starting phase `separate-from-pid1' build process now running as PID 18 phase `separate-from-pid1' succeeded after 0.0 seconds starting phase `set-SOURCE-DATE-EPOCH' phase `set-SOURCE-DATE-EPOCH' succeeded after 0.0 seconds starting phase `set-paths' environment variable `PATH' set to `/gnu/store/lcfbfljdfz9d74cy1llfvq502rzlah2m-python-wrapper-3.10.7/bin:/gnu/store/9qcvl6rg6idqns39ra2jbm2kdz1rwicx-tar-1.34/bin:/gnu/store/5yv24flz74w2bjbpl4fy9n8brcnhhg0m-gzip-1.13/bin:/gnu/store/pdsn19r59s8mbac1z7qj17738b0yng92-bzip2-1.0.8/bin:/gnu/store/z7r7qf08p6qgaw27qy86d8fgbknz8c0s-file-5.45/bin:/gnu/store/nq9418ayx64v9ahnwldvihlv4mddg64c-diffutils-3.10/bin:/gnu/store/drgzs1dic48b1rz090b39yw09wvjs0qa-patch-2.7.6/bin:/gnu/store/r4r6zdsgqc1wmxmy3lasxj1z1bg9ciqc-findutils-4.9.0/bin:/gnu/store/5wsbh52qwg83h2zap0pgic5fn985cq2z-gawk-5.3.0/bin:/gnu/store/swsr50qcmki242ka78gwvqyw821463rv-zstd-1.5.2/bin:/gnu/store/rjjzvnkk4cv57859wvjchgdsd0zrjnim-sed-4.8/bin:/gnu/store/iy4f97nh5mrn7q7miw2ypxnz4fp19k6k-grep-3.11/bin:/gnu/store/ylddhkxf92aq06m28nzz671jbcmdw48j-xz-5.4.5/bin:/gnu/store/3bg5qfsmjw6p7bh1xadarbaq246zis0d-coreutils-9.1/bin:/gnu/store/m3fxyhpqp774hi0kx8vmxibsqz99lqa7-make-4.4.1/bin:/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin:/gnu/store/mg6dkhs9w5a46b4nvdx1nmmdgbp0cfcd-ld-wrapper-0/bin:/gnu/store/byb1pwq6pw3j8mmx3p7491jx7a6a03c5-binutils-2.41/bin:/gnu/store/bqxrv6awpk0y1k67c040qm28imk7xds1-gcc-11.4.0/bin:/gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/bin:/gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/sbin:/gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/bin' environment variable `GUIX_PYTHONPATH' set to `/gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/lib/python3.10/site-packages' environment variable `PYTHONTZPATH' unset environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/jac1blp3miqs1730q0r2lxs5yf0jnqzi-zlib-1.3/include:/gnu/store/pdsn19r59s8mbac1z7qj17738b0yng92-bzip2-1.0.8/include:/gnu/store/z7r7qf08p6qgaw27qy86d8fgbknz8c0s-file-5.45/include:/gnu/store/5wsbh52qwg83h2zap0pgic5fn985cq2z-gawk-5.3.0/include:/gnu/store/ylddhkxf92aq06m28nzz671jbcmdw48j-xz-5.4.5/include:/gnu/store/m3fxyhpqp774hi0kx8vmxibsqz99lqa7-make-4.4.1/include:/gnu/store/byb1pwq6pw3j8mmx3p7491jx7a6a03c5-binutils-2.41/include:/gnu/store/bqxrv6awpk0y1k67c040qm28imk7xds1-gcc-11.4.0/include:/gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/include:/gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/include:/gnu/store/j0w4q2cbzjbg7s4yf9lip8dcbslbw3hi-linux-libre-headers-5.15.49/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/jac1blp3miqs1730q0r2lxs5yf0jnqzi-zlib-1.3/include:/gnu/store/pdsn19r59s8mbac1z7qj17738b0yng92-bzip2-1.0.8/include:/gnu/store/z7r7qf08p6qgaw27qy86d8fgbknz8c0s-file-5.45/include:/gnu/store/5wsbh52qwg83h2zap0pgic5fn985cq2z-gawk-5.3.0/include:/gnu/store/ylddhkxf92aq06m28nzz671jbcmdw48j-xz-5.4.5/include:/gnu/store/m3fxyhpqp774hi0kx8vmxibsqz99lqa7-make-4.4.1/include:/gnu/store/byb1pwq6pw3j8mmx3p7491jx7a6a03c5-binutils-2.41/include:/gnu/store/bqxrv6awpk0y1k67c040qm28imk7xds1-gcc-11.4.0/include/c++:/gnu/store/bqxrv6awpk0y1k67c040qm28imk7xds1-gcc-11.4.0/include:/gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/include:/gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/include:/gnu/store/j0w4q2cbzjbg7s4yf9lip8dcbslbw3hi-linux-libre-headers-5.15.49/include' environment variable `OBJC_INCLUDE_PATH' set to `/gnu/store/jac1blp3miqs1730q0r2lxs5yf0jnqzi-zlib-1.3/include:/gnu/store/pdsn19r59s8mbac1z7qj17738b0yng92-bzip2-1.0.8/include:/gnu/store/z7r7qf08p6qgaw27qy86d8fgbknz8c0s-file-5.45/include:/gnu/store/5wsbh52qwg83h2zap0pgic5fn985cq2z-gawk-5.3.0/include:/gnu/store/ylddhkxf92aq06m28nzz671jbcmdw48j-xz-5.4.5/include:/gnu/store/m3fxyhpqp774hi0kx8vmxibsqz99lqa7-make-4.4.1/include:/gnu/store/byb1pwq6pw3j8mmx3p7491jx7a6a03c5-binutils-2.41/include:/gnu/store/bqxrv6awpk0y1k67c040qm28imk7xds1-gcc-11.4.0/include:/gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/include:/gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/include:/gnu/store/j0w4q2cbzjbg7s4yf9lip8dcbslbw3hi-linux-libre-headers-5.15.49/include' environment variable `OBJCPLUS_INCLUDE_PATH' set to `/gnu/store/jac1blp3miqs1730q0r2lxs5yf0jnqzi-zlib-1.3/include:/gnu/store/pdsn19r59s8mbac1z7qj17738b0yng92-bzip2-1.0.8/include:/gnu/store/z7r7qf08p6qgaw27qy86d8fgbknz8c0s-file-5.45/include:/gnu/store/5wsbh52qwg83h2zap0pgic5fn985cq2z-gawk-5.3.0/include:/gnu/store/ylddhkxf92aq06m28nzz671jbcmdw48j-xz-5.4.5/include:/gnu/store/m3fxyhpqp774hi0kx8vmxibsqz99lqa7-make-4.4.1/include:/gnu/store/byb1pwq6pw3j8mmx3p7491jx7a6a03c5-binutils-2.41/include:/gnu/store/bqxrv6awpk0y1k67c040qm28imk7xds1-gcc-11.4.0/include/c++:/gnu/store/bqxrv6awpk0y1k67c040qm28imk7xds1-gcc-11.4.0/include:/gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/include:/gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/include:/gnu/store/j0w4q2cbzjbg7s4yf9lip8dcbslbw3hi-linux-libre-headers-5.15.49/include' environment variable `LIBRARY_PATH' set to `/gnu/store/jac1blp3miqs1730q0r2lxs5yf0jnqzi-zlib-1.3/lib:/gnu/store/pdsn19r59s8mbac1z7qj17738b0yng92-bzip2-1.0.8/lib:/gnu/store/z7r7qf08p6qgaw27qy86d8fgbknz8c0s-file-5.45/lib:/gnu/store/5wsbh52qwg83h2zap0pgic5fn985cq2z-gawk-5.3.0/lib:/gnu/store/ylddhkxf92aq06m28nzz671jbcmdw48j-xz-5.4.5/lib:/gnu/store/byb1pwq6pw3j8mmx3p7491jx7a6a03c5-binutils-2.41/lib:/gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/lib:/gnu/store/hwzlxqp51gl75fni0vzyshsfbn062bhz-glibc-2.39-static/lib:/gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/lib/locale' environment variable `TZDIR' unset phase `set-paths' succeeded after 0.0 seconds starting phase `install-locale' using 'C.UTF-8' locale for category "LC_ALL" phase `install-locale' succeeded after 0.0 seconds starting phase `unpack' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/Makefile' -> `./Makefile' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/pairs_format_specification.md' -> `./pairs_format_specification.md' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/VERSION.txt' -> `./VERSION.txt' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/.travis.yml' -> `./.travis.yml' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/pairix_indexing_benchmarking_large_files.20170505.png' -> `./pairix_indexing_benchmarking_large_files.20170505.png' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/README.md' -> `./README.md' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/LICENSE.txt' -> `./LICENSE.txt' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/setup.py' -> `./setup.py' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/.gitignore' -> `./.gitignore' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/pairix_indexing_benchmarking_large_files.20170505.pdf' -> `./pairix_indexing_benchmarking_large_files.20170505.pdf' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/setup.cfg' -> `./setup.cfg' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/MANIFEST.in' -> `./MANIFEST.in' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_old_merged_nodups.bsorted.pairs.gz' -> `./samples/test_old_merged_nodups.bsorted.