[package - 124i386-quarterly][biology/bcftools] Failed for bcftools-1.17 in lib-depends
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Date: Thu, 25 May 2023 09:23:39 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: jwb@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy4/data/124i386-quarterly/56368df6bdde/logs/bcftools-1.17.log
Build URL: https://pkg-status.freebsd.org/beefy4/build.html?mastername=124i386-quarterly&build=56368df6bdde
Log:
=>> Building biology/bcftools
build started at Thu May 25 09:23:29 UTC 2023
port directory: /usr/ports/biology/bcftools
package name: bcftools-1.17
building for: FreeBSD 124i386-quarterly-job-07 12.4-RELEASE-p2 FreeBSD 12.4-RELEASE-p2 i386
maintained by: jwb@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400078
Jail OSVERSION: 1204000
Job Id: 07
---Begin Environment---
SHELL=/bin/csh
UNAME_p=i386
UNAME_m=i386
OSVERSION=1204000
UNAME_v=FreeBSD 12.4-RELEASE-p2
UNAME_r=12.4-RELEASE-p2
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
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POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/124i386-quarterly/ref/.p/pool
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POUDRIEREPATH=/usr/local/bin/poudriere
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PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for bcftools-1.17:
GPL=on: Enable modules that rely on GPL code
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
jwb@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bcftools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bcftools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bcftools/work/.cache HOME=/wrkdirs/usr/ports/biology/bcftools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bcftools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bcftools/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.71 CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288
--End CONFIGURE_ENV--
--MAKE_ENV--
USE_GPL=1 PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bcftools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bcftools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bcftools/work/.cache HOME=/wrkdirs/usr/ports/biology/bcftools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bcftools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bcftools/work/.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 DEFAULT_AUTOCONF=2.71 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing
-isystem /usr/local/include " 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/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd12 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=12.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.1 PERL_VER=5.32 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.32 DOCSDIR="share/doc/bcftools" EXAMPLESDIR="share/examples/bcftools" DATADIR="share/bcftools" WWWDIR="www/bcftools" ETCDIR="etc/bcftools"
--End PLIST_SUB--
--SUB_LIST--
PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd12 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bcftools DOCSDIR=/usr/local/share/doc/bcftools EXAMPLESDIR=/usr/local/share/examples/bcftools WWWDIR=/usr/local/www/bcftools ETCDIR=/usr/local/etc/bcftools
--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
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
#### /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
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#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
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CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=yes
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CC_OUTPUT_921dbbb2_f2776b26=yes
CC_OUTPUT_921dbbb2_53255a77=yes
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CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
CC_OUTPUT_921dbbb2_af59ad06=yes
CC_OUTPUT_921dbbb2_a15f3fcf=yes
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ARCH=i386
OPSYS=FreeBSD
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OSREL=12.4
OSVERSION=1204000
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) 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) 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 MIT GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> bcftools-1.17 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1_1.pkg
[124i386-quarterly-job-07] Installing pkg-1.19.1_1...
[124i386-quarterly-job-07] Extracting pkg-1.19.1_1: .......... done
===> bcftools-1.17 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of bcftools-1.17
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT GPLv3 accepted by the user
===> Fetching all distfiles required by bcftools-1.17 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT GPLv3 accepted by the user
===> Fetching all distfiles required by bcftools-1.17 for building
=> SHA256 Checksum OK for samtools-bcftools-1.17_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License MIT GPLv3 accepted by the user
===> Fetching all distfiles required by bcftools-1.17 for building
===> Extracting for bcftools-1.17
=> SHA256 Checksum OK for samtools-bcftools-1.17_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for bcftools-1.17
===> Applying FreeBSD patches for bcftools-1.17 from /usr/ports/biology/bcftools/files
===========================================================================
=======================<phase: build-depends >============================
===> bcftools-1.17 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[124i386-quarterly-job-07] Installing gmake-4.3_2...
[124i386-quarterly-job-07] `-- Installing gettext-runtime-0.21.1...
[124i386-quarterly-job-07] | `-- Installing indexinfo-0.3.1...
