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Date: Fri, 26 Nov 2021 07:00:55 GMT
From: pkg-fallout@FreeBSD.org
Message-Id: <202111260700.1AQ70tN4015732@ampere1.nyi.freebsd.org>
To: pkg-fallout@FreeBSD.org
Subject: [package - 130arm64-quarterly][biology/py-scikit-bio] Failed for py38-scikit-bio-0.5.6 in build
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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
Log URL: http://ampere1.nyi.freebsd.org/data/130arm64-quarterly/06d01a3e6b0a/logs/py38-scikit-bio-0.5.6.log
Build URL: http://ampere1.nyi.freebsd.org/build.html?mastername=130arm64-quarterly&build=06d01a3e6b0a
Log:
=>> Building biology/py-scikit-bio
build started at Fri Nov 26 07:00:24 UTC 2021
port directory: /usr/ports/biology/py-scikit-bio
package name: py38-scikit-bio-0.5.6
building for: FreeBSD 130arm64-quarterly-job-10 13.0-RELEASE-p5 FreeBSD 13.0-RELEASE-p5 arm64
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400008
Jail OSVERSION: 1300139
Job Id: 10
---Begin Environment---
SHELL=/bin/csh
OSVERSION=1300139
UNAME_v=FreeBSD 13.0-RELEASE-p5
UNAME_r=13.0-RELEASE-p5
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
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=3.2.8-21-g883afb07
MASTERMNT=/usr/local/poudriere/data/.m/130arm64-quarterly/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/130arm64-quarterly/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=130arm64-quarterly
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/130arm64-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=py38
DEPENDS_ARGS=
MAKE_ARGS= FLAVOR=py38
---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/python3.8" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py38 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py38 HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py38 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py38/.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-py38 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py38 HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py38 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py38/.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/python3.8 PYTHON_LIBDIR=lib/python3.8 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.8/site-packages PYTHON_SUFFIX=38 PYTHON_EXT_SUFFIX=.cpython-38 PYTHON_VER=3.8 PYTHON_VERSION=python3.8 PYTHON2="@comment " PYTHON3="" OSREL=13.0 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 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: aarch64-unknown-freebsd13.0 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 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=aarch64
OPSYS=FreeBSD
_OSRELEASE=13.0-RELEASE-p5
OSREL=13.0
OSVERSION=1300139
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 >============================
===> py38-scikit-bio-0.5.6 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.5.pkg
[130arm64-quarterly-job-10] Installing pkg-1.17.5...
[130arm64-quarterly-job-10] Extracting pkg-1.17.5: .......... done
===> py38-scikit-bio-0.5.6 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py38-scikit-bio-0.5.6
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py38-scikit-bio-0.5.6 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py38-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 py38-scikit-bio-0.5.6 for building
===> Extracting for py38-scikit-bio-0.5.6
=> SHA256 Checksum OK for scikit-bio-0.5.6.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for py38-scikit-bio-0.5.6
===========================================================================
=======================<phase: build-depends >============================
===> py38-scikit-bio-0.5.6 depends on package: py38-numpy>=1.16,1<1.20,1 - not found
===> Installing existing package /packages/All/py38-numpy-1.16.6_2,1.pkg
[130arm64-quarterly-job-10] Installing py38-numpy-1.16.6_2,1...
[130arm64-quarterly-job-10] `-- Installing gcc10-10.3.0...
[130arm64-quarterly-job-10] | `-- Installing binutils-2.37_2,1...
[130arm64-quarterly-job-10] | | `-- Installing gettext-runtime-0.21...
[130arm64-quarterly-job-10] | | `-- Installing indexinfo-0.3.1...
[130arm64-quarterly-job-10] | | `-- Extracting indexinfo-0.3.1: .... done
[130arm64-quarterly-job-10] | | `-- Extracting gettext-runtime-0.21: .......... done
[130arm64-quarterly-job-10] | `-- Extracting binutils-2.37_2,1: .......... done
[130arm64-quarterly-job-10] | `-- Installing gmp-6.2.1...
[130arm64-quarterly-job-10] | `-- Extracting gmp-6.2.1: .......... done
[130arm64-quarterly-job-10] | `-- Installing mpc-1.2.1...
[130arm64-quarterly-job-10] | | `-- Installing mpfr-4.1.0_1...
[130arm64-quarterly-job-10] | | `-- Extracting mpfr-4.1.0_1: .......... done
[130arm64-quarterly-job-10] | `-- Extracting mpc-1.2.1: ......... done
[130arm64-quarterly-job-10] `-- Extracting gcc10-10.3.0: .......... done
[130arm64-quarterly-job-10] `-- Installing openblas-0.3.16,1...
[130arm64-quarterly-job-10] `-- Extracting openblas-0.3.16,1: .......... done
[130arm64-quarterly-job-10] `-- Installing py38-setuptools-57.0.0...