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/4dn.bsorted.chr21_22_only.largechr.pairs' -> `./samples/4dn.bsorted.chr21_22_only.largechr.pairs' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/merged_nodups.space.chrblock_sorted.subsample1.txt.gz' -> `./samples/merged_nodups.space.chrblock_sorted.subsample1.txt.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_juicer_shortform.pairs' -> `./samples/test_juicer_shortform.pairs' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_4dn_2.bsorted.pairs.gz' -> `./samples/test_4dn_2.bsorted.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/mock.largechr.pairs.gz' -> `./samples/mock.largechr.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_merged_nodups.txt' -> `./samples/test_merged_nodups.txt' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/merged_nodup.tab.chrblock_sorted.txt.gz.px2' -> `./samples/merged_nodup.tab.chrblock_sorted.txt.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/4dn.bsorted.chr21_22_only.pairs.gz' -> `./samples/4dn.bsorted.chr21_22_only.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/merged_nodups.space.chrblock_sorted.subsample3.txt.gz' -> `./samples/merged_nodups.space.chrblock_sorted.subsample3.txt.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_old_merged_nodups.pairs' -> `./samples/test_old_merged_nodups.pairs' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/hg19.chrom.sizes.chr21_22_only' -> `./samples/hg19.chrom.sizes.chr21_22_only' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz' -> `./samples/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.pairs.gz' -> `./samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_merged_nodups.bsorted.pairs.gz.px2' -> `./samples/test_merged_nodups.bsorted.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_4dn_2.bsorted.pairs.gz.px2' -> `./samples/test_4dn_2.bsorted.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_4dn.cp.pairs' -> `./samples/test_4dn.cp.pairs' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/hg19.chrom.sizes.-chr' -> `./samples/hg19.chrom.sizes.-chr' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_merged_nodups.txt.bsorted.gz' -> `./samples/test_merged_nodups.txt.bsorted.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_juicer_shortform.bsorted.pairs.gz' -> `./samples/test_juicer_shortform.bsorted.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/merged_nodups.space.chrblock_sorted.subsample3.txt.gz.px2' -> `./samples/merged_nodups.space.chrblock_sorted.subsample3.txt.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_merged_nodups.bsorted.pairs.gz' -> `./samples/test_merged_nodups.bsorted.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.nofrag.pairs.gz' -> `./samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.nofrag.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_juicer_shortform.bsorted.pairs.gz.px2' -> `./samples/test_juicer_shortform.bsorted.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test.bed' -> `./samples/test.bed' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/SRR1171591.variants.snp.vqsr.p.vcf.gz.px2' -> `./samples/SRR1171591.variants.snp.vqsr.p.vcf.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/merged_nodups.space.chrblock_sorted.subsample1.txt.gz.px2' -> `./samples/merged_nodups.space.chrblock_sorted.subsample1.txt.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/merged_nodups.space.chrblock_sorted.subsample3.pairs' -> `./samples/merged_nodups.space.chrblock_sorted.subsample3.pairs' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/merged_nodup.tab.chrblock_sorted.txt.gz' -> `./samples/merged_nodup.tab.chrblock_sorted.txt.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_old_merged_nodups.bsorted.pairs.gz.px2' -> `./samples/test_old_merged_nodups.bsorted.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/hg19.chrom.sizes.chr21_22_only:50000' -> `./samples/hg19.chrom.sizes.chr21_22_only:50000' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_old_merged_nodups.txt.bsorted.gz' -> `./samples/test_old_merged_nodups.txt.bsorted.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/mock.largechr.pairs.gz.px2' -> `./samples/mock.largechr.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.pairs.gz.px2' -> `./samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_juicer_shortform.txt' -> `./samples/test_juicer_shortform.txt' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_old_merged_nodups.txt.bsorted.gz.px2' -> `./samples/test_old_merged_nodups.txt.bsorted.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/merged_nodups.space.chrblock_sorted.subsample2.txt.gz' -> `./samples/merged_nodups.space.chrblock_sorted.subsample2.txt.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.ff.pairs.gz.px2' -> `./samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.ff.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/merged_nodups.space.chrblock_sorted.subsample2.txt.gz.px2' -> `./samples/merged_nodups.space.chrblock_sorted.subsample2.txt.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.nofrag.pairs.gz.px2' -> `./samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.nofrag.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_old_merged_nodups.txt' -> `./samples/test_old_merged_nodups.txt' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_merged_nodups.txt.bsorted.gz.px2' -> `./samples/test_merged_nodups.txt.bsorted.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/4dn.bsorted.chr21_22_only.pairs.gz.px2' -> `./samples/4dn.bsorted.chr21_22_only.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.ff.pairs.gz' -> `./samples/merged_nodups.space.chrblock_sorted.subsample3.bsorted.ff.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_4dn.pairs.gz' -> `./samples/test_4dn.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_merged_nodups.pairs' -> `./samples/test_merged_nodups.pairs' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/SRR1171591.variants.snp.vqsr.p.vcf.gz' -> `./samples/SRR1171591.variants.snp.vqsr.p.vcf.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test.regions' -> `./samples/test.regions' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test.regions2' -> `./samples/test.regions2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/test_4dn.pairs.gz.px2' -> `./samples/test_4dn.