/oxli/assembler.cc:38:
> include/oxli/assembler.hh: In constructor ‘oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)’:
> include/oxli/assembler.hh:80:23: warning: ‘oxli::LinearAssembler::graph’ will be initialized after [-Wreorder]
> 80 | const Hashgraph * graph;
> | ^~~~~
> include/oxli/assembler.hh:79:16: warning: ‘oxli::WordLength oxli::LinearAssembler::_ksize’ [-Wreorder]
> 79 | WordLength _ksize;
> | ^~~~~~
> src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder]
> 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) :
> | ^~~~~~~~~~~~~~~
> src/oxli/assembler.cc: In destructor ‘oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()’:
> src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type ‘oxli::LinearAssembler’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
> 189 | delete this->linear_asm;
> | ^~~~~~~~~~~~~~~~~~~~~~~
> In file included from src/oxli/assembler.cc:38:
> include/oxli/assembler.hh: In constructor ‘oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)’:
> include/oxli/assembler.hh:158:16: warning: ‘oxli::JunctionCountAssembler::_ksize’ will be initialized after [-Wreorder]
> 158 | WordLength _ksize;
> | ^~~~~~
> include/oxli/assembler.hh:153:15: warning: ‘oxli::Traverser oxli::JunctionCountAssembler::traverser’ [-Wreorder]
> 153 | Traverser traverser;
> | ^~~~~~~~~
> src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder]
> 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) :
> | ^~~~~~~~~~~~~~~~~~~~~~
> In file included from src/oxli/assembler.cc:38:
> include/oxli/assembler.hh:153:15: warning: ‘oxli::JunctionCountAssembler::traverser’ will be initialized after [-Wreorder]
> 153 | Traverser traverser;
> | ^~~~~~~~~
> include/oxli/assembler.hh:151:21: warning: ‘oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm’ [-Wreorder]
> 151 | LinearAssembler linear_asm;
> | ^~~~~~~~~~
> src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder]
> 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) :
> | ^~~~~~~~~~~~~~~~~~~~~~
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp
> src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr<SeqIO>&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr<SeqIO> = std::unique_ptr<oxli::read_parsers::ReadParser<oxli::read_parsers::FastxReader> >]’:
> src/oxli/hashtable.cc:512:1: required from here
> src/oxli/hashtable.cc:103:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=]
> 103 | } catch (NoMoreReadsAvailable) {
> | ^~~~~~~~~~~~~~~~~~~~
> src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr<SeqIO>&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr<SeqIO> = std::unique_ptr<oxli::read_parsers::ReadParser<oxli::read_parsers::FastxReader> >]’:
> src/oxli/hashtable.cc:529:1: required from here
> src/oxli/hashtable.cc:133:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=]
> 133 | } catch (NoMoreReadsAvailable) {
> | ^~~~~~~~~~~~~~~~~~~~
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp
> src/oxli/hllcounter.cc: In instantiation of ‘void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr<SeqIO>&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr<SeqIO> = std::unique_ptr<oxli::read_parsers::ReadParser<oxli::read_parsers::FastxReader> >]’:
> src/oxli/hllcounter.cc:524:1: required from here
> src/oxli/hllcounter.cc:428:40: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=]
> 428 | } catch (read_parsers::NoMoreReadsAvailable) {
> | ^~~~~~~~~~~~~~~~~~~~
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp
> In file included from third-party/seqan/core/include/seqan/basic.h:62,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 92 | std::auto_ptr<Test> instance;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 105 | std::auto_ptr<Stream<GZFile> > _gzStream;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 108 | std::auto_ptr<Stream<BZ2File> > _bz2Stream;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 110 | std::auto_ptr<String<char, MMap<> > > _mmapString;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 111 | std::auto_ptr<std::ifstream> _plainStream;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 116 | std::auto_ptr<RecordReader<Stream<GZFile>, SinglePass<> > > _gzReader;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 119 | std::auto_ptr<RecordReader<Stream<BZ2File>, SinglePass<> > > _bz2Reader;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 121 | std::auto_ptr<RecordReader<String<char, MMap<> >, SinglePass<StringReader> > > _mmapReaderSinglePass;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 122 | std::auto_ptr<RecordReader<String<char, MMap<> >, DoublePass<StringReader> > > _mmapReaderDoublePass;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 123 | std::auto_ptr<RecordReader<std::istream, SinglePass<> > > _istreamReader;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/seq_io.h:64,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 124 | std::auto_ptr<RecordReader<std::ifstream, SinglePass<> > > _ifstreamReader;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/align.h:116,
> from third-party/seqan/core/include/seqan/store.h:38,
> from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40,
> from third-party/seqan/core/include/seqan/seq_io.h:83,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function ‘seqan::DPCell_<TScoreValue, seqan::Tag<seqan::AffineGaps_> >& seqan::DPCell_<TScoreValue, seqan::Tag<seqan::AffineGaps_> >::operator=(const seqan::DPCell_<TScoreValue, seqan::Tag<seqan::AffineGaps_> >&)’:
> third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
> 84 | if (this != &other)
> | ^~
> third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
> 86 | _horizontalScore = other._horizontalScore;
> | ^~~~~~~~~~~~~~~~
> In file included from third-party/seqan/core/include/seqan/align.h:166,
> from third-party/seqan/core/include/seqan/store.h:38,
> from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40,
> from third-party/seqan/core/include/seqan/seq_io.h:83,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const seqan::String<TValue, TSpec>&, const seqan::String<TValue2, TSpec2>&, const MyersBitVector&)’:
> third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
> 70 | if (length(seqH) < length(seqV))
> | ^~
> third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
> 74 | const unsigned int BLOCK_SIZE = BitsPerValue<unsigned int>::VALUE;
> | ^~~~~
> In file included from third-party/seqan/core/include/seqan/align.h:174,
> from third-party/seqan/core/include/seqan/store.h:38,
> from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40,
> from third-party/seqan/core/include/seqan/seq_io.h:83,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair<seqan::Pair<TDiagonal> > seqan::_alignBandedSmithWatermanTrace(seqan::LocalAlignmentFinder<TScoreValue>&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’:
> third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
> 409 | if ((actualCol == 0) || (actualRow == 0))
> | ^~
> third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
> 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal);
> | ^~
> In file included from third-party/seqan/core/include/seqan/bam_io.h:107,
> from third-party/seqan/core/include/seqan/store.h:41,
> from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40,
> from third-party/seqan/core/include/seqan/seq_io.h:83,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope:
> third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 180 | std::auto_ptr<XamWriter_> _writer;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/bam_io.h:107,
> from third-party/seqan/core/include/seqan/store.h:41,
> from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40,
> from third-party/seqan/core/include/seqan/seq_io.h:83,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
> 182 | std::auto_ptr<XamReader_> _reader;
> | ^~~~~~~~
> In file included from /usr/include/c++/11/bits/locale_conv.h:41,
> from /usr/include/c++/11/locale:43,
> from /usr/include/c++/11/iomanip:43,
> from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46,
> from third-party/seqan/core/include/seqan/basic/basic_debug.h:52,
> from third-party/seqan/core/include/seqan/basic.h:52,
> from third-party/seqan/core/include/seqan/seq_io.h:44,
> from src/oxli/read_parsers.cc:39:
> /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
> 57 | template<typename> class auto_ptr;
> | ^~~~~~~~
> In file included from third-party/seqan/core/include/seqan/store.h:61,
> from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40,
> from third-party/seqan/core/include/seqan/seq_io.h:83,
> from src/oxli/read_parsers.cc:39:
> third-party/seqan/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(seqan::FragmentStore<TSpec, TConfig>&, const TScore&, const TShrinkMatches&)’:
> third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
> 1733 | if (alignQualityStoreLengthPre == 0u)
> | ^~
> third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
> 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos());
> | ^~~~~~~~~~~~~~~~
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/storage.cc -o build/temp.linux-x86_64-3.9/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/subset.cc -o build/temp.linux-x86_64-3.9/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp
> src/oxli/subset.cc: In member function ‘size_t oxli::SubsetPartition::output_partitioned_file(const string&, const string&, bool, oxli::CallbackFn, void*)’:
> src/oxli/subset.cc:136:24: warning: unused variable ‘ksize’ [-Wunused-variable]
> 136 | const unsigned int ksize = _ht->ksize();
> | ^~~~~
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-3.9/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp
> In file included from src/oxli/traversal.cc:39:
> src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer<direction>::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list<std::function<bool(const oxli::Kmer&)> >]’:
> src/oxli/traversal.cc:202:5: required from here
> include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer<false>::graph’ will be initialized after [-Wreorder]
> 79 | const Hashgraph * graph;
> | ^~~~~
> include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer<false>::filters’ [-Wreorder]
> 76 | KmerFilterList filters;
> | ^~~~~~~
> src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder]
> 53 | NodeGatherer<direction>::NodeGatherer(const Hashgraph * ht,
> | ^~~~~~~~~~~~~~~~~~~~~~~
> In file included from src/oxli/traversal.cc:39:
> src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer<direction>::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list<std::function<bool(const oxli::Kmer&)> >]’:
> src/oxli/traversal.cc:203:5: required from here
> include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer<true>::graph’ will be initialized after [-Wreorder]
> 79 | const Hashgraph * graph;
> | ^~~~~
> include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer<true>::filters’ [-Wreorder]
> 76 | KmerFilterList filters;
> | ^~~~~~~
> src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder]
> 53 | NodeGatherer<direction>::NodeGatherer(const Hashgraph * ht,
> | ^~~~~~~~~~~~~~~~~~~~~~~
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp
> x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_khmer.cpython-39-x86_64-linux-gnu.so -fopenmp
> running build_scripts
> running install_lib
> creating /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9
> creating /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages
> creating /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/oxli/__init__.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/oxli/build_graph.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/oxli/functions.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/oxli/partition.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/oxli
> creating /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/__init__.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/khmer_args.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/kfile.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/trimming.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer
