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/aain9m7r37jlzd21kvgvrkhc2pm7mk1w-cmake-minimal-3.21.3/bin:/gnu/store/wc7lqi6kgki5qzr01g3gvriwdadjiwpc-pkg-config-0.29.2/bin:/gnu/store/q0lqlhnbg35fkhb1gmd918d05fpn4cjj-gflags-2.2.2/bin:/gnu/store/ikc2qn1h260f8mdhjz2cwndv2i7n753z-tar-1.34/bin:/gnu/store/v5l2251ck0r4n3w2rjw3l5dzyqsb9zj1-gzip-1.10/bin:/gnu/store/w6zv2mz56wyxr471q38a3cmzm4iqimy8-bzip2-1.0.8/bin:/gnu/store/72kpdqplq4nc87fm7ch47kxy3nlkzsyx-xz-5.2.5/bin:/gnu/store/jazwfsj2v41yih2yzw5nydqgdz1hgfm4-file-5.39/bin:/gnu/store/s49sxmz9g4xmzz222cay9k04ziy3qgmj-diffutils-3.8/bin:/gnu/store/m96snvbl92ivkd32giqh5f3d21bc2n5x-patch-2.7.6/bin:/gnu/store/l8l2y2dlya5rs9hfypmcb4saay7iwn0q-findutils-4.8.0/bin:/gnu/store/v45pjc1yqmy59j9ff913p3ywn9qk4lqx-gawk-5.1.0/bin:/gnu/store/7cddr79rydhc1m4hxr921mq17pz1jj3z-sed-4.8/bin:/gnu/store/ldkm5jwql0qsrfh3ax6rljjsrk0jzv7z-grep-3.6/bin:/gnu/store/25gv43v5rm05i26z39ajrd6nsxa5r461-coreutils-8.32/bin:/gnu/store/l8kxrs01lll3pzjrd590p45l8k045q6q-make-4.3/bin:/gnu/store/vx6vfbmmazvfi7vp8xyjn2mcyylvw9gn-bash-minimal-5.1.8/bin:/gnu/store/k452f0r5bk6n0cbsf5ndxbp5qcf6bpfw-ld-wrapper-0/bin:/gnu/store/6mqcv52gwn2dnbislgv9k99525mzmrrs-binutils-2.37/bin:/gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin:/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/bin:/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/sbin'
environment variable `CMAKE_PREFIX_PATH' set to `/gnu/store/aain9m7r37jlzd21kvgvrkhc2pm7mk1w-cmake-minimal-3.21.3/:/gnu/store/wc7lqi6kgki5qzr01g3gvriwdadjiwpc-pkg-config-0.29.2/:/gnu/store/2vsqj5xkpr6jw5bfw7q9y70kj9a02cbl-concurrentqueue-1.0.3/:/gnu/store/q0lqlhnbg35fkhb1gmd918d05fpn4cjj-gflags-2.2.2/:/gnu/store/rx3yfw1m7ibx7fm2z3c4bl9sa683swy0-rapidjson-1.1.0/:/gnu/store/5v3fp2v0bb7kk8rbkfw38ri2wf7cn34w-rocksdb-6.26.1/:/gnu/store/2i0zpa5w320y8m4zbqk1va8vs6dbawv0-zlib-1.2.11/:/gnu/store/ikc2qn1h260f8mdhjz2cwndv2i7n753z-tar-1.34/:/gnu/store/v5l2251ck0r4n3w2rjw3l5dzyqsb9zj1-gzip-1.10/:/gnu/store/w6zv2mz56wyxr471q38a3cmzm4iqimy8-bzip2-1.0.8/:/gnu/store/72kpdqplq4nc87fm7ch47kxy3nlkzsyx-xz-5.2.5/:/gnu/store/jazwfsj2v41yih2yzw5nydqgdz1hgfm4-file-5.39/:/gnu/store/s49sxmz9g4xmzz222cay9k04ziy3qgmj-diffutils-3.8/:/gnu/store/m96snvbl92ivkd32giqh5f3d21bc2n5x-patch-2.7.6/:/gnu/store/l8l2y2dlya5rs9hfypmcb4saay7iwn0q-findutils-4.8.0/:/gnu/store/v45pjc1yqmy59j9ff913p3ywn9qk4lqx-gawk-5.1.0/:/gnu/store/7cddr79rydhc1m4hxr921mq17pz1jj3z-sed-4.8/:/gnu/store/ldkm5jwql0qsrfh3ax6rljjsrk0jzv7z-grep-3.6/:/gnu/store/25gv43v5rm05i26z39ajrd6nsxa5r461-coreutils-8.32/:/gnu/store/l8kxrs01lll3pzjrd590p45l8k045q6q-make-4.3/:/gnu/store/vx6vfbmmazvfi7vp8xyjn2mcyylvw9gn-bash-minimal-5.1.8/:/gnu/store/k452f0r5bk6n0cbsf5ndxbp5qcf6bpfw-ld-wrapper-0/:/gnu/store/6mqcv52gwn2dnbislgv9k99525mzmrrs-binutils-2.37/:/gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/:/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/:/gnu/store/3ywv7s8d38rgcq7ljmc1s084358a2m3h-glibc-2.33-static/:/gnu/store/0brdikxqk59hdr47qabcm3sya001d8vf-glibc-utf8-locales-2.33/:/gnu/store/99a2njzz22dkzd8pz75fsi5nbgv9ww0x-linux-libre-headers-5.10.35/'
environment variable `SSL_CERT_DIR' unset
environment variable `SSL_CERT_FILE' unset
environment variable `PKG_CONFIG_PATH' set to `/gnu/store/q0lqlhnbg35fkhb1gmd918d05fpn4cjj-gflags-2.2.2/lib/pkgconfig:/gnu/store/rx3yfw1m7ibx7fm2z3c4bl9sa683swy0-rapidjson-1.1.0/lib/pkgconfig:/gnu/store/2i0zpa5w320y8m4zbqk1va8vs6dbawv0-zlib-1.2.11/lib/pkgconfig:/gnu/store/72kpdqplq4nc87fm7ch47kxy3nlkzsyx-xz-5.2.5/lib/pkgconfig:/gnu/store/jazwfsj2v41yih2yzw5nydqgdz1hgfm4-file-5.39/lib/pkgconfig'
environment variable `BASH_LOADABLES_PATH' unset
environment variable `C_INCLUDE_PATH' set to `/gnu/store/2vsqj5xkpr6jw5bfw7q9y70kj9a02cbl-concurrentqueue-1.0.3/include:/gnu/store/q0lqlhnbg35fkhb1gmd918d05fpn4cjj-gflags-2.2.2/include:/gnu/store/rx3yfw1m7ibx7fm2z3c4bl9sa683swy0-rapidjson-1.1.0/include:/gnu/store/5v3fp2v0bb7kk8rbkfw38ri2wf7cn34w-rocksdb-6.26.1/include:/gnu/store/2i0zpa5w320y8m4zbqk1va8vs6dbawv0-zlib-1.2.11/include:/gnu/store/w6zv2mz56wyxr471q38a3cmzm4iqimy8-bzip2-1.0.8/include:/gnu/store/72kpdqplq4nc87fm7ch47kxy3nlkzsyx-xz-5.2.5/include:/gnu/store/jazwfsj2v41yih2yzw5nydqgdz1hgfm4-file-5.39/include:/gnu/store/v45pjc1yqmy59j9ff913p3ywn9qk4lqx-gawk-5.1.0/include:/gnu/store/l8kxrs01lll3pzjrd590p45l8k045q6q-make-4.3/include:/gnu/store/6mqcv52gwn2dnbislgv9k99525mzmrrs-binutils-2.37/include:/gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/include:/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/include:/gnu/store/99a2njzz22dkzd8pz75fsi5nbgv9ww0x-linux-libre-headers-5.10.35/include'
environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/2vsqj5xkpr6jw5bfw7q9y70kj9a02cbl-concurrentqueue-1.0.3/include:/gnu/store/q0lqlhnbg35fkhb1gmd918d05fpn4cjj-gflags-2.2.2/include:/gnu/store/rx3yfw1m7ibx7fm2z3c4bl9sa683swy0-rapidjson-1.1.0/include:/gnu/store/5v3fp2v0bb7kk8rbkfw38ri2wf7cn34w-rocksdb-6.26.1/include:/gnu/store/2i0zpa5w320y8m4zbqk1va8vs6dbawv0-zlib-1.2.11/include:/gnu/store/w6zv2mz56wyxr471q38a3cmzm4iqimy8-bzip2-1.0.8/include:/gnu/store/72kpdqplq4nc87fm7ch47kxy3nlkzsyx-xz-5.2.5/include:/gnu/store/jazwfsj2v41yih2yzw5nydqgdz1hgfm4-file-5.39/include:/gnu/store/v45pjc1yqmy59j9ff913p3ywn9qk4lqx-gawk-5.1.0/include:/gnu/store/l8kxrs01lll3pzjrd590p45l8k045q6q-make-4.3/include:/gnu/store/6mqcv52gwn2dnbislgv9k99525mzmrrs-binutils-2.37/include:/gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/include/c++:/gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/include:/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/include:/gnu/store/99a2njzz22dkzd8pz75fsi5nbgv9ww0x-linux-libre-headers-5.10.35/include'
environment variable `LIBRARY_PATH' set to `/gnu/store/q0lqlhnbg35fkhb1gmd918d05fpn4cjj-gflags-2.2.2/lib:/gnu/store/rx3yfw1m7ibx7fm2z3c4bl9sa683swy0-rapidjson-1.1.0/lib:/gnu/store/5v3fp2v0bb7kk8rbkfw38ri2wf7cn34w-rocksdb-6.26.1/lib:/gnu/store/2i0zpa5w320y8m4zbqk1va8vs6dbawv0-zlib-1.2.11/lib:/gnu/store/w6zv2mz56wyxr471q38a3cmzm4iqimy8-bzip2-1.0.8/lib:/gnu/store/72kpdqplq4nc87fm7ch47kxy3nlkzsyx-xz-5.2.5/lib:/gnu/store/jazwfsj2v41yih2yzw5nydqgdz1hgfm4-file-5.39/lib:/gnu/store/v45pjc1yqmy59j9ff913p3ywn9qk4lqx-gawk-5.1.0/lib:/gnu/store/6mqcv52gwn2dnbislgv9k99525mzmrrs-binutils-2.37/lib:/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/lib:/gnu/store/3ywv7s8d38rgcq7ljmc1s084358a2m3h-glibc-2.33-static/lib:/gnu/store/0brdikxqk59hdr47qabcm3sya001d8vf-glibc-utf8-locales-2.33/lib'
environment variable `GUIX_LOCPATH' set to `/gnu/store/0brdikxqk59hdr47qabcm3sya001d8vf-glibc-utf8-locales-2.33/lib/locale'
phase `set-paths' succeeded after 0.0 seconds
starting phase `install-locale'
using 'en_US.utf8' locale for category "LC_ALL"
phase `install-locale' succeeded after 0.0 seconds
starting phase `unpack'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/.gitignore' -> `./.gitignore'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/.travis.yml' -> `./.travis.yml'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/AUTHORS' -> `./AUTHORS'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/BUILD.md' -> `./BUILD.md'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/CMakeLists.txt' -> `./CMakeLists.txt'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/COPYING' -> `./COPYING'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/COPYING.LESSER.txt' -> `./COPYING.LESSER.txt'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/ChangeLog' -> `./ChangeLog'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/Dockerfile' -> `./Dockerfile'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/LICENSE.LESSER.txt' -> `./LICENSE.LESSER.txt'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/LICENSE.txt' -> `./LICENSE.txt'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/README.md' -> `./README.md'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/tests/sortmerna/CMakeLists.txt' -> `./tests/sortmerna/CMakeLists.txt'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/tests/sortmerna/kvdb.cpp' -> `./tests/sortmerna/kvdb.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/tests/sortmerna/main.cpp' -> `./tests/sortmerna/main.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/.dirstamp' -> `./src/.dirstamp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/winapi/CMakeLists.txt' -> `./src/winapi/CMakeLists.txt'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/winapi/unistd.cpp' -> `./src/winapi/unistd.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/winapi/wintime.cpp' -> `./src/winapi/wintime.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/winapi/include/unistd.h' -> `./src/winapi/include/unistd.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/winapi/include/sys/time.h' -> `./src/winapi/include/sys/time.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/util/build_version.cpp.in' -> `./src/util/build_version.cpp.in'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/CMakeLists.txt' -> `./src/sortmerna/CMakeLists.txt'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/alignment.cpp' -> `./src/sortmerna/alignment.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/bitvector.cpp' -> `./src/sortmerna/bitvector.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/cmd.cpp' -> `./src/sortmerna/cmd.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/index.cpp' -> `./src/sortmerna/index.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/indexdb.cpp' -> `./src/sortmerna/indexdb.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/izlib.cpp' -> `./src/sortmerna/izlib.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/kseq_load.cpp' -> `./src/sortmerna/kseq_load.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/kvdb.cpp' -> `./src/sortmerna/kvdb.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/main.cpp' -> `./src/sortmerna/main.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/minoccur.cpp' -> `./src/sortmerna/minoccur.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/options.cpp' -> `./src/sortmerna/options.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/otumap.cpp' -> `./src/sortmerna/otumap.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/output.cpp' -> `./src/sortmerna/output.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/paralleltraversal.cpp' -> `./src/sortmerna/paralleltraversal.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/processor.cpp' -> `./src/sortmerna/processor.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/read.cpp' -> `./src/sortmerna/read.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/read_control.cpp' -> `./src/sortmerna/read_control.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/readfeed.cpp' -> `./src/sortmerna/readfeed.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/readstats.cpp' -> `./src/sortmerna/readstats.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/references.cpp' -> `./src/sortmerna/references.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/refstats.cpp' -> `./src/sortmerna/refstats.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/report.cpp' -> `./src/sortmerna/report.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/report_biom.cpp' -> `./src/sortmerna/report_biom.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/report_blast.cpp' -> `./src/sortmerna/report_blast.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/report_denovo.cpp' -> `./src/sortmerna/report_denovo.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/report_fastx.cpp' -> `./src/sortmerna/report_fastx.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/report_fx_base.cpp' -> `./src/sortmerna/report_fx_base.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/report_fx_other.cpp' -> `./src/sortmerna/report_fx_other.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/report_sam.cpp' -> `./src/sortmerna/report_sam.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/ssw.c' -> `./src/sortmerna/ssw.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/ssw_example.c' -> `./src/sortmerna/ssw_example.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/summary.cpp' -> `./src/sortmerna/summary.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/traverse_bursttrie.cpp' -> `./src/sortmerna/traverse_bursttrie.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/util.cpp' -> `./src/sortmerna/util.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/sortmerna/writer.cpp' -> `./src/sortmerna/writer.