[exp - 140amd64-default-build-as-user][biology/py-pywgsim] Failed for py311-pywgsim-0.5.2 in build
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Date: Mon, 03 Jun 2024 04:52:50 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/package19/data/140amd64-default-build-as-user/1d1d7ac81d64/logs/py311-pywgsim-0.5.2.log
Build URL: https://pkg-status.freebsd.org/package19/build.html?mastername=140amd64-default-build-as-user&build=1d1d7ac81d64
Log:
=>> Building biology/py-pywgsim
build started at Mon Jun 3 04:52:41 UTC 2024
port directory: /usr/ports/biology/py-pywgsim
package name: py311-pywgsim-0.5.2
building for: FreeBSD 140amd64-default-build-as-user-job-09 14.0-RELEASE-p6 FreeBSD 14.0-RELEASE-p6 amd64
maintained by: jwb@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 398 Jan 13 2023 /usr/ports/biology/py-pywgsim/Makefile
Ports top last git commit: 1d1d7ac81d6
Ports top unclean checkout: no
Port dir last git commit: 77d68471ade
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-30-g79e3edcd
Host OSVERSION: 1500018
Jail OSVERSION: 1400097
Job Id: 09
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PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-pywgsim/work-py311 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-pywgsim/work-py311 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-pywgsim/work-py311/.cache HOME=/wrkdirs/usr/ports/biology/py-pywgsim/work-py311 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-pywgsim/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-pywgsim/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
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--End PLIST_SUB--
--SUB_LIST--
PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 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/pywgsim DOCSDIR=/usr/local/share/doc/pywgsim EXAMPLESDIR=/usr/local/share/examples/pywgsim WWWDIR=/usr/local/www/pywgsim ETCDIR=/usr/local/etc/pywgsim
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--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py311-pywgsim-0.5.2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.3.pkg
[140amd64-default-build-as-user-job-09] Installing pkg-1.21.3...
[140amd64-default-build-as-user-job-09] Extracting pkg-1.21.3: .......... done
===> py311-pywgsim-0.5.2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py311-pywgsim-0.5.2
===========================================================================
=======================<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 MIT accepted by the user
===> Fetching all distfiles required by py311-pywgsim-0.5.2 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===> Fetching all distfiles required by py311-pywgsim-0.5.2 for building
=> SHA256 Checksum OK for pywgsim-0.5.2.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534
===> License MIT accepted by the user
===> Fetching all distfiles required by py311-pywgsim-0.5.2 for building
===> Extracting for py311-pywgsim-0.5.2
=> SHA256 Checksum OK for pywgsim-0.5.2.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534
===> Patching for py311-pywgsim-0.5.2
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py311-pywgsim-0.5.2 depends on package: py311-setuptools>=63.1.0 - not found
===> Installing existing package /packages/All/py311-setuptools-63.1.0_1.pkg
[140amd64-default-build-as-user-job-09] Installing py311-setuptools-63.1.0_1...
[140amd64-default-build-as-user-job-09] `-- Installing python311-3.11.9...
[140amd64-default-build-as-user-job-09] | `-- Installing gettext-runtime-0.22.5...
[140amd64-default-build-as-user-job-09] | | `-- Installing indexinfo-0.3.1...
[140amd64-default-build-as-user-job-09] | | `-- Extracting indexinfo-0.3.1: .... done
[140amd64-default-build-as-user-job-09] | `-- Extracting gettext-runtime-0.22.5: .......... done
[140amd64-default-build-as-user-job-09] | `-- Installing libffi-3.4.6...
[140amd64-default-build-as-user-job-09] | `-- Extracting libffi-3.4.6: .......... done
[140amd64-default-build-as-user-job-09] | `-- Installing mpdecimal-4.0.0...
[140amd64-default-build-as-user-job-09] | `-- Extracting mpdecimal-4.0.0: .......... done
[140amd64-default-build-as-user-job-09] | `-- Installing readline-8.2.10...
