WARNING: (guile-user): imported module (guix build utils) overrides core binding `delete' starting phase `separate-from-pid1' build process now running as PID 10 phase `separate-from-pid1' succeeded after 0.0 seconds starting phase `set-SOURCE-DATE-EPOCH' phase `set-SOURCE-DATE-EPOCH' succeeded after 0.0 seconds starting phase `set-paths' environment variable `PATH' set to `/gnu/store/rifdrl2924k51285x4k9sbhjz07pph9s-python-wrapper-3.10.7/bin:/gnu/store/8psgrz9j2jn7pxqy5mkzhfcf1x00wics-python-cffi-1.17.1/bin:/gnu/store/pg4wj6kljl46ngn6wdy997fwwmxr2a7x-python-wheel-0.40.0/bin:/gnu/store/m8h0hv6g549nh9n9xfjphjrzqg8g2r2w-tar-1.34/bin:/gnu/store/b3mdz7n6j9dzkyi0scdbldnzrwcc3nlg-gzip-1.13/bin:/gnu/store/2aqa6wi5y81yprflz59cjk91pgwvy48w-bzip2-1.0.8/bin:/gnu/store/k4ycd4b9zqrzxmdivjbhakjjymg8bfsv-file-5.45/bin:/gnu/store/ra6mdl923hpjw0yyrrj3j1snhibs32z0-diffutils-3.10/bin:/gnu/store/p76jj9sv007cj4hmfskjjsscy9z0vrc6-patch-2.7.6/bin:/gnu/store/p1g6q2qnp1m0iza4d09mknyqx1xspws3-findutils-4.9.0/bin:/gnu/store/mbgs4jl3vbhi6vya4p64hjfyj3739qzi-gawk-5.3.0/bin:/gnu/store/542d6rh6ci06ngcgiprnambqfws09i4f-zstd-1.5.2/bin:/gnu/store/mqb37w640rg4hx9nx00274r2kz54kc3w-sed-4.8/bin:/gnu/store/wpykxc5blf6vcw7bmqa4k21sqs44p8as-grep-3.11/bin:/gnu/store/cnv0rzdrdmlb3c43sr9n5vagjh3qn0k1-xz-5.4.5/bin:/gnu/store/yxcrwcdd7blcczlc50i6lgcnj2w7nlja-coreutils-9.1/bin:/gnu/store/c6i7ihy40368732m574lpgvygikd4ql9-make-4.4.1/bin:/gnu/store/ak41ci13apcxh5ahd8lc9rv6l7bqnwym-bash-minimal-5.1.16/bin:/gnu/store/d7ayy457nq3a42myfgqs2mc2zbx7z406-ld-wrapper-0/bin:/gnu/store/zf310q29z3apmkp3g6hck29z1d39ajly-binutils-2.41/bin:/gnu/store/xgqbv2lkh6z9x6wgyfjvcpr8paw0zd9a-gcc-11.4.0/bin:/gnu/store/g88kcslhrdmd0b5bap2f2ghj26i7jdlm-glibc-2.39/bin:/gnu/store/g88kcslhrdmd0b5bap2f2ghj26i7jdlm-glibc-2.39/sbin:/gnu/store/h619s650q7w3sv9nagrzlnynsrnds8yf-python-3.10.7/bin' environment variable `GUIX_PYTHONPATH' set to `/gnu/store/8psgrz9j2jn7pxqy5mkzhfcf1x00wics-python-cffi-1.17.1/lib/python3.10/site-packages:/gnu/store/rx7xh6iyij7qh7r5gyq5r1ah5gq6kff5-python-setuptools-67.6.1/lib/python3.10/site-packages:/gnu/store/pg4wj6kljl46ngn6wdy997fwwmxr2a7x-python-wheel-0.40.0/lib/python3.10/site-packages:/gnu/store/h619s650q7w3sv9nagrzlnynsrnds8yf-python-3.10.7/lib/python3.10/site-packages:/gnu/store/idjj9zd331y5lakisw2am6pcjs395l4j-python-pycparser-2.21/lib/python3.10/site-packages' environment variable `PYTHONTZPATH' unset environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/sfp3ncqmf8nyznjkgywi0jv11j8ps0a3-zlib-1.3/include:/gnu/store/2aqa6wi5y81yprflz59cjk91pgwvy48w-bzip2-1.0.8/include:/gnu/store/k4ycd4b9zqrzxmdivjbhakjjymg8bfsv-file-5.45/include:/gnu/store/mbgs4jl3vbhi6vya4p64hjfyj3739qzi-gawk-5.3.0/include:/gnu/store/cnv0rzdrdmlb3c43sr9n5vagjh3qn0k1-xz-5.4.5/include:/gnu/store/c6i7ihy40368732m574lpgvygikd4ql9-make-4.4.1/include:/gnu/store/zf310q29z3apmkp3g6hck29z1d39ajly-binutils-2.41/include:/gnu/store/xgqbv2lkh6z9x6wgyfjvcpr8paw0zd9a-gcc-11.4.0/include:/gnu/store/g88kcslhrdmd0b5bap2f2ghj26i7jdlm-glibc-2.39/include:/gnu/store/h619s650q7w3sv9nagrzlnynsrnds8yf-python-3.10.7/include:/gnu/store/hpcf3359y90qb3c8c1x5syr0ivrj54bg-linux-libre-headers-5.15.49/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/sfp3ncqmf8nyznjkgywi0jv11j8ps0a3-zlib-1.3/include:/gnu/store/2aqa6wi5y81yprflz59cjk91pgwvy48w-bzip2-1.0.8/include:/gnu/store/k4ycd4b9zqrzxmdivjbhakjjymg8bfsv-file-5.45/include:/gnu/store/mbgs4jl3vbhi6vya4p64hjfyj3739qzi-gawk-5.3.0/include:/gnu/store/cnv0rzdrdmlb3c43sr9n5vagjh3qn0k1-xz-5.4.5/include:/gnu/store/c6i7ihy40368732m574lpgvygikd4ql9-make-4.4.1/include:/gnu/store/zf310q29z3apmkp3g6hck29z1d39ajly-binutils-2.41/include:/gnu/store/xgqbv2lkh6z9x6wgyfjvcpr8paw0zd9a-gcc-11.4.0/include/c++:/gnu/store/xgqbv2lkh6z9x6wgyfjvcpr8paw0zd9a-gcc-11.4.0/include:/gnu/store/g88kcslhrdmd0b5bap2f2ghj26i7jdlm-glibc-2.39/include:/gnu/store/h619s650q7w3sv9nagrzlnynsrnds8yf-python-3.10.7/include:/gnu/store/hpcf3359y90qb3c8c1x5syr0ivrj54bg-linux-libre-headers-5.15.49/include' environment variable `OBJC_INCLUDE_PATH' set to `/gnu/store/sfp3ncqmf8nyznjkgywi0jv11j8ps0a3-zlib-1.3/include:/gnu/store/2aqa6wi5y81yprflz59cjk91pgwvy48w-bzip2-1.0.8/include:/gnu/store/k4ycd4b9zqrzxmdivjbhakjjymg8bfsv-file-5.45/include:/gnu/store/mbgs4jl3vbhi6vya4p64hjfyj3739qzi-gawk-5.3.0/include:/gnu/store/cnv0rzdrdmlb3c43sr9n5vagjh3qn0k1-xz-5.4.5/include:/gnu/store/c6i7ihy40368732m574lpgvygikd4ql9-make-4.4.1/include:/gnu/store/zf310q29z3apmkp3g6hck29z1d39ajly-binutils-2.41/include:/gnu/store/xgqbv2lkh6z9x6wgyfjvcpr8paw0zd9a-gcc-11.4.0/include:/gnu/store/g88kcslhrdmd0b5bap2f2ghj26i7jdlm-glibc-2.39/include:/gnu/store/h619s650q7w3sv9nagrzlnynsrnds8yf-python-3.10.7/include:/gnu/store/hpcf3359y90qb3c8c1x5syr0ivrj54bg-linux-libre-headers-5.15.49/include' environment variable `OBJCPLUS_INCLUDE_PATH' set to `/gnu/store/sfp3ncqmf8nyznjkgywi0jv11j8ps0a3-zlib-1.3/include:/gnu/store/2aqa6wi5y81yprflz59cjk91pgwvy48w-bzip2-1.0.8/include:/gnu/store/k4ycd4b9zqrzxmdivjbhakjjymg8bfsv-file-5.45/include:/gnu/store/mbgs4jl3vbhi6vya4p64hjfyj3739qzi-gawk-5.3.0/include:/gnu/store/cnv0rzdrdmlb3c43sr9n5vagjh3qn0k1-xz-5.4.5/include:/gnu/store/c6i7ihy40368732m574lpgvygikd4ql9-make-4.4.1/include:/gnu/store/zf310q29z3apmkp3g6hck29z1d39ajly-binutils-2.41/include:/gnu/store/xgqbv2lkh6z9x6wgyfjvcpr8paw0zd9a-gcc-11.4.0/include/c++:/gnu/store/xgqbv2lkh6z9x6wgyfjvcpr8paw0zd9a-gcc-11.4.0/include:/gnu/store/g88kcslhrdmd0b5bap2f2ghj26i7jdlm-glibc-2.39/include:/gnu/store/h619s650q7w3sv9nagrzlnynsrnds8yf-python-3.10.7/include:/gnu/store/hpcf3359y90qb3c8c1x5syr0ivrj54bg-linux-libre-headers-5.15.49/include' environment