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/src/.deps/.dirstamp' -> `./src/.deps/.dirstamp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/scripts/build.py' -> `./scripts/build.py'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/scripts/env.jinja.yaml' -> `./scripts/env.jinja.yaml'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/scripts/run.py' -> `./scripts/run.py'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/scripts/test.jinja.yaml' -> `./scripts/test.jinja.yaml'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/ThreadPool.hpp' -> `./include/ThreadPool.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/alignment.hpp' -> `./include/alignment.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/baserec.hpp' -> `./include/baserec.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/bitvector.hpp' -> `./include/bitvector.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/build_version.h' -> `./include/build_version.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/cmd.hpp' -> `./include/cmd.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/common' -> `./include/common'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/common.hpp' -> `./include/common.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/config.h' -> `./include/config.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/config.h.in' -> `./include/config.h.in'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/index.hpp' -> `./include/index.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/indexdb.hpp' -> `./include/indexdb.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/izlib.hpp' -> `./include/izlib.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/kseq.h' -> `./include/kseq.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/kseq_load.hpp' -> `./include/kseq_load.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/kvdb.hpp' -> `./include/kvdb.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/loadgenome.hpp' -> `./include/loadgenome.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/memcheck.h' -> `./include/memcheck.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/minoccur.hpp' -> `./include/minoccur.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/options.hpp' -> `./include/options.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/otumap.h' -> `./include/otumap.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/output.hpp' -> `./include/output.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/paralleltraversal.hpp' -> `./include/paralleltraversal.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/processor.hpp' -> `./include/processor.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/read.hpp' -> `./include/read.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/readfeed.hpp' -> `./include/readfeed.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/readfile.h' -> `./include/readfile.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/readsqueue.hpp' -> `./include/readsqueue.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/readstate.h' -> `./include/readstate.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/readstats.hpp' -> `./include/readstats.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/references.hpp' -> `./include/references.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/refstats.hpp' -> `./include/refstats.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/report.h' -> `./include/report.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/report_biom.h' -> `./include/report_biom.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/report_blast.h' -> `./include/report_blast.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/report_denovo.h' -> `./include/report_denovo.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/report_fastx.h' -> `./include/report_fastx.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/report_fx_base.h' -> `./include/report_fx_base.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/report_fx_other.h' -> `./include/report_fx_other.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/report_sam.h' -> `./include/report_sam.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/ssw.h' -> `./include/ssw.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/ssw.hpp' -> `./include/ssw.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/stamp-h1' -> `./include/stamp-h1'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/summary.hpp' -> `./include/summary.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/traverse_bursttrie.hpp' -> `./include/traverse_bursttrie.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/triestats.hpp' -> `./include/triestats.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/version.h' -> `./include/version.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/include/writer.hpp' -> `./include/writer.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/docs/img/smr_1_arch.graphml' -> `./docs/img/smr_1_arch.graphml'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/docs/img/smr_1_arch.svg' -> `./docs/img/smr_1_arch.svg'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/docs/img/smr_3_processing_pipeline.graphml' -> `./docs/img/smr_3_processing_pipeline.graphml'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/docs/img/smr_3_processing_pipeline.svg' -> `./docs/img/smr_3_processing_pipeline.svg'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/docs/img/algorithm/min_lis.png' -> `./docs/img/algorithm/min_lis.png'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/docs/img/algorithm/min_lis_small.png' -> `./docs/img/algorithm/min_lis_small.png'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/empty_file.fasta' -> `./data/empty_file.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/gg_13_8_ref_set.fasta' -> `./data/gg_13_8_ref_set.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/illumina_GQ099317.fasta' -> `./data/illumina_GQ099317.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/ref_GQ099317_forward_and_rc.fasta' -> `./data/ref_GQ099317_forward_and_rc.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/ref_short_seqs.fasta' -> `./data/ref_short_seqs.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/set2_environmental_study_550_amplicon.fasta' -> `./data/set2_environmental_study_550_amplicon.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/set2_environmental_study_550_amplicon.fasta.gz' -> `./data/set2_environmental_study_550_amplicon.fasta.gz'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/set4_mate_pairs_metatranscriptomics.fastq' -> `./data/set4_mate_pairs_metatranscriptomics.fastq'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/set4_mate_pairs_metatranscriptomics_1.fastq' -> `./data/set4_mate_pairs_metatranscriptomics_1.fastq'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/set4_mate_pairs_metatranscriptomics_1.fastq.gz' -> `./data/set4_mate_pairs_metatranscriptomics_1.fastq.gz'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/set4_mate_pairs_metatranscriptomics_2.fastq' -> `./data/set4_mate_pairs_metatranscriptomics_2.fastq'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/set4_mate_pairs_metatranscriptomics_2.fastq.gz' -> `./data/set4_mate_pairs_metatranscriptomics_2.fastq.gz'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/set5_simulated_amplicon_silva_bac_16s.fasta' -> `./data/set5_simulated_amplicon_silva_bac_16s.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/set7_arc_bac_16S_database_match.fasta' -> `./data/set7_arc_bac_16S_database_match.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/silva-arc-16s-database-id95.fasta' -> `./data/silva-arc-16s-database-id95.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/silva-bac-16s-database-id85.fasta' -> `./data/silva-bac-16s-database-id85.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/t0_expected_alignment.blast' -> `./data/t0_expected_alignment.blast'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/test_read.fasta' -> `./data/test_read.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/test_ref.fasta' -> `./data/test_ref.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/rRNA_databases/README.txt' -> `./data/rRNA_databases/README.txt'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/rRNA_databases/rfam-5.8s-database-id98.fasta' -> `./data/rRNA_databases/rfam-5.8s-database-id98.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/rRNA_databases/rfam-5s-database-id98.fasta' -> `./data/rRNA_databases/rfam-5s-database-id98.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/rRNA_databases/silva-arc-16s-id95.fasta' -> `./data/rRNA_databases/silva-arc-16s-id95.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/rRNA_databases/silva-arc-23s-id98.fasta' -> `./data/rRNA_databases/silva-arc-23s-id98.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/rRNA_databases/silva-bac-16s-id90.fasta' -> `./data/rRNA_databases/silva-bac-16s-id90.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/rRNA_databases/silva-bac-23s-id98.fasta' -> `./data/rRNA_databases/silva-bac-23s-id98.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/rRNA_databases/silva-euk-18s-id95.fasta' -> `./data/rRNA_databases/silva-euk-18s-id95.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/rRNA_databases/silva-euk-28s-id98.fasta' -> `./data/rRNA_databases/silva-euk-28s-id98.fasta'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/rRNA_databases/silva_ids_acc_tax.tar.gz' -> `./data/rRNA_databases/silva_ids_acc_tax.tar.gz'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/rRNA_databases/scripts/edit_U_to_T_rna.py' -> `./data/rRNA_databases/scripts/edit_U_to_T_rna.py'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/rRNA_databases/scripts/generate_databases.sh' -> `./data/rRNA_databases/scripts/generate_databases.sh'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/data/rRNA_databases/scripts/hmmer_clean.sh' -> `./data/rRNA_databases/scripts/hmmer_clean.sh'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/cmake/sortmernaConfig.cmake.in' -> `./cmake/sortmernaConfig.cmake.in'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/cmake/modules/FindRapidJson.cmake' -> `./cmake/modules/FindRapidJson.cmake'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/cmake/modules/smr_utils.cmake' -> `./cmake/modules/smr_utils.cmake'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/CMakeLists.txt' -> `./3rdparty/cmph/CMakeLists.txt'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/bdz.c' -> `./3rdparty/cmph/bdz.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/bdz.h' -> `./3rdparty/cmph/bdz.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/bdz_ph.c' -> `./3rdparty/cmph/bdz_ph.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/bdz_ph.h' -> `./3rdparty/cmph/bdz_ph.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/bdz_structs.h' -> `./3rdparty/cmph/bdz_structs.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/bdz_structs_ph.h' -> `./3rdparty/cmph/bdz_structs_ph.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/bitbool.h' -> `./3rdparty/cmph/bitbool.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/bmz.c' -> `./3rdparty/cmph/bmz.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/bmz.h' -> `./3rdparty/cmph/bmz.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/bmz8.c' -> `./3rdparty/cmph/bmz8.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/bmz8.h' -> `./3rdparty/cmph/bmz8.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/bmz8_structs.h' -> `./3rdparty/cmph/bmz8_structs.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/bmz_structs.h' -> `./3rdparty/cmph/bmz_structs.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/brz.c' -> `./3rdparty/cmph/brz.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/brz.h' -> `./3rdparty/cmph/brz.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/brz_structs.h' -> `./3rdparty/cmph/brz_structs.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/buffer_entry.c' -> `./3rdparty/cmph/buffer_entry.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/buffer_entry.h' -> `./3rdparty/cmph/buffer_entry.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/buffer_manager.c' -> `./3rdparty/cmph/buffer_manager.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/buffer_manager.h' -> `./3rdparty/cmph/buffer_manager.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/chd.c' -> `./3rdparty/cmph/chd.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/chd.h' -> `./3rdparty/cmph/chd.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/chd_ph.c' -> `./3rdparty/cmph/chd_ph.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/chd_ph.h' -> `./3rdparty/cmph/chd_ph.