[package - main-armv7-default][biology/py-scikit-bio] Failed for py311-scikit-bio-0.6.2 in build
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Date: Wed, 13 Nov 2024 03:51:55 UTC
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: https://pkg-status.freebsd.org/ampere2/data/main-armv7-default/p380be9c7980a_s5036d9652a/logs/py311-scikit-bio-0.6.2.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=p380be9c7980a_s5036d9652a
Log:
=>> Building biology/py-scikit-bio
build started at Wed Nov 13 03:50:45 UTC 2024
port directory: /usr/ports/biology/py-scikit-bio
package name: py311-scikit-bio-0.6.2
building for: FreeBSD main-armv7-default-job-02 15.0-CURRENT FreeBSD 15.0-CURRENT 1500026 arm
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 2276 Jul 14 01:02 /usr/ports/biology/py-scikit-bio/Makefile
Ports top last git commit: 380be9c7980
Ports top unclean checkout: no
Port dir last git commit: e9af3287f78
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2
Host OSVERSION: 1500023
Jail OSVERSION: 1500026
Job Id: 02
!!! Jail is newer than host. (Jail: 1500026, Host: 1500023) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1500026
UNAME_v=FreeBSD 15.0-CURRENT 1500026
UNAME_r=15.0-CURRENT
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
MAKE_OBJDIR_CHECK_WRITABLE=0
LOCALBASE=/usr/local
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.2
MASTERMNT=/usr/local/poudriere/data/.m/main-armv7-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
PWD=/usr/local/poudriere/data/.m/main-armv7-default/02/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-armv7-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-armv7-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.2
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=py311
MAKE_ARGS= FLAVOR=py311
---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/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py311/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-scikit-bio/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES 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 " 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/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=15.0 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--
PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" 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---
# 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 3 jobs
MAKE_JOBS_NUMBER=3
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### ####
# 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 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
UID=0
---End make.conf---
--Resource limits--
ulimit: can't get limit: Invalid argument
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 524288
stack size (kbytes, -s) 65536
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) 8192
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 >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py311-scikit-bio-0.6.2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.3.pkg
[main-armv7-default-job-02] Installing pkg-1.21.3...
[main-armv7-default-job-02] Extracting pkg-1.21.3: .......... done
===> py311-scikit-bio-0.6.2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py311-scikit-bio-0.6.2
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py311-scikit-bio-0.6.2 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py311-scikit-bio-0.6.2 for building
=> SHA256 Checksum OK for scikit-bio-0.6.2.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py311-scikit-bio-0.6.2 for building
===> Extracting for py311-scikit-bio-0.6.2
=> SHA256 Checksum OK for scikit-bio-0.6.2.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for py311-scikit-bio-0.6.2
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py311-scikit-bio-0.6.2 depends on package: py311-numpy>=1.16,1<1.27,1 - not found
===> Installing existing package /packages/All/py311-numpy-1.26.4_2,1.pkg
[main-armv7-default-job-02] Installing py311-numpy-1.26.4_2,1...
[main-armv7-default-job-02] `-- Installing gcc13-13.3.0...
[main-armv7-default-job-02] | `-- Installing binutils-2.43.1,1...
[main-armv7-default-job-02] | | `-- Installing indexinfo-0.3.1...
[main-armv7-default-job-02] | | `-- Extracting indexinfo-0.3.1: .... done
[main-armv7-default-job-02] | | `-- Installing zstd-1.5.6...
[main-armv7-default-job-02] | | `-- Installing liblz4-1.10.0,1...