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2' -> `./samples/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index2/merged_nodups.space.chrblock_sorted.subsample1.txt.gz' -> `./samples/old_index2/merged_nodups.space.chrblock_sorted.subsample1.txt.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index2/mock.largechr.pairs.gz' -> `./samples/old_index2/mock.largechr.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index2/merged_nodup.tab.chrblock_sorted.txt.gz.px2' -> `./samples/old_index2/merged_nodup.tab.chrblock_sorted.txt.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index2/4dn.bsorted.chr21_22_only.pairs.gz' -> `./samples/old_index2/4dn.bsorted.chr21_22_only.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index2/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz' -> `./samples/old_index2/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index2/SRR1171591.variants.snp.vqsr.p.vcf.gz.px2' -> `./samples/old_index2/SRR1171591.variants.snp.vqsr.p.vcf.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index2/merged_nodups.space.chrblock_sorted.subsample1.txt.gz.px2' -> `./samples/old_index2/merged_nodups.space.chrblock_sorted.subsample1.txt.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index2/merged_nodup.tab.chrblock_sorted.txt.gz' -> `./samples/old_index2/merged_nodup.tab.chrblock_sorted.txt.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index2/mock.largechr.pairs.gz.px2' -> `./samples/old_index2/mock.largechr.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index2/4dn.bsorted.chr21_22_only.pairs.gz.px2' -> `./samples/old_index2/4dn.bsorted.chr21_22_only.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index2/test_4dn.pairs.gz' -> `./samples/old_index2/test_4dn.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index2/SRR1171591.variants.snp.vqsr.p.vcf.gz' -> `./samples/old_index2/SRR1171591.variants.snp.vqsr.p.vcf.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index2/test_4dn.pairs.gz.px2' -> `./samples/old_index2/test_4dn.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index2/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2' -> `./samples/old_index2/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_old_merged_nodups.bsorted.pairs.gz' -> `./samples/old_index/test_old_merged_nodups.bsorted.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/merged_nodups.space.chrblock_sorted.subsample1.txt.gz' -> `./samples/old_index/merged_nodups.space.chrblock_sorted.subsample1.txt.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_juicer_shortform.pairs' -> `./samples/old_index/test_juicer_shortform.pairs' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_4dn_2.bsorted.pairs.gz' -> `./samples/old_index/test_4dn_2.bsorted.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/mock.largechr.pairs.gz' -> `./samples/old_index/mock.largechr.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_merged_nodups.txt' -> `./samples/old_index/test_merged_nodups.txt' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/merged_nodup.tab.chrblock_sorted.txt.gz.px2' -> `./samples/old_index/merged_nodup.tab.chrblock_sorted.txt.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/4dn.bsorted.chr21_22_only.pairs.gz' -> `./samples/old_index/4dn.bsorted.chr21_22_only.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.txt.gz' -> `./samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.txt.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_old_merged_nodups.pairs' -> `./samples/old_index/test_old_merged_nodups.pairs' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/hg19.chrom.sizes.chr21_22_only' -> `./samples/old_index/hg19.chrom.sizes.chr21_22_only' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz' -> `./samples/old_index/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.pairs.gz' -> `./samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_merged_nodups.bsorted.pairs.gz.px2' -> `./samples/old_index/test_merged_nodups.bsorted.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_4dn_2.bsorted.pairs.gz.px2' -> `./samples/old_index/test_4dn_2.bsorted.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_4dn.cp.pairs' -> `./samples/old_index/test_4dn.cp.pairs' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/hg19.chrom.sizes.-chr' -> `./samples/old_index/hg19.chrom.sizes.-chr' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_merged_nodups.txt.bsorted.gz' -> `./samples/old_index/test_merged_nodups.txt.bsorted.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_juicer_shortform.bsorted.pairs.gz' -> `./samples/old_index/test_juicer_shortform.bsorted.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.txt.gz.px2' -> `./samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.txt.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_merged_nodups.bsorted.pairs.gz' -> `./samples/old_index/test_merged_nodups.bsorted.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.nofrag.pairs.gz' -> `./samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.nofrag.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_juicer_shortform.bsorted.pairs.gz.px2' -> `./samples/old_index/test_juicer_shortform.bsorted.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test.bed' -> `./samples/old_index/test.bed' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/SRR1171591.variants.snp.vqsr.p.vcf.gz.px2' -> `./samples/old_index/SRR1171591.variants.snp.vqsr.p.vcf.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/merged_nodups.space.chrblock_sorted.subsample1.txt.gz.px2' -> `./samples/old_index/merged_nodups.space.chrblock_sorted.subsample1.txt.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.pairs' -> `./samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.pairs' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/merged_nodup.tab.chrblock_sorted.txt.gz' -> `./samples/old_index/merged_nodup.tab.chrblock_sorted.txt.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_old_merged_nodups.bsorted.pairs.gz.px2' -> `./samples/old_index/test_old_merged_nodups.bsorted.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/hg19.chrom.sizes.chr21_22_only:50000' -> `./samples/old_index/hg19.chrom.sizes.chr21_22_only:50000' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_old_merged_nodups.txt.bsorted.gz' -> `./samples/old_index/test_old_merged_nodups.txt.bsorted.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/mock.largechr.pairs.gz.px2' -> `./samples/old_index/mock.largechr.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.pairs.gz.px2' -> `./samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_juicer_shortform.txt' -> `./samples/old_index/test_juicer_shortform.txt' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_old_merged_nodups.txt.bsorted.gz.px2' -> `./samples/old_index/test_old_merged_nodups.txt.bsorted.