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/chd_structs.h' -> `./3rdparty/cmph/chd_structs.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/chd_structs_ph.h' -> `./3rdparty/cmph/chd_structs_ph.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/chm.c' -> `./3rdparty/cmph/chm.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/chm.h' -> `./3rdparty/cmph/chm.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/chm_structs.h' -> `./3rdparty/cmph/chm_structs.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/cmph.c' -> `./3rdparty/cmph/cmph.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/cmph.h' -> `./3rdparty/cmph/cmph.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/cmph_structs.c' -> `./3rdparty/cmph/cmph_structs.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/cmph_structs.h' -> `./3rdparty/cmph/cmph_structs.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/cmph_time.h' -> `./3rdparty/cmph/cmph_time.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/cmph_types.h' -> `./3rdparty/cmph/cmph_types.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/compressed_rank.c' -> `./3rdparty/cmph/compressed_rank.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/compressed_rank.h' -> `./3rdparty/cmph/compressed_rank.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/compressed_seq.c' -> `./3rdparty/cmph/compressed_seq.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/compressed_seq.h' -> `./3rdparty/cmph/compressed_seq.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/debug.h' -> `./3rdparty/cmph/debug.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/fch.c' -> `./3rdparty/cmph/fch.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/fch.h' -> `./3rdparty/cmph/fch.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/fch_buckets.c' -> `./3rdparty/cmph/fch_buckets.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/fch_buckets.h' -> `./3rdparty/cmph/fch_buckets.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/fch_structs.h' -> `./3rdparty/cmph/fch_structs.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/graph.c' -> `./3rdparty/cmph/graph.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/graph.h' -> `./3rdparty/cmph/graph.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/hash.c' -> `./3rdparty/cmph/hash.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/hash.h' -> `./3rdparty/cmph/hash.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/hash_state.h' -> `./3rdparty/cmph/hash_state.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/jenkins_hash.c' -> `./3rdparty/cmph/jenkins_hash.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/jenkins_hash.h' -> `./3rdparty/cmph/jenkins_hash.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/miller_rabin.c' -> `./3rdparty/cmph/miller_rabin.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/miller_rabin.h' -> `./3rdparty/cmph/miller_rabin.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/select.c' -> `./3rdparty/cmph/select.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/select.h' -> `./3rdparty/cmph/select.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/select_lookup_tables.h' -> `./3rdparty/cmph/select_lookup_tables.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/vqueue.c' -> `./3rdparty/cmph/vqueue.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/vqueue.h' -> `./3rdparty/cmph/vqueue.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/vstack.c' -> `./3rdparty/cmph/vstack.c'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/cmph/vstack.h' -> `./3rdparty/cmph/vstack.h'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/CMakeLists.txt' -> `./3rdparty/alp/CMakeLists.txt'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_approx.hpp' -> `./3rdparty/alp/njn_approx.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_doubletype.hpp' -> `./3rdparty/alp/njn_doubletype.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_dynprogprob.cpp' -> `./3rdparty/alp/njn_dynprogprob.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_dynprogprob.hpp' -> `./3rdparty/alp/njn_dynprogprob.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_dynprogproblim.cpp' -> `./3rdparty/alp/njn_dynprogproblim.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_dynprogproblim.hpp' -> `./3rdparty/alp/njn_dynprogproblim.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_dynprogprobproto.cpp' -> `./3rdparty/alp/njn_dynprogprobproto.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_dynprogprobproto.hpp' -> `./3rdparty/alp/njn_dynprogprobproto.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_function.hpp' -> `./3rdparty/alp/njn_function.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_integer.hpp' -> `./3rdparty/alp/njn_integer.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_ioutil.cpp' -> `./3rdparty/alp/njn_ioutil.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_ioutil.hpp' -> `./3rdparty/alp/njn_ioutil.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_localmaxstat.cpp' -> `./3rdparty/alp/njn_localmaxstat.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_localmaxstat.hpp' -> `./3rdparty/alp/njn_localmaxstat.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_localmaxstatmatrix.cpp' -> `./3rdparty/alp/njn_localmaxstatmatrix.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_localmaxstatmatrix.hpp' -> `./3rdparty/alp/njn_localmaxstatmatrix.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_localmaxstatutil.cpp' -> `./3rdparty/alp/njn_localmaxstatutil.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_localmaxstatutil.hpp' -> `./3rdparty/alp/njn_localmaxstatutil.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_matrix.hpp' -> `./3rdparty/alp/njn_matrix.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_memutil.hpp' -> `./3rdparty/alp/njn_memutil.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_random.cpp' -> `./3rdparty/alp/njn_random.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_random.hpp' -> `./3rdparty/alp/njn_random.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_root.hpp' -> `./3rdparty/alp/njn_root.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_uniform.hpp' -> `./3rdparty/alp/njn_uniform.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/njn_vector.hpp' -> `./3rdparty/alp/njn_vector.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/sls_alignment_evaluer.cpp' -> `./3rdparty/alp/sls_alignment_evaluer.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/sls_alignment_evaluer.hpp' -> `./3rdparty/alp/sls_alignment_evaluer.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/sls_alp.cpp' -> `./3rdparty/alp/sls_alp.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/sls_alp.hpp' -> `./3rdparty/alp/sls_alp.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/sls_alp_data.cpp' -> `./3rdparty/alp/sls_alp_data.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/sls_alp_data.hpp' -> `./3rdparty/alp/sls_alp_data.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/sls_alp_regression.cpp' -> `./3rdparty/alp/sls_alp_regression.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/sls_alp_regression.hpp' -> `./3rdparty/alp/sls_alp_regression.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/sls_alp_sim.cpp' -> `./3rdparty/alp/sls_alp_sim.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/sls_alp_sim.hpp' -> `./3rdparty/alp/sls_alp_sim.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/sls_basic.cpp' -> `./3rdparty/alp/sls_basic.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/sls_basic.hpp' -> `./3rdparty/alp/sls_basic.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/sls_normal_distr_array.hpp' -> `./3rdparty/alp/sls_normal_distr_array.hpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/sls_pvalues.cpp' -> `./3rdparty/alp/sls_pvalues.cpp'
`/gnu/store/rw9rnxy5x3ynkz4hx8b5cckcjrrcgcyb-sortmerna-4.3.4-checkout/3rdparty/alp/sls_pvalues.hpp' -> `./3rdparty/alp/sls_pvalues.hpp'
phase `unpack' succeeded after 0.3 seconds
starting phase `find-concurrentqueue-headers'
phase `find-concurrentqueue-headers' 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: ./data/rRNA_databases/scripts/generate_databases.sh: changing `/bin/bash' to `/gnu/store/vx6vfbmmazvfi7vp8xyjn2mcyylvw9gn-bash-minimal-5.1.8/bin/bash'
patch-shebang: ./data/rRNA_databases/scripts/hmmer_clean.sh: changing `/bin/bash' to `/gnu/store/vx6vfbmmazvfi7vp8xyjn2mcyylvw9gn-bash-minimal-5.1.8/bin/bash'
phase `patch-source-shebangs' succeeded after 0.0 seconds
starting phase `configure'
source directory: "/tmp/guix-build-sortmerna-4.3.4.drv-0/source" (relative from build: "../source")
build directory: "/tmp/guix-build-sortmerna-4.3.4.drv-0/build"
running 'cmake' with arguments ("../source" "-DCMAKE_BUILD_TYPE=RelWithDebInfo" "-DCMAKE_INSTALL_PREFIX=/gnu/store/ngqb6mvsm4816dm6iqvfdpjyh84myhly-sortmerna-4.3.4" "-DCMAKE_INSTALL_LIBDIR=lib" "-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE" "-DCMAKE_INSTALL_RPATH=/gnu/store/ngqb6mvsm4816dm6iqvfdpjyh84myhly-sortmerna-4.3.4/lib" "-DCMAKE_VERBOSE_MAKEFILE=ON" "-DWITH_TESTS=ON" "-DCMAKE_CXX_FLAGS=-pthread" "-DZLIB_STATIC=OFF" "-DROCKSDB_STATIC=OFF" "-DPORTABLE=OFF" "-DROCKSDB_HOME=/gnu/store/5v3fp2v0bb7kk8rbkfw38ri2wf7cn34w-rocksdb-6.26.1" "-DRAPIDJSON_HOME=/gnu/store/rx3yfw1m7ibx7fm2z3c4bl9sa683swy0-rapidjson-1.1.0" "-DRapidJson_DIR=/gnu/store/rx3yfw1m7ibx7fm2z3c4bl9sa683swy0-rapidjson-1.1.0/lib/cmake/RapidJSON" "-DRapidJSON_INCLUDE_DIR=/gnu/store/rx3yfw1m7ibx7fm2z3c4bl9sa683swy0-rapidjson-1.1.0/include")
-- The CXX compiler identification is GNU 10.3.0
-- The C compiler identification is GNU 10.3.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Could NOT find Git (missing: GIT_EXECUTABLE) 
CMAKE_CXX_COMPILER_ID = GNU
CMAKE_CONFIGURATION_TYPES = 
CMAKE_HOST_SYSTEM_NAME = Linux
CMAKE_HOST_SYSTEM_VERSION = 5.14.21-gnu
CMAKE_HOST_SYSTEM = Linux-5.14.21-gnu
PROJECT_BINARY_DIR = /tmp/guix-build-sortmerna-4.3.4.drv-0/build
CMAKE_BINARY_DIR = /tmp/guix-build-sortmerna-4.3.4.drv-0/build
CMAKE_CURRENT_BINARY_DIR = /tmp/guix-build-sortmerna-4.3.4.drv-0/build
RUNTIME_OUTPUT_DIRECTORY_RELEASE = 
CMAKE_CURRENT_LIST_DIR: /tmp/guix-build-sortmerna-4.3.4.drv-0/source
CMAKE_CXX_FLAGS_DEBUG: -g
CMAKE_C_FLAGS_DEBUG: -g
CMAKE_CXX_FLAGS_RELEASE: -O3 -DNDEBUG
EXTRA_CXX_FLAGS_RELEASE: 
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
RocksDB package OK
RocksDB::rocksdb-shared LOCATION: /gnu/store/5v3fp2v0bb7kk8rbkfw38ri2wf7cn34w-rocksdb-6.26.1/lib/librocksdb.so.6.26.1
RocksDB::rocksdb-shared LOCATION_DEBUG: /gnu/store/5v3fp2v0bb7kk8rbkfw38ri2wf7cn34w-rocksdb-6.26.1/lib/librocksdb.so.6.26.1
RocksDB::rocksdb-shared LOCATION_DEBUG: lib-NOTFOUND
RocksDB::rocksdb-shared IMPORTED_CONFIGURATIONS: RELWITHDEBINFO
RocksDB::rocksdb-shared IMPORTED_IMPLIB: lib-NOTFOUND
RocksDB::rocksdb LIBRARY_OUTPUT_NAME: lib-NOTFOUND
Using Shared RocksDB lib
RocksDB::rocksdb-shared transitive link dependencies: 
rocksdb transitive link dependencies AFTER modification: $<LINK_ONLY:gflags::gflags_shared>;$<LINK_ONLY:-lpthread>
-- Found ZLIB: /gnu/store/2i0zpa5w320y8m4zbqk1va8vs6dbawv0-zlib-1.2.11/lib/libz.so (found version "1.2.11") 
RapidJson_DIR: /gnu/store/rx3yfw1m7ibx7fm2z3c4bl9sa683swy0-rapidjson-1.1.0/lib/cmake/RapidJSON
RapidJSON_INCLUDE_DIR: /gnu/store/rx3yfw1m7ibx7fm2z3c4bl9sa683swy0-rapidjson-1.1.0/include
version_line: SET(PACKAGE_VERSION "1.1.0")
CMAKE_MATCH_0: 1.1.0
-- Found RapidJSON: /gnu/store/rx3yfw1m7ibx7fm2z3c4bl9sa683swy0-rapidjson-1.1.0/include (found version "1.1.0") 
RapidJSON_FOUND: TRUE
RapidJSON_VERSION: 1.1.0
RapidJson_DIR: /gnu/store/rx3yfw1m7ibx7fm2z3c4bl9sa683swy0-rapidjson-1.1.0/lib/cmake/RapidJSON
RapidJSON_INCLUDE_DIR: /gnu/store/rx3yfw1m7ibx7fm2z3c4bl9sa683swy0-rapidjson-1.1.0/include
version_line: SET(PACKAGE_VERSION "1.1.0")
CMAKE_MATCH_0: 1.1.0
CMake Warning (dev) at /gnu/store/aain9m7r37jlzd21kvgvrkhc2pm7mk1w-cmake-minimal-3.21.3/share/cmake-3.21/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
  The package name passed to `find_package_handle_standard_args` (RapidJSON)
  does not match the name of the calling package (RapidJson).  This can lead
  to problems in calling code that expects `find_package` result variables
  (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  cmake/modules/FindRapidJson.cmake:43 (find_package_handle_standard_args)
  src/sortmerna/CMakeLists.txt:76 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

RapidJSON_FOUND: TRUE
RapidJSON_VERSION: 1.1.0
SMR Objects transitive link dependencies: alp;RocksDB::rocksdb-shared;RapidJSON::RapidJSON;ZLIB::ZLIB
