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/y808025ygal6skd4fxl96ysn6bpyfq8j-perl-5.36.0/bin:/gnu/store/4vs95giv3b18mr7422adf7r7l917ad41-tar-1.34/bin:/gnu/store/cmp43qav05qdfx8l7am699nngvrcymmf-gzip-1.12/bin:/gnu/store/jyj45lhbdv3ck62qvblhv4rdygszjv3w-bzip2-1.0.8/bin:/gnu/store/54jpx6ymfslv25n1h92ls72z87r9ja2i-file-5.44/bin:/gnu/store/9raglzgr029gila3bl3832h2ry564ayi-diffutils-3.8/bin:/gnu/store/gpcv5f7wsw56kysrlnqpq4g4ij37j1aj-patch-2.7.6/bin:/gnu/store/fs50ippbz10zl55zwwxl04zfvlgjmr7s-findutils-4.9.0/bin:/gnu/store/cdwc7qmxhfmjhhhzrvbhmwal65sshm6z-gawk-5.2.1/bin:/gnu/store/ams1v0vks47c950hym908a4lismsdl6z-sed-4.8/bin:/gnu/store/amm36qk60pnyl3v0vbl72w6agi5xkh07-grep-3.8/bin:/gnu/store/la6c6k6h32bddrf1171n0dp8dm47k656-xz-5.2.8/bin:/gnu/store/g3pv7a535y9h5dsvzv5zr669zzd1hx73-coreutils-9.1/bin:/gnu/store/ly36q12ji4l2fr2kpqf2api2dvg0rmfa-make-4.3/bin:/gnu/store/vza0n6gb01lbc9cgwx2hygvq15qiczn6-bash-minimal-5.1.16/bin:/gnu/store/lymlgi1qapfyr9jxmps1x95qwfgrwmgd-ld-wrapper-0/bin:/gnu/store/b4x9dk21q93na0cg28xmnis3g943nc3p-binutils-2.38/bin:/gnu/store/7pnvpswg5khkrj7gdaq4b5cipr9z2j00-gcc-11.3.0/bin:/gnu/store/r6gm2il1kkyyb6k1881lwilcij2kmbcq-glibc-2.35/bin:/gnu/store/r6gm2il1kkyyb6k1881lwilcij2kmbcq-glibc-2.35/sbin' environment variable `PERL5LIB' set to `/gnu/store/y808025ygal6skd4fxl96ysn6bpyfq8j-perl-5.36.0/lib/perl5/site_perl' environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/include:/gnu/store/jyj45lhbdv3ck62qvblhv4rdygszjv3w-bzip2-1.0.8/include:/gnu/store/54jpx6ymfslv25n1h92ls72z87r9ja2i-file-5.44/include:/gnu/store/cdwc7qmxhfmjhhhzrvbhmwal65sshm6z-gawk-5.2.1/include:/gnu/store/la6c6k6h32bddrf1171n0dp8dm47k656-xz-5.2.8/include:/gnu/store/ly36q12ji4l2fr2kpqf2api2dvg0rmfa-make-4.3/include:/gnu/store/b4x9dk21q93na0cg28xmnis3g943nc3p-binutils-2.38/include:/gnu/store/7pnvpswg5khkrj7gdaq4b5cipr9z2j00-gcc-11.3.0/include:/gnu/store/r6gm2il1kkyyb6k1881lwilcij2kmbcq-glibc-2.35/include:/gnu/store/4w2igc2gchw1xwh1gb1phgbfjy06ram8-linux-libre-headers-5.15.49/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/include:/gnu/store/jyj45lhbdv3ck62qvblhv4rdygszjv3w-bzip2-1.0.8/include:/gnu/store/54jpx6ymfslv25n1h92ls72z87r9ja2i-file-5.44/include:/gnu/store/cdwc7qmxhfmjhhhzrvbhmwal65sshm6z-gawk-5.2.1/include:/gnu/store/la6c6k6h32bddrf1171n0dp8dm47k656-xz-5.2.8/include:/gnu/store/ly36q12ji4l2fr2kpqf2api2dvg0rmfa-make-4.3/include:/gnu/store/b4x9dk21q93na0cg28xmnis3g943nc3p-binutils-2.38/include:/gnu/store/7pnvpswg5khkrj7gdaq4b5cipr9z2j00-gcc-11.3.0/include/c++:/gnu/store/7pnvpswg5khkrj7gdaq4b5cipr9z2j00-gcc-11.3.0/include:/gnu/store/r6gm2il1kkyyb6k1881lwilcij2kmbcq-glibc-2.35/include:/gnu/store/4w2igc2gchw1xwh1gb1phgbfjy06ram8-linux-libre-headers-5.15.49/include' environment variable `LIBRARY_PATH' set to `/gnu/store/y808025ygal6skd4fxl96ysn6bpyfq8j-perl-5.36.0/lib:/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib:/gnu/store/jyj45lhbdv3ck62qvblhv4rdygszjv3w-bzip2-1.0.8/lib:/gnu/store/54jpx6ymfslv25n1h92ls72z87r9ja2i-file-5.44/lib:/gnu/store/cdwc7qmxhfmjhhhzrvbhmwal65sshm6z-gawk-5.2.1/lib:/gnu/store/la6c6k6h32bddrf1171n0dp8dm47k656-xz-5.2.8/lib:/gnu/store/b4x9dk21q93na0cg28xmnis3g943nc3p-binutils-2.38/lib:/gnu/store/r6gm2il1kkyyb6k1881lwilcij2kmbcq-glibc-2.35/lib:/gnu/store/s0cscf8lbg5ipm7gwz41jxcfwv43jzsp-glibc-2.35-static/lib:/gnu/store/zjm02y5r97anpgngbvfvn7mfd2sh9d78-glibc-utf8-locales-2.35/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/zjm02y5r97anpgngbvfvn7mfd2sh9d78-glibc-utf8-locales-2.35/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/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/Makefile' -> `./Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/LICENSE.txt' -> `./LICENSE.txt' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/Doxyfile' -> `./Doxyfile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/.gitignore' -> `./.gitignore' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/binary_install.sh' -> `./binary_install.sh' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/README.txt' -> `./README.txt' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/version' -> `./version' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/phastCons/simple-coding.hmm' -> `./data/phastCons/simple-coding.hmm' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/phastCons/simple-coding-indels.hmm' -> `./data/phastCons/simple-coding-indels.hmm' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/models-no-cns-gc1' -> `./data/exoniphy/models-no-cns-gc1' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/models-gc2' -> `./data/exoniphy/models-gc2' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/models-gc1' -> `./data/exoniphy/models-gc1' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/models-gc4' -> `./data/exoniphy/models-gc4' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/models-no-cns' -> `./data/exoniphy/models-no-cns' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/models-gc3' -> `./data/exoniphy/models-gc3' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/models-gc5' -> `./data/exoniphy/models-gc5' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/default.cm' -> `./data/exoniphy/default.cm' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/models-no-cns-gc2' -> `./data/exoniphy/models-no-cns-gc2' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/models-no-cns-gc4' -> `./data/exoniphy/models-no-cns-gc4' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/models' -> `./data/exoniphy/models' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/default-no-cns.cm' -> `./data/exoniphy/default-no-cns.cm' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/models-no-cns-gc3' -> `./data/exoniphy/models-no-cns-gc3' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/models-no-cns-gc5' -> `./data/exoniphy/models-no-cns-gc5' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.ncns.gc1.mod' -> `./data/exoniphy/mammals/r3.ncns.gc1.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.cds3'ss.mod' -> `./data/exoniphy/mammals/hky.cds3'ss.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.ncns.gc3.mod' -> `./data/exoniphy/mammals/r3.ncns.gc3.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.5'splice-1.mod' -> `./data/exoniphy/mammals/hky.5'splice-1.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/default-no-cns.hmm' -> `./data/exoniphy/mammals/default-no-cns.hmm' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-3.gc4.mod' -> `./data/exoniphy/mammals/r3.cds-3.gc4.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-1.gc1.mod' -> `./data/exoniphy/mammals/r3.cds-1.gc1.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.ncns.gc5.mod' -> `./data/exoniphy/mammals/r3.ncns.gc5.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.cds5'ss-3.mod' -> `./data/exoniphy/mammals/hky.cds5'ss-3.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-1.gc5.mod' -> `./data/exoniphy/mammals/r3.cds-1.gc5.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.noncoding.gc1.mod' -> `./data/exoniphy/mammals/r3.noncoding.gc1.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.noncoding.mod' -> `./data/exoniphy/mammals/r3.noncoding.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.noncoding.gc3.mod' -> `./data/exoniphy/mammals/r3.noncoding.gc3.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.3'splice-4.mod' -> `./data/exoniphy/mammals/hky.3'splice-4.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.start-1.mod' -> `./data/exoniphy/mammals/hky.start-1.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-3.mod' -> `./data/exoniphy/mammals/r3.cds-3.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-3.gc3.mod' -> `./data/exoniphy/mammals/r3.cds-3.gc3.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cns.mod' -> `./data/exoniphy/mammals/r3.cns.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.ncns.mod' -> `./data/exoniphy/mammals/r3.ncns.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.prestart-4.mod' -> `./data/exoniphy/mammals/hky.prestart-4.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cns.gc1.mod' -> `./data/exoniphy/mammals/r3.cns.gc1.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-2.gc2.mod' -> `./data/exoniphy/mammals/r3.cds-2.gc2.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.5'splice-2.mod' -> `./data/exoniphy/mammals/hky.5'splice-2.