[package - head-powerpc64-default][biology/vcflib] Failed for vcflib-1.0.0.r1.130_1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu Oct 29 20:24:22 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: jwb at FreeBSD.org
Last committer: jwb at FreeBSD.org
Ident: $FreeBSD: head/biology/vcflib/Makefile 544090 2020-08-03 17:40:04Z jwb $
Log URL: http://pylon.nyi.freebsd.org/data/head-powerpc64-default/p552783_s366865/logs/vcflib-1.0.0.r1.130_1.log
Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=head-powerpc64-default&build=p552783_s366865
Log:
=>> Building biology/vcflib
build started at Thu Oct 29 20:22:50 UTC 2020
port directory: /usr/ports/biology/vcflib
package name: vcflib-1.0.0.r1.130_1
building for: FreeBSD head-powerpc64-default-job-10 13.0-CURRENT FreeBSD 13.0-CURRENT 1300122 powerpc
maintained by: jwb at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/vcflib/Makefile 544090 2020-08-03 17:40:04Z jwb $
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!!! Jail is newer than host. (Jail: 1300122, Host: 1300084) !!!
!!! This is not supported. !!!
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!!! Expect build failures. !!!
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=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> vcflib-1.0.0.r1.130_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.15.10.txz
[head-powerpc64-default-job-10] Installing pkg-1.15.10...
[head-powerpc64-default-job-10] Extracting pkg-1.15.10: .......... done
===> vcflib-1.0.0.r1.130_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of vcflib-1.0.0.r1.130_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by vcflib-1.0.0.r1.130_1 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by vcflib-1.0.0.r1.130_1 for building
=> SHA256 Checksum OK for ekg-vcflib-v1.0.0-rc1-130-g7e3d806_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by vcflib-1.0.0.r1.130_1 for building
===> Extracting for vcflib-1.0.0.r1.130_1
=> SHA256 Checksum OK for ekg-vcflib-v1.0.0-rc1-130-g7e3d806_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for vcflib-1.0.0.r1.130_1
===> Applying FreeBSD patches for vcflib-1.0.0.r1.130_1 from /usr/ports/biology/vcflib/files
===========================================================================
=======================<phase: build-depends >============================
===> vcflib-1.0.0.r1.130_1 depends on executable: fastahack - not found
===> Installing existing package /packages/All/fastahack-1.0.0.txz
[head-powerpc64-default-job-10] Installing fastahack-1.0.0...
[head-powerpc64-default-job-10] Extracting fastahack-1.0.0: .......... done
===> vcflib-1.0.0.r1.130_1 depends on executable: fastahack - found
===> Returning to build of vcflib-1.0.0.r1.130_1
===> vcflib-1.0.0.r1.130_1 depends on executable: filevercmp - not found
===> Installing existing package /packages/All/filevercmp-g20151117.txz
[head-powerpc64-default-job-10] Installing filevercmp-g20151117...
[head-powerpc64-default-job-10] Extracting filevercmp-g20151117: ...... done
<snip>
===> Returning to build of vcflib-1.0.0.r1.130_1
===> vcflib-1.0.0.r1.130_1 depends on executable: fsom - not found
===> Installing existing package /packages/All/fsom-g20151117_2.txz
[head-powerpc64-default-job-10] Installing fsom-g20151117_2...
[head-powerpc64-default-job-10] Extracting fsom-g20151117_2: ........ done
===> vcflib-1.0.0.r1.130_1 depends on executable: fsom - found
===> Returning to build of vcflib-1.0.0.r1.130_1
===> vcflib-1.0.0.r1.130_1 depends on package: multichoose>=1.0.3 - not found
===> Installing existing package /packages/All/multichoose-1.0.3.2.txz
[head-powerpc64-default-job-10] Installing multichoose-1.0.3.2...
[head-powerpc64-default-job-10] `-- Installing python37-3.7.9_1...
[head-powerpc64-default-job-10] | `-- Installing gettext-runtime-0.21...
[head-powerpc64-default-job-10] | | `-- Installing indexinfo-0.3.1...
[head-powerpc64-default-job-10] | | `-- Extracting indexinfo-0.3.1: .... done
[head-powerpc64-default-job-10] | `-- Extracting gettext-runtime-0.21: .......... done
[head-powerpc64-default-job-10] | `-- Installing libffi-3.3_1...
[head-powerpc64-default-job-10] | `-- Extracting libffi-3.3_1: .......... done
[head-powerpc64-default-job-10] | `-- Installing readline-8.0.4...