SMR Objects COMPILE_OPT: COMPILE_OPT-NOTFOUND  COMPILE_FLG: COMPILE_FLG-NOTFOUND
tests PROJECT_NAME = tests
tests PROJECT_BINARY_DIR = /tmp/guix-build-sortmerna-4.3.4.drv-0/build/tests/sortmerna
tests CMAKE_BUILD_TYPE = RelWithDebInfo
tests CMAKE_CFG_INTDIR = .
package_config_destination: /gnu/store/ngqb6mvsm4816dm6iqvfdpjyh84myhly-sortmerna-4.3.4/cmake/sortmerna
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_INSTALL_LIBDIR


-- Build files have been written to: /tmp/guix-build-sortmerna-4.3.4.drv-0/build
phase `configure' succeeded after 1.2 seconds
starting phase `patch-generated-file-shebangs'
phase `patch-generated-file-shebangs' succeeded after 0.0 seconds
starting phase `build'
/gnu/store/aain9m7r37jlzd21kvgvrkhc2pm7mk1w-cmake-minimal-3.21.3/bin/cmake -S/tmp/guix-build-sortmerna-4.3.4.drv-0/source -B/tmp/guix-build-sortmerna-4.3.4.drv-0/build --check-build-system CMakeFiles/Makefile.cmake 0
/gnu/store/aain9m7r37jlzd21kvgvrkhc2pm7mk1w-cmake-minimal-3.21.3/bin/cmake -E cmake_progress_start /tmp/guix-build-sortmerna-4.3.4.drv-0/build/CMakeFiles /tmp/guix-build-sortmerna-4.3.4.drv-0/build//CMakeFiles/progress.marks
make  -f CMakeFiles/Makefile2 all
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make[2]: Entering directory '/tmp/guix-build-sortmerna-4.3.4.drv-0/build'
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build && /gnu/store/aain9m7r37jlzd21kvgvrkhc2pm7mk1w-cmake-minimal-3.21.3/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/guix-build-sortmerna-4.3.4.drv-0/source /tmp/guix-build-sortmerna-4.3.4.drv-0/source /tmp/guix-build-sortmerna-4.3.4.drv-0/build /tmp/guix-build-sortmerna-4.3.4.drv-0/build /tmp/guix-build-sortmerna-4.3.4.drv-0/build/CMakeFiles/build_version.dir/DependInfo.cmake --color=
make[2]: Entering directory '/tmp/guix-build-sortmerna-4.3.4.drv-0/build'
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build && /gnu/store/aain9m7r37jlzd21kvgvrkhc2pm7mk1w-cmake-minimal-3.21.3/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/guix-build-sortmerna-4.3.4.drv-0/source /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp /tmp/guix-build-sortmerna-4.3.4.drv-0/build /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/alp /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/alp/CMakeFiles/alp.dir/DependInfo.cmake --color=
make[2]: Entering directory '/tmp/guix-build-sortmerna-4.3.4.drv-0/build'
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build && /gnu/store/aain9m7r37jlzd21kvgvrkhc2pm7mk1w-cmake-minimal-3.21.3/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/guix-build-sortmerna-4.3.4.drv-0/source /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph /tmp/guix-build-sortmerna-4.3.4.drv-0/build /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph/CMakeFiles/cmph.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/tmp/guix-build-sortmerna-4.3.4.drv-0/build'
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make[2]: Leaving directory '/tmp/guix-build-sortmerna-4.3.4.drv-0/build'
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make  -f 3rdparty/alp/CMakeFiles/alp.dir/build.make 3rdparty/alp/CMakeFiles/alp.dir/build
make[2]: Entering directory '/tmp/guix-build-sortmerna-4.3.4.drv-0/build'
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make[2]: Entering directory '/tmp/guix-build-sortmerna-4.3.4.drv-0/build'
[  4%] Building CXX object CMakeFiles/build_version.dir/build_version.cpp.o
[  4%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o
[  4%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o
[  5%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o
[  6%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o
[  8%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o
[  9%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o
/gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -pthread -O2 -g -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/build_version.dir/build_version.cpp.o -MF CMakeFiles/build_version.dir/build_version.cpp.o.d -o CMakeFiles/build_version.dir/build_version.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/build/build_version.cpp
[ 10%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o
[ 13%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_entry.c.o
[ 13%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o -MF CMakeFiles/cmph.dir/bdz_ph.c.o.d -o CMakeFiles/cmph.dir/bdz_ph.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/bdz_ph.c
[ 14%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o
[ 16%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o
[ 17%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o
[ 18%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o
[ 20%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/alp && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -O2 -g -DNDEBUG -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o -MF CMakeFiles/alp.dir/njn_dynprogprob.cpp.o.d -o CMakeFiles/alp.dir/njn_dynprogprob.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp/njn_dynprogprob.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o -MF CMakeFiles/cmph.dir/bmz.c.o.d -o CMakeFiles/cmph.dir/bmz.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/bmz.c
[ 21%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chd_ph.c.o
[ 22%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chd.c.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o -MF CMakeFiles/cmph.dir/bmz8.c.o.d -o CMakeFiles/cmph.dir/bmz8.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/bmz8.c
[ 24%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o -MF CMakeFiles/cmph.dir/brz.c.o.d -o CMakeFiles/cmph.dir/brz.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/brz.c
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/alp && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -O2 -g -DNDEBUG -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o -MF CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o.d -o CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp/njn_dynprogproblim.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_entry.c.o -MF CMakeFiles/cmph.dir/buffer_entry.c.o.d -o CMakeFiles/cmph.dir/buffer_entry.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/buffer_entry.c
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/alp && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -O2 -g -DNDEBUG -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o -MF CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o.d -o CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp/njn_dynprogprobproto.cpp
[ 25%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/alp && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -O2 -g -DNDEBUG -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o -MF CMakeFiles/alp.dir/njn_ioutil.cpp.o.d -o CMakeFiles/alp.dir/njn_ioutil.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp/njn_ioutil.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/alp && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -O2 -g -DNDEBUG -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o -MF CMakeFiles/alp.dir/njn_localmaxstat.cpp.o.d -o CMakeFiles/alp.dir/njn_localmaxstat.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp/njn_localmaxstat.cpp
[ 27%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o -MF CMakeFiles/cmph.dir/buffer_manager.c.o.d -o CMakeFiles/cmph.dir/buffer_manager.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/buffer_manager.c
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/chd.c.o -MF CMakeFiles/cmph.dir/chd.c.o.d -o CMakeFiles/cmph.dir/chd.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/chd.c
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/alp && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -O2 -g -DNDEBUG -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o -MF CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o.d -o CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp/njn_localmaxstatmatrix.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/chd_ph.c.o -MF CMakeFiles/cmph.dir/chd_ph.c.o.d -o CMakeFiles/cmph.dir/chd_ph.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/chd_ph.c
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o -MF CMakeFiles/cmph.dir/bdz.c.o.d -o CMakeFiles/cmph.dir/bdz.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/bdz.c
[ 28%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/alp && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -O2 -g -DNDEBUG -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o -MF CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o.d -o CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp/njn_localmaxstatutil.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/alp && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -O2 -g -DNDEBUG -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o -MF CMakeFiles/alp.dir/njn_random.cpp.o.d -o CMakeFiles/alp.dir/njn_random.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp/njn_random.cpp
[ 31%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o
[ 31%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chm.c.o
[ 32%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/cmph.c.o
[ 33%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/cmph_structs.c.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/chm.c.o -MF CMakeFiles/cmph.dir/chm.c.o.d -o CMakeFiles/cmph.dir/chm.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/chm.c
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/cmph.c.o -MF CMakeFiles/cmph.dir/cmph.c.o.d -o CMakeFiles/cmph.dir/cmph.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/cmph.c
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/alp && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -O2 -g -DNDEBUG -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o -MF CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o.d -o CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp/sls_alignment_evaluer.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/alp && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -O2 -g -DNDEBUG -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o -MF CMakeFiles/alp.dir/sls_alp.cpp.o.d -o CMakeFiles/alp.dir/sls_alp.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp/sls_alp.cpp
make[2]: Leaving directory '/tmp/guix-build-sortmerna-4.3.4.drv-0/build'
[ 35%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/compressed_rank.c.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/cmph_structs.c.o -MF CMakeFiles/cmph.dir/cmph_structs.c.o.d -o CMakeFiles/cmph.dir/cmph_structs.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/cmph_structs.c
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/alp && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -O2 -g -DNDEBUG -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o -MF CMakeFiles/alp.dir/sls_alp_data.cpp.o.d -o CMakeFiles/alp.dir/sls_alp_data.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp/sls_alp_data.cpp
[ 36%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/compressed_seq.c.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/alp && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -O2 -g -DNDEBUG -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o -MF CMakeFiles/alp.dir/sls_alp_regression.cpp.o.d -o CMakeFiles/alp.dir/sls_alp_regression.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp/sls_alp_regression.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/compressed_rank.c.o -MF CMakeFiles/cmph.dir/compressed_rank.c.o.d -o CMakeFiles/cmph.dir/compressed_rank.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/compressed_rank.c
[ 36%] Built target build_version
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/compressed_seq.c.o -MF CMakeFiles/cmph.dir/compressed_seq.c.o.d -o CMakeFiles/cmph.dir/compressed_seq.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/compressed_seq.c
[ 37%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_sim.cpp.o
[ 39%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/fch.c.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/alp && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -O2 -g -DNDEBUG -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_sim.cpp.o -MF CMakeFiles/alp.dir/sls_alp_sim.cpp.o.d -o CMakeFiles/alp.dir/sls_alp_sim.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp/sls_alp_sim.cpp