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/default-indels-no-cns.hmm' -> `./data/exoniphy/mammals/default-indels-no-cns.hmm' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.3'splice-5.mod' -> `./data/exoniphy/mammals/hky.3'splice-5.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/cftr25_hybrid.nh' -> `./data/exoniphy/mammals/cftr25_hybrid.nh' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.prestart-2.mod' -> `./data/exoniphy/mammals/hky.prestart-2.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-2.gc1.mod' -> `./data/exoniphy/mammals/r3.cds-2.gc1.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.prestart-3.mod' -> `./data/exoniphy/mammals/hky.prestart-3.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cns.gc5.mod' -> `./data/exoniphy/mammals/r3.cns.gc5.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.ncns.gc4.mod' -> `./data/exoniphy/mammals/r3.ncns.gc4.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/default-indels.hmm' -> `./data/exoniphy/mammals/default-indels.hmm' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.3'splice-6.mod' -> `./data/exoniphy/mammals/hky.3'splice-6.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.ncns.gc2.mod' -> `./data/exoniphy/mammals/r3.ncns.gc2.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.5'splice-4.mod' -> `./data/exoniphy/mammals/hky.5'splice-4.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.stop-3.mod' -> `./data/exoniphy/mammals/hky.stop-3.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.start-2.mod' -> `./data/exoniphy/mammals/hky.start-2.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.start-3.mod' -> `./data/exoniphy/mammals/hky.start-3.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-3.gc2.mod' -> `./data/exoniphy/mammals/r3.cds-3.gc2.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.stop-2.mod' -> `./data/exoniphy/mammals/hky.stop-2.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-1.gc4.mod' -> `./data/exoniphy/mammals/r3.cds-1.gc4.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cns.gc4.mod' -> `./data/exoniphy/mammals/r3.cns.gc4.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-1.mod' -> `./data/exoniphy/mammals/r3.cds-1.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.prestart-1.mod' -> `./data/exoniphy/mammals/hky.prestart-1.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-2.gc4.mod' -> `./data/exoniphy/mammals/r3.cds-2.gc4.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.noncoding.gc4.mod' -> `./data/exoniphy/mammals/r3.noncoding.gc4.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.5'splice-3.mod' -> `./data/exoniphy/mammals/hky.5'splice-3.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/default.hmm' -> `./data/exoniphy/mammals/default.hmm' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.noncoding.gc5.mod' -> `./data/exoniphy/mammals/r3.noncoding.gc5.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.cds5'ss-2.mod' -> `./data/exoniphy/mammals/hky.cds5'ss-2.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-2.mod' -> `./data/exoniphy/mammals/r3.cds-2.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.cds5'ss-1.mod' -> `./data/exoniphy/mammals/hky.cds5'ss-1.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.noncoding.gc2.mod' -> `./data/exoniphy/mammals/r3.noncoding.gc2.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-3.gc1.mod' -> `./data/exoniphy/mammals/r3.cds-3.gc1.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-1.gc3.mod' -> `./data/exoniphy/mammals/r3.cds-1.gc3.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-2.gc5.mod' -> `./data/exoniphy/mammals/r3.cds-2.gc5.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.3'splice-2.mod' -> `./data/exoniphy/mammals/hky.3'splice-2.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-2.gc3.mod' -> `./data/exoniphy/mammals/r3.cds-2.gc3.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.5'splice-6.mod' -> `./data/exoniphy/mammals/hky.5'splice-6.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.stop-1.mod' -> `./data/exoniphy/mammals/hky.stop-1.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.3'splice-3.mod' -> `./data/exoniphy/mammals/hky.3'splice-3.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cns.gc3.mod' -> `./data/exoniphy/mammals/r3.cns.gc3.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.5'splice-5.mod' -> `./data/exoniphy/mammals/hky.5'splice-5.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-1.gc2.mod' -> `./data/exoniphy/mammals/r3.cds-1.gc2.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/hky.3'splice-1.mod' -> `./data/exoniphy/mammals/hky.3'splice-1.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cns.gc2.mod' -> `./data/exoniphy/mammals/r3.cns.gc2.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/data/exoniphy/mammals/r3.cds-3.gc5.mod' -> `./data/exoniphy/mammals/r3.cds-3.gc5.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/Makefile' -> `./test/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/chr22.14500000-15500000.fa' -> `./test/chr22.14500000-15500000.fa' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/rev-hmc.postprob' -> `./test/rev-hmc.postprob' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/rev-lnl.mod' -> `./test/rev-lnl.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/hpmrc-rev-dg-global.mod' -> `./test/hpmrc-rev-dg-global.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/rev-gaps.mod' -> `./test/rev-gaps.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/hky-em.mod' -> `./test/hky-em.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/test_phast.sh' -> `./test/test_phast.sh' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/jc.mod' -> `./test/jc.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/chr22.14500000-15500000.maf' -> `./test/chr22.14500000-15500000.maf' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/rev-dg.mod' -> `./test/rev-dg.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/chr22_correct.oss.gz' -> `./test/chr22_correct.oss.gz' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/elemcfa.bed' -> `./test/elemcfa.bed' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/rev-em.mod' -> `./test/rev-em.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/hky-dg.mod' -> `./test/hky-dg.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/rev-hmc-lnl.mod' -> `./test/rev-hmc-lnl.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/hmrc_correct.fa' -> `./test/hmrc_correct.fa' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/elements_correct.bed' -> `./test/elements_correct.bed' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/hpmrc.ss' -> `./test/hpmrc.ss' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/rev.mod' -> `./test/rev.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/rev-hmr2.mod' -> `./test/rev-hmr2.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/cons-4way_correct.dat' -> `./test/cons-4way_correct.dat' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/hpmrc.fa' -> `./test/hpmrc.fa' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/hky.mod' -> `./test/hky.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/cons_correct.dat' -> `./test/cons_correct.dat' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/elements-4way_correct.bed' -> `./test/elements-4way_correct.bed' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/unrest.mod' -> `./test/unrest.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/chr22.14500000-15500000.gp' -> `./test/chr22.14500000-15500000.gp' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/f81.mod' -> `./test/f81.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/cons-hmr_correct.dat' -> `./test/cons-hmr_correct.dat' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/testPhast.pl' -> `./test/testPhast.pl' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/rev.postprob' -> `./test/rev.postprob' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/rev-hm.mod' -> `./test/rev-hm.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/hmrc.ss' -> `./test/hmrc.ss' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/rev-hmr.mod' -> `./test/rev-hmr.