variable `LIBRARY_PATH' set to `/gnu/store/sfp3ncqmf8nyznjkgywi0jv11j8ps0a3-zlib-1.3/lib:/gnu/store/8psgrz9j2jn7pxqy5mkzhfcf1x00wics-python-cffi-1.17.1/lib:/gnu/store/rx7xh6iyij7qh7r5gyq5r1ah5gq6kff5-python-setuptools-67.6.1/lib:/gnu/store/pg4wj6kljl46ngn6wdy997fwwmxr2a7x-python-wheel-0.40.0/lib:/gnu/store/2aqa6wi5y81yprflz59cjk91pgwvy48w-bzip2-1.0.8/lib:/gnu/store/k4ycd4b9zqrzxmdivjbhakjjymg8bfsv-file-5.45/lib:/gnu/store/mbgs4jl3vbhi6vya4p64hjfyj3739qzi-gawk-5.3.0/lib:/gnu/store/cnv0rzdrdmlb3c43sr9n5vagjh3qn0k1-xz-5.4.5/lib:/gnu/store/zf310q29z3apmkp3g6hck29z1d39ajly-binutils-2.41/lib:/gnu/store/g88kcslhrdmd0b5bap2f2ghj26i7jdlm-glibc-2.39/lib:/gnu/store/3wg51p14zipq2rl2k59pw7i8hirbdnb5-glibc-2.39-static/lib:/gnu/store/h619s650q7w3sv9nagrzlnynsrnds8yf-python-3.10.7/lib:/gnu/store/idjj9zd331y5lakisw2am6pcjs395l4j-python-pycparser-2.21/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/g88kcslhrdmd0b5bap2f2ghj26i7jdlm-glibc-2.39/lib/locale' environment variable `TZDIR' unset phase `set-paths' succeeded after 0.0 seconds starting phase `install-locale' using 'C.UTF-8' locale for category "LC_ALL" phase `install-locale' succeeded after 0.0 seconds starting phase `unpack' bwapy-0.1.4/ bwapy-0.1.4/LICENSE.md bwapy-0.1.4/MANIFEST.in bwapy-0.1.4/Makefile bwapy-0.1.4/PKG-INFO bwapy-0.1.4/README.md bwapy-0.1.4/bwa/ bwapy-0.1.4/bwa/.git bwapy-0.1.4/bwa/.gitignore bwapy-0.1.4/bwa/.travis.yml bwapy-0.1.4/bwa/COPYING bwapy-0.1.4/bwa/ChangeLog bwapy-0.1.4/bwa/Makefile bwapy-0.1.4/bwa/NEWS.md bwapy-0.1.4/bwa/QSufSort.c bwapy-0.1.4/bwa/QSufSort.h bwapy-0.1.4/bwa/README-alt.md bwapy-0.1.4/bwa/README.md bwapy-0.1.4/bwa/bamlite.c bwapy-0.1.4/bwa/bamlite.h bwapy-0.1.4/bwa/bntseq.c bwapy-0.1.4/bwa/bntseq.h bwapy-0.1.4/bwa/bwa.1 bwapy-0.1.4/bwa/bwa.c bwapy-0.1.4/bwa/bwa.h bwapy-0.1.4/bwa/bwakit/ bwapy-0.1.4/bwa/bwakit/README.md bwapy-0.1.4/bwa/bwakit/bwa-postalt.js bwapy-0.1.4/bwa/bwakit/run-HLA bwapy-0.1.4/bwa/bwakit/run-bwamem bwapy-0.1.4/bwa/bwakit/run-gen-ref bwapy-0.1.4/bwa/bwakit/typeHLA-selctg.js bwapy-0.1.4/bwa/bwakit/typeHLA.js bwapy-0.1.4/bwa/bwakit/typeHLA.sh bwapy-0.1.4/bwa/bwamem.c bwapy-0.1.4/bwa/bwamem.h bwapy-0.1.4/bwa/bwamem_extra.c bwapy-0.1.4/bwa/bwamem_pair.c bwapy-0.1.4/bwa/bwape.c bwapy-0.1.4/bwa/bwase.c bwapy-0.1.4/bwa/bwase.h