[package - main-amd64-default][science/py-netCDF4] Failed for py39-netCDF4-1.6.2 in build
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Date: Sat, 18 Feb 2023 15:46:59 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: bofh@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/p9d6358b286b5_sff8da9b2ba/logs/py39-netCDF4-1.6.2.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p9d6358b286b5_sff8da9b2ba
Log:
=>> Building science/py-netCDF4
build started at Sat Feb 18 15:46:36 UTC 2023
port directory: /usr/ports/science/py-netCDF4
package name: py39-netCDF4-1.6.2
building for: FreeBSD main-amd64-default-job-07 14.0-CURRENT FreeBSD 14.0-CURRENT 1400081 amd64
maintained by: bofh@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400073
Jail OSVERSION: 1400081
Job Id: 07
!!! Jail is newer than host. (Jail: 1400081, Host: 1400073) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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===> The following configuration options are available for py39-netCDF4-1.6.2:
DOCS=on: Build and/or install documentation
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
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bofh@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> py39-netCDF4-1.6.2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1_1.pkg
[main-amd64-default-job-07] Installing pkg-1.19.1_1...
[main-amd64-default-job-07] Extracting pkg-1.19.1_1: .......... done
===> py39-netCDF4-1.6.2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py39-netCDF4-1.6.2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by py39-netCDF4-1.6.2 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by py39-netCDF4-1.6.2 for building
=> SHA256 Checksum OK for Unidata-netcdf4-python-v1.6.2rel_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by py39-netCDF4-1.6.2 for building
===> Extracting for py39-netCDF4-1.6.2
=> SHA256 Checksum OK for Unidata-netcdf4-python-v1.6.2rel_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for py39-netCDF4-1.6.2
===========================================================================
=======================<phase: build-depends >============================
===> py39-netCDF4-1.6.2 depends on package: py39-numpy>=1.16,1<1.25,1 - not found
<snip>
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
=====
Message from python39-3.9.16_1:
--
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
=====
Message from metis-5.1.0_9:
--
===> NOTICE:
The metis port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> py39-netCDF4-1.6.2 depends on package: py39-numpy>=1.16,1<1.25,1 - found
===> Returning to build of py39-netCDF4-1.6.2
===> py39-netCDF4-1.6.2 depends on executable: cython-3.9 - not found
===> Installing existing package /packages/All/py39-cython-0.29.33.pkg
[main-amd64-default-job-07] Installing py39-cython-0.29.33...
[main-amd64-default-job-07] Extracting py39-cython-0.29.33: .......... done
>=> Cleaning stale bytecode files...
>=> Byte-compiling Python source files...
===> py39-netCDF4-1.6.2 depends on executable: cython-3.9 - found
===> Returning to build of py39-netCDF4-1.6.2
===> py39-netCDF4-1.6.2 depends on package: py39-setuptools>=63.1.0 - found
===> py39-netCDF4-1.6.2 depends on file: /usr/local/bin/python3.9 - found
===========================================================================
=======================<phase: lib-depends >============================
===> py39-netCDF4-1.6.2 depends on shared library: libhdf5.so - not found
===> Installing existing package /packages/All/hdf5-1.12.2_1,1.pkg
[main-amd64-default-job-07] Installing hdf5-1.12.2_1,1...
[main-amd64-default-job-07] `-- Installing libaec-1.0.6...
[main-amd64-default-job-07] `-- Extracting libaec-1.0.6: .......... done
[main-amd64-default-job-07] Extracting hdf5-1.12.2_1,1: .......... done
===> py39-netCDF4-1.6.2 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so)
===> Returning to build of py39-netCDF4-1.6.2
===> py39-netCDF4-1.6.2 depends on shared library: libnetcdf.so - not found
===> Installing existing package /packages/All/netcdf-4.9.0_2.pkg
[main-amd64-default-job-07] Installing netcdf-4.9.0_2...
[main-amd64-default-job-07] `-- Installing curl-7.87.0_1...
[main-amd64-default-job-07] | `-- Installing ca_root_nss-3.88.1...
[main-amd64-default-job-07] | `-- Extracting ca_root_nss-3.88.1: .......... done
[main-amd64-default-job-07] | `-- Installing libnghttp2-1.51.0_1...
[main-amd64-default-job-07] | `-- Extracting libnghttp2-1.51.0_1: .......... done
[main-amd64-default-job-07] | `-- Installing libpsl-0.21.2_2...
[main-amd64-default-job-07] | | `-- Installing libidn2-2.3.4...
[main-amd64-default-job-07] | | `-- Installing libunistring-1.1...
[main-amd64-default-job-07] | | `-- Extracting libunistring-1.1: .......... done
[main-amd64-default-job-07] | | `-- Extracting libidn2-2.3.4: .......... done
[main-amd64-default-job-07] | `-- Extracting libpsl-0.21.2_2: .......... done
[main-amd64-default-job-07] | `-- Installing libssh2-1.10.0_1,3...
[main-amd64-default-job-07] | `-- Extracting libssh2-1.10.0_1,3: .......... done
[main-amd64-default-job-07] `-- Extracting curl-7.87.0_1: .......... done
[main-amd64-default-job-07] `-- Installing pkgconf-1.8.1,1...
[main-amd64-default-job-07] `-- Extracting pkgconf-1.8.1,1: .......... done
[main-amd64-default-job-07] Extracting netcdf-4.9.0_2: .......... done
=====
Message from ca_root_nss-3.88.1:
--
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
===> py39-netCDF4-1.6.2 depends on shared library: libnetcdf.so - found (/usr/local/lib/libnetcdf.so)
===> Returning to build of py39-netCDF4-1.6.2
===========================================================================
=======================<phase: configure >============================
===> Configuring for py39-netCDF4-1.6.2
reading from setup.cfg...
using /usr/local/bin/nc-config...
checking /usr/local/include ...