[124i386-quarterly-job-07] | `-- Extracting indexinfo-0.3.1: .... done
[124i386-quarterly-job-07] `-- Extracting gettext-runtime-0.21.1: .......... done
[124i386-quarterly-job-07] Extracting gmake-4.3_2: .......... done
===> bcftools-1.17 depends on package: gmake>=4.3 - found
===> Returning to build of bcftools-1.17
===> bcftools-1.17 depends on package: autoconf>=2.71 - not found
===> Installing existing package /packages/All/autoconf-2.71.pkg
[124i386-quarterly-job-07] Installing autoconf-2.71...
[124i386-quarterly-job-07] `-- Installing autoconf-switch-20220527...
[124i386-quarterly-job-07] `-- Extracting autoconf-switch-20220527: .......... done
[124i386-quarterly-job-07] `-- Installing m4-1.4.19,1...
[124i386-quarterly-job-07] `-- Extracting m4-1.4.19,1: .......... done
[124i386-quarterly-job-07] `-- Installing perl5-5.32.1_3...
[124i386-quarterly-job-07] `-- Extracting perl5-5.32.1_3: .......... done
[124i386-quarterly-job-07] Extracting autoconf-2.71: .......... done
===> bcftools-1.17 depends on package: autoconf>=2.71 - found
===> Returning to build of bcftools-1.17
===> bcftools-1.17 depends on package: automake>=1.16.5 - not found
===> Installing existing package /packages/All/automake-1.16.5.pkg
[124i386-quarterly-job-07] Installing automake-1.16.5...
[124i386-quarterly-job-07] Extracting automake-1.16.5: .......... done
===> bcftools-1.17 depends on package: automake>=1.16.5 - found
===> Returning to build of bcftools-1.17
===========================================================================
=======================<phase: lib-depends >============================
===> bcftools-1.17 depends on shared library: libhts.so - not found
===> Installing existing package /packages/All/htslib-1.17.pkg
[124i386-quarterly-job-07] Installing htslib-1.17...
[124i386-quarterly-job-07] `-- Installing curl-8.1.1...
[124i386-quarterly-job-07] | `-- Installing ca_root_nss-3.89...
[124i386-quarterly-job-07] | `-- Extracting ca_root_nss-3.89: .......... done
[124i386-quarterly-job-07] | `-- Installing libnghttp2-1.52.0...
[124i386-quarterly-job-07] | `-- Extracting libnghttp2-1.52.0: .......... done
[124i386-quarterly-job-07] | `-- Installing libpsl-0.21.2_2...
[124i386-quarterly-job-07] | | `-- Installing libidn2-2.3.4...
[124i386-quarterly-job-07] | | `-- Installing libunistring-1.1...
[124i386-quarterly-job-07] | | `-- Extracting libunistring-1.1: .......... done
[124i386-quarterly-job-07] | | `-- Extracting libidn2-2.3.4: .......... done
[124i386-quarterly-job-07] | `-- Extracting libpsl-0.21.2_2: .......... done
[124i386-quarterly-job-07] | `-- Installing libssh2-1.10.0_1,3...
[124i386-quarterly-job-07] | `-- Extracting libssh2-1.10.0_1,3: .......... done
[124i386-quarterly-job-07] `-- Extracting curl-8.1.1: .......... done
[124i386-quarterly-job-07] `-- Installing libdeflate-1.18...
[124i386-quarterly-job-07] `-- Extracting libdeflate-1.18: .......... done
[124i386-quarterly-job-07] Extracting htslib-1.17: .......... done
=====
Message from ca_root_nss-3.89:
--
FreeBSD does not, and can not warrant that the certification authorities
whose certificates are included in this package have in any way been
audited for trustworthiness or RFC 3647 compliance.
Assessment and verification of trust is the complete responsibility of the
system administrator.
This package installs symlinks to support root certificates discovery by
default for software that uses OpenSSL.
This enables SSL Certificate Verification by client software without manual
intervention.
If you prefer to do this manually, replace the following symlinks with
either an empty file or your site-local certificate bundle.
* /etc/ssl/cert.pem
* /usr/local/etc/ssl/cert.pem
* /usr/local/openssl/cert.pem
===> bcftools-1.17 depends on shared library: libhts.soSegmentation fault
- not found
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/bcftools