bwapy-0.1.4/bwa/bwaseqio.c bwapy-0.1.4/bwa/bwashm.c bwapy-0.1.4/bwa/bwt.c bwapy-0.1.4/bwa/bwt.h bwapy-0.1.4/bwa/bwt_gen.c bwapy-0.1.4/bwa/bwt_lite.c bwapy-0.1.4/bwa/bwt_lite.h bwapy-0.1.4/bwa/bwtaln.c bwapy-0.1.4/bwa/bwtaln.h bwapy-0.1.4/bwa/bwtgap.c bwapy-0.1.4/bwa/bwtgap.h bwapy-0.1.4/bwa/bwtindex.c bwapy-0.1.4/bwa/bwtsw2.h bwapy-0.1.4/bwa/bwtsw2_aux.c bwapy-0.1.4/bwa/bwtsw2_chain.c bwapy-0.1.4/bwa/bwtsw2_core.c bwapy-0.1.4/bwa/bwtsw2_main.c bwapy-0.1.4/bwa/bwtsw2_pair.c bwapy-0.1.4/bwa/example.c bwapy-0.1.4/bwa/fastmap.c bwapy-0.1.4/bwa/is.c bwapy-0.1.4/bwa/kbtree.h bwapy-0.1.4/bwa/khash.h bwapy-0.1.4/bwa/kopen.c bwapy-0.1.4/bwa/kseq.h bwapy-0.1.4/bwa/ksort.h bwapy-0.1.4/bwa/kstring.c bwapy-0.1.4/bwa/kstring.h bwapy-0.1.4/bwa/ksw.c bwapy-0.1.4/bwa/ksw.h bwapy-0.1.4/bwa/kthread.c bwapy-0.1.4/bwa/kvec.h bwapy-0.1.4/bwa/libbwa.a bwapy-0.1.4/bwa/main.c bwapy-0.1.4/bwa/malloc_wrap.c bwapy-0.1.4/bwa/malloc_wrap.h bwapy-0.1.4/bwa/maxk.c bwapy-0.1.4/bwa/pemerge.c bwapy-0.1.4/bwa/qualfa2fq.pl bwapy-0.1.4/bwa/rle.c bwapy-0.1.4/bwa/rle.h bwapy-0.1.4/bwa/rope.c bwapy-0.1.4/bwa/rope.h bwapy-0.1.4/bwa/utils.c bwapy-0.1.4/bwa/utils.h bwapy-0.1.4/bwa/xa2multi.pl bwapy-0.1.4/bwapy/ bwapy-0.1.4/bwapy/__init__.py bwapy-0.1.4/bwapy/libbwa.py bwapy-0.1.4/bwapy/libbwapy.c bwapy-0.1.4/bwapy/memopts.c bwapy-0.1.4/bwapy.egg-info/ bwapy-0.1.4/bwapy.egg-info/PKG-INFO bwapy-0.1.4/bwapy.egg-info/SOURCES.txt bwapy-0.1.4/bwapy.egg-info/dependency_links.txt bwapy-0.1.4/bwapy.egg-info/entry_points.txt bwapy-0.1.4/bwapy.egg-info/not-zip-safe bwapy-0.1.4/bwapy.egg-info/requires.txt bwapy-0.1.4/bwapy.egg-info/top_level.txt bwapy-0.1.4/requirements.txt bwapy-0.1.4/setup.cfg bwapy-0.1.4/setup.py phase `unpack' succeeded after 0.0 seconds starting phase `relax-requirements' phase `relax-requirements' succeeded after 0.0 seconds starting phase `ensure-no-mtimes-pre-1980' phase `ensure-no-mtimes-pre-1980' succeeded after 0.0 seconds starting phase `enable-bytecode-determinism' phase `enable-bytecode-determinism' succeeded after 0.0 seconds starting phase `ensure-no-cythonized-files' phase `ensure-no-cythonized-files' succeeded after 0.0 seconds starting phase `patch-usr-bin-file' phase `patch-usr-bin-file' succeeded after 0.0 seconds starting phase `patch-source-shebangs' patch-shebang: ./bwa/bwakit/run-HLA: changing `/bin/bash' to `/gnu/store/ak41ci13apcxh5ahd8lc9rv6l7bqnwym-bash-minimal-5.1.16/bin/bash' patch-shebang: ./bwa/bwakit/run-bwamem: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./bwa/bwakit/run-gen-ref: changing `/bin/bash' to `/gnu/store/ak41ci13apcxh5ahd8lc9rv6l7bqnwym-bash-minimal-5.1.16/bin/bash' patch-shebang: ./bwa/bwakit/typeHLA.sh: changing `/bin/bash' to `/gnu/store/ak41ci13apcxh5ahd8lc9rv6l7bqnwym-bash-minimal-5.1.16/bin/bash' patch-shebang: ./bwa/qualfa2fq.