> creating /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/__init__.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/oxli_types.pxd -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.cpp -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.cpp -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.pxd -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.cpp -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.cpp -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.pxd -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hllcounter.pxd -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.pxd -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.pxd -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.pyx -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.pyx -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/traversal.pxd -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.pyx -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.pxd -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.cpp -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.pyx -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.pyx -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_khmer.cpython-39-x86_64-linux-gnu.so -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/thread_utils.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer
> creating /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__init__.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_script_output.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_normalize_by_median.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_read_aligner.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_tabletype.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_functions.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_sandbox_scripts.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_subset_graph.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_nodegraph.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_oxli_functions.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_filter_abund.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_hll.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/graph_features.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_labelhash.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_sequence_validation.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_read_handling.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_threaded_sequence_processor.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_counting_single.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_cython_assembly.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_nibblestorage.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/khmer_tst_utils.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_cython_parsing.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_counttable.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_banding.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_read_parsers.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_lump.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/.gitignore -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_hashset.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_streaming_io.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> creating /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.gz -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-transcript.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-reads.fq.gz -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/biglump-random-20-a.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-large.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.1 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/fakelump.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k32.tagset -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-sweep-reads.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fq.1 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fq.pe -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-graph.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-overlap1.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/empty-file.gz -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k12.ht.gz -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/simple-genome-reads.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken3.fq.2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-fastq-reads.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.malformat.fq.2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.malformat.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/real-partition-small.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-impaired.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/dn-test-some-paired-all-keep.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-paired.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/single-read.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.paired_bad -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-paired.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/unclean-reads.fastq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-overlap2.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-output-partitions.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-short.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-empty.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken4.fq.1 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed-broken.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/real-partition-tiny.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-reads.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/filter-test-A.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.gz -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.bz2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/empty-file -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/casava_18-pe.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/dn-test-none-paired.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-fastq-n-reads.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-labels.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-3.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.bz2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-slash1.fq.1 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-X2.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa.bz2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-sweep-reads.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-graph5.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k32.tagset -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fa.se -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k12.ht -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fq.2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/multi-output.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/empty-file.bz2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-b.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.paired2.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired_one.base.dif.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-graph2.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fa.2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/bogus.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.paired.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.bz2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fa.pe -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/valid-read-testing.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/readaligner-k12.json -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken4.fq.2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k12.ht -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fq.gz -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-multi.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken3.fq.1 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.gz -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-slash1.fq.2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.badleft -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/readaligner-default.json -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa.part -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fa.1 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.badright -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.even.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/filter-test-B.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-31-c.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-filter-abund-Ns.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fq.bz2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-slash1.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/README.rst -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed-2.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-fastq-reads.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/combine_parts_1.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken2.fq.1 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed-witherror.fa.pe -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/normC20k20.ct -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-error-reads.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-empty.fa.bz2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.odd.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k32.stoptags -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/banding-reads.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/single-read.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/truncated.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fq.se -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken2.fq.2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k32.stoptags -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa.gz -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/simple-genome.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/dn-test-all-paired-all-keep.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/fakelump.fa.stoptags.txt -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-sweep-contigs.fp -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k12.ct -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-reads.fq.bz2 -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/old-style-format-w-comments.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fq -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/all-A.fa -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_countgraph.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_scripts.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_script_arguments.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_version.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_graph.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_cpython_hierarchy.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/khmer_logger.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer
> copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build/khmer/utils.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/oxli/__init__.py to __init__.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/oxli/build_graph.py to build_graph.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/oxli/functions.py to functions.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/oxli/partition.py to partition.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/__init__.py to __init__.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/khmer_args.py to khmer_args.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/kfile.py to kfile.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/trimming.py to trimming.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli/__init__.py to __init__.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/thread_utils.py to thread_utils.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__init__.py to __init__.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_script_output.py to test_script_output.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_normalize_by_median.py to test_normalize_by_median.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_read_aligner.py to test_read_aligner.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_tabletype.py to test_tabletype.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_functions.py to test_functions.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_sandbox_scripts.py to test_sandbox_scripts.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py to test_subset_graph.cpython-39.pyc
> /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:61: SyntaxWarning: "is" with a literal. Did you mean "=="?