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/merged_nodups.space.chrblock_sorted.subsample2.txt.gz' -> `./samples/old_index/merged_nodups.space.chrblock_sorted.subsample2.txt.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.ff.pairs.gz.px2' -> `./samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.ff.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/merged_nodups.space.chrblock_sorted.subsample2.txt.gz.px2' -> `./samples/old_index/merged_nodups.space.chrblock_sorted.subsample2.txt.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.nofrag.pairs.gz.px2' -> `./samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.nofrag.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_old_merged_nodups.txt' -> `./samples/old_index/test_old_merged_nodups.txt' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_merged_nodups.txt.bsorted.gz.px2' -> `./samples/old_index/test_merged_nodups.txt.bsorted.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/4dn.bsorted.chr21_22_only.pairs.gz.px2' -> `./samples/old_index/4dn.bsorted.chr21_22_only.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.ff.pairs.gz' -> `./samples/old_index/merged_nodups.space.chrblock_sorted.subsample3.bsorted.ff.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_4dn.pairs.gz' -> `./samples/old_index/test_4dn.pairs.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_merged_nodups.pairs' -> `./samples/old_index/test_merged_nodups.pairs' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/SRR1171591.variants.snp.vqsr.p.vcf.gz' -> `./samples/old_index/SRR1171591.variants.snp.vqsr.p.vcf.gz' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test.regions' -> `./samples/old_index/test.regions' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test.regions2' -> `./samples/old_index/test.regions2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/test_4dn.pairs.gz.px2' -> `./samples/old_index/test_4dn.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/samples/old_index/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2' -> `./samples/old_index/4dn.bsorted.chr21_22_only.nontriangle.pairs.gz.px2' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/test/test.py' -> `./test/test.py' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/test/test_c_oldindex.sh' -> `./test/test_c_oldindex.sh' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/test/test_c.sh' -> `./test/test_c.sh' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/test/test_c_oldindex2.sh' -> `./test/test_c_oldindex2.sh' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/test/test_oldindex2.py' -> `./test/test_oldindex2.py' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/test/test_oldindex.py' -> `./test/test_oldindex.py' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/test/reindex_samples.sh' -> `./test/reindex_samples.sh' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/test/inefficient-merger-for-testing' -> `./test/inefficient-merger-for-testing' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/test/__pycache__/test.cpython-35.pyc' -> `./test/__pycache__/test.cpython-35.pyc' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/util/juicer_shortform2pairs.pl' -> `./util/juicer_shortform2pairs.pl' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/util/merged_nodup2pairs.pl' -> `./util/merged_nodup2pairs.pl' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/util/duplicate_header_remover.pl' -> `./util/duplicate_header_remover.pl' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/util/process_old_merged_nodup.sh' -> `./util/process_old_merged_nodup.sh' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/util/column_remover.pl' -> `./util/column_remover.pl' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/util/create_randompairs.pl' -> `./util/create_randompairs.pl' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/util/merge-pairs.sh' -> `./util/merge-pairs.sh' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/util/fragment_4dnpairs.pl' -> `./util/fragment_4dnpairs.pl' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/util/boostchr.pl' -> `./util/boostchr.pl' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/util/old_merged_nodup2pairs.pl' -> `./util/old_merged_nodup2pairs.pl' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/util/process_merged_nodup.sh' -> `./util/process_merged_nodup.sh' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/util/bam2pairs/README.md' -> `./util/bam2pairs/README.md' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/util/bam2pairs/bam2pairs' -> `./util/bam2pairs/bam2pairs' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/Makefile' -> `./src/Makefile' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/pairix.h' -> `./src/pairix.h' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/pairixmodule.c' -> `./src/pairixmodule.c' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/khash.h' -> `./src/khash.h' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/bgzf.c' -> `./src/bgzf.c' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/bgzip.c' -> `./src/bgzip.c' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/ksort.h' -> `./src/ksort.h' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/kseq.h' -> `./src/kseq.h' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/bam_endian.h' -> `./src/bam_endian.h' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/bgzf.h' -> `./src/bgzf.h' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/kstring.h' -> `./src/kstring.h' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/bedidx.c' -> `./src/bedidx.c' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/kstring.c' -> `./src/kstring.c' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/streamer_1d.c' -> `./src/streamer_1d.c' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/pairs_merger.c' -> `./src/pairs_merger.c' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/main.c' -> `./src/main.c' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/knetfile.c' -> `./src/knetfile.c' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/knetfile.h' -> `./src/knetfile.h' `/gnu/store/rvg1faw67hlg2fc9wmmz81gycq00vjzx-python-pypairix-0.3.7-checkout/src/index.c' -> `./src/index.c' phase `unpack' succeeded after 0.3 seconds starting phase `ensure-no-mtimes-pre-1980' phase `ensure-no-mtimes-pre-1980' succeeded after 0.0 seconds starting phase `enable-bytecode-determinism' phase `enable-bytecode-determinism' succeeded after 0.0 seconds starting phase `ensure-no-cythonized-files' phase `ensure-no-cythonized-files' succeeded after 0.0 seconds starting phase `patch-usr-bin-file' phase `patch-usr-bin-file' succeeded after 0.0 seconds starting phase `patch-source-shebangs' patch-shebang: ./setup.py: changing `/usr/bin/env python' to `/gnu/store/lcfbfljdfz9d74cy1llfvq502rzlah2m-python-wrapper-3.10.7/bin/python' patch-shebang: ./test/inefficient-merger-for-testing: changing `/bin/bash' to `/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./test/reindex_samples.sh: changing `/bin/bash' to `/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./test/test.py: changing `/usr/bin/env python' to `/gnu/store/lcfbfljdfz9d74cy1llfvq502rzlah2m-python-wrapper-3.10.7/bin/python' patch-shebang: ./test/test_c.sh: changing `/bin/bash' to `/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./test/test_c_oldindex.sh: changing `/bin/bash' to `/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./test/test_c_oldindex2.sh: changing `/bin/bash' to `/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./test/test_oldindex.py: changing `/usr/bin/env python' to `/gnu/store/lcfbfljdfz9d74cy1llfvq502rzlah2m-python-wrapper-3.10.7/bin/python' patch-shebang: ./test/test_oldindex2.py: changing `/usr/bin/env python' to `/gnu/store/lcfbfljdfz9d74cy1llfvq502rzlah2m-python-wrapper-3.10.7/bin/python' patch-shebang: ./util/bam2pairs/bam2pairs: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./util/boostchr.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./util/column_remover.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./util/create_randompairs.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./util/duplicate_header_remover.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./util/fragment_4dnpairs.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./util/juicer_shortform2pairs.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./util/merge-pairs.sh: changing `/bin/bash' to `/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./util/merged_nodup2pairs.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./util/old_merged_nodup2pairs.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./util/process_merged_nodup.sh: changing `/bin/bash' to `/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin/bash' patch-shebang: ./util/process_old_merged_nodup.sh: changing `/bin/bash' to `/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin/bash' phase `patch-source-shebangs' succeeded after 0.0 seconds starting phase `patch-generated-file-shebangs' patch-shebang: ./util/bam2pairs/bam2pairs: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./util/column_remover.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./util/duplicate_header_remover.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./util/fragment_4dnpairs.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./util/juicer_shortform2pairs.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./util/merged_nodup2pairs.pl: warning: no binary for interpreter `perl' found in $PATH patch-shebang: ./util/old_merged_nodup2pairs.pl: warning: no binary for interpreter `perl' found in $PATH phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `build-programs' cd src; make; cd .. make[1]: Entering directory '/tmp/guix-build-python-pypairix-0.3.7.drv-0/source/src' make[2]: Entering directory '/tmp/guix-build-python-pypairix-0.3.7.drv-0/source/src' gcc -c -g -w -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE bgzf.c -o bgzf.o gcc -c -g -w -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE kstring.c -o kstring.o gcc -c -g -w -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE knetfile.c -o knetfile.o gcc -c -g -w -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE index.c -o index.o gcc -c -g -w -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE bedidx.c -o bedidx.o ar -csru libpairix.a bgzf.o kstring.o knetfile.o index.o bedidx.o ar: `u' modifier ignored since `D' is the default (see `U') gcc -c -g -w -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE main.c -o main.o gcc -g -w -O2 -fPIC -o pairix main.o -L. -lpairix -lm -lz gcc -c -g -w -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE bgzip.c -o bgzip.o gcc -g -w -O2 -fPIC -o bgzip bgzip.o bgzf.o knetfile.o -lz gcc -c -g -w -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE pairs_merger.c -o pairs_merger.o gcc -g -w -O2 -fPIC -o pairs_merger pairs_merger.o -L. -lpairix -lm -lz gcc -c -g -w -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE streamer_1d.c -o streamer_1d.o gcc -g -w -O2 -fPIC -o streamer_1d streamer_1d.o -L. -lpairix -lm -lz mkdir -p ../bin; mv pairix bgzip pairs_merger streamer_1d ../bin; chmod +x ../bin/*; make[2]: Leaving directory '/tmp/guix-build-python-pypairix-0.3.7.drv-0/source/src' make[1]: Leaving directory '/tmp/guix-build-python-pypairix-0.3.7.drv-0/source/src' phase `build-programs' succeeded after 5.6 seconds starting phase `build' running "python setup.py" with command "build" and parameters () /gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/lib/python3.10/site-packages/setuptools/dist.py:771: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running build running build_ext building 'pypairix' extension creating build creating build/temp.linux-ppc64le-cpython-310 creating build/temp.linux-ppc64le-cpython-310/src gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fno-semantic-interposition -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/include/python3.10 -c src/bgzf.c -o build/temp.linux-ppc64le-cpython-310/src/bgzf.o src/bgzf.c: In function ‘bgzf_block_length’: src/bgzf.c:331:34: warning: unused variable ‘remaining’ [-Wunused-variable] 331 | int count, block_length, remaining; | ^~~~~~~~~ src/bgzf.c:330:47: warning: unused variable ‘compressed_block’ [-Wunused-variable] 330 | uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block; | ^~~~~~~~~~~~~~~~ src/bgzf.c: In function ‘bgzf_flush’: src/bgzf.c:419:75: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 419 | if (fwrite(fp->compressed_block, 1, block_length, fp->fp) != block_length) { | ^~ src/bgzf.c: In function ‘bgzf_close’: src/bgzf.c:456:18: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 456 | int ret, count, block_length; | ^~~~~ gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fno-semantic-interposition -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/include/python3.10 -c src/bgzip.c -o build/temp.linux-ppc64le-cpython-310/src/bgzip.o gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fno-semantic-interposition -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/include/python3.10 -c src/index.c -o build/temp.linux-ppc64le-cpython-310/src/index.o src/index.c: In function ‘merge_chunks’: src/index.c:354:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 354 | for (l = 1; l < p->n; ++l) { | ^ src/index.c: In function ‘ti_index_core’: src/index.c:393:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 393 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ src/index.c:399:28: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 399 | if (lineno <= idx->conf.line_skip || str->s[0] == idx->conf.meta_char) { | ^~ src/index.c:423:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 423 | if (intv.bin != last_bin) { // then possibly write the binning index | ^~ src/index.c:431:35: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘uint64_t’ {aka ‘long unsigned int’} [-Wsign-compare] 431 | if (bgzf_tell(fp) <= last_off) { | ^~ src/index.c: In function ‘ti_index_save’: src/index.c:510:31: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 510 | for (i = 0; i < kh_size(idx->tname); ++i) | ^ src/index.c:514:31: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 514 | for (i = 0; i < kh_size(idx->tname); ++i) | ^ src/index.c:534:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 534 | for (x = 0; (int)x < p->n; ++x) { | ^ src/index.c:539:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 539 | for (x = 0; (int)x < p->n; ++x) { | ^ src/index.c: In function ‘ti_index_load_core’: src/index.c:659:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 659 | for (x = 0; x < p->n; ++x) { | ^ src/index.c: In function ‘ti_parse_region2d’: src/index.c:864:69: warning: passing argument 1 of ‘ti_get_region_split_character’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 864 | char region_split_character = ti_get_region_split_character(idx); | ^~~ In file included from src/index.c:11: src/pairix.h:218:56: note: expected ‘ti_index_t *’ {aka ‘struct __ti_index_t *’} but argument is of type ‘const ti_index_t *’ {aka ‘const struct __ti_index_t *’} 218 | char ti_get_region_split_character(ti_index_t *idx); | ~~~~~~~~~~~~^~~ src/index.c:878:30: warning: passing argument 1 of ‘ti_get_sc2’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 878 | int dim = ti_get_sc2(idx)+1==0?1:2; | ^~~ In file included from src/index.c:11: src/pairix.h:209:36: note: expected ‘ti_index_t *’ {aka ‘struct __ti_index_t *’} but argument is of type ‘const ti_index_t *’ {aka ‘const struct __ti_index_t *’} 209 | int ti_get_sc2(ti_index_t *idx); | ~~~~~~~~~~~~^~~ src/index.c: In function ‘reg2bins’: src/index.c:974:56: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 974 | for (k = 1 + (beg>>TAD_LIDX_SHIFT_PL12); k <= 1 + (end>>TAD_LIDX_SHIFT_PL12); ++k) list[i++] = k; | ^~ src/index.c:975:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 975 | for (k = 9 + (beg>>TAD_LIDX_SHIFT_PL9); k <= 9 + (end>>TAD_LIDX_SHIFT_PL9); ++k) list[i++] = k; | ^~ src/index.c:976:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 976 | for (k = 73 + (beg>>TAD_LIDX_SHIFT_PL6); k <= 73 + (end>>TAD_LIDX_SHIFT_PL6); ++k) list[i++] = k; | ^~ src/index.c:977:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 977 | for (k = 585 + (beg>>TAD_LIDX_SHIFT_PL3); k <= 585 + (end>>TAD_LIDX_SHIFT_PL3); ++k) list[i++] = k; | ^~ src/index.c:978:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 978 | for (k = 4681 + (beg>>TAD_LIDX_SHIFT); k <= 4681 + (end>>TAD_LIDX_SHIFT); ++k) list[i++] = k; | ^~ src/index.c: In function ‘ti_iter_query’: src/index.c:1038:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1038 | for (j = 0; j < p->n; ++j) | ^ src/index.c: In function ‘ti_querys_2d_general’: src/index.c:1219:31: warning: initialization of ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 1219 | char **chrpairlist = ti_seqname(t->idx, &n_seqpair_list); | ^~~~~~~~~~ src/index.c:1236:59: warning: passing argument 2 of ‘ti_querys_2d_multi’ from incompatible pointer type [-Wincompatible-pointer-types] 1236 | sequential_iter_t *siter = ti_querys_2d_multi(t, regions, n_sub_list); | ^~~~~~~ | | | char ** In file included from src/index.c:11: src/pairix.h:131:73: note: expected ‘const char **’ but argument is of type ‘char **’ 131 | sequential_iter_t *ti_querys_2d_multi(pairix_t *t, const char **regs, int nRegs); | ~~~~~~~~~~~~~^~~~ src/index.c:1242:30: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1242 | *sp=0; char *chr1 = reg; | ^~~ src/index.c:1246:31: warning: initialization of ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 1246 | char **chrpairlist = ti_seqname(t->idx, &n_seqpair_list); | ^~~~~~~~~~ src/index.c:1263:59: warning: passing argument 2 of ‘ti_querys_2d_multi’ from incompatible pointer type [-Wincompatible-pointer-types] 1263 | sequential_iter_t *siter = ti_querys_2d_multi(t, regions, n_sub_list); | ^~~~~~~ | | | char ** In file included from src/index.c:11: src/pairix.h:131:73: note: expected ‘const char **’ but argument is of type ‘char **’ 131 | sequential_iter_t *ti_querys_2d_multi(pairix_t *t, const char **regs, int nRegs); | ~~~~~~~~~~~~~^~~~ src/index.c: In function ‘ti_query_2d_tid’: src/index.c:1417:31: warning: returning ‘ti_iter_t’ {aka ‘struct __ti_iter_t *’} from a function with return type ‘int’ makes integer from pointer without a cast [-Wint-conversion] 1417 | if (name == 0) return ti_iter_first(); | ^~~~~~~~~~~~~~~ src/index.c: In function ‘create_merged_iter’: src/index.c:1469:10: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 1469 | if( miter->iu = calloc(n,sizeof(iter_unit*))) { | ^~~~~ src/index.c: In function ‘merged_ti_read’: src/index.c:1537:19: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1537 | miu[i]->s = ti_iter_read(miu[i]->t->fp, miu[i]->iter, miu[i]->len, seqonly); | ^ src/index.c:1543:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1543 | miu[0]->s = ti_iter_read(miu[0]->t->fp, miu[0]->iter, miu[0]->len, seqonly); // get next entry for the flushed iter | ^ src/index.c: In function ‘sequential_ti_read’: src/index.c:1573:15: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1573 | char *s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len, 0); | ^~~~~~~~~~~~ src/index.c:1576:9: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1576 | s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len, 0); | ^ src/index.c: In function ‘get_unique_merged_seqname’: src/index.c:1643:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 1643 | seqnames = ti_seqname(tbs[i]->idx,&len); | ^ src/index.c: In function ‘flip_region’: src/index.c:1744:19: warning: variable ‘split_pos’ set but not used [-Wunused-but-set-variable] 1744 | int l, i, l2, split_pos; | ^~~~~~~~~ src/index.c: In function ‘querys_2D_wrapper’: src/index.c:1911:34: warning: passing argument 1 of ‘flip_region’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1911 | char *reg2 = flip_region(reg, get_region_split_character(tb)); | ^~~ src/index.c:1743:27: note: expected ‘char *’ but argument is of type ‘const char *’ 1743 | char *flip_region ( char* s, char region_split_character) { | ~~~~~~^ src/index.c: In function ‘check_triangle’: src/index.c:1971:23: warning: initialization of ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 1971 | char **seqnames = ti_seqname(idx,&len); | ^~~~~~~~~~ src/index.c:1977:64: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1977 | if(ti_get_tid(idx, reg2)!