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./bwa/xa2multi.pl: warning: no binary for interpreter `perl' found in $PATH phase `patch-source-shebangs' succeeded after 0.0 seconds starting phase `patch-generated-file-shebangs' patch-shebang: ./bwa/bwakit/run-bwamem: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./bwa/qualfa2fq.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./bwa/xa2multi.pl: warning: no binary for interpreter `perl' found in $PATH phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `build' running "python setup.py" with command "build" and parameters () running build make: 'bwa/libbwa.a' is up to date. creating build creating build/lib.linux-i686-cpython-310 running build_py creating build/lib.linux-i686-cpython-310/bwapy copying bwapy/__init__.py -> build/lib.linux-i686-cpython-310/bwapy copying bwapy/libbwa.py -> build/lib.linux-i686-cpython-310/bwapy warning: build_py: byte-compiling is disabled, skipping. running build_ext building 'bwalib' extension creating build/temp.linux-i686-cpython-310 creating build/temp.linux-i686-cpython-310/bwapy gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fno-semantic-interposition -fPIC -Ibwa -I/gnu/store/h619s650q7w3sv9nagrzlnynsrnds8yf-python-3.10.7/include/python3.10 -c bwapy/libbwapy.c -o build/temp.linux-i686-cpython-310/bwapy/libbwapy.o -pedantic -Wall -std=c99 -march=native -ffast-math -DUSE_SSE2 -DNDEBUG gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fno-semantic-interposition -fPIC -Ibwa -I/gnu/store/h619s650q7w3sv9nagrzlnynsrnds8yf-python-3.10.7/include/python3.10 -c bwapy/memopts.c -o build/temp.linux-i686-cpython-310/bwapy/memopts.o -pedantic -Wall -std=c99 -march=native -ffast-math -DUSE_SSE2 -DNDEBUG gcc -shared -Wl,-rpath=/gnu/store/h619s650q7w3sv9nagrzlnynsrnds8yf-python-3.10.7/lib -fno-semantic-interposition build/temp.linux-i686-cpython-310/bwapy/libbwapy.o build/temp.linux-i686-cpython-310/bwapy/memopts.o bwa/libbwa.a -L/gnu/store/h619s650q7w3sv9nagrzlnynsrnds8yf-python-3.10.7/lib -lz -o build/lib.linux-i686-cpython-310/bwalib.cpython-310-i386-linux-gnu.so ld: i386:x86-64 architecture of input file `bwa/libbwa.a(bwa.o)' is incompatible with i386 output ld: i386:x86-64 architecture of input file `bwa/libbwa.a(bwamem.o)' is incompatible with i386 output ld: i386:x86-64 architecture of input file `bwa/libbwa.a(bwamem_pair.o)' is incompatible with i386 output ld: i386:x86-64 architecture of input file `bwa/libbwa.a(bwamem_extra.o)' is incompatible with i386 output ld: i386:x86-64 architecture of input file `bwa/libbwa.a(malloc_wrap.o)' is incompatible with i386 output ld: i386:x86-64 architecture of input file `bwa/libbwa.a(utils.o)' is incompatible with i386 output ld: i386:x86-64 architecture of input file `bwa/libbwa.a(kthread.o)' is incompatible with i386 output ld: i386:x86-64 architecture of input file `bwa/libbwa.a(kstring.o)' is incompatible with i386 output ld: i386:x86-64 architecture of input file `bwa/libbwa.a(ksw.o)' is incompatible with i386 output ld: i386:x86-64 architecture of input file `bwa/libbwa.a(bwt.o)' is incompatible with i386 output ld: i386:x86-64 architecture of input file `bwa/libbwa.a(bntseq.o)' is incompatible with i386 output ld: bwa/libbwa.a(bwamem.o): in function `mem_approx_mapq_se': /users/u233287/scratch/code/bwapy/bwa/bwamem.c:964:(.text+0x82e7): undefined reference to `log' ld: /users/u233287/scratch/code/bwapy/bwa/bwamem.c:957:(.text+0x840c): undefined reference to `log' ld: /users/u233287/scratch/code/bwapy/bwa/bwamem.c:961:(.text+0x8449): undefined reference to `log' ld: bwa/libbwa.a(bwamem.o): in function `mem_flt_chained_seeds': /users/u233287/scratch/code/bwapy/bwa/bwamem.c:600:(.text+0x8fd1): undefined reference to `log' ld: bwa/libbwa.a(bwamem_pair.o): in function `mem_pair': /users/u233287/scratch/code/bwapy/bwa/bwamem_pair.c:218:(.text+0x412): undefined reference to `erfc' ld: /users/u233287/scratch/code/bwapy/bwa/bwamem_pair.c:218:(.text+0x41b): undefined reference to `log' ld: bwa/libbwa.a(bwamem_pair.o): in function `mem_sam_pe': /users/u233287/scratch/code/bwapy/bwa/bwamem_pair.c:295:(.text+0x192d): undefined reference to `log' ld: bwa/libbwa.a(bwamem_pair.o): in function `mem_pestat': /users/u233287/scratch/code/bwapy/bwa/bwamem_pair.c:92:(.text+0x278e): undefined reference to `sqrt' collect2: error: ld returned 1 exit status error: command '/gnu/store/xgqbv2lkh6z9x6wgyfjvcpr8paw0zd9a-gcc-11.4.0/bin/gcc' failed with exit code 1 error: in phase 'build': uncaught exception: %exception #<&invoke-error program: "python" arguments: ("-c" "import setuptools, tokenize;__file__='setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\\r\\n', '\\n');f.close();exec(compile(code, __file__, 'exec'))" "build") exit-status: 1 term-signal: #f stop-signal: #f> phase `build' failed after 0.7 seconds command "python" "-c" "import setuptools, tokenize;__file__='setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\\r\\n', '\\n');f.close();exec(compile(code, __file__, 'exec'))" "build" failed with status 1 build process 10 exited with status 256