Date: Sat, 30 Jan 2021 02:10:55 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 121arm64-quarterly][biology/py-scikit-bio] Failed for py37-scikit-bio-0.5.6 in build Message-ID: <202101300210.10U2Atd2038908@ampere1.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Last committer: adamw@FreeBSD.org Ident: $FreeBSD: branches/2021Q1/biology/py-scikit-bio/Makefile 555738 2020-11-20 07:16:06Z adamw $ Log URL: http://ampere1.nyi.freebsd.org/data/121arm64-quarterly/563271/logs/py37-scikit-bio-0.5.6.log Build URL: http://ampere1.nyi.freebsd.org/build.html?mastername=121arm64-quarterly&build=563271 Log: =>> Building biology/py-scikit-bio build started at Sat Jan 30 02:10:24 UTC 2021 port directory: /usr/ports/biology/py-scikit-bio package name: py37-scikit-bio-0.5.6 building for: FreeBSD 121arm64-quarterly-job-03 12.1-RELEASE FreeBSD 12.1-RELEASE arm64 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: branches/2021Q1/biology/py-scikit-bio/Makefile 555738 2020-11-20 07:16:06Z adamw $ Poudriere version: 3.2.8-8-gaf08dbda Host OSVERSION: 1300134 Jail OSVERSION: 1201000 Job Id: 03 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1201000 UNAME_v=FreeBSD 12.1-RELEASE UNAME_r=12.1-RELEASE BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-8-gaf08dbda MASTERMNT=/usr/local/poudriere/data/.m/121arm64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/121arm64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=121arm64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/121arm64-quarterly/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py37 DEPENDS_ARGS= MAKE_ARGS= FLAVOR=py37 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py37 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py37 HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py37 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py37/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py37 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py37 HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py37 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py37/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=freebsd12 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_EXT_SUFFIX= PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=12.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/scikit-bio" EXAMPLESDIR="share/examples/scikit-bio" DATADIR="share/scikit-bio" WWWDIR="www/scikit-bio" ETCDIR="etc/scikit-bio" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/scikit-bio DOCSDIR=/usr/local/share/doc/scikit-bio EXAMPLESDIR=/usr/local/share/examples/scikit-bio WWWDIR=/usr/local/www/scikit-bio ETCDIR=/usr/local/etc/scikit-bio --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd12.1 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd12.1 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd12.1 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=12.1-RELEASE OSREL=12.1 OSVERSION=1201000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===> License BSD3CLAUSE accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> py37-scikit-bio-0.5.6 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.16.1.txz [121arm64-quarterly-job-03] Installing pkg-1.16.1... [121arm64-quarterly-job-03] Extracting pkg-1.16.1: .......... done ===> py37-scikit-bio-0.5.6 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py37-scikit-bio-0.5.6 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py37-scikit-bio-0.5.6 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py37-scikit-bio-0.5.6 for building => SHA256 Checksum OK for scikit-bio-0.5.6.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py37-scikit-bio-0.5.6 for building ===> Extracting for py37-scikit-bio-0.5.6 => SHA256 Checksum OK for scikit-bio-0.5.6.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for py37-scikit-bio-0.5.6 =========================================================================== =======================<phase: build-depends >============================ ===> py37-scikit-bio-0.5.6 depends on package: py37-numpy>=1.16,1<1.20,1 - not found ===> Installing existing package /packages/All/py37-numpy-1.16.6,1.txz [121arm64-quarterly-job-03] Installing py37-numpy-1.16.6,1... [121arm64-quarterly-job-03] `-- Installing gcc9-9.3.0_1... [121arm64-quarterly-job-03] | `-- Installing binutils-2.33.1_4,1... [121arm64-quarterly-job-03] | | `-- Installing gettext-runtime-0.21... [121arm64-quarterly-job-03] | | `-- Installing indexinfo-0.3.1... [121arm64-quarterly-job-03] | | `-- Extracting indexinfo-0.3.1: .... done [121arm64-quarterly-job-03] | | `-- Extracting gettext-runtime-0.21: .......... done [121arm64-quarterly-job-03] | `-- Extracting binutils-2.33.1_4,1: .......... done [121arm64-quarterly-job-03] | `-- Installing gmp-6.2.1... [121arm64-quarterly-job-03] | `-- Extracting gmp-6.2.1: .......... done [121arm64-quarterly-job-03] | `-- Installing mpc-1.1.0_2... [121arm64-quarterly-job-03] | | `-- Installing mpfr-4.1.0... [121arm64-quarterly-job-03] | | `-- Extracting mpfr-4.1.0: .......... done [121arm64-quarterly-job-03] | `-- Extracting mpc-1.1.0_2: ......... done [121arm64-quarterly-job-03] `-- Extracting gcc9-9.3.0_1: .......... done [121arm64-quarterly-job-03] `-- Installing openblas-0.3.12,1... [121arm64-quarterly-job-03] `-- Extracting openblas-0.3.12,1: .......... done [121arm64-quarterly-job-03] `-- Installing py37-setuptools-44.0.0... [121arm64-quarterly-job-03] | `-- Installing python37-3.7.9_1... [121arm64-quarterly-job-03] | | `-- Installing libffi-3.3_1... <snip> copying skbio/io/format/tests/data/fastq_wrapping_as_sanger_no_description -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_blanks_end_of_file -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_blank_start_of_file -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_seq_sanger -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_example3_scores -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_multi_seq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_varied_whitespace_in_seqs -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/tsv_8_fields -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_PCoA_sample_data_3_scores -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_missing_rn_tag -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_ws_lines_end_of_file -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_multiple_trees -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_seq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_runon_gf_with_whitespace -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_missing_header -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_custom_multi_line -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_defaults_extra -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_blank_end_of_file -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_seq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_ws_line_after_seq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/gff3_multi_record -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_wrapping_original_sanger_no_description -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_single_tree_without_id -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_multi_seq_roundtrip -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_too_few_seqs -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_lane -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_custom_minimal -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_whitespace_in_header_3 -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_whitespace_in_header_2 -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_whitespace_in_header_1 -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_wrapping_as_illumina_no_description -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_nonstring_labels -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_metadata_only -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_2_seqs_defaults -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_ws_lines_between_records -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_missing_seq_data_last -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_RDA_site_constraints -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_max_width_5 -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_max_width_1 -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_differing_fields -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_blank_line_within_sequence -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_5_ws_lines_start_of_file -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_id_whitespace_replacement_empty_str -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_whitespace_only_lines -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_ws_line_within_seq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_5_blanks_start_of_file -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_tabs.fastq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_whitespace_only_sequence -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/illumina_full_range_as_sanger.fastq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/sanger_full_range_original_sanger.fastq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_multi_seq_roundtrip -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_data_only -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_multi_line_tree_with_id -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_no_data -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_default_single_line -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_blank_lines -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/longreads_as_illumina.fastq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_multi_seq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_ws_lines_start_of_file -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_after_header -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_single_seq_short -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_different_padding -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_L&L_CA_data_scores -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/solexa_full_range_original_solexa.fastq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_description_newline_replacement_none -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_rna -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_empty_line_before_header -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_runon_references -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_rna_as_illumina.fastq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_single_seq_long -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_custom_mixed_nans -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_single_record -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_long_qual.fastq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_custom_minimal -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_all_data_types -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_null.fastq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_whitespace_only_line_within_sequence -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_RDA_site -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_missing_qual_scores_middle -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_description_newline_replacement_multi_char -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_escape.fastq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_extensive -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/embl_single_record_simple -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_dna_as_sanger.fastq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_dna_as_illumina.fastq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/empty -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_blank_between_records -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_default_single_line -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_missing_reference_items -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_runon_gf_no_whitespace -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_dna_seq_non_defaults -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_missing_qual_scores_first -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_qual_scores_over_255 -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_id_whitespace_replacement_none -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_5_ws_lines_start_of_file -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_whitespace_line_in_seq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_in_title.fastq -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_ws_lines_between_records -> build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/io/format/tests/data running build_ext building 'skbio.metadata._intersection' extension creating build/temp.freebsd-12.1-RELEASE-arm64-3.7 creating build/temp.freebsd-12.1-RELEASE-arm64-3.7/skbio creating build/temp.freebsd-12.1-RELEASE-arm64-3.7/skbio/metadata cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c skbio/metadata/_intersection.c -o build/temp.freebsd-12.1-RELEASE-arm64-3.7/skbio/metadata/_intersection.o skbio/metadata/_intersection.c:2297:5: warning: code will never be executed [-Wunreachable-code] PyErr_SetString(PyExc_ZeroDivisionError, "float division"); ^~~~~~~~~~~~~~~ 1 warning generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-12.1-RELEASE-arm64-3.7/skbio/metadata/_intersection.o -L/usr/local/lib -lpython3.7m -o build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/metadata/_intersection.so building 'skbio.stats.__subsample' extension creating build/temp.freebsd-12.1-RELEASE-arm64-3.7/skbio/stats cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c skbio/stats/__subsample.c -o build/temp.freebsd-12.1-RELEASE-arm64-3.7/skbio/stats/__subsample.o In file included from skbio/stats/__subsample.c:617: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " \ ^ 1 warning generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-12.1-RELEASE-arm64-3.7/skbio/stats/__subsample.o -L/usr/local/lib -lpython3.7m -o build/lib.freebsd-12.1-RELEASE-arm64-3.7/skbio/stats/__subsample.so building 'skbio.alignment._ssw_wrapper' extension creating build/temp.freebsd-12.1-RELEASE-arm64-3.7/skbio/alignment creating build/temp.freebsd-12.1-RELEASE-arm64-3.7/skbio/alignment/_lib cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c skbio/alignment/_ssw_wrapper.c -o build/temp.freebsd-12.1-RELEASE-arm64-3.7/skbio/alignment/_ssw_wrapper.o -Wno-error=declaration-after-statement In file included from skbio/alignment/_ssw_wrapper.c:624: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822: /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " \ ^ In file included from skbio/alignment/_ssw_wrapper.c:626: In file included from skbio/alignment/_lib/ssw.h:17: In file included from /usr/lib/clang/8.0.1/include/emmintrin.h:27: In file included from /usr/lib/clang/8.0.1/include/xmmintrin.h:27: /usr/lib/clang/8.0.1/include/mmintrin.h:64:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_vec_init_v2si(__i, 0); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:143:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_packsswb((__v4hi)__m1, (__v4hi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:173:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_packssdw((__v2si)__m1, (__v2si)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:203:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:230:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:253:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:274:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:301:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:324:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:345:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:366:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:387:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:408:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:430:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_paddsb((__v8qi)__m1, (__v8qi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:453:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_paddsw((__v4hi)__m1, (__v4hi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:475:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_paddusb((__v8qi)__m1, (__v8qi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:497:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_paddusw((__v4hi)__m1, (__v4hi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:518:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_psubb((__v8qi)__m1, (__v8qi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/lib/clang/8.0.1/include/mmintrin.h:539:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_psubw((__v4hi)__m1, (__v4hi)__m2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fatal error: too many errors emitted, stopping now [-ferror-limit=] 1 warning and 20 errors generated. error: command 'cc' failed with exit status 1 *** Error code 1 Stop. make: stopped in /usr/ports/biology/py-scikit-bio
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