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/hmrc_summary_correct' -> `./test/hmrc_summary_correct' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/test/unrest-cow-anc.mod' -> `./test/unrest-cow-anc.mod' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/lists.h' -> `./include/lists.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/hashtable.h' -> `./include/hashtable.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/simplex_grid.h' -> `./include/simplex_grid.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/pssm.h' -> `./include/pssm.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/tree_model.h' -> `./include/tree_model.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/gff.h' -> `./include/gff.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/sufficient_stats.h' -> `./include/sufficient_stats.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/fit_feature.h' -> `./include/fit_feature.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/eigen.h' -> `./include/eigen.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/tree_likelihoods.h' -> `./include/tree_likelihoods.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/ms.h' -> `./include/ms.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/rph_util.h' -> `./include/rph_util.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/numerical_opt.h' -> `./include/numerical_opt.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/subst_distrib.h' -> `./include/subst_distrib.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/multi_msa.h' -> `./include/multi_msa.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/prob_matrix.h' -> `./include/prob_matrix.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/trees.h' -> `./include/trees.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/motif.h' -> `./include/motif.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/stringsplus.h' -> `./include/stringsplus.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/memory_handler.h' -> `./include/memory_handler.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/phylo_hmm.h' -> `./include/phylo_hmm.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/bgc_hmm.h' -> `./include/bgc_hmm.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/msa.h' -> `./include/msa.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/maf_block.h' -> `./include/maf_block.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/markov_matrix.h' -> `./include/markov_matrix.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/prob_vector.h' -> `./include/prob_vector.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/subst_mods.h' -> `./include/subst_mods.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/phylo_p_print.h' -> `./include/phylo_p_print.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/indel_history.h' -> `./include/indel_history.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/matrix.h' -> `./include/matrix.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/vector.h' -> `./include/vector.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/indel_mod.h' -> `./include/indel_mod.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/phylo_fit.h' -> `./include/phylo_fit.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/bd_phylo_hmm.h' -> `./include/bd_phylo_hmm.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/genepred.h' -> `./include/genepred.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/complex_matrix.h' -> `./include/complex_matrix.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/misc.h' -> `./include/misc.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/external_libs.h' -> `./include/external_libs.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/queues.h' -> `./include/queues.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/complex_vector.h' -> `./include/complex_vector.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/fit_column.h' -> `./include/fit_column.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/list_of_lists.h' -> `./include/list_of_lists.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/wig.h' -> `./include/wig.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/gap_patterns.h' -> `./include/gap_patterns.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/phast_cons.h' -> `./include/phast_cons.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/bed.h' -> `./include/bed.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/hmm.h' -> `./include/hmm.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/em.h' -> `./include/em.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/dgamma.h' -> `./include/dgamma.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/local_alignment.h' -> `./include/local_alignment.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/complex.h' -> `./include/complex.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/maf.h' -> `./include/maf.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/tfbs.h' -> `./include/tfbs.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/category_map.h' -> `./include/category_map.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/stacks.h' -> `./include/stacks.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/phylo_p.h' -> `./include/phylo_p.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/puzzler.h' -> `./include/puzzler.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/pbs_code.h' -> `./include/pbs_code.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/include/fit_em.h' -> `./include/fit_em.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/Makefile' -> `./src/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/munge-help.sh' -> `./src/munge-help.sh' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/help2man.pl' -> `./src/help2man.pl' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/make-include.mk' -> `./src/make-include.mk' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/phastCons/Makefile' -> `./src/phastCons/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/phastCons/phastCons.help_src' -> `./src/phastCons/phastCons.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/phastCons/phastCons.c' -> `./src/phastCons/phastCons.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/phastMotif/Makefile' -> `./src/phastMotif/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/phastMotif/phastMotif.c' -> `./src/phastMotif/phastMotif.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/exoniphy/Makefile' -> `./src/exoniphy/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/exoniphy/exoniphy.help_src' -> `./src/exoniphy/exoniphy.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/exoniphy/exoniphy.c' -> `./src/exoniphy/exoniphy.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/dless/Makefile' -> `./src/dless/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/dless/dless.help_src' -> `./src/dless/dless.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/dless/dless.doxy' -> `./src/dless/dless.doxy' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/dless/dless.c' -> `./src/dless/dless.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/dless/dlessP.c' -> `./src/dless/dlessP.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/dless/bd_phylo_hmm.c' -> `./src/dless/bd_phylo_hmm.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/dless/dlessP.help_src' -> `./src/dless/dlessP.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/phyloBoot/Makefile' -> `./src/phyloBoot/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/phyloBoot/phyloBoot.c' -> `./src/phyloBoot/phyloBoot.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/phyloBoot/phyloBoot.help_src' -> `./src/phyloBoot/phyloBoot.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/Makefile' -> `./src/util/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/hmm_view.c' -> `./src/util/hmm_view.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/phast.help_src' -> `./src/util/phast.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/treeGen.c' -> `./src/util/treeGen.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/base_evolve.c' -> `./src/util/base_evolve.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/indelFit.help_src' -> `./src/util/indelFit.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/chooseLines.c' -> `./src/util/chooseLines.