<snip>
copying skbio/io/format/tests/data/fastq_invalid_blank_after_header -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_single_seq_short -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_different_padding -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/ordination_L&L_CA_data_scores -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/solexa_full_range_original_solexa.fastq -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_description_newline_replacement_none -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_rna -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/sample-metadata-complete-types-directive.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_invalid_empty_line_before_header -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_runon_references -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/misc_rna_as_illumina.fastq -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_single_seq_long -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast6_custom_mixed_nans -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/embl_single_record -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/error_long_qual.fastq -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast6_custom_minimal -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_all_data_types -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/error_qual_null.fastq -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_invalid_whitespace_only_line_within_sequence -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/ordination_exp_Ordination_RDA_site -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_invalid_missing_qual_scores_middle -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_description_newline_replacement_multi_char -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/error_qual_escape.fastq -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_extensive -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/embl_single_record_simple -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/misc_dna_as_sanger.fastq -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/misc_dna_as_illumina.fastq -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/empty -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_multi_blank_between_records -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast6_default_single_line -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_missing_reference_items -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_runon_gf_no_whitespace -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_single_dna_seq_non_defaults -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_invalid_missing_qual_scores_first -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_invalid_qual_scores_over_255 -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_id_whitespace_replacement_none -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_5_ws_lines_start_of_file -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_invalid_whitespace_line_in_seq -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/error_trunc_in_title.fastq -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/sample-metadata-comments-mixed-case.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_ws_lines_between_records -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/io/format/tests/data
creating build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/embedding/tests/data
copying skbio/embedding/tests/data/embed1.txt.npy -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/embedding/tests/data
creating build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data
creating build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/invalid-header.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/types-directive-non-numeric.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/directive-before-header.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/directive-after-directives-section.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/duplicate-ids.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/comments-and-empty-rows-only.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/qiime1-empty.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/missing-unknown-scheme.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/column-name-conflicts-with-id-header.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/id-conflicts-with-id-header.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/duplicate-directives.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/whitespace-only-id.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/directive-longer-than-header.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/duplicate-column-names-with-whitespace.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/header-only.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/whitespace-only-column-name.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/simple-utf-16be.txt -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/unrecognized-column-type.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/empty-file -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/data-longer-than-header.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/duplicate-column-names.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/empty-column-name.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/simple-utf-16le.txt -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/non-utf-8.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/unrecognized-directive.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/duplicate-ids-with-whitespace.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/header-only-with-comments-and-empty-rows.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
copying skbio/metadata/tests/data/invalid/empty-id.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/invalid
creating build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/override-insdc.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/non-standard-characters.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/single-column.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/simple.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/simple-with-directive.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/empty-types-directive.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/numeric-column.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/simple.txt -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/case-insensitive-types-directive.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/complete-types-directive.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/windows-line-endings.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/jagged-trailing-columns.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/leading-trailing-whitespace.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/jagged.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/trailing-columns.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/BOM-simple.txt -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/missing-data.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/qiita-preparation-information.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/mac-line-endings.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/recommended-ids.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/qiime1.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/qiita-sample-information.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/no-columns.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/partial-types-directive.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/unix-line-endings.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/no-id-or-column-name-type-cast.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/missing-insdc-no-directive.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/biom-observation-metadata.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/minimal.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/all-cells-padded.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/empty-rows.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/missing-insdc.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/rows-shorter-than-header.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/single-id.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/complete-types-directive_w_sk.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/comments.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/column-order.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
copying skbio/metadata/tests/data/valid/no-newline-at-eof.tsv -> build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/tests/data/valid
running build_ext
building 'skbio.metadata._intersection' extension
creating build/temp.freebsd-15.0-CURRENT-arm-cpython-311
creating build/temp.freebsd-15.0-CURRENT-arm-cpython-311/skbio
creating build/temp.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata
cc -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/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c skbio/metadata/_intersection.c -o build/temp.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/_intersection.o
skbio/metadata/_intersection.c:2503:25: warning: overflow in expression; result is -2'147'483'648 with type 'int' [-Winteger-overflow]
2503 | __pyx_t_2 = (RAND_MAX + 1);
| ~~~~~~~~~^~~
skbio/metadata/_intersection.c:11813:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
11813 | CYTHON_FALLTHROUGH;
| ^
skbio/metadata/_intersection.c:358:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
358 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
| ^
skbio/metadata/_intersection.c:11824:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
11824 | CYTHON_FALLTHROUGH;
| ^
skbio/metadata/_intersection.c:358:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
358 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
| ^
skbio/metadata/_intersection.c:12120:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
12120 | CYTHON_FALLTHROUGH;
| ^
skbio/metadata/_intersection.c:358:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
358 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
| ^
skbio/metadata/_intersection.c:12131:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
12131 | CYTHON_FALLTHROUGH;
| ^
skbio/metadata/_intersection.c:358:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
358 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
| ^
5 warnings generated.
