[package - 140amd64-quarterly][biology/py-pybigwig] Failed for py39-pyBigWig-0.3.21 in build
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Date: Fri, 29 Dec 2023 13:20:02 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/beefy8/data/140amd64-quarterly/d1ac189050da/logs/py39-pyBigWig-0.3.21.log
Build URL: https://pkg-status.freebsd.org/beefy8/build.html?mastername=140amd64-quarterly&build=d1ac189050da
Log:
=>> Building biology/py-pybigwig
build started at Fri Dec 29 13:19:56 UTC 2023
port directory: /usr/ports/biology/py-pybigwig
package name: py39-pyBigWig-0.3.21
building for: FreeBSD 140amd64-quarterly-job-07 14.0-RELEASE-p4 FreeBSD 14.0-RELEASE-p4 amd64
maintained by: jwb@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 495 Oct 7 01:01 /usr/ports/biology/py-pybigwig/Makefile
Ports top last git commit: d1ac18905
Ports top unclean checkout: no
Port dir last git commit: 2b5c95373
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.0
Host OSVERSION: 1500006
Jail OSVERSION: 1400097
Job Id: 07
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PORT_FLAGS=
PKGENV=
FLAVOR=py39
MAKE_ARGS= FLAVOR=py39
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
---End OPTIONS List---
--MAINTAINER--
jwb@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-pybigwig/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-pybigwig/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-pybigwig/work-py39/.cache HOME=/wrkdirs/usr/ports/biology/py-pybigwig/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-pybigwig/work-py39/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-pybigwig/work-py39/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local"
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-pybigwig/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-pybigwig/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-pybigwig/work-py39/.cache HOME=/wrkdirs/usr/ports/biology/py-pybigwig/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-pybigwig/work-py39/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-pybigwig/work-py39/.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 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= 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
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--End MAKE_ENV--
--PLIST_SUB--
PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd14 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=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/pyBigWig" EXAMPLESDIR="share/examples/pyBigWig" DATADIR="share/pyBigWig" WWWDIR="www/pyBigWig" ETCDIR="etc/pyBigWig"
--End PLIST_SUB--
--SUB_LIST--
PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd14 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/pyBigWig DOCSDIR=/usr/local/share/doc/pyBigWig EXAMPLESDIR=/usr/local/share/examples/pyBigWig WWWDIR=/usr/local/www/pyBigWig ETCDIR=/usr/local/etc/pyBigWig
--End SUB_LIST--
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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
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GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
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cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 33554432
stack size (kbytes, -s) 524288
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 MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py39-pyBigWig-0.3.21 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.9.pkg
[140amd64-quarterly-job-07] Installing pkg-1.20.9...
[140amd64-quarterly-job-07] Extracting pkg-1.20.9: .......... done
===> py39-pyBigWig-0.3.21 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py39-pyBigWig-0.3.21
===========================================================================
=======================<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 py39-pyBigWig-0.3.21 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 py39-pyBigWig-0.3.21 for building
=> SHA256 Checksum OK for pyBigWig-0.3.21.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 MIT accepted by the user
===> Fetching all distfiles required by py39-pyBigWig-0.3.21 for building
===> Extracting for py39-pyBigWig-0.3.21
=> SHA256 Checksum OK for pyBigWig-0.3.21.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 py39-pyBigWig-0.3.21
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py39-pyBigWig-0.3.21 depends on package: py39-setuptools>=63.1.0 - not found
===> Installing existing package /packages/All/py39-setuptools-63.1.0_1.pkg
[140amd64-quarterly-job-07] Installing py39-setuptools-63.1.0_1...
[140amd64-quarterly-job-07] `-- Installing python39-3.9.18...
[140amd64-quarterly-job-07] | `-- Installing gettext-runtime-0.22_1...
[140amd64-quarterly-job-07] | | `-- Installing indexinfo-0.3.1...
[140amd64-quarterly-job-07] | | `-- Extracting indexinfo-0.3.1: .... done
[140amd64-quarterly-job-07] | `-- Extracting gettext-runtime-0.22_1: .......... done
[140amd64-quarterly-job-07] | `-- Installing libffi-3.4.4...
[140amd64-quarterly-job-07] | `-- Extracting libffi-3.4.4: .......... done
[140amd64-quarterly-job-07] | `-- Installing mpdecimal-2.5.1...
[140amd64-quarterly-job-07] | `-- Extracting mpdecimal-2.5.1: .......... done
[140amd64-quarterly-job-07] | `-- Installing readline-8.2.1...
[140amd64-quarterly-job-07] | `-- Extracting readline-8.2.1: .......... done
[140amd64-quarterly-job-07] `-- Extracting python39-3.9.18: .......... done
[140amd64-quarterly-job-07] Extracting py39-setuptools-63.1.0_1: .......... done
=====
Message from python39-3.9.18:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py39-gdbm databases/py-gdbm@py39
py39-sqlite3 databases/py-sqlite3@py39
py39-tkinter x11-toolkits/py-tkinter@py39
===> py39-pyBigWig-0.3.21 depends on package: py39-setuptools>=63.1.0 - found
===> Returning to build of py39-pyBigWig-0.3.21
===> py39-pyBigWig-0.3.21 depends on file: /usr/local/bin/python3.9 - found
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> py39-pyBigWig-0.3.21 depends on shared library: libcurl.so - not found
===> Installing existing package /packages/All/curl-8.5.0.pkg
[140amd64-quarterly-job-07] Installing curl-8.5.0...
