[package - head-i386-default][biology/py-scikit-bio] Failed for py37-scikit-bio-0.5.6 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu Jun 11 12:23:21 UTC 2020
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 at FreeBSD.org
Last committer: yuri at FreeBSD.org
Ident: $FreeBSD: head/biology/py-scikit-bio/Makefile 535346 2020-05-16 02:29:20Z yuri $
Log URL: http://beefy17.nyi.freebsd.org/data/head-i386-default/p538447_s362038/logs/py37-scikit-bio-0.5.6.log
Build URL: http://beefy17.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p538447_s362038
Log:
=>> Building biology/py-scikit-bio
build started at Thu Jun 11 12:22:49 UTC 2020
port directory: /usr/ports/biology/py-scikit-bio
package name: py37-scikit-bio-0.5.6
building for: FreeBSD head-i386-default-job-11 13.0-CURRENT FreeBSD 13.0-CURRENT 1300097 i386
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/py-scikit-bio/Makefile 535346 2020-05-16 02:29:20Z yuri $
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!!! Jail is newer than host. (Jail: 1300097, Host: 1300089) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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=======================<phase: check-sanity >============================
===> License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> py37-scikit-bio-0.5.6 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.14.4.txz
[head-i386-default-job-11] Installing pkg-1.14.4...
[head-i386-default-job-11] Extracting pkg-1.14.4: .......... done
ldconfig: aout support is deprecated
===> py37-scikit-bio-0.5.6 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py37-scikit-bio-0.5.6
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py37-scikit-bio-0.5.6 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py37-scikit-bio-0.5.6 for building
=> SHA256 Checksum OK for scikit-bio-0.5.6.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py37-scikit-bio-0.5.6 for building
===> Extracting for py37-scikit-bio-0.5.6
=> SHA256 Checksum OK for scikit-bio-0.5.6.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for py37-scikit-bio-0.5.6
===========================================================================
=======================<phase: build-depends >============================
===> py37-scikit-bio-0.5.6 depends on package: py37-numpy>=1.16,1<1.19,1 - not found
===> Installing existing package /packages/All/py37-numpy-1.16.6,1.txz
[head-i386-default-job-11] Installing py37-numpy-1.16.6,1...
[head-i386-default-job-11] `-- Installing gcc9-9.3.0_1...
[head-i386-default-job-11] | `-- Installing binutils-2.33.1_2,1...
[head-i386-default-job-11] | | `-- Installing gettext-runtime-0.20.2...
<snip>
copying skbio/io/format/tests/data/qual_blanks_end_of_file -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_multi_blank_start_of_file -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_multi_seq_sanger -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/ordination_example3_scores -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_multi_seq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_varied_whitespace_in_seqs -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/tsv_8_fields -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/ordination_PCoA_sample_data_3_scores -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_missing_rn_tag -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_ws_lines_end_of_file -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_multiple_trees -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_single_seq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_runon_gf_with_whitespace -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_invalid_missing_header -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast6_custom_multi_line -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_3_seqs_defaults_extra -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_multi_blank_end_of_file -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_single_seq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_invalid_ws_line_after_seq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/gff3_multi_record -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_wrapping_original_sanger_no_description -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_single_tree_without_id -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_multi_seq_roundtrip -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_invalid_too_few_seqs -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qseq_invalid_lane -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast7_custom_minimal -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_whitespace_in_header_3 -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_whitespace_in_header_2 -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_whitespace_in_header_1 -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_wrapping_as_illumina_no_description -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_nonstring_labels -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_metadata_only -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_2_seqs_defaults -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_ws_lines_between_records -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_invalid_missing_seq_data_last -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/ordination_exp_Ordination_RDA_site_constraints -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_max_width_5 -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_max_width_1 -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast7_invalid_differing_fields -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_invalid_blank_line_within_sequence -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_5_ws_lines_start_of_file -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_id_whitespace_replacement_empty_str -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_whitespace_only_lines -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_invalid_ws_line_within_seq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/genbank_5_blanks_start_of_file -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/error_tabs.fastq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_invalid_whitespace_only_sequence -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/illumina_full_range_as_sanger.fastq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/sanger_full_range_original_sanger.fastq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_multi_seq_roundtrip -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_data_only -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_multi_line_tree_with_id -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast7_invalid_no_data -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast7_default_single_line -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_blank_lines -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/longreads_as_illumina.fastq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_multi_seq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_multi_ws_lines_start_of_file -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_invalid_blank_after_header -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_single_seq_short -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_different_padding -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/ordination_L&L_CA_data_scores -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/solexa_full_range_original_solexa.fastq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_description_newline_replacement_none -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_rna -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_invalid_empty_line_before_header -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_runon_references -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/misc_rna_as_illumina.fastq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/phylip_single_seq_long -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast6_custom_mixed_nans -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/embl_single_record -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/error_long_qual.fastq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast6_custom_minimal -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_all_data_types -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/error_qual_null.fastq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_invalid_whitespace_only_line_within_sequence -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/ordination_exp_Ordination_RDA_site -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_invalid_missing_qual_scores_middle -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_description_newline_replacement_multi_char -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/error_qual_escape.fastq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_extensive -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/embl_single_record_simple -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/misc_dna_as_sanger.fastq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/misc_dna_as_illumina.fastq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/empty -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_multi_blank_between_records -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/blast6_default_single_line -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_missing_reference_items -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/stockholm_runon_gf_no_whitespace -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_single_dna_seq_non_defaults -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_invalid_missing_qual_scores_first -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_invalid_qual_scores_over_255 -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_id_whitespace_replacement_none -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fastq_5_ws_lines_start_of_file -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/qual_invalid_whitespace_line_in_seq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/error_trunc_in_title.fastq -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
copying skbio/io/format/tests/data/fasta_ws_lines_between_records -> build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/io/format/tests/data
running build_ext
building 'skbio.metadata._intersection' extension
creating build/temp.freebsd-13.0-CURRENT-i386-3.7
creating build/temp.freebsd-13.0-CURRENT-i386-3.7/skbio
creating build/temp.freebsd-13.0-CURRENT-i386-3.7/skbio/metadata
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/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c skbio/metadata/_intersection.c -o build/temp.freebsd-13.0-CURRENT-i386-3.7/skbio/metadata/_intersection.o
skbio/metadata/_intersection.c:2297:5: warning: code will never be executed [-Wunreachable-code]
PyErr_SetString(PyExc_ZeroDivisionError, "float division");
^~~~~~~~~~~~~~~
1 warning generated.
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-CURRENT-i386-3.7/skbio/metadata/_intersection.o -L/usr/local/lib -lpython3.7m -o build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/metadata/_intersection.so
building 'skbio.stats.__subsample' extension
creating build/temp.freebsd-13.0-CURRENT-i386-3.7/skbio/stats
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/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c skbio/stats/__subsample.c -o build/temp.freebsd-13.0-CURRENT-i386-3.7/skbio/stats/__subsample.o
In file included from skbio/stats/__subsample.c:617:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
^
1 warning generated.
cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-CURRENT-i386-3.7/skbio/stats/__subsample.o -L/usr/local/lib -lpython3.7m -o build/lib.freebsd-13.0-CURRENT-i386-3.7/skbio/stats/__subsample.so
building 'skbio.alignment._ssw_wrapper' extension
creating build/temp.freebsd-13.0-CURRENT-i386-3.7/skbio/alignment
creating build/temp.freebsd-13.0-CURRENT-i386-3.7/skbio/alignment/_lib
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/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c skbio/alignment/_ssw_wrapper.c -o build/temp.freebsd-13.0-CURRENT-i386-3.7/skbio/alignment/_ssw_wrapper.o -Wno-error=declaration-after-statement
In file included from skbio/alignment/_ssw_wrapper.c:624:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
^
1 warning generated.