[140amd64-default-build-as-user-job-09] | `-- Extracting readline-8.2.10: .......... done
[140amd64-default-build-as-user-job-09] `-- Extracting python311-3.11.9: .......... done
[140amd64-default-build-as-user-job-09] Extracting py311-setuptools-63.1.0_1: .......... done
=====
Message from python311-3.11.9:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py311-gdbm databases/py-gdbm@py311
py311-sqlite3 databases/py-sqlite3@py311
py311-tkinter x11-toolkits/py-tkinter@py311
===> py311-pywgsim-0.5.2 depends on package: py311-setuptools>=63.1.0 - found
===> Returning to build of py311-pywgsim-0.5.2
===> py311-pywgsim-0.5.2 depends on file: /usr/local/bin/python3.11 - found
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534
===> Configuring for py311-pywgsim-0.5.2
running config
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534
===> Building for py311-pywgsim-0.5.2
running build
running build_py
creating build
creating build/lib.freebsd-14.0-RELEASE-p6-amd64-cpython-311
creating build/lib.freebsd-14.0-RELEASE-p6-amd64-cpython-311/pywgsim
copying pywgsim/main.py -> build/lib.freebsd-14.0-RELEASE-p6-amd64-cpython-311/pywgsim
copying pywgsim/__main__.py -> build/lib.freebsd-14.0-RELEASE-p6-amd64-cpython-311/pywgsim
copying pywgsim/__init__.py -> build/lib.freebsd-14.0-RELEASE-p6-amd64-cpython-311/pywgsim
running egg_info
writing pywgsim.egg-info/PKG-INFO
writing dependency_links to pywgsim.egg-info/dependency_links.txt
writing entry points to pywgsim.egg-info/entry_points.txt
writing requirements to pywgsim.egg-info/requires.txt
writing top-level names to pywgsim.egg-info/top_level.txt
reading manifest file 'pywgsim.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'pywgsim.egg-info/SOURCES.txt'
/usr/local/lib/python3.11/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'pywgsim.src' as data is deprecated, please list it in `packages`.
!!
############################
# Package would be ignored #
############################
Python recognizes 'pywgsim.src' as an importable package,
but it is not listed in the `packages` configuration of setuptools.
'pywgsim.src' has been automatically added to the distribution only
because it may contain data files, but this behavior is likely to change
in future versions of setuptools (and therefore is considered deprecated).
Please make sure that 'pywgsim.src' is included as a package by using
the `packages` configuration field or the proper discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" and "data files" on setuptools
documentation page.
!!
check.warn(importable)
copying pywgsim/wgsim_lib.c -> build/lib.freebsd-14.0-RELEASE-p6-amd64-cpython-311/pywgsim
copying pywgsim/wgsim_lib.pyx -> build/lib.freebsd-14.0-RELEASE-p6-amd64-cpython-311/pywgsim
creating build/lib.freebsd-14.0-RELEASE-p6-amd64-cpython-311/pywgsim/src
copying pywgsim/src/Makefile -> build/lib.freebsd-14.0-RELEASE-p6-amd64-cpython-311/pywgsim/src
copying pywgsim/src/kseq.h -> build/lib.freebsd-14.0-RELEASE-p6-amd64-cpython-311/pywgsim/src
copying pywgsim/src/wgsim_mod.c -> build/lib.freebsd-14.0-RELEASE-p6-amd64-cpython-311/pywgsim/src
copying pywgsim/src/wgsim_mod.h -> build/lib.freebsd-14.0-RELEASE-p6-amd64-cpython-311/pywgsim/src
running build_ext
building 'pywgsim.wgsim' extension
creating build/temp.freebsd-14.0-RELEASE-p6-amd64-cpython-311
creating build/temp.freebsd-14.0-RELEASE-p6-amd64-cpython-311/pywgsim
creating build/temp.freebsd-14.0-RELEASE-p6-amd64-cpython-311/pywgsim/src
cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Ipywgsim/src -I/usr/local/include/python3.11 -c pywgsim/src/wgsim_mod.c -o build/temp.freebsd-14.0-RELEASE-p6-amd64-cpython-311/pywgsim/src/wgsim_mod.o
pywgsim/src/wgsim_mod.c:41:1: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
KSEQ_INIT(gzFile, gzread)
^~~~~~~~~~~~~~~~~~~~~~~~~
pywgsim/src/kseq.h:220:2: note: expanded from macro 'KSEQ_INIT'
KSTREAM_INIT(type_t, __read, 4096) \
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pywgsim/src/kseq.h:145:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETUNTIL(__read, __bufsize)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pywgsim/src/kseq.h:120:24: note: expanded from macro '__KS_GETUNTIL'
if (str->m - str->l < i - ks->begin + 1) { \
~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~
pywgsim/src/wgsim_mod.c:114:16: warning: comparison of integers of different signs: 'int' and 'const size_t' (aka 'const unsigned long') [-Wsign-compare]
for (i = 0; i != ks->seq.l; ++i) {
~ ^ ~~~~~~~~~
pywgsim/src/wgsim_mod.c:170:16: warning: comparison of integers of different signs: 'int' and 'const size_t' (aka 'const unsigned long') [-Wsign-compare]
for (i = 0; i != ks->seq.l; ++i) {
~ ^ ~~~~~~~~~
pywgsim/src/wgsim_mod.c:192:21: warning: comparison of integers of different signs: 'int' and 'const size_t' (aka 'const unsigned long') [-Wsign-compare]
for (j = i; j < ks->seq.l && hap1->s[j] == hap2->s[j] && (hap1->s[j]&mutmsk) == DELETE; ++j)
~ ^ ~~~~~~~~~
pywgsim/src/wgsim_mod.c:221:21: warning: comparison of integers of different signs: 'int' and 'const size_t' (aka 'const unsigned long') [-Wsign-compare]
for (j = i; j < ks->seq.l && hap1->s[j] != hap2->s[j] && (hap1->s[j]&mutmsk) == DELETE; ++j)
~ ^ ~~~~~~~~~
pywgsim/src/wgsim_mod.c:231:21: warning: comparison of integers of different signs: 'int' and 'const size_t' (aka 'const unsigned long') [-Wsign-compare]
for (j = i; j < ks->seq.l && hap1->s[j] != hap2->s[j] && (hap2->s[j]&mutmsk) == DELETE; ++j)
~ ^ ~~~~~~~~~
pywgsim/src/wgsim_mod.c:341:56: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
} while (pos < 0 || pos >= ks->seq.l || pos + d - 1 >= ks->seq.l);
~~~~~~~~~~~ ^ ~~~~~~~~~
pywgsim/src/wgsim_mod.c:341:28: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
} while (pos < 0 || pos >= ks->seq.l || pos + d - 1 >= ks->seq.l);
~~~ ^ ~~~~~~~~~
pywgsim/src/wgsim_mod.c:379:4: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
__gen_read(0, pos, ++i);
^~~~~~~~~~~~~~~~~~~~~~~
pywgsim/src/wgsim_mod.c:358:61: note: expanded from macro '__gen_read'
for (i = (start), k = 0, ext_coor[x] = -10; i >= 0 && i < ks->seq.l && k < s[x]; iter) { \
~ ^ ~~~~~~~~~
pywgsim/src/wgsim_mod.c:380:4: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
__gen_read(1, pos + d - 1, --i);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pywgsim/src/wgsim_mod.c:358:61: note: expanded from macro '__gen_read'
for (i = (start), k = 0, ext_coor[x] = -10; i >= 0 && i < ks->seq.l && k < s[x]; iter) { \
~ ^ ~~~~~~~~~
10 warnings generated.
cc -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -Ipywgsim/src -I/usr/local/include/python3.11 -c pywgsim/wgsim_lib.c -o build/temp.freebsd-14.0-RELEASE-p6-amd64-cpython-311/pywgsim/wgsim_lib.o
pywgsim/wgsim_lib.c:220:12: fatal error: 'longintrepr.h' file not found
#include "longintrepr.h"
^~~~~~~~~~~~~~~
1 error generated.
error: command '/usr/bin/cc' failed with exit code 1
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/py-pywgsim