[head-powerpc64-default-job-10] | `-- Extracting readline-8.0.4: .......... done
[head-powerpc64-default-job-10] `-- Extracting python37-3.7.9_1: .......... done
[head-powerpc64-default-job-10] Extracting multichoose-1.0.3.2: .......... done
=====
Message from python37-3.7.9_1:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py37-gdbm databases/py-gdbm at py37
py37-sqlite3 databases/py-sqlite3 at py37
py37-tkinter x11-toolkits/py-tkinter at py37
===> vcflib-1.0.0.r1.130_1 depends on package: multichoose>=1.0.3 - found
===> Returning to build of vcflib-1.0.0.r1.130_1
===> vcflib-1.0.0.r1.130_1 depends on executable: interval_tree_test - not found
===> Installing existing package /packages/All/intervaltree-g20151213_2.txz
[head-powerpc64-default-job-10] Installing intervaltree-g20151213_2...
[head-powerpc64-default-job-10] Extracting intervaltree-g20151213_2: ..... done
===> vcflib-1.0.0.r1.130_1 depends on executable: interval_tree_test - found
===> Returning to build of vcflib-1.0.0.r1.130_1
===> vcflib-1.0.0.r1.130_1 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.txz
[head-powerpc64-default-job-10] Installing gmake-4.3_2...
[head-powerpc64-default-job-10] Extracting gmake-4.3_2: .......... done
===> vcflib-1.0.0.r1.130_1 depends on package: gmake>=4.3 - found
===> Returning to build of vcflib-1.0.0.r1.130_1
===========================================================================
=======================<phase: lib-depends >============================
===> vcflib-1.0.0.r1.130_1 depends on shared library: libhts.so - not found
===> Installing existing package /packages/All/htslib-1.10.2.txz
[head-powerpc64-default-job-10] Installing htslib-1.10.2...
[head-powerpc64-default-job-10] `-- Installing curl-7.73.0...
[head-powerpc64-default-job-10] | `-- Installing ca_root_nss-3.58...
[head-powerpc64-default-job-10] | `-- Extracting ca_root_nss-3.58: ........ done
[head-powerpc64-default-job-10] | `-- Installing libnghttp2-1.41.0...
[head-powerpc64-default-job-10] | `-- Extracting libnghttp2-1.41.0: .......... done
[head-powerpc64-default-job-10] `-- Extracting curl-7.73.0: .......... done
[head-powerpc64-default-job-10] `-- Installing libdeflate-1.6...
[head-powerpc64-default-job-10] `-- Extracting libdeflate-1.6: .......... done
[head-powerpc64-default-job-10] Extracting htslib-1.10.2: .......... done
=====
Message from ca_root_nss-3.58:
--
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
===> vcflib-1.0.0.r1.130_1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
===> Returning to build of vcflib-1.0.0.r1.130_1
===> vcflib-1.0.0.r1.130_1 depends on shared library: libtabix.so - not found
===> Installing existing package /packages/All/tabixpp-1.0.0.10_1.txz
[head-powerpc64-default-job-10] Installing tabixpp-1.0.0.10_1...
[head-powerpc64-default-job-10] Extracting tabixpp-1.0.0.10_1: ........ done
===> vcflib-1.0.0.r1.130_1 depends on shared library: libtabix.so - found (/usr/local/lib/libtabix.so)
===> Returning to build of vcflib-1.0.0.r1.130_1
===> vcflib-1.0.0.r1.130_1 depends on shared library: libsw.so - not found
===> Installing existing package /packages/All/smithwaterman-g20160702.txz
[head-powerpc64-default-job-10] Installing smithwaterman-g20160702...
[head-powerpc64-default-job-10] Extracting smithwaterman-g20160702: .......... done
===> vcflib-1.0.0.r1.130_1 depends on shared library: libsw.so - found (/usr/local/lib/libsw.so)
===> Returning to build of vcflib-1.0.0.r1.130_1
===========================================================================
=======================<phase: configure >============================
===> Configuring for vcflib-1.0.0.r1.130_1
===========================================================================
=======================<phase: build >============================
===> Building for vcflib-1.0.0.r1.130_1
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.0-rc1-130-g7e3d806'
c++ -c -o src/Variant.o src/Variant.cpp -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11
c++ -c -o src/rnglib.o src/rnglib.cpp -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11
src/Variant.cpp:174:1: warning: non-void function does not return a value in all control paths [-Wreturn-type]
};
^
c++ -c -o src/var.o src/var.cpp -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11
src/Variant.cpp:502:5: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
src/Variant.cpp:627:5: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
src/Variant.cpp:661:5: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
src/Variant.cpp:699:5: warning: non-void function does not return a value in all control paths [-Wreturn-type]
}
^
c++ -c -o src/pdflib.o src/pdflib.cpp -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11
c++ -c -o src/cdflib.o src/cdflib.cpp -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11
c++ -c -o src/split.o src/split.cpp -I/usr/local/include -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/smithwaterman -I/usr/local/include/multichoose -I/usr/local/include/filevercmp -I/usr/local/include/fastahack -I/usr/local/include/intervaltree -DVERSION='"1.0.0.r1.130"' -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -fPIC --std=c++11 -c -o src/ssw.o src/ssw.cpp
In file included from src/ssw.cpp:38:
In file included from /usr/lib/clang/11.0.0/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.0/include/xmmintrin.h:13:
/usr/lib/clang/11.0.0/include/mmintrin.h:33:5: error: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'?