=-1) { free(seqnames); free(reg2); return(0); } // not a triangle | ^~~~ In file included from src/khash.h:94, from src/index.c:4: /gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/include/stdlib.h:687:25: note: expected ‘void *’ but argument is of type ‘const char *’ 687 | extern void free (void *__ptr) __THROW; | ~~~~~~^~~~~ src/index.c:1978:14: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1978 | free(reg2); | ^~~~ In file included from src/khash.h:94, from src/index.c:4: /gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/include/stdlib.h:687:25: note: expected ‘void *’ but argument is of type ‘const char *’ 687 | extern void free (void *__ptr) __THROW; | ~~~~~~^~~~~ In file included from src/index.c:4: src/index.c: In function ‘ti_index_load_core’: src/khash.h:185:60: note: the layout of aggregates containing vectors with 8-byte alignment has changed in GCC 5 185 | if (kh_is_map) val = h->vals[j]; \ | ~~~~^~~~~~~~~~~~ src/khash.h:453:9: note: in expansion of macro ‘KHASH_INIT’ 453 | KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) | ^~~~~~~~~~ src/index.c:51:1: note: in expansion of macro ‘KHASH_MAP_INIT_INT’ 51 | KHASH_MAP_INIT_INT(i, ti_binlist_t) | ^~~~~~~~~~~~~~~~~~ gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fno-semantic-interposition -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/include/python3.10 -c src/knetfile.c -o build/temp.linux-ppc64le-cpython-310/src/knetfile.o gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fno-semantic-interposition -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/include/python3.10 -c src/kstring.c -o build/temp.linux-ppc64le-cpython-310/src/kstring.o src/kstring.c: In function ‘ksprintf’: src/kstring.c:15:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 15 | if (l + 1 > s->m - s->l) { | ^ gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fno-semantic-interposition -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/include/python3.10 -c src/pairixmodule.c -o build/temp.linux-ppc64le-cpython-310/src/pairixmodule.o src/pairixmodule.c: In function ‘pairix_new’: src/pairixmodule.c:367:9: warning: unused variable ‘i’ [-Wunused-variable] 367 | int i; | ^ src/pairixmodule.c: In function ‘pairix_querys_2D’: src/pairixmodule.c:559:28: warning: passing argument 1 of ‘flip_region’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 559 | reg2 = flip_region(reg, get_region_split_character(self->tb)); | ^~~ In file included from src/pairixmodule.c:34: src/pairix.h:223:33: note: expected ‘char *’ but argument is of type ‘const char *’ 223 | char* flip_region(char *s, char region_split_character); | ~~~~~~^ src/pairixmodule.c: In function ‘pairix_get_blocknames’: src/pairixmodule.c:603:23: warning: initialization of ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 603 | char **blocknames = ti_seqname(self->tb->idx, &n); | ^~~~~~~~~~ src/pairixmodule.c: In function ‘pairix_get_header’: src/pairixmodule.c:693:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 693 | while ((s = sequential_ti_read(siter, &len)) != 0) { | ^ src/pairixmodule.c:704:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 704 | while ((s = sequential_ti_read(siter, &len)) != 0) { | ^ src/pairixmodule.c: In function ‘pairix_get_chromsize’: src/pairixmodule.c:726:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 726 | while ((s = sequential_ti_read(siter, &len)) != 0) { | ^ src/pairixmodule.c:738:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 738 | while ((s = sequential_ti_read(siter, &len)) != 0) { | ^ creating build/lib.linux-ppc64le-cpython-310 gcc -shared -Wl,-rpath=/gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/lib -fno-semantic-interposition build/temp.linux-ppc64le-cpython-310/src/bgzf.o build/temp.linux-ppc64le-cpython-310/src/bgzip.o build/temp.linux-ppc64le-cpython-310/src/index.o build/temp.linux-ppc64le-cpython-310/src/knetfile.o build/temp.linux-ppc64le-cpython-310/src/kstring.o build/temp.linux-ppc64le-cpython-310/src/pairixmodule.o -L/gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/lib -lz -o build/lib.linux-ppc64le-cpython-310/pypairix.cpython-310-powerpc64le-linux-gnu.so phase `build' succeeded after 6.8 seconds starting phase `install' running "python setup.py" with command "install" and parameters ("--prefix=/gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7" "--no-compile" "--single-version-externally-managed" "--root=/") /gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/lib/python3.10/site-packages/setuptools/dist.py:771: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running install /gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/lib/python3.10/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_ext running install_lib creating /gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7 creating /gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/lib creating /gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/lib/python3.10 creating /gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/lib/python3.10/site-packages copying build/lib.linux-ppc64le-cpython-310/pypairix.cpython-310-powerpc64le-linux-gnu.so -> /gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/lib/python3.10/site-packages warning: install_lib: byte-compiling is disabled, skipping. running install_egg_info running egg_info creating pypairix.egg-info writing pypairix.egg-info/PKG-INFO writing dependency_links to pypairix.egg-info/dependency_links.txt writing top-level names to pypairix.egg-info/top_level.txt writing manifest file 'pypairix.egg-info/SOURCES.txt' reading manifest file 'pypairix.