<snip>
copying skbio/io/format/tests/data/fastq_wrapping_as_sanger_no_description -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_blanks_end_of_file -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_multi_blank_start_of_file -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_multi_seq_sanger -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/ordination_example3_scores -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_multi_seq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_varied_whitespace_in_seqs -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/tsv_8_fields -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/ordination_PCoA_sample_data_3_scores -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_missing_rn_tag -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_ws_lines_end_of_file -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_multiple_trees -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_single_seq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_runon_gf_with_whitespace -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_invalid_missing_header -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast6_custom_multi_line -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_3_seqs_defaults_extra -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_multi_blank_end_of_file -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_single_seq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_invalid_ws_line_after_seq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/gff3_multi_record -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_wrapping_original_sanger_no_description -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_single_tree_without_id -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_multi_seq_roundtrip -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_invalid_too_few_seqs -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qseq_invalid_lane -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast7_custom_minimal -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_whitespace_in_header_3 -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_whitespace_in_header_2 -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_whitespace_in_header_1 -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_wrapping_as_illumina_no_description -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_nonstring_labels -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_metadata_only -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_2_seqs_defaults -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_ws_lines_between_records -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_invalid_missing_seq_data_last -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/ordination_exp_Ordination_RDA_site_constraints -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_max_width_5 -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_max_width_1 -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast7_invalid_differing_fields -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_invalid_blank_line_within_sequence -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_5_ws_lines_start_of_file -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_id_whitespace_replacement_empty_str -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_whitespace_only_lines -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_invalid_ws_line_within_seq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/genbank_5_blanks_start_of_file -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/error_tabs.fastq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_invalid_whitespace_only_sequence -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/illumina_full_range_as_sanger.fastq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/sanger_full_range_original_sanger.fastq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_multi_seq_roundtrip -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_data_only -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_multi_line_tree_with_id -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast7_invalid_no_data -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast7_default_single_line -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_blank_lines -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/longreads_as_illumina.fastq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_multi_seq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_multi_ws_lines_start_of_file -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_invalid_blank_after_header -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_single_seq_short -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_different_padding -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/ordination_L&L_CA_data_scores -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/solexa_full_range_original_solexa.fastq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_description_newline_replacement_none -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_rna -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_invalid_empty_line_before_header -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_runon_references -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/misc_rna_as_illumina.fastq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_single_seq_long -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast6_custom_mixed_nans -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/embl_single_record -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/error_long_qual.fastq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast6_custom_minimal -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_all_data_types -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/error_qual_null.fastq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_invalid_whitespace_only_line_within_sequence -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/ordination_exp_Ordination_RDA_site -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_invalid_missing_qual_scores_middle -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_description_newline_replacement_multi_char -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/error_qual_escape.fastq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_extensive -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/embl_single_record_simple -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/misc_dna_as_sanger.fastq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/misc_dna_as_illumina.fastq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/empty -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_multi_blank_between_records -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast6_default_single_line -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_missing_reference_items -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_runon_gf_no_whitespace -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_single_dna_seq_non_defaults -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_invalid_missing_qual_scores_first -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_invalid_qual_scores_over_255 -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_id_whitespace_replacement_none -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_5_ws_lines_start_of_file -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_invalid_whitespace_line_in_seq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/error_trunc_in_title.fastq -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_ws_lines_between_records -> build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/io/format/tests/data
running build_ext
building 'skbio.metadata._intersection' extension
creating build/temp.freebsd-13.0-RELEASE-p5-arm64-3.8
creating build/temp.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio
creating build/temp.freebsd-13.0-RELEASE-p5-arm64-3.8/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/python3.8/site-packages/numpy/core/include -I/usr/local/include/python3.8 -c skbio/metadata/_intersection.c -o build/temp.freebsd-13.0-RELEASE-p5-arm64-3.8/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-13.0-RELEASE-p5-arm64-3.8/skbio/metadata/_intersection.o -L/usr/local/lib -o build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/metadata/_intersection.cpython-38.so
building 'skbio.stats.__subsample' extension
creating build/temp.freebsd-13.0-RELEASE-p5-arm64-3.8/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/python3.8/site-packages/numpy/core/include -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/usr/local/include/python3.8 -c skbio/stats/__subsample.c -o build/temp.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/stats/__subsample.o
In file included from skbio/stats/__subsample.c:617:
In file included from /usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/usr/local/lib/python3.8/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-13.0-RELEASE-p5-arm64-3.8/skbio/stats/__subsample.o -L/usr/local/lib -o build/lib.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/stats/__subsample.cpython-38.so
building 'skbio.alignment._ssw_wrapper' extension
creating build/temp.freebsd-13.0-RELEASE-p5-arm64-3.8/skbio/alignment
creating build/temp.freebsd-13.0-RELEASE-p5-arm64-3.8/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/python3.8/site-packages/numpy/core/include -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/usr/local/include/python3.8 -c skbio/alignment/_ssw_wrapper.c -o build/temp.freebsd-13.0-RELEASE-p5-arm64-3.8/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/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/usr/local/lib/python3.8/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/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:50:12: 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/11.0.1/include/mmintrin.h:129:12: 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/11.0.1/include/mmintrin.h:159:12: 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/11.0.1/include/mmintrin.h:189:12: 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/11.0.1/include/mmintrin.h:216:12: 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/11.0.1/include/mmintrin.h:239:12: 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/11.0.1/include/mmintrin.h:260:12: 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/11.0.1/include/mmintrin.h:287:12: 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/11.0.1/include/mmintrin.h:310:12: 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/11.0.1/include/mmintrin.h:331:12: 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/11.0.1/include/mmintrin.h:352:12: 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/11.0.1/include/mmintrin.h:373:12: 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/11.0.1/include/mmintrin.h:394:12: 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/11.0.1/include/mmintrin.h:416:12: 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/11.0.1/include/mmintrin.h:439:12: 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/11.0.1/include/mmintrin.h:461:12: 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/11.0.1/include/mmintrin.h:483:12: 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/11.0.1/include/mmintrin.h:504:12: 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/11.0.1/include/mmintrin.h:525:12: 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