HDF5 library version: 1.12.2 headers found in /usr/local/include
using netcdf library version b'4.9.0'
using Cython to compile netCDF4.pyx...
netcdf lib has group rename capability
netcdf lib has nc_inq_path function
netcdf lib has nc_inq_format_extended function
netcdf lib has nc_open_mem function
netcdf lib has nc_create_mem function
netcdf lib has cdf-5 format capability
netcdf lib does not have netcdf4 parallel functions
netcdf lib does not have pnetcdf parallel functions
netcdf lib has bit-grooming/quantization functions
netcdf lib has zstandard compression functions
netcdf lib has bzip2 compression functions
netcdf lib has blosc compression functions
netcdf lib has szip compression functions
netcdf lib has nc_set_alignment function
netcdf lib has nc_inq_filter_avail function
NETCDF_PLUGIN_DIR not set, no netcdf compression plugins installed
running config
===========================================================================
=======================<phase: build >============================
===> Building for py39-netCDF4-1.6.2
reading from setup.cfg...
using /usr/local/bin/nc-config...
checking /usr/local/include ...
HDF5 library version: 1.12.2 headers found in /usr/local/include
using netcdf library version b'4.9.0'
using Cython to compile netCDF4.pyx...
netcdf lib has group rename capability
netcdf lib has nc_inq_path function
netcdf lib has nc_inq_format_extended function
netcdf lib has nc_open_mem function
netcdf lib has nc_create_mem function
netcdf lib has cdf-5 format capability
netcdf lib does not have netcdf4 parallel functions
netcdf lib does not have pnetcdf parallel functions
netcdf lib has bit-grooming/quantization functions
netcdf lib has zstandard compression functions
netcdf lib has bzip2 compression functions
netcdf lib has blosc compression functions
netcdf lib has szip compression functions
netcdf lib has nc_set_alignment function
netcdf lib has nc_inq_filter_avail function
NETCDF_PLUGIN_DIR not set, no netcdf compression plugins installed
running build
running build_py
creating build
creating build/lib.freebsd-14.0-CURRENT-amd64-cpython-39
creating build/lib.freebsd-14.0-CURRENT-amd64-cpython-39/netCDF4
copying src/netCDF4/__init__.py -> build/lib.freebsd-14.0-CURRENT-amd64-cpython-39/netCDF4
copying src/netCDF4/utils.py -> build/lib.freebsd-14.0-CURRENT-amd64-cpython-39/netCDF4
running build_ext
cythoning src/netCDF4/_netCDF4.pyx to src/netCDF4/_netCDF4.c
building 'netCDF4._netCDF4' extension
creating build/temp.freebsd-14.0-CURRENT-amd64-cpython-39
creating build/temp.freebsd-14.0-CURRENT-amd64-cpython-39/src
creating build/temp.freebsd-14.0-CURRENT-amd64-cpython-39/src/netCDF4
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 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I/usr/local/include -I/usr/local/lib/python3.9/site-packages/numpy/core/include -Iinclude -I/usr/local/include/python3.9 -c src/netCDF4/_netCDF4.c -o build/temp.freebsd-14.0-CURRENT-amd64-cpython-39/src/netCDF4/_netCDF4.o
src/netCDF4/_netCDF4.c:4971:8: warning: passing 'const void *' to parameter of type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
free(__pyx_v_self->memory);
^~~~~~~~~~~~~~~~~~~~
/usr/include/stdlib.h:102:18: note: passing argument to parameter here
void free(void *);
^
src/netCDF4/_netCDF4.c:9587:106: warning: passing 'char **' to parameter of type 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_ierr = nc_put_att_string(__pyx_v_grpid, __pyx_v_varid, __pyx_v_attname, __pyx_v_N, __pyx_v_string_ptrs);
^~~~~~~~~~~~~~~~~~~
/usr/local/include/netcdf.h:1110:44: note: passing argument to parameter 'op' here
size_t len, const char **op);
^
src/netCDF4/_netCDF4.c:10084:102: warning: passing 'char **' to parameter of type 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
__pyx_v_ierr = nc_put_att_string(__pyx_v_grpid, __pyx_v_varid, __pyx_v_attname, 1, (&__pyx_v_datstring));
^~~~~~~~~~~~~~~~~~~~
/usr/local/include/netcdf.h:1110:44: note: passing argument to parameter 'op' here
size_t len, const char **op);
^
src/netCDF4/_netCDF4.c:69249:35: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
for (__pyx_v_nf = 0; __pyx_v_nf < __pyx_t_4; __pyx_v_nf++) {
~~~~~~~~~~ ^ ~~~~~~~~~
src/netCDF4/_netCDF4.c:73259:39: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
for (__pyx_v_nmem = 0; __pyx_v_nmem < __pyx_t_11; __pyx_v_nmem++) {
~~~~~~~~~~~~ ^ ~~~~~~~~~~
src/netCDF4/_netCDF4.c:93376:3: error: incompatible pointer to integer conversion returning 'void *' from a function with result type 'int' [-Wint-conversion]
import_array();
^~~~~~~~~~~~~~
/usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/__multiarray_api.h:1553:151: note: expanded from macro 'import_array'
#define import_array() {if (_import_array() < 0) {PyErr_Print(); PyErr_SetString(PyExc_ImportError, "numpy.core.multiarray failed to import"); return NULL; } }
^~~~
/usr/include/sys/_null.h:34:14: note: expanded from macro 'NULL'
#define NULL ((void *)0)
^~~~~~~~~~~
5 warnings and 1 error generated.
error: command '/usr/bin/cc' failed with exit code 1
*** Error code 1
Stop.
make: stopped in /usr/ports/science/py-netCDF4