[package - main-riscv64-default][biology/py-pysam] Failed for py38-pysam-0.19.1 in build
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Date: Tue, 14 Jun 2022 23:48:07 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: http://beefy7.nyi.freebsd.org/data/main-riscv64-default/p89cfb00e410e_sc7f14adfda/logs/py38-pysam-0.19.1.log
Build URL: http://beefy7.nyi.freebsd.org/build.html?mastername=main-riscv64-default&build=p89cfb00e410e_sc7f14adfda
Log:
=>> Building biology/py-pysam
build started at Tue Jun 14 23:41:40 UTC 2022
port directory: /usr/ports/biology/py-pysam
package name: py38-pysam-0.19.1
building for: FreeBSD main-riscv64-default-job-13 14.0-CURRENT FreeBSD 14.0-CURRENT 1400061 riscv
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400050
Jail OSVERSION: 1400061
Job Id: 13
!!! Jail is newer than host. (Jail: 1400061, Host: 1400050) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/pysam DOCSDIR=/usr/local/share/doc/pysam EXAMPLESDIR=/usr/local/share/examples/pysam WWWDIR=/usr/local/www/pysam ETCDIR=/usr/local/etc/pysam
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=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> py38-pysam-0.19.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.5_1.pkg
pkg-static: Warning: Major OS version upgrade detected. Running "pkg bootstrap -f" recommended
[main-riscv64-default-job-13] Installing pkg-1.17.5_1...
[main-riscv64-default-job-13] Extracting pkg-1.17.5_1: .......... done
===> py38-pysam-0.19.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py38-pysam-0.19.1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by py38-pysam-0.19.1 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
<snip>
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:18249:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:18394:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:18527:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:18644:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:18740:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:18836:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:18932:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:22477:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libctabixproxies.c:336:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libctabixproxies.c:22488:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libctabixproxies.c:336:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libctabixproxies.c:23443:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0,
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libctabixproxies.c:25816:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0,
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
17 warnings generated.
/nxb-bin/usr/bin/cc -shared -fstack-protector-strong -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.0-CURRENT-riscv-cpython-38/pysam/libctabixproxies.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/build/lib.freebsd-14.0-CURRENT-riscv-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-r
iscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-38 -lcutils.cpython-38 -o build/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam/libctabixproxies.cpython-38.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
/nxb-bin/usr/bin/cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1 -I/usr/local/include/python3.8 -c pysam/libcvcf.c -o build/temp.freebsd-14.0-CURRENT-riscv-cpython-38/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcvcf.c:31912:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libcvcf.c:32034:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libcvcf.c:32159:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0, /*tp_print*/
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libcvcf.c:35701:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libcvcf.c:351:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libcvcf.c:35712:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libcvcf.c:351:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libcvcf.c:36710:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libcvcf.c:351:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libcvcf.c:36721:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libcvcf.c:351:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libcvcf.c:37042:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libcvcf.c:351:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libcvcf.c:37053:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libcvcf.c:351:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libcvcf.c:37177:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libcvcf.c:351:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libcvcf.c:37188:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libcvcf.c:351:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libcvcf.c:38596:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0,
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pysam/libcvcf.c:40547:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations]
0,
^
/usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here
Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int);
^
/usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
13 warnings generated.
/nxb-bin/usr/bin/cc -shared -fstack-protector-strong -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.0-CURRENT-riscv-cpython-38/pysam/libcvcf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.1/build/lib.freebsd-14.0-CURRENT-riscv-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpyt
hon-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -Lbuild/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-38 -lcutils.cpython-38 -o build/lib.freebsd-14.0-CURRENT-riscv-cpython-38/pysam/libcvcf.cpython-38.so -Wl,-rpath,$ORIGIN
conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): .Lline_table_start0
error: symbols defined in multiple extensions
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/py-pysam