[ 40%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_basic.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/fch.c.o -MF CMakeFiles/cmph.dir/fch.c.o.d -o CMakeFiles/cmph.dir/fch.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/fch.c
[ 41%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/fch_buckets.c.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/alp && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -O2 -g -DNDEBUG -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_basic.cpp.o -MF CMakeFiles/alp.dir/sls_basic.cpp.o.d -o CMakeFiles/alp.dir/sls_basic.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp/sls_basic.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/fch_buckets.c.o -MF CMakeFiles/cmph.dir/fch_buckets.c.o.d -o CMakeFiles/cmph.dir/fch_buckets.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/fch_buckets.c
[ 43%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_pvalues.cpp.o
[ 44%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/graph.c.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/alp && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -O2 -g -DNDEBUG -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_pvalues.cpp.o -MF CMakeFiles/alp.dir/sls_pvalues.cpp.o.d -o CMakeFiles/alp.dir/sls_pvalues.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp/sls_pvalues.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/graph.c.o -MF CMakeFiles/cmph.dir/graph.c.o.d -o CMakeFiles/cmph.dir/graph.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/graph.c
[ 45%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/hash.c.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/hash.c.o -MF CMakeFiles/cmph.dir/hash.c.o.d -o CMakeFiles/cmph.dir/hash.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/hash.c
[ 47%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/jenkins_hash.c.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/jenkins_hash.c.o -MF CMakeFiles/cmph.dir/jenkins_hash.c.o.d -o CMakeFiles/cmph.dir/jenkins_hash.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/jenkins_hash.c
[ 48%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/miller_rabin.c.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/miller_rabin.c.o -MF CMakeFiles/cmph.dir/miller_rabin.c.o.d -o CMakeFiles/cmph.dir/miller_rabin.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/miller_rabin.c
[ 50%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o -MF CMakeFiles/cmph.dir/vqueue.c.o.d -o CMakeFiles/cmph.dir/vqueue.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/vqueue.c
[ 51%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/select.c.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/select.c.o -MF CMakeFiles/cmph.dir/select.c.o.d -o CMakeFiles/cmph.dir/select.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/select.c
[ 52%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/3rdparty/cmph && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -O2 -g -DNDEBUG -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o -MF CMakeFiles/cmph.dir/vstack.c.o.d -o CMakeFiles/cmph.dir/vstack.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph/vstack.c
make[2]: Leaving directory '/tmp/guix-build-sortmerna-4.3.4.drv-0/build'
[ 52%] Built target cmph
make[2]: Leaving directory '/tmp/guix-build-sortmerna-4.3.4.drv-0/build'
[ 52%] Built target alp
make  -f src/sortmerna/CMakeFiles/smr_objs.dir/build.make src/sortmerna/CMakeFiles/smr_objs.dir/depend
make[2]: Entering directory '/tmp/guix-build-sortmerna-4.3.4.drv-0/build'
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build && /gnu/store/aain9m7r37jlzd21kvgvrkhc2pm7mk1w-cmake-minimal-3.21.3/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/guix-build-sortmerna-4.3.4.drv-0/source /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna /tmp/guix-build-sortmerna-4.3.4.drv-0/build /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna/CMakeFiles/smr_objs.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/tmp/guix-build-sortmerna-4.3.4.drv-0/build'
make  -f src/sortmerna/CMakeFiles/smr_objs.dir/build.make src/sortmerna/CMakeFiles/smr_objs.dir/build
make[2]: Entering directory '/tmp/guix-build-sortmerna-4.3.4.drv-0/build'
[ 56%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.cpp.o
[ 56%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/indexdb.cpp.o
[ 56%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/index.cpp.o
[ 58%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/izlib.cpp.o
[ 62%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/alignment.cpp.o
[ 62%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/bitvector.cpp.o
[ 62%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/cmd.cpp.o
[ 63%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kvdb.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/izlib.cpp.o -MF CMakeFiles/smr_objs.dir/izlib.cpp.o.d -o CMakeFiles/smr_objs.dir/izlib.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/izlib.cpp
[ 64%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/options.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/index.cpp.o -MF CMakeFiles/smr_objs.dir/index.cpp.o.d -o CMakeFiles/smr_objs.dir/index.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/index.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/alignment.cpp.o -MF CMakeFiles/smr_objs.dir/alignment.cpp.o.d -o CMakeFiles/smr_objs.dir/alignment.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/alignment.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/bitvector.cpp.o -MF CMakeFiles/smr_objs.dir/bitvector.cpp.o.d -o CMakeFiles/smr_objs.dir/bitvector.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/bitvector.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/cmd.cpp.o -MF CMakeFiles/smr_objs.dir/cmd.cpp.o.d -o CMakeFiles/smr_objs.dir/cmd.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/cmd.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/indexdb.cpp.o -MF CMakeFiles/smr_objs.dir/indexdb.cpp.o.d -o CMakeFiles/smr_objs.dir/indexdb.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/indexdb.cpp
[ 66%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/output.cpp.o
[ 67%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/summary.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.cpp.o -MF CMakeFiles/smr_objs.dir/kseq_load.cpp.o.d -o CMakeFiles/smr_objs.dir/kseq_load.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/kseq_load.cpp
[ 68%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o
[ 70%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/read.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/kvdb.cpp.o -MF CMakeFiles/smr_objs.dir/kvdb.cpp.o.d -o CMakeFiles/smr_objs.dir/kvdb.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/kvdb.cpp
[ 71%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/processor.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/options.cpp.o -MF CMakeFiles/smr_objs.dir/options.cpp.o.d -o CMakeFiles/smr_objs.dir/options.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp
[ 72%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/output.cpp.o -MF CMakeFiles/smr_objs.dir/output.cpp.o.d -o CMakeFiles/smr_objs.dir/output.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/output.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/summary.cpp.o -MF CMakeFiles/smr_objs.dir/summary.cpp.o.d -o CMakeFiles/smr_objs.dir/summary.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/summary.cpp
[ 74%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o -MF CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o.d -o CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/paralleltraversal.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/processor.cpp.o -MF CMakeFiles/smr_objs.dir/processor.cpp.o.d -o CMakeFiles/smr_objs.dir/processor.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/processor.cpp
[ 75%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/read.cpp.o -MF CMakeFiles/smr_objs.dir/read.cpp.o.d -o CMakeFiles/smr_objs.dir/read.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/read.cpp
[ 78%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o
[ 78%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o
[ 79%] Building C object src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o
[ 81%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/otumap.cpp.o
[ 82%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report.cpp.o
[ 83%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/util.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o -MF CMakeFiles/smr_objs.dir/readfeed.cpp.o.d -o CMakeFiles/smr_objs.dir/readfeed.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/readfeed.cpp
[ 85%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_base.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o -MF CMakeFiles/smr_objs.dir/readstats.cpp.o.d -o CMakeFiles/smr_objs.dir/readstats.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/readstats.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o -MF CMakeFiles/smr_objs.dir/references.cpp.o.d -o CMakeFiles/smr_objs.dir/references.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/references.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o -MF CMakeFiles/smr_objs.dir/refstats.cpp.o.d -o CMakeFiles/smr_objs.dir/refstats.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/refstats.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/gcc  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -O2 -g -DNDEBUG -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o -MF CMakeFiles/smr_objs.dir/ssw.c.o.d -o CMakeFiles/smr_objs.dir/ssw.c.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/ssw.c
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o -MF CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o.d -o CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/traverse_bursttrie.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/util.cpp.o -MF CMakeFiles/smr_objs.dir/util.cpp.o.d -o CMakeFiles/smr_objs.dir/util.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/util.cpp
[ 86%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fastx.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/otumap.cpp.o -MF CMakeFiles/smr_objs.dir/otumap.cpp.o.d -o CMakeFiles/smr_objs.dir/otumap.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/otumap.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report.cpp.o -MF CMakeFiles/smr_objs.dir/report.cpp.o.d -o CMakeFiles/smr_objs.dir/report.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/report.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_base.cpp.o -MF CMakeFiles/smr_objs.dir/report_fx_base.cpp.o.d -o CMakeFiles/smr_objs.dir/report_fx_base.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/report_fx_base.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_fastx.cpp.o -MF CMakeFiles/smr_objs.dir/report_fastx.cpp.o.d -o CMakeFiles/smr_objs.dir/report_fastx.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/report_fastx.cpp
[ 87%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_other.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_other.cpp.o -MF CMakeFiles/smr_objs.dir/report_fx_other.cpp.o.d -o CMakeFiles/smr_objs.dir/report_fx_other.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/report_fx_other.cpp
[ 90%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_blast.cpp.o
[ 90%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_denovo.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_blast.cpp.o -MF CMakeFiles/smr_objs.dir/report_blast.cpp.o.d -o CMakeFiles/smr_objs.dir/report_blast.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/report_blast.cpp
[ 91%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_biom.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_denovo.cpp.o -MF CMakeFiles/smr_objs.dir/report_denovo.cpp.o.d -o CMakeFiles/smr_objs.dir/report_denovo.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/report_denovo.cpp
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_biom.cpp.o -MF CMakeFiles/smr_objs.dir/report_biom.cpp.o.d -o CMakeFiles/smr_objs.dir/report_biom.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/report_biom.cpp
[ 93%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_sam.cpp.o
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_sam.cpp.o -MF CMakeFiles/smr_objs.dir/report_sam.cpp.o.d -o CMakeFiles/smr_objs.dir/report_sam.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/report_sam.cpp
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/izlib.cpp: In member function ‘int Izlib::inflatez(std::ifstream&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/izlib.cpp:243:8: warning: this statement may fall through [-Wimplicit-fallthrough=]