> /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:82: SyntaxWarning: "is" with a literal. Did you mean "=="?
> /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:278: SyntaxWarning: "is" with a literal. Did you mean "=="?
> /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:476: SyntaxWarning: "is" with a literal. Did you mean "=="?
> /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:509: SyntaxWarning: "is" with a literal. Did you mean "=="?
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_nodegraph.py to test_nodegraph.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_oxli_functions.py to test_oxli_functions.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_filter_abund.py to test_filter_abund.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_hll.py to test_hll.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/graph_features.py to graph_features.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_labelhash.py to test_labelhash.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_sequence_validation.py to test_sequence_validation.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_read_handling.py to test_read_handling.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_threaded_sequence_processor.py to test_threaded_sequence_processor.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_counting_single.py to test_counting_single.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_cython_assembly.py to test_cython_assembly.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_nibblestorage.py to test_nibblestorage.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/khmer_tst_utils.py to khmer_tst_utils.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_cython_parsing.py to test_cython_parsing.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_counttable.py to test_counttable.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_banding.py to test_banding.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_read_parsers.py to test_read_parsers.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_lump.py to test_lump.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_hashset.py to test_hashset.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_streaming_io.py to test_streaming_io.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_countgraph.py to test_countgraph.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_scripts.py to test_scripts.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_script_arguments.py to test_script_arguments.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_version.py to test_version.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_graph.py to test_graph.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_cpython_hierarchy.py to test_cpython_hierarchy.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/khmer_logger.py to khmer_logger.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_version.py to _version.cpython-39.pyc
> byte-compiling /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer/utils.py to utils.cpython-39.pyc
> running install_egg_info
> Copying khmer.egg-info to /<<PKGBUILDDIR>>/debian/khmer/usr/lib/python3.9/dist-packages/khmer-2.1.2.egg-info
> Skipping SOURCES.txt
> running install_scripts
> copying build/scripts-3.9/abundance-dist.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/do-partition.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/extract-paired-reads.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/normalize-by-median.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/make-initial-stoptags.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/interleave-reads.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/count-median.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/extract-partitions.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/load-graph.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/fastq-to-fasta.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/filter-abund.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/extract-long-sequences.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/filter-stoptags.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/load-into-counting.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/readstats.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/partition-graph.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/abundance-dist-single.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/filter-abund-single.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/trim-low-abund.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/annotate-partitions.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/merge-partitions.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/find-knots.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/sample-reads-randomly.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/split-paired-reads.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> copying build/scripts-3.9/unique-kmers.py -> /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/abundance-dist.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/do-partition.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/extract-paired-reads.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/normalize-by-median.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/make-initial-stoptags.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/interleave-reads.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/count-median.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/extract-partitions.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/load-graph.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/fastq-to-fasta.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/filter-abund.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/extract-long-sequences.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/filter-stoptags.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/load-into-counting.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/readstats.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/partition-graph.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/abundance-dist-single.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/filter-abund-single.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/trim-low-abund.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/annotate-partitions.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/merge-partitions.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/find-knots.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/split-paired-reads.py to 755
> changing mode of /<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin/unique-kmers.py to 755
> PYBUILD_SYSTEM=custom \
> PYBUILD_TEST_ARGS="cd {dir}; export PATH={destdir}/usr/lib/khmer/bin:$PATH ; \
> cd {build_dir}; export PYTHONPATH=$(pwd); {interpreter} -m pytest \
> -m 'not known_failing and not jenkins and not huge and not noroot'\
> -q" dh_auto_test
> pybuild --test --test-pytest -i python{version} -p "3.10 3.9"
> I: pybuild base:237: cd /<<PKGBUILDDIR>>; export PATH=/<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games ; cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build; export PYTHONPATH=/<<PKGBUILDDIR>>; python3.10 -m pytest -m 'not known_failing and not jenkins and not huge and not noroot' -q
> ============================= test session starts ==============================
> platform linux -- Python 3.10.4, pytest-6.2.5, py-1.10.0, pluggy-1.0.0
> rootdir: /<<PKGBUILDDIR>>, configfile: pytest.ini
> collected 2732 items / 52 deselected / 2680 selected
>
> khmer/tests/test_banding.py ............ [ 0%]
> khmer/tests/test_countgraph.py ......................................... [ 1%]
> .................................................. [ 3%]
> khmer/tests/test_counting_single.py ......................... [ 4%]