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/phastBias.c' -> `./src/util/phastBias.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/msa_diff.help_src' -> `./src/util/msa_diff.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/indelHistory.c' -> `./src/util/indelHistory.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/clean_genes.help_src' -> `./src/util/clean_genes.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/treeGen.help_src' -> `./src/util/treeGen.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/convert_coords.c' -> `./src/util/convert_coords.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/modFreqs.help_src' -> `./src/util/modFreqs.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/consEntropy.c' -> `./src/util/consEntropy.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/maf_parse.c' -> `./src/util/maf_parse.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/modFreqs.c' -> `./src/util/modFreqs.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/makeHKY.c' -> `./src/util/makeHKY.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/draw_tree.c' -> `./src/util/draw_tree.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/indelHistory.help_src' -> `./src/util/indelHistory.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/phastBias.help_src' -> `./src/util/phastBias.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/display_rate_matrix.c' -> `./src/util/display_rate_matrix.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/consEntropy.help_src' -> `./src/util/consEntropy.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/refeature.c' -> `./src/util/refeature.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/hmm_train.c' -> `./src/util/hmm_train.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/indelFit.c' -> `./src/util/indelFit.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/msa_view.c' -> `./src/util/msa_view.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/eval_predictions.c' -> `./src/util/eval_predictions.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/tree_doctor.c' -> `./src/util/tree_doctor.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/stringiphy.c' -> `./src/util/stringiphy.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/msa_split.c' -> `./src/util/msa_split.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/hmm_tweak.c' -> `./src/util/hmm_tweak.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/msa_diff.c' -> `./src/util/msa_diff.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/makeHKY.help_src' -> `./src/util/makeHKY.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/phast.c' -> `./src/util/phast.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/base_evolve.help_src' -> `./src/util/base_evolve.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/all_dists.c' -> `./src/util/all_dists.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/util/clean_genes.c' -> `./src/util/clean_genes.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/Makefile' -> `./src/lib/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/base/Makefile' -> `./src/lib/base/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/base/lists.c' -> `./src/lib/base/lists.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/base/prob_vector.c' -> `./src/lib/base/prob_vector.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/base/prob_matrix.c' -> `./src/lib/base/prob_matrix.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/base/hashtable.c' -> `./src/lib/base/hashtable.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/base/base.doxy' -> `./src/lib/base/base.doxy' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/base/matrix.c' -> `./src/lib/base/matrix.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/base/list_of_lists.c' -> `./src/lib/base/list_of_lists.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/base/numerical_opt.c' -> `./src/lib/base/numerical_opt.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/base/memory_handler.c' -> `./src/lib/base/memory_handler.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/base/misc.c' -> `./src/lib/base/misc.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/base/markov_matrix.c' -> `./src/lib/base/markov_matrix.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/base/stringsplus.c' -> `./src/lib/base/stringsplus.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/base/complex_vector.c' -> `./src/lib/base/complex_vector.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/base/vector.c' -> `./src/lib/base/vector.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/base/complex_matrix.c' -> `./src/lib/base/complex_matrix.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/base/eigen.c' -> `./src/lib/base/eigen.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/Makefile' -> `./src/lib/pcre/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_valid_utf8.c' -> `./src/lib/pcre/pcre_valid_utf8.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_try_flipped.c' -> `./src/lib/pcre/pcre_try_flipped.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_ucd.c' -> `./src/lib/pcre/pcre_ucd.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/ucp.h' -> `./src/lib/pcre/ucp.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_printint.src' -> `./src/lib/pcre/pcre_printint.src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre.h' -> `./src/lib/pcre/pcre.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_fullinfo.c' -> `./src/lib/pcre/pcre_fullinfo.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_get.c' -> `./src/lib/pcre/pcre_get.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/LICENCE' -> `./src/lib/pcre/LICENCE' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_exec.c' -> `./src/lib/pcre/pcre_exec.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_globals.c' -> `./src/lib/pcre/pcre_globals.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_newline.c' -> `./src/lib/pcre/pcre_newline.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_dfa_exec.c' -> `./src/lib/pcre/pcre_dfa_exec.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/README' -> `./src/lib/pcre/README' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_ord2utf8.c' -> `./src/lib/pcre/pcre_ord2utf8.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_internal.h' -> `./src/lib/pcre/pcre_internal.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_info.c' -> `./src/lib/pcre/pcre_info.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_chartables.c' -> `./src/lib/pcre/pcre_chartables.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_config.c' -> `./src/lib/pcre/pcre_config.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_study.c' -> `./src/lib/pcre/pcre_study.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/config.h' -> `./src/lib/pcre/config.h' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_compile.c' -> `./src/lib/pcre/pcre_compile.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_xclass.c' -> `./src/lib/pcre/pcre_xclass.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_tables.c' -> `./src/lib/pcre/pcre_tables.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_maketables.c' -> `./src/lib/pcre/pcre_maketables.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_version.c' -> `./src/lib/pcre/pcre_version.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/pcre/pcre_refcount.c' -> `./src/lib/pcre/pcre_refcount.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/feature/Makefile' -> `./src/lib/feature/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/feature/bed.c' -> `./src/lib/feature/bed.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/feature/genepred.c' -> `./src/lib/feature/genepred.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/feature/feature.doxy' -> `./src/lib/feature/feature.doxy' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/feature/category_map.c' -> `./src/lib/feature/category_map.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/feature/wig.c' -> `./src/lib/feature/wig.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/feature/gff.c' -> `./src/lib/feature/gff.