  243 |    ret = Z_DATA_ERROR; /* and fall through */
      |        ^
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/izlib.cpp:244:3: note: here
  244 |   case Z_DATA_ERROR:
      |   ^~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/report_biom.cpp: In member function ‘virtual void ReportBiom::init(Readfeed&, Runopts&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/report_biom.cpp:41:33: warning: unused parameter ‘readfeed’ [-Wunused-parameter]
   41 | void ReportBiom::init(Readfeed& readfeed, Runopts& opts)
      |                       ~~~~~~~~~~^~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/report_biom.cpp:41:52: warning: unused parameter ‘opts’ [-Wunused-parameter]
   41 | void ReportBiom::init(Readfeed& readfeed, Runopts& opts)
      |                                           ~~~~~~~~~^~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/report.cpp: In constructor ‘Report::Report(Runopts&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/report.cpp:39:25: warning: unused parameter ‘opts’ [-Wunused-parameter]
   39 | Report::Report(Runopts& opts) : pid_str(std::to_string(getpid())), is_zip(false) {}
      |                ~~~~~~~~~^~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/readfeed.cpp: In member function ‘void Readfeed::init(std::vector<std::__cxx11::basic_string<char> >&, const int&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/readfeed.cpp:105:69: warning: unused parameter ‘dbg’ [-Wunused-parameter]
  105 | void Readfeed::init(std::vector<std::string>& readfiles, const int& dbg)
      |                                                          ~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/readfeed.cpp: In static member function ‘static bool Readfeed::loadReadByIdx(Read&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/readfeed.cpp:187:37: warning: unused parameter ‘read’ [-Wunused-parameter]
  187 | bool Readfeed::loadReadByIdx(Read & read)
      |                              ~~~~~~~^~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/readfeed.cpp: In static member function ‘static bool Readfeed::loadReadById(Read&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/readfeed.cpp:271:35: warning: unused parameter ‘read’ [-Wunused-parameter]
  271 | bool Readfeed::loadReadById(Read& read)
      |                             ~~~~~~^~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/readfeed.cpp: In static member function ‘static bool Readfeed::hasnext(std::ifstream&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/readfeed.cpp:553:39: warning: unused parameter ‘ifs’ [-Wunused-parameter]
  553 | bool Readfeed::hasnext(std::ifstream& ifs)
      |                        ~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In constructor ‘Runopts::Runopts(int, char**, bool)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:79:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   79 |   for (int i = 0; i < indexfiles.size(); ++i)
      |                   ~~^~~~~~~~~~~~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/indexdb.cpp: In function ‘int build_index(Runopts&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/indexdb.cpp:1121:10: warning: unused variable ‘t’ [-Wunused-variable]
 1121 |  timeval t;
      |          ^
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/indexdb.cpp:1130:7: warning: unused variable ‘mem_is_set’ [-Wunused-variable]
 1130 |  bool mem_is_set = false;
      |       ^~~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/indexdb.cpp:1131:7: warning: unused variable ‘lnwin_set’ [-Wunused-variable]
 1131 |  bool lnwin_set = false;
      |       ^~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/indexdb.cpp:1132:7: warning: unused variable ‘interval_set’ [-Wunused-variable]
 1132 |  bool interval_set = false;
      |       ^~~~~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/indexdb.cpp:1133:7: warning: unused variable ‘max_pos_set’ [-Wunused-variable]
 1133 |  bool max_pos_set = false;
      |       ^~~~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/readfeed.cpp: In member function ‘bool Readfeed::define_format(const int&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/readfeed.cpp:891:15: warning: comparison is always false due to limited range of data type [-Wtype-limits]
  891 |    if (str[i] > 127 || str[i] < 0) {
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_log(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:283:42: warning: unused parameter ‘val’ [-Wunused-parameter]
  283 | void Runopts::opt_log(const std::string& val)
      |                       ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_denovo_otu(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:289:49: warning: unused parameter ‘val’ [-Wunused-parameter]
  289 | void Runopts::opt_denovo_otu(const std::string& val)
      |                              ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_otu_map(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:294:46: warning: unused parameter ‘val’ [-Wunused-parameter]
  294 | void Runopts::opt_otu_map(const std::string &val)
      |                           ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_print_all_reads(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:299:54: warning: unused parameter ‘val’ [-Wunused-parameter]
  299 | void Runopts::opt_print_all_reads(const std::string &val)
      |                                   ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_pid(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:304:42: warning: unused parameter ‘val’ [-Wunused-parameter]
  304 | void Runopts::opt_pid(const std::string &val)
      |                       ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_paired(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:309:45: warning: unused parameter ‘val’ [-Wunused-parameter]
  309 | void Runopts::opt_paired(const std::string& val)
      |                          ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_paired_in(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:323:48: warning: unused parameter ‘val’ [-Wunused-parameter]
  323 | void Runopts::opt_paired_in(const std::string &val)
      |                             ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_paired_out(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:328:49: warning: unused parameter ‘val’ [-Wunused-parameter]
  328 | void Runopts::opt_paired_out(const std::string &val)
      |                              ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_out2(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:337:43: warning: unused parameter ‘val’ [-Wunused-parameter]
  337 | void Runopts::opt_out2(const std::string& val)
      |                        ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_sout(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:342:43: warning: unused parameter ‘val’ [-Wunused-parameter]
  342 | void Runopts::opt_sout(const std::string& val)
      |                        ~~~~~~~~~~~~~~~~~~~^~~
In file included from /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/paralleltraversal.cpp:47:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include/ThreadPool.hpp: In member function ‘void ThreadPool::threadEntry(int)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include/ThreadPool.hpp:92:24: warning: unused parameter ‘i’ [-Wunused-parameter]
   92 |   void threadEntry(int i)
      |                    ~~~~^
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_fastx(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:470:44: warning: unused parameter ‘val’ [-Wunused-parameter]
  470 | void Runopts::opt_fastx(const std::string &val)
      |                         ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_sam(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:483:42: warning: unused parameter ‘val’ [-Wunused-parameter]
  483 | void Runopts::opt_sam(const std::string &val)
      |                       ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_no_best(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:592:46: warning: unused parameter ‘val’ [-Wunused-parameter]
  592 | void Runopts::opt_no_best(const std::string &val)
      |                           ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_edges(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:635:8: warning: unused variable ‘end’ [-Wunused-variable]
  635 |  char *end = 0;
      |        ^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_full_search(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:650:50: warning: unused parameter ‘val’ [-Wunused-parameter]
  650 | void Runopts::opt_full_search(const std::string &val)
      |                               ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_SQ(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:660:41: warning: unused parameter ‘val’ [-Wunused-parameter]
  660 | void Runopts::opt_SQ(const std::string &val)
      |                      ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_version(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:739:46: warning: unused parameter ‘val’ [-Wunused-parameter]
  739 | void Runopts::opt_version(const std::string &val)
      |                           ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_unknown(char**, int&, char*)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:749:34: warning: unused parameter ‘argv’ [-Wunused-parameter]
  749 | void Runopts::opt_unknown(char **argv, int &narg, char * opt)
      |                           ~~~~~~~^~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:749:45: warning: unused parameter ‘narg’ [-Wunused-parameter]
  749 | void Runopts::opt_unknown(char **argv, int &narg, char * opt)
      |                                        ~~~~~^~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_F(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:783:40: warning: unused parameter ‘val’ [-Wunused-parameter]
  783 | void Runopts::opt_F(const std::string &val)
      |                     ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_R(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:797:40: warning: unused parameter ‘val’ [-Wunused-parameter]
  797 | void Runopts::opt_R(const std::string &val)
      |                     ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_h(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:811:40: warning: unused parameter ‘val’ [-Wunused-parameter]
  811 | void Runopts::opt_h(const std::string &val)
      |                     ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_v(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:818:40: warning: unused parameter ‘val’ [-Wunused-parameter]
  818 | void Runopts::opt_v(const std::string &val)
      |                     ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_dbg_put_db(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:936:49: warning: unused parameter ‘val’ [-Wunused-parameter]
  936 | void Runopts::opt_dbg_put_db(const std::string& val)
      |                              ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_cmd(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:979:42: warning: unused parameter ‘val’ [-Wunused-parameter]
  979 | void Runopts::opt_cmd(const std::string &val)
      |                       ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_tmpdir(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:1035:45: warning: unused parameter ‘val’ [-Wunused-parameter]
 1035 | void Runopts::opt_tmpdir(const std::string &val)
      |                          ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/paralleltraversal.cpp: In function ‘void traverse(Runopts&, Index&, References&, Readstats&, Refstats&, Read&, bool)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/paralleltraversal.cpp:291:85: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  291 |   bool is_last_idx = (index.index_num == opts.indexfiles.size() - 1) && (index.part == refstats.num_index_parts[index.index_num] - 1);
      |                                                                          ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/paralleltraversal.cpp:93:7: warning: unused variable ‘read_to_count’ [-Wunused-variable]
   93 |  bool read_to_count = true; // passed directly to compute_lis_alignment. TODO: What's the point?