> khmer/tests/test_counttable.py .......... [ 5%]
> khmer/tests/test_cpython_hierarchy.py .... [ 5%]
> khmer/tests/test_cython_assembly.py .................................... [ 6%]
> ........................................................................ [ 9%]
> ........................................................................ [ 12%]
> ........................................................................ [ 14%]
> ........................................................................ [ 17%]
> ......... [ 17%]
> khmer/tests/test_cython_parsing.py ..................................... [ 19%]
> .... [ 19%]
> khmer/tests/test_filter_abund.py ................... [ 19%]
> khmer/tests/test_functions.py .................. [ 20%]
> khmer/tests/test_graph.py ............................ [ 21%]
> khmer/tests/test_hashset.py ............. [ 22%]
> khmer/tests/test_hll.py ...................... [ 22%]
> khmer/tests/test_labelhash.py ................. [ 23%]
> khmer/tests/test_lump.py ...... [ 23%]
> khmer/tests/test_nibblestorage.py ..... [ 24%]
> khmer/tests/test_nodegraph.py .......................................... [ 25%]
> ........................ [ 26%]
> khmer/tests/test_normalize_by_median.py ............F................... [ 27%]
> ...... [ 27%]
> khmer/tests/test_oxli_functions.py .... [ 28%]
> khmer/tests/test_read_aligner.py ..................x. [ 28%]
> khmer/tests/test_read_handling.py ................................ [ 30%]
> khmer/tests/test_read_parsers.py .............................. [ 31%]
> khmer/tests/test_sandbox_scripts.py sssssssssss [ 31%]
> khmer/tests/test_script_arguments.py ............................ [ 32%]
> khmer/tests/test_script_output.py ........... [ 32%]
> khmer/tests/test_scripts.py ............................................ [ 34%]
> .............................................................F.......... [ 37%]
> .............................. [ 38%]
> khmer/tests/test_sequence_validation.py ................................ [ 39%]
> ............ [ 40%]
> khmer/tests/test_streaming_io.py ............................ [ 41%]
> khmer/tests/test_subset_graph.py ........................... [ 42%]
> khmer/tests/test_tabletype.py .....................................s.s.s [ 43%]
> ........................................................................ [ 46%]
> ........................................................................ [ 49%]
> .................. [ 49%]
> khmer/tests/test_threaded_sequence_processor.py ...... [ 49%]
> khmer/tests/test_version.py . [ 50%]
> tests/test_banding.py ............ [ 50%]
> tests/test_countgraph.py ............................................... [ 52%]
> ............................................ [ 53%]
> tests/test_counting_single.py ......................... [ 54%]
> tests/test_counttable.py .......... [ 55%]
> tests/test_cpython_hierarchy.py .... [ 55%]
> tests/test_cython_assembly.py .......................................... [ 56%]
> ........................................................................ [ 59%]
> ........................................................................ [ 62%]
> ........................................................................ [ 64%]
> ........................................................................ [ 67%]
> ... [ 67%]
> tests/test_cython_parsing.py ......................................... [ 69%]
> tests/test_filter_abund.py ................... [ 69%]
> tests/test_functions.py .................. [ 70%]
> tests/test_graph.py ............................ [ 71%]
> tests/test_hashset.py ............. [ 72%]
> tests/test_hll.py ...................... [ 72%]
> tests/test_labelhash.py ................. [ 73%]
> tests/test_lump.py ...... [ 73%]
> tests/test_nibblestorage.py ..... [ 74%]
> tests/test_nodegraph.py ................................................ [ 75%]
> .................. [ 76%]
> tests/test_normalize_by_median.py ............F......................... [ 77%]
> [ 77%]
> tests/test_oxli_functions.py .... [ 78%]
> tests/test_read_aligner.py ..................x. [ 78%]
> tests/test_read_handling.py ................................ [ 80%]
> tests/test_read_parsers.py .............................. [ 81%]
> tests/test_sandbox_scripts.py sssssssssss [ 81%]
> tests/test_script_arguments.py ............................ [ 82%]
> tests/test_script_output.py ........... [ 82%]
> tests/test_scripts.py .................................................. [ 84%]
> .......................................................F................ [ 87%]
> ........................ [ 88%]
> tests/test_sequence_validation.py ...................................... [ 89%]
> ...... [ 90%]
> tests/test_streaming_io.py ............................ [ 91%]
> tests/test_subset_graph.py ........................... [ 92%]
> tests/test_tabletype.py .....................................s.s.s...... [ 93%]
> ........................................................................ [ 96%]
> ........................................................................ [ 99%]
> ............ [ 99%]
> tests/test_threaded_sequence_processor.py ...... [ 99%]
> tests/test_version.py . [100%]
>
> =================================== FAILURES ===================================
> ______________________ test_normalize_by_median_stdout_3 _______________________
>
> def test_normalize_by_median_stdout_3():
> CUTOFF = '1'
>
> infile = utils.copy_test_data('test-abund-read-2.fa')
> in_dir = os.path.dirname(infile)
>
> script = 'normalize-by-median.py'
> args = ['-C', CUTOFF, '-k', '17', infile, '--out', '-']
> > (_, _, err) = utils.runscript(script, args, in_dir)
>
> khmer/tests/test_normalize_by_median.py:233:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> khmer/tests/khmer_tst_utils.py:188: in runscript
> status = _runscript(scriptname, sandbox=sandbox)
> khmer/tests/khmer_tst_utils.py:144: in _runscript
> exec(compile(open(scriptfile).read(), scriptfile, 'exec'),
> ../../../debian/khmer/usr/lib/khmer/bin/normalize-by-median.py:420: in <module>
> main()
> ../../../debian/khmer/usr/lib/khmer/bin/normalize-by-median.py:304: in main
> args = parser.parse_args()
> khmer/khmer_args.py:149: in parse_args
> args = super(KhmerArgumentParser, self).parse_args(args=args,
> /usr/lib/python3.10/argparse.py:1837: in parse_args
> args, argv = self.parse_known_args(args, namespace)
> /usr/lib/python3.10/argparse.py:1870: in parse_known_args
> namespace, args = self._parse_known_args(args, namespace)
> /usr/lib/python3.10/argparse.py:2079: in _parse_known_args
> start_index = consume_optional(start_index)
> /usr/lib/python3.10/argparse.py:2019: in consume_optional
> take_action(action, args, option_string)
> /usr/lib/python3.10/argparse.py:1931: in take_action
> argument_values = self._get_values(action, argument_strings)
> /usr/lib/python3.10/argparse.py:2462: in _get_values
> value = self._get_value(action, arg_string)
> /usr/lib/python3.10/argparse.py:2495: in _get_value
> result = type_func(arg_string)
> khmer/khmer_args.py:174: in __call__
> return super(FileType, self).__call__(fname)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> self = FileType('wb'), string = '-'
>
> def __call__(self, string):
> # the special argument "-" means sys.std{in,out}
> if string == '-':
> if 'r' in self._mode:
> return _sys.stdin.buffer if 'b' in self._mode else _sys.stdin
> elif any(c in self._mode for c in 'wax'):
> > return _sys.stdout.buffer if 'b' in self._mode else _sys.stdout
> E AttributeError: '_io.StringIO' object has no attribute 'buffer'
>
> /usr/lib/python3.10/argparse.py:1273: AttributeError
> ----------------------------- Captured stdout call -----------------------------
> running: normalize-by-median.py in: /tmp/khmertest_oy8tyqsi
> arguments ['normalize-by-median.py', '-C', '1', '-k', '17', '/tmp/khmertest_oy8tyqsi/test-abund-read-2.fa', '--out', '-']