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/rphast/Makefile' -> `./src/lib/rphast/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/rphast/rph_phyloFit.c' -> `./src/lib/rphast/rph_phyloFit.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/rphast/rph_tfbs.c' -> `./src/lib/rphast/rph_tfbs.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/rphast/rph_category_map.c' -> `./src/lib/rphast/rph_category_map.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/rphast/rph_util.c' -> `./src/lib/rphast/rph_util.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/rphast/rph_phyloP.c' -> `./src/lib/rphast/rph_phyloP.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/rphast/rph_trees.c' -> `./src/lib/rphast/rph_trees.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/rphast/rph_phastCons.c' -> `./src/lib/rphast/rph_phastCons.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/rphast/rph_gff.c' -> `./src/lib/rphast/rph_gff.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/rphast/rph_subst_mods.c' -> `./src/lib/rphast/rph_subst_mods.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/rphast/rph_wig.c' -> `./src/lib/rphast/rph_wig.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/rphast/rph_phylo_hmm.c' -> `./src/lib/rphast/rph_phylo_hmm.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/rphast/rph_tree_model.c' -> `./src/lib/rphast/rph_tree_model.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/rphast/rph_bgc_hmm.c' -> `./src/lib/rphast/rph_bgc_hmm.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/rphast/rph_list_of_lists.c' -> `./src/lib/rphast/rph_list_of_lists.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/rphast/rph_hmm.c' -> `./src/lib/rphast/rph_hmm.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/rphast/rph_msa.c' -> `./src/lib/rphast/rph_msa.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/msa/Makefile' -> `./src/lib/msa/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/msa/sufficient_stats.c' -> `./src/lib/msa/sufficient_stats.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/msa/msa.doxy' -> `./src/lib/msa/msa.doxy' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/msa/maf.c' -> `./src/lib/msa/maf.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/msa/local_alignment.c' -> `./src/lib/msa/local_alignment.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/msa/.cvsignore' -> `./src/lib/msa/.cvsignore' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/msa/maf_block.c' -> `./src/lib/msa/maf_block.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/msa/msa.c' -> `./src/lib/msa/msa.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/msa/multi_msa.c' -> `./src/lib/msa/multi_msa.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo_hmm/Makefile' -> `./src/lib/phylo_hmm/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo_hmm/gap_patterns.c' -> `./src/lib/phylo_hmm/gap_patterns.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo_hmm/phylo_hmm.c' -> `./src/lib/phylo_hmm/phylo_hmm.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/motif/Makefile' -> `./src/lib/motif/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/motif/motif.c' -> `./src/lib/motif/motif.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/motif/tfbs.c' -> `./src/lib/motif/tfbs.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/Makefile' -> `./src/lib/phylo/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/tree_model.c' -> `./src/lib/phylo/tree_model.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/dgamma.c' -> `./src/lib/phylo/dgamma.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/fit_em.c' -> `./src/lib/phylo/fit_em.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/fit_column.c' -> `./src/lib/phylo/fit_column.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/tree_likelihoods.c' -> `./src/lib/phylo/tree_likelihoods.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/indel_history.c' -> `./src/lib/phylo/indel_history.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/trees.c' -> `./src/lib/phylo/trees.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/phylo_p_print.c' -> `./src/lib/phylo/phylo_p_print.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/subst_distrib.c' -> `./src/lib/phylo/subst_distrib.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/subst_mods.c' -> `./src/lib/phylo/subst_mods.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/phast_cons.c' -> `./src/lib/phylo/phast_cons.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/fit_feature.c' -> `./src/lib/phylo/fit_feature.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/bgc_hmm.c' -> `./src/lib/phylo/bgc_hmm.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/phylo_p.c' -> `./src/lib/phylo/phylo_p.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/phylo.doxy' -> `./src/lib/phylo/phylo.doxy' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/indel_mod.c' -> `./src/lib/phylo/indel_mod.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/phylo/phylo_fit.c' -> `./src/lib/phylo/phylo_fit.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/hmm/Makefile' -> `./src/lib/hmm/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/hmm/em.c' -> `./src/lib/hmm/em.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/lib/hmm/hmm.c' -> `./src/lib/hmm/hmm.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/prequel/Makefile' -> `./src/prequel/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/prequel/pbs_code.c' -> `./src/prequel/pbs_code.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/prequel/simplex_grid.c' -> `./src/prequel/simplex_grid.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/prequel/pbsTrain.help_src' -> `./src/prequel/pbsTrain.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/prequel/prequel.c' -> `./src/prequel/prequel.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/prequel/pbsDecode.c' -> `./src/prequel/pbsDecode.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/prequel/pbsEncode.help_src' -> `./src/prequel/pbsEncode.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/prequel/pbsEncode.c' -> `./src/prequel/pbsEncode.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/prequel/pbsScoreMatrix.help_src' -> `./src/prequel/pbsScoreMatrix.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/prequel/pbsTrain.c' -> `./src/prequel/pbsTrain.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/prequel/prequel.doxy' -> `./src/prequel/prequel.doxy' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/prequel/prequel.help_src' -> `./src/prequel/prequel.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/prequel/pbsDecode.help_src' -> `./src/prequel/pbsDecode.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/prequel/pbsScoreMatrix.c' -> `./src/prequel/pbsScoreMatrix.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/phastOdds/Makefile' -> `./src/phastOdds/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/phastOdds/phastOdds.c' -> `./src/phastOdds/phastOdds.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/phastOdds/phastOdds.help_src' -> `./src/phastOdds/phastOdds.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/phyloFit/Makefile' -> `./src/phyloFit/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/phyloFit/phyloFit.help_src' -> `./src/phyloFit/phyloFit.help_src' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/phyloFit/phyloFit.c' -> `./src/phyloFit/phyloFit.