      |       ^~~~~~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/paralleltraversal.cpp: In function ‘bool is_aligned(Runopts&, Readstats&, Output&, Index&, KeyValueDatabase&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/paralleltraversal.cpp:314:26: warning: unused parameter ‘opts’ [-Wunused-parameter]
  314 | bool is_aligned(Runopts& opts, Readstats& readstats, Output& output, Index& index, KeyValueDatabase& kvdb)
      |                 ~~~~~~~~~^~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/paralleltraversal.cpp:314:43: warning: unused parameter ‘readstats’ [-Wunused-parameter]
  314 | bool is_aligned(Runopts& opts, Readstats& readstats, Output& output, Index& index, KeyValueDatabase& kvdb)
      |                                ~~~~~~~~~~~^~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/paralleltraversal.cpp:314:62: warning: unused parameter ‘output’ [-Wunused-parameter]
  314 | bool is_aligned(Runopts& opts, Readstats& readstats, Output& output, Index& index, KeyValueDatabase& kvdb)
      |                                                      ~~~~~~~~^~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/paralleltraversal.cpp:314:77: warning: unused parameter ‘index’ [-Wunused-parameter]
  314 | bool is_aligned(Runopts& opts, Readstats& readstats, Output& output, Index& index, KeyValueDatabase& kvdb)
      |                                                                      ~~~~~~~^~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/paralleltraversal.cpp:314:102: warning: unused parameter ‘kvdb’ [-Wunused-parameter]
  314 | bool is_aligned(Runopts& opts, Readstats& readstats, Output& output, Index& index, KeyValueDatabase& kvdb)
      |                                                                                    ~~~~~~~~~~~~~~~~~~^~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_align(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:1172:44: warning: unused parameter ‘val’ [-Wunused-parameter]
 1172 | void Runopts::opt_align(const std::string& val)
      |                         ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::opt_filter(const string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:1177:45: warning: unused parameter ‘val’ [-Wunused-parameter]
 1177 | void Runopts::opt_filter(const std::string& val)
      |                          ~~~~~~~~~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::process(int, char**, bool)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:1351:50: warning: unused parameter ‘dryrun’ [-Wunused-parameter]
 1351 | void Runopts::process(int argc, char**argv, bool dryrun)
      |                                             ~~~~~^~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/kvdb.cpp: In member function ‘int KeyValueDatabase::clear(std::string)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/kvdb.cpp:58:41: warning: unused parameter ‘dbpath’ [-Wunused-parameter]
   58 | int KeyValueDatabase::clear(std::string dbpath)
      |                             ~~~~~~~~~~~~^~~~~~
In file included from /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/read.cpp:42:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include/read.hpp: In constructor ‘Read::Read()’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include/read.hpp:110:11: warning: ‘Read::n_denovo’ will be initialized after [-Wreorder]
  110 |  unsigned n_denovo; // count of alignment !ID + !COV
      |           ^~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include/read.hpp:100:7: warning:   ‘bool Read::reversed’ [-Wreorder]
  100 |  bool reversed; // indicates the read is reverse-complement i.e. 'revIntStr' was applied
      |       ^~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/read.cpp:116:1: warning:   when initialized here [-Wreorder]
  116 | Read::Read()
      | ^~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/indexdb.cpp: At global scope:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/indexdb.cpp:916:7: warning: ‘void {anonymous}::help()’ defined but not used [-Wunused-function]
  916 |  void help()
      |       ^~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/read.cpp: In constructor ‘Read::Read(std::string, std::string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/read.cpp:147:41: warning: unused parameter ‘read’ [-Wunused-parameter]
  147 | Read::Read(std::string id, std::string& read) : Read() { id = id; }
      |                            ~~~~~~~~~~~~~^~~~
In file included from /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/read.cpp:42:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include/read.hpp: In constructor ‘Read::Read(std::string, std::string, std::string, std::string, BIO_FORMAT)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include/read.hpp:96:13: warning: ‘Read::format’ will be initialized after [-Wreorder]
   96 |  BIO_FORMAT format; // fasta | fastq
      |             ^~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include/read.hpp:87:7: warning:   ‘bool Read::isEmpty’ [-Wreorder]
   87 |  bool isEmpty; // flags the Read object is empty i.e. just a placeholder for copy assignment
      |       ^~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/read.cpp:149:1: warning:   when initialized here [-Wreorder]
  149 | Read::Read(std::string id, std::string header, std::string sequence, std::string quality, BIO_FORMAT format)
      | ^~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/read.cpp: In member function ‘void Read::revIntStr()’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/read.cpp:346:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  346 |  for (int i = 0; i < isequence.length(); i++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/read.cpp: In member function ‘std::string Read::get04alphaSeq()’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/read.cpp:357:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  357 |  for (int i = 0; i < isequence.size(); ++i)
      |                  ~~^~~~~~~~~~~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp: In member function ‘void Runopts::print_help()’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:1732:6: warning: unused variable ‘req_w’ [-Wunused-variable]
 1732 |  int req_w   = 9;
      |      ^~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:1733:6: warning: unused variable ‘descr_w’ [-Wunused-variable]
 1733 |  int descr_w = 47; // description width
      |      ^~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/options.cpp:1734:6: warning: unused variable ‘def_w’ [-Wunused-variable]
 1734 |  int def_w = 20;
      |      ^~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/read.cpp: In member function ‘bool Read::load_db(KeyValueDatabase&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/read.cpp:462:6: warning: unused variable ‘id_win_hits_len’ [-Wunused-variable]
  462 |  int id_win_hits_len = 0;
      |      ^~~~~~~~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/read.cpp: In member function ‘void Read::unmarshallJson(KeyValueDatabase&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/read.cpp:536:46: warning: unused parameter ‘kvdb’ [-Wunused-parameter]
  536 | void Read::unmarshallJson(KeyValueDatabase & kvdb)
      |                           ~~~~~~~~~~~~~~~~~~~^~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/read.cpp: In member function ‘std::tuple<unsigned int, unsigned int, unsigned int, double, double> Read::calc_miss_gap_match(const References&, const s_align2&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/read.cpp:579:7: warning: unused variable ‘align_len’ [-Wunused-variable]
  579 |  auto align_len = align.read_end1 - align.read_begin1 + 1;
      |       ^~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/index.cpp: In constructor ‘Index::Index(Runopts&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/index.cpp:69:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   69 |   for (int idx = 0; idx < opts.indexfiles.size(); ++idx)
      |                     ~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/index.cpp:99:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   99 |   if (count_indexed == opts.indexfiles.size() * sfxarr.size())
      |       ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/index.cpp:118:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  118 |    for (int idx = 0; idx < opts.indexfiles.size(); ++idx) {
      |                      ~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/index.cpp: In member function ‘void Index::load(uint32_t, uint32_t, std::vector<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >&, Refstats&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/index.cpp:211:23: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  211 |      ((NodeElement *&)dst) += 4;
      |                       ^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/index.cpp:257:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
  257 |         ((NodeElement *&)dst) += 4;
      |                          ^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/index.cpp: In member function ‘void Index::unload()’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/index.cpp:360:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<kmer>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  360 |  for (int i = 0; i < lookup_tbl.size(); i++)
      |                  ~~^~~~~~~~~~~~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/index.cpp:377:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<kmer_origin>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  377 |  for (int i = 0; i < positions_tbl.size(); i++)
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/report_fx_base.cpp: In member function ‘void ReportFxBase::write_a_read(std::ostream&, Read&, Readstate&, Izlib&, bool, const int&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/report_fx_base.cpp:200:123: warning: unused parameter ‘dbg’ [-Wunused-parameter]
  200 | void ReportFxBase::write_a_read(std::ostream& strm, Read& read, Readstate& rstate, Izlib& izlib, bool is_last, const int& dbg)
      |                                                                                                                ~~~~~~~~~~~^~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/output.cpp: In member function ‘void Output::init(Readfeed&, Runopts&, Readstats&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/output.cpp:65:65: warning: unused parameter ‘readstats’ [-Wunused-parameter]
   65 | void Output::init(Readfeed& readfeed, Runopts& opts, Readstats& readstats)
      |                                                      ~~~~~~~~~~~^~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/cmd.cpp: In member function ‘void CmdSession::cmdIndex(Runopts&, std::string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/cmd.cpp:250:47: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  250 |    if (index.positions_tbl[it->id].arr[i].seq == std::stoi(refid))
      |        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
In file included from /tmp/guix-build-sortmerna-4.3.4.drv-0/source/include/kseq_load.hpp:40,
                 from /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/readstats.cpp:52:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include/kseq.h:171:13: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function]
  171 |  static int kseq_read(kseq_t *seq)         \
      |             ^~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include/kseq.h:221:2: note: in expansion of macro ‘__KSEQ_READ’
  221 |  __KSEQ_READ
      |  ^~~~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include/kseq_load.hpp:43:1: note: in expansion of macro ‘KSEQ_INIT’
   43 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/cmd.cpp: In member function ‘void CmdSession::cmdTest(Runopts&, std::string&)’:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/cmd.cpp:317:36: warning: unused parameter ‘opts’ [-Wunused-parameter]
  317 | void CmdSession::cmdTest(Runopts & opts, std::string & cmd)
      |                          ~~~~~~~~~~^~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/cmd.cpp:317:56: warning: unused parameter ‘cmd’ [-Wunused-parameter]
  317 | void CmdSession::cmdTest(Runopts & opts, std::string & cmd)
      |                                          ~~~~~~~~~~~~~~^~~
In file included from /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/paralleltraversal.cpp:41:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include/kseq_load.hpp: At global scope:
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include/kseq.h:171:13: warning: ‘int kseq_read(kseq_t*)’ defined but not used [-Wunused-function]
  171 |  static int kseq_read(kseq_t *seq)         \
      |             ^~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include/kseq.h:221:2: note: in expansion of macro ‘__KSEQ_READ’
  221 |  __KSEQ_READ
      |  ^~~~~~~~~~~
/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include/kseq_load.hpp:43:1: note: in expansion of macro ‘KSEQ_INIT’
   43 | KSEQ_INIT(gzFile, gzread)
      | ^~~~~~~~~