> __________________________ test_trim_low_abund_stdout __________________________
>
> def test_trim_low_abund_stdout():
> infile = utils.copy_test_data('test-abund-read-2.fa')
> in_dir = os.path.dirname(infile)
>
> args = ["-k", "17", "-x", "1e7", "-N", "2", infile, "-o", "-"]
> > _, out, err = utils.runscript('trim-low-abund.py', args, in_dir)
>
> khmer/tests/test_scripts.py:2642:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> khmer/tests/khmer_tst_utils.py:188: in runscript
> status = _runscript(scriptname, sandbox=sandbox)
> khmer/tests/khmer_tst_utils.py:144: in _runscript
> exec(compile(open(scriptfile).read(), scriptfile, 'exec'),
> ../../../debian/khmer/usr/lib/khmer/bin/trim-low-abund.py:549: in <module>
> main()
> ../../../debian/khmer/usr/lib/khmer/bin/trim-low-abund.py:305: in main
> args = parser.parse_args()
> khmer/khmer_args.py:149: in parse_args
> args = super(KhmerArgumentParser, self).parse_args(args=args,
> /usr/lib/python3.10/argparse.py:1837: in parse_args
> args, argv = self.parse_known_args(args, namespace)
> /usr/lib/python3.10/argparse.py:1870: in parse_known_args
> namespace, args = self._parse_known_args(args, namespace)
> /usr/lib/python3.10/argparse.py:2079: in _parse_known_args
> start_index = consume_optional(start_index)
> /usr/lib/python3.10/argparse.py:2019: in consume_optional
> take_action(action, args, option_string)
> /usr/lib/python3.10/argparse.py:1931: in take_action
> argument_values = self._get_values(action, argument_strings)
> /usr/lib/python3.10/argparse.py:2462: in _get_values
> value = self._get_value(action, arg_string)
> /usr/lib/python3.10/argparse.py:2495: in _get_value
> result = type_func(arg_string)
> khmer/khmer_args.py:174: in __call__
> return super(FileType, self).__call__(fname)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> self = FileType('wb'), string = '-'
>
> def __call__(self, string):
> # the special argument "-" means sys.std{in,out}
> if string == '-':
> if 'r' in self._mode:
> return _sys.stdin.buffer if 'b' in self._mode else _sys.stdin
> elif any(c in self._mode for c in 'wax'):
> > return _sys.stdout.buffer if 'b' in self._mode else _sys.stdout
> E AttributeError: '_io.StringIO' object has no attribute 'buffer'
>
> /usr/lib/python3.10/argparse.py:1273: AttributeError
> ----------------------------- Captured stdout call -----------------------------
> running: trim-low-abund.py in: /tmp/khmertest_2n43jcic
> arguments ['trim-low-abund.py', '-k', '17', '-x', '1e7', '-N', '2', '/tmp/khmertest_2n43jcic/test-abund-read-2.fa', '-o', '-']
> ______________________ test_normalize_by_median_stdout_3 _______________________
>
> def test_normalize_by_median_stdout_3():
> CUTOFF = '1'
>
> infile = utils.copy_test_data('test-abund-read-2.fa')
> in_dir = os.path.dirname(infile)
>
> script = 'normalize-by-median.py'
> args = ['-C', CUTOFF, '-k', '17', infile, '--out', '-']
> > (_, _, err) = utils.runscript(script, args, in_dir)
>
> tests/test_normalize_by_median.py:233:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> tests/khmer_tst_utils.py:188: in runscript
> status = _runscript(scriptname, sandbox=sandbox)
> tests/khmer_tst_utils.py:144: in _runscript
> exec(compile(open(scriptfile).read(), scriptfile, 'exec'),
> ../../../debian/khmer/usr/lib/khmer/bin/normalize-by-median.py:420: in <module>
> main()
> ../../../debian/khmer/usr/lib/khmer/bin/normalize-by-median.py:304: in main
> args = parser.parse_args()
> khmer/khmer_args.py:149: in parse_args
> args = super(KhmerArgumentParser, self).parse_args(args=args,
> /usr/lib/python3.10/argparse.py:1837: in parse_args
> args, argv = self.parse_known_args(args, namespace)
> /usr/lib/python3.10/argparse.py:1870: in parse_known_args
> namespace, args = self._parse_known_args(args, namespace)
> /usr/lib/python3.10/argparse.py:2079: in _parse_known_args
> start_index = consume_optional(start_index)
> /usr/lib/python3.10/argparse.py:2019: in consume_optional
> take_action(action, args, option_string)
> /usr/lib/python3.10/argparse.py:1931: in take_action
> argument_values = self._get_values(action, argument_strings)
> /usr/lib/python3.10/argparse.py:2462: in _get_values
> value = self._get_value(action, arg_string)
> /usr/lib/python3.10/argparse.py:2495: in _get_value
> result = type_func(arg_string)
> khmer/khmer_args.py:174: in __call__
> return super(FileType, self).__call__(fname)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> self = FileType('wb'), string = '-'
>
> def __call__(self, string):
> # the special argument "-" means sys.std{in,out}
> if string == '-':
> if 'r' in self._mode:
> return _sys.stdin.buffer if 'b' in self._mode else _sys.stdin
> elif any(c in self._mode for c in 'wax'):
> > return _sys.stdout.buffer if 'b' in self._mode else _sys.stdout
> E AttributeError: '_io.StringIO' object has no attribute 'buffer'
>
> /usr/lib/python3.10/argparse.py:1273: AttributeError
> ----------------------------- Captured stdout call -----------------------------
> running: normalize-by-median.py in: /tmp/khmertest_lhsu6qae
> arguments ['normalize-by-median.py', '-C', '1', '-k', '17', '/tmp/khmertest_lhsu6qae/test-abund-read-2.fa', '--out', '-']
> __________________________ test_trim_low_abund_stdout __________________________
>
> def test_trim_low_abund_stdout():
> infile = utils.copy_test_data('test-abund-read-2.fa')
> in_dir = os.path.dirname(infile)
>
> args = ["-k", "17", "-x", "1e7", "-N", "2", infile, "-o", "-"]
> > _, out, err = utils.runscript('trim-low-abund.py', args, in_dir)
>
> tests/test_scripts.py:2642:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> tests/khmer_tst_utils.py:188: in runscript
> status = _runscript(scriptname, sandbox=sandbox)
> tests/khmer_tst_utils.py:144: in _runscript
> exec(compile(open(scriptfile).read(), scriptfile, 'exec'),
> ../../../debian/khmer/usr/lib/khmer/bin/trim-low-abund.py:549: in <module>
> main()
> ../../../debian/khmer/usr/lib/khmer/bin/trim-low-abund.py:305: in main
> args = parser.parse_args()
> khmer/khmer_args.py:149: in parse_args
> args = super(KhmerArgumentParser, self).parse_args(args=args,
> /usr/lib/python3.10/argparse.py:1837: in parse_args
> args, argv = self.parse_known_args(args, namespace)
> /usr/lib/python3.10/argparse.py:1870: in parse_known_args
> namespace, args = self._parse_known_args(args, namespace)
> /usr/lib/python3.10/argparse.py:2079: in _parse_known_args
> start_index = consume_optional(start_index)
> /usr/lib/python3.10/argparse.py:2019: in consume_optional
> take_action(action, args, option_string)
> /usr/lib/python3.10/argparse.py:1931: in take_action
> argument_values = self._get_values(action, argument_strings)
> /usr/lib/python3.10/argparse.py:2462: in _get_values
> value = self._get_value(action, arg_string)
> /usr/lib/python3.10/argparse.py:2495: in _get_value
> result = type_func(arg_string)
> khmer/khmer_args.py:174: in __call__
> return super(FileType, self).__call__(fname)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> self = FileType('wb'), string = '-'
>
> def __call__(self, string):
> # the special argument "-" means sys.std{in,out}
> if string == '-':
> if 'r' in self._mode:
> return _sys.stdin.buffer if 'b' in self._mode else _sys.stdin
> elif any(c in self._mode for c in 'wax'):
> > return _sys.stdout.buffer if 'b' in self._mode else _sys.stdout
> E AttributeError: '_io.StringIO' object has no attribute 'buffer'
>
> /usr/lib/python3.10/argparse.py:1273: AttributeError
> ----------------------------- Captured stdout call -----------------------------
> running: trim-low-abund.py in: /tmp/khmertest_x7hd3rph
> arguments ['trim-low-abund.py', '-k', '17', '-x', '1e7', '-N', '2', '/tmp/khmertest_x7hd3rph/test-abund-read-2.fa', '-o', '-']
> =========================== short test summary info ============================
> FAILED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_stdout_3
> FAILED khmer/tests/test_scripts.py::test_trim_low_abund_stdout - AttributeErr...