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/phyloP/Makefile' -> `./src/phyloP/Makefile' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/phyloP/phyloP.c' -> `./src/phyloP/phyloP.c' `/gnu/store/3ml5g52y4afq0p3bjyi0fyr5h0apadr9-phast-1.5-checkout/src/phyloP/phyloP.help_src' -> `./src/phyloP/phyloP.help_src' phase `unpack' succeeded after 0.2 seconds starting phase `bootstrap' no 'configure.ac' or anything like that, doing nothing phase `bootstrap' 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: ./binary_install.sh: changing `/bin/bash' to `/gnu/store/vza0n6gb01lbc9cgwx2hygvq15qiczn6-bash-minimal-5.1.16/bin/bash' patch-shebang: ./src/help2man.pl: changing `/usr/bin/perl' to `/gnu/store/y808025ygal6skd4fxl96ysn6bpyfq8j-perl-5.36.0/bin/perl' patch-shebang: ./src/munge-help.sh: changing `/bin/bash' to `/gnu/store/vza0n6gb01lbc9cgwx2hygvq15qiczn6-bash-minimal-5.1.16/bin/bash' patch-shebang: ./test/testPhast.pl: changing `/usr/bin/perl' to `/gnu/store/y808025ygal6skd4fxl96ysn6bpyfq8j-perl-5.36.0/bin/perl' phase `patch-source-shebangs' succeeded after 0.0 seconds starting phase `configure' phase `configure' succeeded after 0.0 seconds starting phase `patch-generated-file-shebangs' phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `build' Type "make package" to create a tarball reflecting the current state of the CVS tree. (cd src; make DESTDIR=/gnu/store/32qv7x3a6rir7cqwvxkvvllh27kqbfgc-phast-1.5 CLAPACKPATH=/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib ) make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[1]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src' mkdir -p ../bin ../lib for dir in lib dless exoniphy phastCons phastOdds phastMotif phyloFit phyloBoot phyloP prequel util ; do cd /tmp/guix-build-phast-1.5.drv-0/source/src/$dir && make ; done make[2]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib' for dir in base msa feature hmm phylo phylo_hmm motif pcre; do cd /tmp/guix-build-phast-1.5.drv-0/source/src/lib/$dir && make ; done make[3]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base' gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c complex_matrix.c -o complex_matrix.o complex_matrix.c: In function ‘zmat_create_copy’: complex_matrix.c:86:19: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 86 | Zmatrix *dest = zmat_new(src->nrows, src->ncols); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c complex_vector.c -o complex_vector.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c eigen.c -o eigen.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c hashtable.c -o hashtable.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c list_of_lists.c -o list_of_lists.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c lists.c -o lists.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c markov_matrix.c -o markov_matrix.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c matrix.c -o matrix.o matrix.c: In function ‘mat_create_copy’: matrix.c:98:18: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 98 | Matrix *dest = mat_new(src->nrows, src->ncols); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c memory_handler.c -o memory_handler.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c misc.c -o misc.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c numerical_opt.c -o numerical_opt.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c prob_matrix.c -o prob_matrix.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c prob_vector.c -o prob_vector.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c stringsplus.c -o stringsplus.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c vector.c -o vector.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar: creating /tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../lib/libphast.a ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o make[3]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib/base' make[3]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa' gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c local_alignment.c -o local_alignment.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c maf_block.c -o maf_block.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c maf.c -o maf.o maf.c: In function ‘maf_read_cats_subset’: maf.c:29:41: warning: variable ‘block_no’ set but not used [-Wunused-but-set-variable] 29 | int i, start_idx, length, max_tuples, block_no, | ^~~~~~~~ gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c msa.c -o msa.o msa.c: In function ‘msa_read_fasta’: msa.c:257:40: warning: variable ‘line_no’ set but not used [-Wunused-but-set-variable] 257 | int maxlen, i, nseqs, j, do_toupper, line_no; | ^~~~~~~ gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c multi_msa.c -o multi_msa.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c sufficient_stats.c -o sufficient_stats.o sufficient_stats.c: In function ‘ss_from_msas’: sufficient_stats.c:140:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 140 | else | ^~~~ sufficient_stats.c:142:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 142 | max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1, | ^~~~~~~~~~ ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../lib/libphast.a local_alignment.o maf_block.o maf.o msa.o multi_msa.o sufficient_stats.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../lib/libphast.a local_alignment.o maf_block.o maf.o msa.o multi_msa.o sufficient_stats.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../lib/libphast.a local_alignment.o maf_block.o maf.o msa.o multi_msa.o sufficient_stats.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../lib/libphast.a local_alignment.o maf_block.o maf.o msa.o multi_msa.o sufficient_stats.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../lib/libphast.a local_alignment.o maf_block.o maf.o msa.o multi_msa.o sufficient_stats.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa/../../../lib/libphast.a local_alignment.o maf_block.o maf.o msa.o multi_msa.o sufficient_stats.o make[3]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib/msa' make[3]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature' gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c bed.c -o bed.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c category_map.c -o category_map.o category_map.c: In function ‘cm_create_trivial’: category_map.c:559:20: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 559 | cr->start_cat_no = start_cat_no; | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c genepred.c -o genepred.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c gff.c -o gff.o gff.c: In function ‘gff_new_feature_copy’: gff.c:423:14: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 423 | GFF_Feature *gff_new_feature_copy(GFF_Feature *orig) { | ^~~~~~~~~~~~~~~~~~~~ gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c wig.c -o wig.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o make[3]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib/feature' make[3]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib/hmm' gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/hmm/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/hmm/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c em.c -o em.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/hmm/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/hmm/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c hmm.c -o hmm.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/hmm/../../../lib/libphast.a em.o hmm.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/hmm/../../../lib/libphast.a em.o hmm.o make[3]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib/hmm' make[3]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo' gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c bgc_hmm.c -o bgc_hmm.o bgc_hmm.c: In function ‘bgcHmm’: bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 241 | sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars); | ^~ bgc_hmm.c:241:7: note: ‘sprintf’ output 3 or more bytes (assuming 10002) into a destination of size 10000 241 | sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bgc_hmm.c:241:7: warning: ‘sprintf’ argument 3 overlaps destination object ‘warning_str’ [-Wrestrict] bgc_hmm.c:235:10: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here 235 | char warning_str[10000]; | ^~~~~~~~~~~ bgc_hmm.c:242:29: warning: ‘) ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=] 242 | sprintf(warning_str, "%s)\n", warning_str); | ^~~ bgc_hmm.c:242:5: note: ‘sprintf’ output between 3 and 10002 bytes into a destination of size 10000 242 | sprintf(warning_str, "%s)\n", warning_str); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bgc_hmm.c:242:5: warning: ‘sprintf’ argument 3 overlaps destination object ‘warning_str’ [-Wrestrict] bgc_hmm.c:235:10: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here 235 | char warning_str[10000]; | ^~~~~~~~~~~ gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c dgamma.c -o dgamma.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c fit_column.c -o fit_column.