[140amd64-quarterly-job-07] `-- Installing libnghttp2-1.57.0...
[140amd64-quarterly-job-07] `-- Extracting libnghttp2-1.57.0: .......... done
[140amd64-quarterly-job-07] `-- Installing libpsl-0.21.2_3...
[140amd64-quarterly-job-07] | `-- Installing libidn2-2.3.4...
[140amd64-quarterly-job-07] | | `-- Installing libunistring-1.1...
[140amd64-quarterly-job-07] | | `-- Extracting libunistring-1.1: .......... done
[140amd64-quarterly-job-07] | `-- Extracting libidn2-2.3.4: .......... done
[140amd64-quarterly-job-07] `-- Extracting libpsl-0.21.2_3: .......... done
[140amd64-quarterly-job-07] `-- Installing libssh2-1.11.0,3...
[140amd64-quarterly-job-07] `-- Extracting libssh2-1.11.0,3: .......... done
[140amd64-quarterly-job-07] Extracting curl-8.5.0: .......... done
===> py39-pyBigWig-0.3.21 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so)
===> Returning to build of py39-pyBigWig-0.3.21
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for py39-pyBigWig-0.3.21
/usr/local/lib/python3.9/site-packages/setuptools/config/pyprojecttoml.py:104: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*.
warnings.warn(msg, _BetaConfiguration)
running config
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for py39-pyBigWig-0.3.21
/usr/local/lib/python3.9/site-packages/setuptools/config/pyprojecttoml.py:104: _BetaConfiguration: Support for `[tool.setuptools]` in `pyproject.toml` is still *beta*.
warnings.warn(msg, _BetaConfiguration)
running build
running build_py
creating build
creating build/lib.freebsd-14.0-RELEASE-p4-amd64-cpython-39
creating build/lib.freebsd-14.0-RELEASE-p4-amd64-cpython-39/pyBigWigTest
copying pyBigWigTest/__init__.py -> build/lib.freebsd-14.0-RELEASE-p4-amd64-cpython-39/pyBigWigTest
copying pyBigWigTest/test.py -> build/lib.freebsd-14.0-RELEASE-p4-amd64-cpython-39/pyBigWigTest
running egg_info
writing pyBigWig.egg-info/PKG-INFO
writing dependency_links to pyBigWig.egg-info/dependency_links.txt
writing top-level names to pyBigWig.egg-info/top_level.txt
reading manifest file 'pyBigWig.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE.txt'
writing manifest file 'pyBigWig.egg-info/SOURCES.txt'
copying pyBigWigTest/test.bigBed -> build/lib.freebsd-14.0-RELEASE-p4-amd64-cpython-39/pyBigWigTest
copying pyBigWigTest/test.bw -> build/lib.freebsd-14.0-RELEASE-p4-amd64-cpython-39/pyBigWigTest
running build_ext
building 'pyBigWig' extension
creating build/temp.freebsd-14.0-RELEASE-p4-amd64-cpython-39
creating build/temp.freebsd-14.0-RELEASE-p4-amd64-cpython-39/libBigWig
cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -IlibBigWig -I/usr/local/include/python3.9 -I/usr/local/include/python3.9 -c libBigWig/bwRead.c -o build/temp.freebsd-14.0-RELEASE-p4-amd64-cpython-39/libBigWig/bwRead.o
cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -IlibBigWig -I/usr/local/include/python3.9 -I/usr/local/include/python3.9 -c libBigWig/bwStats.c -o build/temp.freebsd-14.0-RELEASE-p4-amd64-cpython-39/libBigWig/bwStats.o
cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -IlibBigWig -I/usr/local/include/python3.9 -I/usr/local/include/python3.9 -c libBigWig/bwValues.c -o build/temp.freebsd-14.0-RELEASE-p4-amd64-cpython-39/libBigWig/bwValues.o
libBigWig/bwValues.c:8:35: error: too few arguments provided to function-like macro invocation
static uint32_t roundup(uint32_t v) {
^
/usr/include/sys/param.h:326:9: note: macro 'roundup' defined here
#define roundup(x, y) ((((x)+((y)-1))/(y))*(y)) /* to any y */
^
libBigWig/bwValues.c:8:24: error: expected ';' after top level declarator
static uint32_t roundup(uint32_t v) {
^
;
libBigWig/bwValues.c:349:30: error: too few arguments provided to function-like macro invocation
o->m = roundup(o->l+1);
^
/usr/include/sys/param.h:326:9: note: macro 'roundup' defined here
#define roundup(x, y) ((((x)+((y)-1))/(y))*(y)) /* to any y */
^
libBigWig/bwValues.c:369:30: error: too few arguments provided to function-like macro invocation
o->m = roundup(o->l+1);
^
/usr/include/sys/param.h:326:9: note: macro 'roundup' defined here
#define roundup(x, y) ((((x)+((y)-1))/(y))*(y)) /* to any y */
^
4 errors generated.
error: command '/usr/bin/cc' failed with exit code 1
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/py-pybigwig