> FAILED tests/test_normalize_by_median.py::test_normalize_by_median_stdout_3
> FAILED tests/test_scripts.py::test_trim_low_abund_stdout - AttributeError: '_...
> = 4 failed, 2646 passed, 28 skipped, 52 deselected, 2 xfailed in 93.47s (0:01:33) =
> E: pybuild pybuild:367: test: plugin custom failed with: exit code=1: cd /<<PKGBUILDDIR>>; export PATH=/<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games ; cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build; export PYTHONPATH=/<<PKGBUILDDIR>>; python3.10 -m pytest -m 'not known_failing and not jenkins and not huge and not noroot' -q
> I: pybuild base:237: cd /<<PKGBUILDDIR>>; export PATH=/<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games ; cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build; export PYTHONPATH=/<<PKGBUILDDIR>>; python3.9 -m pytest -m 'not known_failing and not jenkins and not huge and not noroot' -q
> ============================= test session starts ==============================
> platform linux -- Python 3.9.12, pytest-6.2.5, py-1.10.0, pluggy-1.0.0
> rootdir: /<<PKGBUILDDIR>>, configfile: pytest.ini
> collected 2732 items / 52 deselected / 2680 selected
>
> khmer/tests/test_banding.py ............ [ 0%]
> khmer/tests/test_countgraph.py ......................................... [ 1%]
> .................................................. [ 3%]
> khmer/tests/test_counting_single.py ......................... [ 4%]
> khmer/tests/test_counttable.py .......... [ 5%]
> khmer/tests/test_cpython_hierarchy.py .... [ 5%]
> khmer/tests/test_cython_assembly.py .................................... [ 6%]
> ........................................................................ [ 9%]
> ........................................................................ [ 12%]
> ........................................................................ [ 14%]
> ........................................................................ [ 17%]
> ......... [ 17%]
> khmer/tests/test_cython_parsing.py ..................................... [ 19%]
> .... [ 19%]
> khmer/tests/test_filter_abund.py ................... [ 19%]
> khmer/tests/test_functions.py .................. [ 20%]
> khmer/tests/test_graph.py ............................ [ 21%]
> khmer/tests/test_hashset.py ............. [ 22%]
> khmer/tests/test_hll.py ...................... [ 22%]
> khmer/tests/test_labelhash.py ................. [ 23%]
> khmer/tests/test_lump.py ...... [ 23%]
> khmer/tests/test_nibblestorage.py ..... [ 24%]
> khmer/tests/test_nodegraph.py .......................................... [ 25%]
> ........................ [ 26%]
> khmer/tests/test_normalize_by_median.py ............F................... [ 27%]
> ...... [ 27%]
> khmer/tests/test_oxli_functions.py .... [ 28%]
> khmer/tests/test_read_aligner.py ..................x. [ 28%]
> khmer/tests/test_read_handling.py ................................ [ 30%]
> khmer/tests/test_read_parsers.py .............................. [ 31%]
> khmer/tests/test_sandbox_scripts.py sssssssssss [ 31%]
> khmer/tests/test_script_arguments.py ............................ [ 32%]
> khmer/tests/test_script_output.py ........... [ 32%]
> khmer/tests/test_scripts.py ............................................ [ 34%]
> .............................................................F.......... [ 37%]
> .............................. [ 38%]
> khmer/tests/test_sequence_validation.py ................................ [ 39%]
> ............ [ 40%]
> khmer/tests/test_streaming_io.py ............................ [ 41%]
> khmer/tests/test_subset_graph.py ........................... [ 42%]
> khmer/tests/test_tabletype.py .....................................s.s.s [ 43%]
> ........................................................................ [ 46%]
> ........................................................................ [ 49%]
> .................. [ 49%]
> khmer/tests/test_threaded_sequence_processor.py ...... [ 49%]
> khmer/tests/test_version.py . [ 50%]
> tests/test_banding.py ............ [ 50%]
> tests/test_countgraph.py ............................................... [ 52%]
> ............................................ [ 53%]
> tests/test_counting_single.py ......................... [ 54%]
> tests/test_counttable.py .......... [ 55%]
> tests/test_cpython_hierarchy.py .... [ 55%]
> tests/test_cython_assembly.py .......................................... [ 56%]
> ........................................................................ [ 59%]
> ........................................................................ [ 62%]
> ........................................................................ [ 64%]
> ........................................................................ [ 67%]
> ... [ 67%]
> tests/test_cython_parsing.py ......................................... [ 69%]
> tests/test_filter_abund.py ................... [ 69%]
> tests/test_functions.py .................. [ 70%]
> tests/test_graph.py ............................ [ 71%]
> tests/test_hashset.py ............. [ 72%]
> tests/test_hll.py ...................... [ 72%]
> tests/test_labelhash.py ................. [ 73%]
> tests/test_lump.py ...... [ 73%]
> tests/test_nibblestorage.py ..... [ 74%]
> tests/test_nodegraph.py ................................................ [ 75%]
> .................. [ 76%]
> tests/test_normalize_by_median.py ............F......................... [ 77%]
> [ 77%]
> tests/test_oxli_functions.py .... [ 78%]
> tests/test_read_aligner.py ..................x. [ 78%]
> tests/test_read_handling.py ................................ [ 80%]
> tests/test_read_parsers.py .............................. [ 81%]
> tests/test_sandbox_scripts.py sssssssssss [ 81%]
> tests/test_script_arguments.py ............................ [ 82%]
> tests/test_script_output.py ........... [ 82%]
> tests/test_scripts.py .................................................. [ 84%]
> .......................................................F................ [ 87%]
> ........................ [ 88%]
> tests/test_sequence_validation.py ...................................... [ 89%]