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c fit_em.c -o fit_em.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c fit_feature.c -o fit_feature.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c indel_history.c -o indel_history.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c indel_mod.c -o indel_mod.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c phast_cons.c -o phast_cons.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c phylo_fit.c -o phylo_fit.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c phylo_p.c -o phylo_p.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c phylo_p_print.c -o phylo_p_print.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c subst_distrib.c -o subst_distrib.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c subst_mods.c -o subst_mods.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c tree_likelihoods.c -o tree_likelihoods.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c tree_model.c -o tree_model.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c trees.c -o trees.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o make[3]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo' make[3]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo_hmm' gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo_hmm/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo_hmm/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c gap_patterns.c -o gap_patterns.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo_hmm/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo_hmm/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c phylo_hmm.c -o phylo_hmm.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo_hmm/../../../lib/libphast.a gap_patterns.o phylo_hmm.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo_hmm/../../../lib/libphast.a gap_patterns.o phylo_hmm.o make[3]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib/phylo_hmm' make[3]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib/motif' gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/motif/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/motif/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c motif.c -o motif.o motif.c: In function ‘mtf_print’: motif.c:1411:7: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 1411 | fprintf(F, "\t%s\n", (char*)lst_get_ptr(notfound, i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ motif.c: In function ‘mtf_print_html’: motif.c:1604:7: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 1604 | fprintf(F, "
  • %s\n", (char*)lst_get_ptr(notfound, i)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/motif/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/motif/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c tfbs.c -o tfbs.o tfbs.c: In function ‘ms_read’: tfbs.c:219:32: warning: variable ‘line_no’ set but not used [-Wunused-but-set-variable] 219 | int i, nseqs, j, do_toupper, line_no; | ^~~~~~~ ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/motif/../../../lib/libphast.a motif.o tfbs.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/motif/../../../lib/libphast.a motif.o tfbs.o make[3]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib/motif' make[3]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre' gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_chartables.c -o pcre_chartables.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_compile.c -o pcre_compile.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_config.c -o pcre_config.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_dfa_exec.c -o pcre_dfa_exec.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_exec.c -o pcre_exec.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_fullinfo.c -o pcre_fullinfo.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_get.c -o pcre_get.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_globals.c -o pcre_globals.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_info.c -o pcre_info.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_maketables.c -o pcre_maketables.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_newline.c -o pcre_newline.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_ord2utf8.c -o pcre_ord2utf8.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_refcount.c -o pcre_refcount.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_study.c -o pcre_study.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_tables.c -o pcre_tables.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_try_flipped.c -o pcre_try_flipped.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_ucd.c -o pcre_ucd.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_valid_utf8.c -o pcre_valid_utf8.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_version.c -o pcre_version.o gcc -I. -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -DHAVE_CONFIG_H -c pcre_xclass.c -o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o ar rs /tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre/../../../lib/libphast.a pcre_chartables.o pcre_compile.o pcre_config.o pcre_dfa_exec.o pcre_exec.o pcre_fullinfo.o pcre_get.o pcre_globals.o pcre_info.o pcre_maketables.o pcre_newline.o pcre_ord2utf8.o pcre_refcount.o pcre_study.o pcre_tables.o pcre_try_flipped.o pcre_ucd.o pcre_valid_utf8.o pcre_version.o pcre_xclass.o make[3]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib/pcre' make[2]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/lib' make[2]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/dless' ../munge-help.sh dless.help_src > dless.help ../munge-help.sh dlessP.help_src > dlessP.help gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/dless/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/dless/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/dless/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c dless.c -o dless.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/dless/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/dless/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/dless/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c bd_phylo_hmm.c -o bd_phylo_hmm.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/dless/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/dless/../../bin/dless dless.o bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/dless/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/dless/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/dless/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c dlessP.c -o dlessP.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/dless/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/dless/../../bin/dlessP dlessP.o bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm make[2]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/dless' make[2]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/exoniphy' ../munge-help.sh exoniphy.help_src > exoniphy.help gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/exoniphy/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/exoniphy/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/exoniphy/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c exoniphy.c -o exoniphy.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/exoniphy/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm make[2]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/exoniphy' make[2]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/phastCons' ../munge-help.sh phastCons.help_src > phastCons.help gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/phastCons/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/phastCons/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/phastCons/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c phastCons.c -o phastCons.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/phastCons/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm make[2]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/phastCons' make[2]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/phastOdds' ../munge-help.sh phastOdds.help_src > phastOdds.help gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/phastOdds/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/phastOdds/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/phastOdds/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c phastOdds.c -o phastOdds.