make[2]: Leaving directory '/tmp/guix-build-sortmerna-4.3.4.drv-0/build'
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cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build && /gnu/store/aain9m7r37jlzd21kvgvrkhc2pm7mk1w-cmake-minimal-3.21.3/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/guix-build-sortmerna-4.3.4.drv-0/source /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna /tmp/guix-build-sortmerna-4.3.4.drv-0/build /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna/CMakeFiles/sortmerna.dir/DependInfo.cmake --color=
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cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++  -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/concurrentqueue -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/include -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/cmph -I/tmp/guix-build-sortmerna-4.3.4.drv-0/source/3rdparty/alp -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/sortmerna.dir/main.cpp.o -MF CMakeFiles/sortmerna.dir/main.cpp.o.d -o CMakeFiles/sortmerna.dir/main.cpp.o -c /tmp/guix-build-sortmerna-4.3.4.drv-0/source/src/sortmerna/main.cpp
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[ 98%] Linking CXX executable sortmerna
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/src/sortmerna && /gnu/store/aain9m7r37jlzd21kvgvrkhc2pm7mk1w-cmake-minimal-3.21.3/bin/cmake -E cmake_link_script CMakeFiles/sortmerna.dir/link.txt --verbose=1
/gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++ -pthread -W -Wextra -Wall -Xlinker -v -O2 -g -DNDEBUG CMakeFiles/sortmerna.dir/main.cpp.o ../../CMakeFiles/build_version.dir/build_version.cpp.o CMakeFiles/smr_objs.dir/alignment.cpp.o CMakeFiles/smr_objs.dir/bitvector.cpp.o CMakeFiles/smr_objs.dir/cmd.cpp.o CMakeFiles/smr_objs.dir/izlib.cpp.o CMakeFiles/smr_objs.dir/index.cpp.o CMakeFiles/smr_objs.dir/indexdb.cpp.o CMakeFiles/smr_objs.dir/kseq_load.cpp.o CMakeFiles/smr_objs.dir/kvdb.cpp.o CMakeFiles/smr_objs.dir/options.cpp.o CMakeFiles/smr_objs.dir/output.cpp.o CMakeFiles/smr_objs.dir/summary.cpp.o CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o CMakeFiles/smr_objs.dir/processor.cpp.o CMakeFiles/smr_objs.dir/read.cpp.o CMakeFiles/smr_objs.dir/readfeed.cpp.o CMakeFiles/smr_objs.dir/readstats.cpp.o CMakeFiles/smr_objs.dir/references.cpp.o CMakeFiles/smr_objs.dir/refstats.cpp.o CMakeFiles/smr_objs.dir/ssw.c.o CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o CMakeFiles/smr_objs.dir/util.cpp.o CMakeFiles/smr_objs.dir/otumap.cpp.o CMakeFiles/smr_objs.dir/report.cpp.o CMakeFiles/smr_objs.dir/report_fx_base.cpp.o CMakeFiles/smr_objs.dir/report_fastx.cpp.o CMakeFiles/smr_objs.dir/report_fx_other.cpp.o CMakeFiles/smr_objs.dir/report_blast.cpp.o CMakeFiles/smr_objs.dir/report_denovo.cpp.o CMakeFiles/smr_objs.dir/report_biom.cpp.o CMakeFiles/smr_objs.dir/report_sam.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_sim.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_basic.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_pvalues.cpp.o -o sortmerna  -Wl,-rpath,::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: ../../3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/buffer_entry.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chd.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chd_ph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chm.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/cmph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/cmph_structs.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/compressed_rank.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/compressed_seq.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/fch.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/fch_buckets.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/graph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/hash.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/jenkins_hash.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/miller_rabin.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/select.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o /gnu/store/5v3fp2v0bb7kk8rbkfw38ri2wf7cn34w-rocksdb-6.26.1/lib/librocksdb.so.6.26.1 -ldl /gnu/store/2i0zpa5w320y8m4zbqk1va8vs6dbawv0-zlib-1.2.11/lib/libz.so 
collect2 version 10.3.0
/gnu/store/k452f0r5bk6n0cbsf5ndxbp5qcf6bpfw-ld-wrapper-0/bin/ld -plugin /gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/libexec/gcc/x86_64-unknown-linux-gnu/10.3.0/liblto_plugin.so -plugin-opt=/gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/libexec/gcc/x86_64-unknown-linux-gnu/10.3.0/lto-wrapper -plugin-opt=-fresolution=/tmp/guix-build-sortmerna-4.3.4.drv-0/ccJYeuzg.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lpthread -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --eh-frame-hdr -m elf_x86_64 -dynamic-linker /gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/lib/ld-linux-x86-64.so.2 -o sortmerna /gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/lib/crt1.o /gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/lib/crti.o /gnu/store/90lbavffg0csrf208nw0ayj1bz5knl47-gcc-10.3.0-lib/lib/gcc/x86_64-unknown-linux-gnu/10.3.0/crtbegin.o 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-L/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/lib -v CMakeFiles/sortmerna.dir/main.cpp.o ../../CMakeFiles/build_version.dir/build_version.cpp.o CMakeFiles/smr_objs.dir/alignment.cpp.o CMakeFiles/smr_objs.dir/bitvector.cpp.o CMakeFiles/smr_objs.dir/cmd.cpp.o CMakeFiles/smr_objs.dir/izlib.cpp.o CMakeFiles/smr_objs.dir/index.cpp.o CMakeFiles/smr_objs.dir/indexdb.cpp.o CMakeFiles/smr_objs.dir/kseq_load.cpp.o CMakeFiles/smr_objs.dir/kvdb.cpp.o CMakeFiles/smr_objs.dir/options.cpp.o CMakeFiles/smr_objs.dir/output.cpp.o CMakeFiles/smr_objs.dir/summary.cpp.o CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o CMakeFiles/smr_objs.dir/processor.cpp.o CMakeFiles/smr_objs.dir/read.cpp.o CMakeFiles/smr_objs.dir/readfeed.cpp.o CMakeFiles/smr_objs.dir/readstats.cpp.o CMakeFiles/smr_objs.dir/references.cpp.o CMakeFiles/smr_objs.dir/refstats.cpp.o CMakeFiles/smr_objs.dir/ssw.c.o CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o CMakeFiles/smr_objs.dir/util.cpp.o CMakeFiles/smr_objs.dir/otumap.cpp.o CMakeFiles/smr_objs.dir/report.cpp.o CMakeFiles/smr_objs.dir/report_fx_base.cpp.o CMakeFiles/smr_objs.dir/report_fastx.cpp.o CMakeFiles/smr_objs.dir/report_fx_other.cpp.o CMakeFiles/smr_objs.dir/report_blast.cpp.o CMakeFiles/smr_objs.dir/report_denovo.cpp.o CMakeFiles/smr_objs.dir/report_biom.cpp.o CMakeFiles/smr_objs.dir/report_sam.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_sim.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_basic.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_pvalues.cpp.o -rpath ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: ../../3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/buffer_entry.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chd.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chd_ph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chm.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/cmph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/cmph_structs.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/compressed_rank.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/compressed_seq.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/fch.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/fch_buckets.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/graph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/hash.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/jenkins_hash.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/miller_rabin.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/select.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o /gnu/store/5v3fp2v0bb7kk8rbkfw38ri2wf7cn34w-rocksdb-6.26.1/lib/librocksdb.so.6.26.1 -ldl /gnu/store/2i0zpa5w320y8m4zbqk1va8vs6dbawv0-zlib-1.2.11/lib/libz.so -lstdc++ -lm -lgcc_s -lgcc -L/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/lib -rpath=/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/lib -rpath=/gnu/store/90lbavffg0csrf208nw0ayj1bz5knl47-gcc-10.3.0-lib/lib -lgcc_s -lpthread -lc -lgcc_s 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GNU ld (GNU Binutils) 2.37
make[2]: Leaving directory '/tmp/guix-build-sortmerna-4.3.4.drv-0/build'
[ 98%] Built target sortmerna
[100%] Linking CXX executable tests
cd /tmp/guix-build-sortmerna-4.3.4.drv-0/build/tests/sortmerna && /gnu/store/aain9m7r37jlzd21kvgvrkhc2pm7mk1w-cmake-minimal-3.21.3/bin/cmake -E cmake_link_script CMakeFiles/tests.dir/link.txt --verbose=1
/gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin/c++ -pthread -O2 -g -DNDEBUG CMakeFiles/tests.dir/kvdb.cpp.o CMakeFiles/tests.dir/main.cpp.o ../../CMakeFiles/build_version.dir/build_version.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_sim.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_basic.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_pvalues.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/alignment.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/bitvector.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/cmd.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/izlib.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/index.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/indexdb.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/kvdb.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/options.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/output.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/summary.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/processor.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/read.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/util.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/otumap.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/report.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_base.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/report_fastx.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_other.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/report_blast.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/report_denovo.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/report_biom.cpp.o ../../src/sortmerna/CMakeFiles/smr_objs.dir/report_sam.cpp.o -o tests  ../../3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/buffer_entry.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chd.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chd_ph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chm.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/cmph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/cmph_structs.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/compressed_rank.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/compressed_seq.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/fch.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/fch_buckets.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/graph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/hash.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/jenkins_hash.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/miller_rabin.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/select.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o /gnu/store/5v3fp2v0bb7kk8rbkfw38ri2wf7cn34w-rocksdb-6.26.1/lib/librocksdb.so.6.26.1 /gnu/store/2i0zpa5w320y8m4zbqk1va8vs6dbawv0-zlib-1.2.11/lib/libz.so 
make[2]: Leaving directory '/tmp/guix-build-sortmerna-4.3.4.drv-0/build'
[100%] Built target tests
make[1]: Leaving directory '/tmp/guix-build-sortmerna-4.3.4.drv-0/build'
/gnu/store/aain9m7r37jlzd21kvgvrkhc2pm7mk1w-cmake-minimal-3.21.3/bin/cmake -E cmake_progress_start /tmp/guix-build-sortmerna-4.3.4.drv-0/build/CMakeFiles 0
phase `build' succeeded after 30.6 seconds
starting phase `check'
test suite not run
phase `check' succeeded after 0.0 seconds
starting phase `install'
phase `install' succeeded after 0.1 seconds
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phase `patch-shebangs' succeeded after 0.0 seconds
starting phase `strip'
stripping binaries in "/gnu/store/ngqb6mvsm4816dm6iqvfdpjyh84myhly-sortmerna-4.3.4/bin" with "strip" and flags ("--strip-debug")
phase `strip' succeeded after 0.0 seconds
starting phase `validate-runpath'
validating RUNPATH of 0 binaries in "/gnu/store/ngqb6mvsm4816dm6iqvfdpjyh84myhly-sortmerna-4.3.4/bin"...
phase `validate-runpath' succeeded after 0.0 seconds
starting phase `validate-documentation-location'
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phase `patch-dot-desktop-files' succeeded after 0.0 seconds
starting phase `make-dynamic-linker-cache'
phase `make-dynamic-linker-cache' succeeded after 0.0 seconds
starting phase `install-license-files'
installing 4 license files from '../source'
phase `install-license-files' succeeded after 0.0 seconds
starting phase `reset-gzip-timestamps'
phase `reset-gzip-timestamps' succeeded after 0.0 seconds
starting phase `compress-documentation'
phase `compress-documentation' succeeded after 0.0 seconds