> ...... [ 90%]
> tests/test_streaming_io.py ............................ [ 91%]
> tests/test_subset_graph.py ........................... [ 92%]
> tests/test_tabletype.py .....................................s.s.s...... [ 93%]
> ........................................................................ [ 96%]
> ........................................................................ [ 99%]
> ............ [ 99%]
> tests/test_threaded_sequence_processor.py ...... [ 99%]
> tests/test_version.py . [100%]
>
> =================================== FAILURES ===================================
> ______________________ test_normalize_by_median_stdout_3 _______________________
>
> def test_normalize_by_median_stdout_3():
> CUTOFF = '1'
>
> infile = utils.copy_test_data('test-abund-read-2.fa')
> in_dir = os.path.dirname(infile)
>
> script = 'normalize-by-median.py'
> args = ['-C', CUTOFF, '-k', '17', infile, '--out', '-']
> > (_, _, err) = utils.runscript(script, args, in_dir)
>
> khmer/tests/test_normalize_by_median.py:233:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> khmer/tests/khmer_tst_utils.py:188: in runscript
> status = _runscript(scriptname, sandbox=sandbox)
> khmer/tests/khmer_tst_utils.py:144: in _runscript
> exec(compile(open(scriptfile).read(), scriptfile, 'exec'),
> ../../../debian/khmer/usr/lib/khmer/bin/normalize-by-median.py:420: in <module>
> main()
> ../../../debian/khmer/usr/lib/khmer/bin/normalize-by-median.py:304: in main
> args = parser.parse_args()
> khmer/khmer_args.py:149: in parse_args
> args = super(KhmerArgumentParser, self).parse_args(args=args,
> /usr/lib/python3.9/argparse.py:1836: in parse_args
> args, argv = self.parse_known_args(args, namespace)
> /usr/lib/python3.9/argparse.py:1869: in parse_known_args
> namespace, args = self._parse_known_args(args, namespace)
> /usr/lib/python3.9/argparse.py:2078: in _parse_known_args
> start_index = consume_optional(start_index)
> /usr/lib/python3.9/argparse.py:2018: in consume_optional
> take_action(action, args, option_string)
> /usr/lib/python3.9/argparse.py:1930: in take_action
> argument_values = self._get_values(action, argument_strings)
> /usr/lib/python3.9/argparse.py:2461: in _get_values
> value = self._get_value(action, arg_string)
> /usr/lib/python3.9/argparse.py:2494: in _get_value
> result = type_func(arg_string)
> khmer/khmer_args.py:174: in __call__
> return super(FileType, self).__call__(fname)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> self = FileType('wb'), string = '-'
>
> def __call__(self, string):
> # the special argument "-" means sys.std{in,out}
> if string == '-':
> if 'r' in self._mode:
> return _sys.stdin.buffer if 'b' in self._mode else _sys.stdin
> elif any(c in self._mode for c in 'wax'):
> > return _sys.stdout.buffer if 'b' in self._mode else _sys.stdout
> E AttributeError: '_io.StringIO' object has no attribute 'buffer'
>
> /usr/lib/python3.9/argparse.py:1273: AttributeError
> ----------------------------- Captured stdout call -----------------------------
> running: normalize-by-median.py in: /tmp/khmertest_4h6r6flu
> arguments ['normalize-by-median.py', '-C', '1', '-k', '17', '/tmp/khmertest_4h6r6flu/test-abund-read-2.fa', '--out', '-']
> __________________________ test_trim_low_abund_stdout __________________________
>
> def test_trim_low_abund_stdout():
> infile = utils.copy_test_data('test-abund-read-2.fa')
> in_dir = os.path.dirname(infile)
>
> args = ["-k", "17", "-x", "1e7", "-N", "2", infile, "-o", "-"]
> > _, out, err = utils.runscript('trim-low-abund.py', args, in_dir)
>
> khmer/tests/test_scripts.py:2642:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> khmer/tests/khmer_tst_utils.py:188: in runscript
> status = _runscript(scriptname, sandbox=sandbox)
> khmer/tests/khmer_tst_utils.py:144: in _runscript
> exec(compile(open(scriptfile).read(), scriptfile, 'exec'),
> ../../../debian/khmer/usr/lib/khmer/bin/trim-low-abund.py:549: in <module>
> main()
> ../../../debian/khmer/usr/lib/khmer/bin/trim-low-abund.py:305: in main
> args = parser.parse_args()
> khmer/khmer_args.py:149: in parse_args
> args = super(KhmerArgumentParser, self).parse_args(args=args,
> /usr/lib/python3.9/argparse.py:1836: in parse_args
> args, argv = self.parse_known_args(args, namespace)
> /usr/lib/python3.9/argparse.py:1869: in parse_known_args
> namespace, args = self._parse_known_args(args, namespace)
> /usr/lib/python3.9/argparse.py:2078: in _parse_known_args
> start_index = consume_optional(start_index)
> /usr/lib/python3.9/argparse.py:2018: in consume_optional
> take_action(action, args, option_string)
> /usr/lib/python3.9/argparse.py:1930: in take_action
> argument_values = self._get_values(action, argument_strings)
> /usr/lib/python3.9/argparse.py:2461: in _get_values
> value = self._get_value(action, arg_string)
> /usr/lib/python3.9/argparse.py:2494: in _get_value
> result = type_func(arg_string)
> khmer/khmer_args.py:174: in __call__
> return super(FileType, self).__call__(fname)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> self = FileType('wb'), string = '-'
>
> def __call__(self, string):
> # the special argument "-" means sys.std{in,out}
> if string == '-':
> if 'r' in self._mode:
> return _sys.stdin.buffer if 'b' in self._mode else _sys.stdin
> elif any(c in self._mode for c in 'wax'):
> > return _sys.stdout.buffer if 'b' in self._mode else _sys.stdout
> E AttributeError: '_io.StringIO' object has no attribute 'buffer'
>
> /usr/lib/python3.9/argparse.py:1273: AttributeError
> ----------------------------- Captured stdout call -----------------------------
> running: trim-low-abund.py in: /tmp/khmertest_jh705pw6
> arguments ['trim-low-abund.py', '-k', '17', '-x', '1e7', '-N', '2', '/tmp/khmertest_jh705pw6/test-abund-read-2.fa', '-o', '-']
> ______________________ test_normalize_by_median_stdout_3 _______________________
>
> def test_normalize_by_median_stdout_3():
> CUTOFF = '1'
>
> infile = utils.copy_test_data('test-abund-read-2.fa')
> in_dir = os.path.dirname(infile)
>
> script = 'normalize-by-median.py'