cc -shared -L/usr/local/lib -fstack-protector-strong -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/_intersection.o -L/usr/local/lib -o build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/metadata/_intersection.cpython-311.so
building 'skbio.alignment._ssw_wrapper' extension
creating build/temp.freebsd-15.0-CURRENT-arm-cpython-311/skbio/alignment
creating build/temp.freebsd-15.0-CURRENT-arm-cpython-311/skbio/alignment/_lib
cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Iskbio/alignment -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c skbio/alignment/_lib/ssw.c -o build/temp.freebsd-15.0-CURRENT-arm-cpython-311/skbio/alignment/_lib/ssw.o -I. -fopenmp-simd -DSIMDE_ENABLE_OPENMP
cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Iskbio/alignment -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c skbio/alignment/_ssw_wrapper.c -o build/temp.freebsd-15.0-CURRENT-arm-cpython-311/skbio/alignment/_ssw_wrapper.o -I. -fopenmp-simd -DSIMDE_ENABLE_OPENMP
In file included from skbio/alignment/_ssw_wrapper.c:783:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:
/usr/local/lib/python3.11/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]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^
skbio/alignment/_ssw_wrapper.c:11948:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
11948 | CYTHON_FALLTHROUGH;
| ^
skbio/alignment/_ssw_wrapper.c:375:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
375 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
| ^
skbio/alignment/_ssw_wrapper.c:11959:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
11959 | CYTHON_FALLTHROUGH;
| ^
skbio/alignment/_ssw_wrapper.c:375:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
375 | #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
| ^
3 warnings generated.
cc -shared -L/usr/local/lib -fstack-protector-strong -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.0-CURRENT-arm-cpython-311/skbio/alignment/_lib/ssw.o build/temp.freebsd-15.0-CURRENT-arm-cpython-311/skbio/alignment/_ssw_wrapper.o -L/usr/local/lib -o build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/alignment/_ssw_wrapper.cpython-311.so
building 'skbio.diversity._phylogenetic' extension
creating build/temp.freebsd-15.0-CURRENT-arm-cpython-311/skbio/diversity
cc -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/python3.11/site-packages/numpy/core/include -I/usr/local/lib/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c skbio/diversity/_phylogenetic.c -o build/temp.freebsd-15.0-CURRENT-arm-cpython-311/skbio/diversity/_phylogenetic.o
In file included from skbio/diversity/_phylogenetic.c:774:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/arrayobject.h:5:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.11/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:
/usr/local/lib/python3.11/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]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^
1 warning generated.
cc -shared -L/usr/local/lib -fstack-protector-strong -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-15.0-CURRENT-arm-cpython-311/skbio/diversity/_phylogenetic.o -L/usr/local/lib -o build/lib.freebsd-15.0-CURRENT-arm-cpython-311/skbio/diversity/_phylogenetic.cpython-311.so
building 'skbio.stats.ordination._cutils' extension
creating build/temp.freebsd-15.0-CURRENT-arm-cpython-311/skbio/stats
creating build/temp.freebsd-15.0-CURRENT-arm-cpython-311/skbio/stats/ordination
cc -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/python3.11/site-packages/numpy/core/include -I/usr/local/include/python3.11 -c skbio/stats/ordination/_cutils.c -o build/temp.freebsd-15.0-CURRENT-arm-cpython-311/skbio/stats/ordination/_cutils.o -I. -fopenmp-simd -DSIMDE_ENABLE_OPENMP -fopenmp
skbio/stats/ordination/_cutils.c:778:10: fatal error: 'omp.h' file not found
778 | #include <omp.h>
| ^~~~~~~
1 error generated.
error: command '/usr/bin/cc' failed with exit code 1
ERROR Backend subprocess exited when trying to invoke build_wheel
*** Error code 1
Stop.
make: stopped making "build" in /usr/ports/biology/py-scikit-bio