[package - main-arm64-default][biology/py-pysam] Failed for py38-pysam-0.19.0 in build
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Date: Mon, 16 May 2022 12:20:35 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://ampere2.nyi.freebsd.org/data/main-arm64-default/p9fe69f91ad22_s9b2a35b3a9/logs/py38-pysam-0.19.0.log
Build URL: http://ampere2.nyi.freebsd.org/build.html?mastername=main-arm64-default&build=p9fe69f91ad22_s9b2a35b3a9
Log:
=>> Building biology/py-pysam
build started at Mon May 16 12:11:09 UTC 2022
port directory: /usr/ports/biology/py-pysam
package name: py38-pysam-0.19.0
building for: FreeBSD main-arm64-default-job-03 14.0-CURRENT FreeBSD 14.0-CURRENT 1400059 arm64
maintained by: yuri@FreeBSD.org
Makefile ident:
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Host OSVERSION: 1400050
Jail OSVERSION: 1400059
Job Id: 03
!!! Jail is newer than host. (Jail: 1400059, Host: 1400050) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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yuri@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> py38-pysam-0.19.0 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.5_1.pkg
[main-arm64-default-job-03] Installing pkg-1.17.5_1...
[main-arm64-default-job-03] Extracting pkg-1.17.5_1: .......... done
===> py38-pysam-0.19.0 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py38-pysam-0.19.0
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by py38-pysam-0.19.0 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by py38-pysam-0.19.0 for building
=> SHA256 Checksum OK for pysam-0.19.0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by py38-pysam-0.19.0 for building
===> Extracting for py38-pysam-0.19.0
=> SHA256 Checksum OK for pysam-0.19.0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for py38-pysam-0.19.0
===> Applying FreeBSD patches for py38-pysam-0.19.0 from /usr/ports/biology/py-pysam/files
===========================================================================
=======================<phase: build-depends >============================
===> py38-pysam-0.19.0 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[main-arm64-default-job-03] Installing gmake-4.3_2...
[main-arm64-default-job-03] `-- Installing gettext-runtime-0.21...
[main-arm64-default-job-03] | `-- Installing indexinfo-0.3.1...
[main-arm64-default-job-03] | `-- Extracting indexinfo-0.3.1: .... done
[main-arm64-default-job-03] `-- Extracting gettext-runtime-0.21: .......... done
[main-arm64-default-job-03] Extracting gmake-4.3_2: .......... done
===> py38-pysam-0.19.0 depends on package: gmake>=4.3 - found
<snip>
^
/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:18364:3: 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:18497:3: 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:18614:3: 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:18710:3: 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:18806:3: 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:18902:3: 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:22442:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libctabixproxies.c:327:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libctabixproxies.c:22453:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libctabixproxies.c:327:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libctabixproxies.c:23405:5: 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:25736:5: 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.
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.0-CURRENT-arm64-3.8/pysam/libctabixproxies.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0 -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/build/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pys
am -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-38 -lcutils.cpython-38 -o build/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam/libctabixproxies.cpython-38.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0 -I/usr/local/include/python3.8 -c pysam/libcvcf.c -o build/temp.freebsd-14.0-CURRENT-arm64-3.8/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcvcf.c:31888:3: 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:32010:3: 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:32135:3: 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:35664:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libcvcf.c:342:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libcvcf.c:35675:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libcvcf.c:342:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libcvcf.c:36673:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libcvcf.c:342:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libcvcf.c:36684:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libcvcf.c:342:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libcvcf.c:37005:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libcvcf.c:342:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libcvcf.c:37016:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libcvcf.c:342:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libcvcf.c:37140:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libcvcf.c:342:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libcvcf.c:37151:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough]
CYTHON_FALLTHROUGH;
^
pysam/libcvcf.c:342:34: note: expanded from macro 'CYTHON_FALLTHROUGH'
#define CYTHON_FALLTHROUGH __attribute__((fallthrough))
^
pysam/libcvcf.c:38536:5: 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:40465:5: 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.
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-14.0-CURRENT-arm64-3.8/pysam/libcvcf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0 -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/build/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuil
d/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -Lbuild/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-38 -lcutils.cpython-38 -o build/lib.freebsd-14.0-CURRENT-arm64-3.8/pysam/libcvcf.cpython-38.so -Wl,-rpath,$ORIGIN
conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.1
conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.3
conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.9
conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.8
conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.5
conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.6
conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.4
conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.2
error: symbols defined in multiple extensions
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/py-pysam