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/phastOdds/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm make[2]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/phastOdds' make[2]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/phastMotif' gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/phastMotif/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/phastMotif/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/phastMotif/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c phastMotif.c -o phastMotif.o phastMotif.c: In function ‘main’: phastMotif.c:131:13: warning: variable ‘separate_backgd’ set but not used [-Wunused-but-set-variable] 131 | int i, j, separate_backgd = 0, | ^~~~~~~~~~~~~~~ gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/phastMotif/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm make[2]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/phastMotif' make[2]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/phyloFit' ../munge-help.sh phyloFit.help_src > phyloFit.help gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/phyloFit/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/phyloFit/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/phyloFit/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c phyloFit.c -o phyloFit.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/phyloFit/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/phyloFit/../../bin/phyloFit phyloFit.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm make[2]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/phyloFit' make[2]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/phyloBoot' ../munge-help.sh phyloBoot.help_src > phyloBoot.help gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/phyloBoot/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/phyloBoot/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c phyloBoot.c -o phyloBoot.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/phyloBoot/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm make[2]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/phyloBoot' make[2]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/phyloP' ../munge-help.sh phyloP.help_src > phyloP.help gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/phyloP/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/phyloP/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/phyloP/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c phyloP.c -o phyloP.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/phyloP/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm make[2]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/phyloP' make[2]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/prequel' ../munge-help.sh pbsDecode.help_src > pbsDecode.help ../munge-help.sh pbsEncode.help_src > pbsEncode.help ../munge-help.sh pbsScoreMatrix.help_src > pbsScoreMatrix.help ../munge-help.sh pbsTrain.help_src > pbsTrain.help ../munge-help.sh prequel.help_src > prequel.help gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c pbsDecode.c -o pbsDecode.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c simplex_grid.c -o simplex_grid.o gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c pbs_code.c -o pbs_code.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../bin/pbsDecode pbsDecode.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c pbsEncode.c -o pbsEncode.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../bin/pbsEncode pbsEncode.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c pbsScoreMatrix.c -o pbsScoreMatrix.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../bin/pbsScoreMatrix pbsScoreMatrix.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c pbsTrain.c -o pbsTrain.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../bin/pbsTrain pbsTrain.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c prequel.c -o prequel.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/prequel/../../bin/prequel prequel.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm make[2]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/prequel' make[2]: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/src/util' ../munge-help.sh base_evolve.help_src > base_evolve.help ../munge-help.sh clean_genes.help_src > clean_genes.help ../munge-help.sh consEntropy.help_src > consEntropy.help ../munge-help.sh indelFit.help_src > indelFit.help ../munge-help.sh indelHistory.help_src > indelHistory.help ../munge-help.sh makeHKY.help_src > makeHKY.help ../munge-help.sh modFreqs.help_src > modFreqs.help ../munge-help.sh msa_diff.help_src > msa_diff.help ../munge-help.sh phastBias.help_src > phastBias.help ../munge-help.sh phast.help_src > phast.help ../munge-help.sh treeGen.help_src > treeGen.help gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c all_dists.c -o all_dists.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c base_evolve.c -o base_evolve.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c chooseLines.c -o chooseLines.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c clean_genes.c -o clean_genes.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c consEntropy.c -o consEntropy.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c convert_coords.c -o convert_coords.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c display_rate_matrix.c -o display_rate_matrix.o display_rate_matrix.c: In function ‘do_context_dependent_ti_tv’: display_rate_matrix.c:204:8: warning: variable ‘tuple_i’ set but not used [-Wunused-but-set-variable] 204 | char tuple_i[mod->order+2], tuple_j[mod->order+2]; | ^~~~~~~ gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c draw_tree.c -o draw_tree.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c eval_predictions.c -o eval_predictions.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c hmm_train.c -o hmm_train.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c hmm_tweak.c -o hmm_tweak.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c hmm_view.c -o hmm_view.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c indelFit.c -o indelFit.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c indelHistory.c -o indelHistory.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c maf_parse.c -o maf_parse.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c makeHKY.c -o makeHKY.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c modFreqs.c -o modFreqs.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c msa_diff.c -o msa_diff.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c msa_split.c -o msa_split.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c msa_view.c -o msa_view.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c phastBias.c -o phastBias.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c phast.c -o phast.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c refeature.c -o refeature.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c stringiphy.c -o stringiphy.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c tree_doctor.c -o tree_doctor.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm gcc -O3 -Wall -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/tmp/guix-build-phast-1.5.drv-0/source/src/util/../..\" -I/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../src/lib/pcre -fno-strict-aliasing -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/INCLUDE -I/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -c treeGen.c -o treeGen.o gcc -L/tmp/guix-build-phast-1.5.drv-0/source/src/util/../../lib -L/gnu/store/mgicxrfxrmqh9vny8w4saj8542abzvlv-clapack-3.2.1/lib/F2CLIBS -o /tmp/guix-build-phast-1.5.drv-0/source/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lf2c -lm make[2]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src/util' mkdir -p ../doc/man/ Generating man pages... Done. make[1]: Leaving directory '/tmp/guix-build-phast-1.5.drv-0/source/src' phase `build' succeeded after 64.3 seconds starting phase `check' make: Entering directory '/tmp/guix-build-phast-1.5.drv-0/source/test' *** Testing msa_view *** msa_view hmrc.ss -i SS --end 10000 > hmrc.fa