__builtin_ia32_emms();
^
/usr/lib/clang/11.0.0/include/mmintrin.h:33:5: note: '__builtin_isless' declared here
/usr/lib/clang/11.0.0/include/mmintrin.h:33:25: error: too few arguments to function call, expected 2, have 0
__builtin_ia32_emms();
^
/usr/lib/clang/11.0.0/include/mmintrin.h:50:19: error: use of undeclared identifier '__builtin_ia32_vec_init_v2si'
return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
^
/usr/lib/clang/11.0.0/include/mmintrin.h:67:12: error: use of undeclared identifier '__builtin_ia32_vec_ext_v2si'
return __builtin_ia32_vec_ext_v2si((__v2si)__m, 0);
^
/usr/lib/clang/11.0.0/include/mmintrin.h:129:19: error: use of undeclared identifier '__builtin_ia32_packsswb'
return (__m64)__builtin_ia32_packsswb((__v4hi)__m1, (__v4hi)__m2);
^
/usr/lib/clang/11.0.0/include/mmintrin.h:159:19: error: use of undeclared identifier '__builtin_ia32_packssdw'
return (__m64)__builtin_ia32_packssdw((__v2si)__m1, (__v2si)__m2);
^
/usr/lib/clang/11.0.0/include/mmintrin.h:189:19: error: use of undeclared identifier '__builtin_ia32_packuswb'
return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2);
^
/usr/lib/clang/11.0.0/include/mmintrin.h:216:19: error: use of undeclared identifier '__builtin_ia32_punpckhbw'
return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);
^
/usr/lib/clang/11.0.0/include/mmintrin.h:239:19: error: use of undeclared identifier '__builtin_ia32_punpckhwd'
return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2);
^
/usr/lib/clang/11.0.0/include/mmintrin.h:260:19: error: use of undeclared identifier '__builtin_ia32_punpckhdq'
return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2);
^
/usr/lib/clang/11.0.0/include/mmintrin.h:287:19: error: use of undeclared identifier '__builtin_ia32_punpcklbw'
return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2);
^
/usr/lib/clang/11.0.0/include/mmintrin.h:310:19: error: use of undeclared identifier '__builtin_ia32_punpcklwd'
return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2);
^
/usr/lib/clang/11.0.0/include/mmintrin.h:331:19: error: use of undeclared identifier '__builtin_ia32_punpckldq'
return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2);
^
/usr/lib/clang/11.0.0/include/mmintrin.h:352:19: error: use of undeclared identifier '__builtin_ia32_paddb'
return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2);
^
/usr/lib/clang/11.0.0/include/mmintrin.h:373:19: error: use of undeclared identifier '__builtin_ia32_paddw'
return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2);
^
/usr/lib/clang/11.0.0/include/mmintrin.h:394:19: error: use of undeclared identifier '__builtin_ia32_paddd'
return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2);
^
/usr/lib/clang/11.0.0/include/mmintrin.h:416:19: error: use of undeclared identifier '__builtin_ia32_paddsb'
return (__m64)__builtin_ia32_paddsb((__v8qi)__m1, (__v8qi)__m2);
^
/usr/lib/clang/11.0.0/include/mmintrin.h:439:19: error: use of undeclared identifier '__builtin_ia32_paddsw'
return (__m64)__builtin_ia32_paddsw((__v4hi)__m1, (__v4hi)__m2);
^
/usr/lib/clang/11.0.0/include/mmintrin.h:461:19: error: use of undeclared identifier '__builtin_ia32_paddusb'
return (__m64)__builtin_ia32_paddusb((__v8qi)__m1, (__v8qi)__m2);
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
gmake[1]: *** [<builtin>: src/ssw.o] Error 1
gmake[1]: *** Waiting for unfinished jobs....
5 warnings generated.
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.0-rc1-130-g7e3d806'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/vcflib
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