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/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c skbio/alignment/_lib/ssw.c -o build/temp.freebsd-13.0-CURRENT-i386-3.7/skbio/alignment/_lib/ssw.o -Wno-error=declaration-after-statement
skbio/alignment/_lib/ssw.c:155:21: error: always_inline function '_mm_set1_epi32' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
__m128i vZero = _mm_set1_epi32(0);
^
skbio/alignment/_lib/ssw.c:164:21: error: always_inline function '_mm_set1_epi8' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
__m128i vGapO = _mm_set1_epi8(weight_gapO);
^
skbio/alignment/_lib/ssw.c:167:21: error: always_inline function '_mm_set1_epi8' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
__m128i vGapE = _mm_set1_epi8(weight_gapE);
^
skbio/alignment/_lib/ssw.c:170:21: error: always_inline function '_mm_set1_epi8' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
__m128i vBias = _mm_set1_epi8(bias);
^
skbio/alignment/_lib/ssw.c:195:14: error: '__builtin_ia32_pslldqi128_byteshift' needs target feature sse2
vH = _mm_slli_si128 (vH, 1); /* Shift the 128-bit value in vH left by 1 byte. */
^
/usr/lib/clang/10.0.1/include/emmintrin.h:2821:12: note: expanded from macro '_mm_slli_si128'
(__m128i)__builtin_ia32_pslldqi128_byteshift((__v2di)(__m128i)(a), (int)(imm))
^
skbio/alignment/_lib/ssw.c:205:36: error: always_inline function '_mm_load_si128' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
vH = _mm_adds_epu8(vH, _mm_load_si128(vP + j));
^
skbio/alignment/_lib/ssw.c:205:18: error: always_inline function '_mm_adds_epu8' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
vH = _mm_adds_epu8(vH, _mm_load_si128(vP + j));
^
skbio/alignment/_lib/ssw.c:206:18: error: always_inline function '_mm_subs_epu8' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
vH = _mm_subs_epu8(vH, vBias); /* vH will be always > 0 */
^
skbio/alignment/_lib/ssw.c:214:17: error: always_inline function '_mm_load_si128' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
e = _mm_load_si128(pvE + j);
^
skbio/alignment/_lib/ssw.c:215:18: error: always_inline function '_mm_max_epu8' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
vH = _mm_max_epu8(vH, e);
^
skbio/alignment/_lib/ssw.c:216:18: error: always_inline function '_mm_max_epu8' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
vH = _mm_max_epu8(vH, vF);
^
skbio/alignment/_lib/ssw.c:217:26: error: always_inline function '_mm_max_epu8' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
vMaxColumn = _mm_max_epu8(vMaxColumn, vH);
^
skbio/alignment/_lib/ssw.c:224:13: error: always_inline function '_mm_store_si128' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
_mm_store_si128(pvHStore + j, vH);
^
skbio/alignment/_lib/ssw.c:227:18: error: always_inline function '_mm_subs_epu8' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
vH = _mm_subs_epu8(vH, vGapO); /* saturation arithmetic, result >= 0 */
^
skbio/alignment/_lib/ssw.c:228:17: error: always_inline function '_mm_subs_epu8' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
e = _mm_subs_epu8(e, vGapE);
^
skbio/alignment/_lib/ssw.c:229:17: error: always_inline function '_mm_max_epu8' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
e = _mm_max_epu8(e, vH);
^
skbio/alignment/_lib/ssw.c:230:13: error: always_inline function '_mm_store_si128' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
_mm_store_si128(pvE + j, e);
^
skbio/alignment/_lib/ssw.c:233:18: error: always_inline function '_mm_subs_epu8' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
vF = _mm_subs_epu8(vF, vGapE);
^
skbio/alignment/_lib/ssw.c:234:18: error: always_inline function '_mm_max_epu8' requires target feature 'sse2', but would be inlined into function 'sw_sse2_byte' that is compiled without support for 'sse2'
vF = _mm_max_epu8(vF, vH);
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
error: command 'cc' failed with exit status 1
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/py-scikit-bio
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