> args = ['-C', CUTOFF, '-k', '17', infile, '--out', '-']
> > (_, _, err) = utils.runscript(script, args, in_dir)
>
> tests/test_normalize_by_median.py:233:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> tests/khmer_tst_utils.py:188: in runscript
> status = _runscript(scriptname, sandbox=sandbox)
> tests/khmer_tst_utils.py:144: in _runscript
> exec(compile(open(scriptfile).read(), scriptfile, 'exec'),
> ../../../debian/khmer/usr/lib/khmer/bin/normalize-by-median.py:420: in <module>
> main()
> ../../../debian/khmer/usr/lib/khmer/bin/normalize-by-median.py:304: in main
> args = parser.parse_args()
> khmer/khmer_args.py:149: in parse_args
> args = super(KhmerArgumentParser, self).parse_args(args=args,
> /usr/lib/python3.9/argparse.py:1836: in parse_args
> args, argv = self.parse_known_args(args, namespace)
> /usr/lib/python3.9/argparse.py:1869: in parse_known_args
> namespace, args = self._parse_known_args(args, namespace)
> /usr/lib/python3.9/argparse.py:2078: in _parse_known_args
> start_index = consume_optional(start_index)
> /usr/lib/python3.9/argparse.py:2018: in consume_optional
> take_action(action, args, option_string)
> /usr/lib/python3.9/argparse.py:1930: in take_action
> argument_values = self._get_values(action, argument_strings)
> /usr/lib/python3.9/argparse.py:2461: in _get_values
> value = self._get_value(action, arg_string)
> /usr/lib/python3.9/argparse.py:2494: in _get_value
> result = type_func(arg_string)
> khmer/khmer_args.py:174: in __call__
> return super(FileType, self).__call__(fname)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> self = FileType('wb'), string = '-'
>
> def __call__(self, string):
> # the special argument "-" means sys.std{in,out}
> if string == '-':
> if 'r' in self._mode:
> return _sys.stdin.buffer if 'b' in self._mode else _sys.stdin
> elif any(c in self._mode for c in 'wax'):
> > return _sys.stdout.buffer if 'b' in self._mode else _sys.stdout
> E AttributeError: '_io.StringIO' object has no attribute 'buffer'
>
> /usr/lib/python3.9/argparse.py:1273: AttributeError
> ----------------------------- Captured stdout call -----------------------------
> running: normalize-by-median.py in: /tmp/khmertest_3hayp1m8
> arguments ['normalize-by-median.py', '-C', '1', '-k', '17', '/tmp/khmertest_3hayp1m8/test-abund-read-2.fa', '--out', '-']
> __________________________ test_trim_low_abund_stdout __________________________
>
> def test_trim_low_abund_stdout():
> infile = utils.copy_test_data('test-abund-read-2.fa')
> in_dir = os.path.dirname(infile)
>
> args = ["-k", "17", "-x", "1e7", "-N", "2", infile, "-o", "-"]
> > _, out, err = utils.runscript('trim-low-abund.py', args, in_dir)
>
> tests/test_scripts.py:2642:
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> tests/khmer_tst_utils.py:188: in runscript
> status = _runscript(scriptname, sandbox=sandbox)
> tests/khmer_tst_utils.py:144: in _runscript
> exec(compile(open(scriptfile).read(), scriptfile, 'exec'),
> ../../../debian/khmer/usr/lib/khmer/bin/trim-low-abund.py:549: in <module>
> main()
> ../../../debian/khmer/usr/lib/khmer/bin/trim-low-abund.py:305: in main
> args = parser.parse_args()
> khmer/khmer_args.py:149: in parse_args
> args = super(KhmerArgumentParser, self).parse_args(args=args,
> /usr/lib/python3.9/argparse.py:1836: in parse_args
> args, argv = self.parse_known_args(args, namespace)
> /usr/lib/python3.9/argparse.py:1869: in parse_known_args
> namespace, args = self._parse_known_args(args, namespace)
> /usr/lib/python3.9/argparse.py:2078: in _parse_known_args
> start_index = consume_optional(start_index)
> /usr/lib/python3.9/argparse.py:2018: in consume_optional
> take_action(action, args, option_string)
> /usr/lib/python3.9/argparse.py:1930: in take_action
> argument_values = self._get_values(action, argument_strings)
> /usr/lib/python3.9/argparse.py:2461: in _get_values
> value = self._get_value(action, arg_string)
> /usr/lib/python3.9/argparse.py:2494: in _get_value
> result = type_func(arg_string)
> khmer/khmer_args.py:174: in __call__
> return super(FileType, self).__call__(fname)
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
>
> self = FileType('wb'), string = '-'
>
> def __call__(self, string):
> # the special argument "-" means sys.std{in,out}
> if string == '-':
> if 'r' in self._mode:
> return _sys.stdin.buffer if 'b' in self._mode else _sys.stdin
> elif any(c in self._mode for c in 'wax'):
> > return _sys.stdout.buffer if 'b' in self._mode else _sys.stdout
> E AttributeError: '_io.StringIO' object has no attribute 'buffer'
>
> /usr/lib/python3.9/argparse.py:1273: AttributeError
> ----------------------------- Captured stdout call -----------------------------
> running: trim-low-abund.py in: /tmp/khmertest_qe3wx8nc
> arguments ['trim-low-abund.py', '-k', '17', '-x', '1e7', '-N', '2', '/tmp/khmertest_qe3wx8nc/test-abund-read-2.fa', '-o', '-']
> =========================== short test summary info ============================
> FAILED khmer/tests/test_normalize_by_median.py::test_normalize_by_median_stdout_3
> FAILED khmer/tests/test_scripts.py::test_trim_low_abund_stdout - AttributeErr...
> FAILED tests/test_normalize_by_median.py::test_normalize_by_median_stdout_3
> FAILED tests/test_scripts.py::test_trim_low_abund_stdout - AttributeError: '_...
> = 4 failed, 2646 passed, 28 skipped, 52 deselected, 2 xfailed in 89.53s (0:01:29) =
> E: pybuild pybuild:367: test: plugin custom failed with: exit code=1: cd /<<PKGBUILDDIR>>; export PATH=/<<PKGBUILDDIR>>/debian/khmer/usr/lib/khmer/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games ; cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_khmer/build; export PYTHONPATH=/<<PKGBUILDDIR>>; python3.9 -m pytest -m 'not known_failing and not jenkins and not huge and not noroot' -q
> rm -fr -- /tmp/dh-xdg-rundir-81obpoi4
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.10 3.9" returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2022/03/26/khmer_2.1.2+dfsg-10_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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