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.txt' writing manifest file 'pypairix.egg-info/SOURCES.txt' Copying pypairix.egg-info to /gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/lib/python3.10/site-packages/pypairix-0.3.7-py3.10.egg-info running install_scripts Listing '/gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7'... Listing '/gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/lib'... Listing '/gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/lib/python3.10'... Listing '/gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/lib/python3.10/site-packages'... Listing '/gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/lib/python3.10/site-packages/pypairix-0.3.7-py3.10.egg-info'... phase `install' succeeded after 1.0 seconds starting phase `install-programs' `bin/streamer_1d' -> `/gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/bin/streamer_1d' `bin/pairs_merger' -> `/gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/bin/pairs_merger' `bin/bgzip' -> `/gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/bin/bgzip' `bin/pairix' -> `/gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/bin/pairix' phase `install-programs' succeeded after 0.0 seconds starting phase `add-install-to-pythonpath' phase `add-install-to-pythonpath' succeeded after 0.0 seconds starting phase `add-install-to-path' phase `add-install-to-path' succeeded after 0.0 seconds starting phase `wrap' find-files: /gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/sbin: No such file or directory phase `wrap' succeeded after 0.0 seconds starting phase `check' running "python setup.py" with command "test" and parameters () /gnu/store/kk7kf15fc9n0z66bbqaprfr51nsq4iiw-python-3.10.7/lib/python3.10/site-packages/setuptools/dist.py:771: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead warnings.warn( running test WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox. running egg_info writing pypairix.egg-info/PKG-INFO writing dependency_links to pypairix.egg-info/dependency_links.txt writing top-level names to pypairix.egg-info/top_level.txt reading manifest file 'pypairix.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.txt' writing manifest file 'pypairix.egg-info/SOURCES.txt' running build_ext copying build/lib.linux-ppc64le-cpython-310/pypairix.cpython-310-powerpc64le-linux-gnu.so -> test_CleanImport (test.test_support.TestSupport) ... ok test_DirsOnSysPath (test.test_support.TestSupport) ... ok test_HOST (test.test_support.TestSupport) ... ok test_args_from_interpreter_flags (test.test_support.TestSupport) ... ok test_bind_port (test.test_support.TestSupport) ... ok test_captured_stderr (test.test_support.TestSupport) ... ok test_captured_stdin (test.test_support.TestSupport) ... ok test_captured_stdout (test.test_support.TestSupport) ... ok test_change_cwd (test.test_support.TestSupport) ... ok test_change_cwd__chdir_warning (test.test_support.TestSupport) Check the warning message when os.chdir() fails. ... ok test_change_cwd__non_existent_dir (test.test_support.TestSupport) Test passing a non-existent directory. ... ok test_change_cwd__non_existent_dir__quiet_true (test.test_support.TestSupport) Test passing a non-existent directory with quiet=True. ... ok test_check__all__ (test.test_support.TestSupport) ... ok test_check_syntax_error (test.test_support.TestSupport) ... ok test_detect_api_mismatch (test.test_support.TestSupport) ... ok test_detect_api_mismatch__ignore (test.test_support.TestSupport) ... ok test_fd_count (test.test_support.TestSupport) ... ok test_find_unused_port (test.test_support.TestSupport) ... ok test_forget (test.test_support.TestSupport) ... ok test_gc_collect (test.test_support.TestSupport) ... ok test_get_attribute (test.test_support.TestSupport) ... ok test_get_original_stdout (test.test_support.TestSupport) ... skipped 'failing buildbots' test_ignored_deprecations_are_silent (test.test_support.TestSupport) Test support.ignore_deprecations_from() silences warnings ... ok test_import_fresh_module (test.test_support.TestSupport) ... ok test_import_module (test.test_support.TestSupport) ... ok test_make_bad_fd (test.test_support.TestSupport) ... ok test_match_test (test.test_support.TestSupport) ... ok test_optim_args_from_interpreter_flags (test.test_support.TestSupport) ... ok test_print_warning (test.test_support.TestSupport) ... ok test_python_is_optimized (test.test_support.TestSupport) ... ok test_reap_children (test.test_support.TestSupport) ... ok test_rmtree (test.test_support.TestSupport) ... ok test_sortdict (test.test_support.TestSupport) ... ok test_swap_attr (test.test_support.TestSupport) ... ok test_swap_item (test.test_support.TestSupport) ... ok test_temp_cwd (test.test_support.TestSupport) ... ok test_temp_cwd__name_none (test.test_support.TestSupport) Test passing None to temp_cwd(). ... ok test_temp_dir (test.test_support.TestSupport) Test that temp_dir() creates and destroys its directory. ... ok test_temp_dir__existing_dir__quiet_default (test.test_support.TestSupport) Test passing a directory that already exists. ... ok test_temp_dir__existing_dir__quiet_true (test.test_support.TestSupport) Test passing a directory that already exists with quiet=True. ... ok test_temp_dir__forked_child (test.test_support.TestSupport) Test that a forked child process does not remove the directory. ... ok test_temp_dir__path_none (test.test_support.TestSupport) Test passing no path. ... ok test_unlink (test.test_support.TestSupport) ... ok test_unload (test.test_support.TestSupport) ... ok ---------------------------------------------------------------------- Ran 44 tests in 4.146s OK (skipped=1) phase `check' succeeded after 5.0 seconds starting phase `sanity-check' validating 'pypairix' /gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/lib/python3.10/site-packages ...checking requirements: OK ...trying to load module pypairix: OK phase `sanity-check' succeeded after 0.3 seconds starting phase `patch-shebangs' phase `patch-shebangs' succeeded after 0.0 seconds starting phase `rename-pth-file' phase `rename-pth-file' succeeded after 0.0 seconds starting phase `strip' stripping binaries in "/gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/lib" with "strip" and flags ("--strip-unneeded" "--enable-deterministic-archives") stripping binaries in "/gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/bin" with "strip" and flags ("--strip-unneeded" "--enable-deterministic-archives") phase `strip' succeeded after 0.0 seconds starting phase `validate-runpath' validating RUNPATH of 1 binaries in "/gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/lib"... validating RUNPATH of 4 binaries in "/gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/bin"... phase `validate-runpath' succeeded after 0.0 seconds starting phase `validate-documentation-location' phase `validate-documentation-location' succeeded after 0.0 seconds starting phase `delete-info-dir-file' phase `delete-info-dir-file' succeeded after 0.0 seconds starting phase `patch-dot-desktop-files' phase `patch-dot-desktop-files' succeeded after 0.0 seconds starting phase `make-dynamic-linker-cache' created '/gnu/store/xylwy0djnh9cj31g77vw39rkari0bcn8-python-pypairix-0.3.7/etc/ld.so.cache' from 4 library search path entries phase `make-dynamic-linker-cache' succeeded after 0.2 seconds starting phase `install-license-files' installing 1 license files from '.' phase `install-license-files' succeeded after 0.0 seconds starting phase `reset-gzip-timestamps' phase `reset-gzip-timestamps' succeeded after 0.0 seconds starting phase `compress-documentation' phase `compress-documentation' succeeded after 0.0 seconds