[package - 131powerpc-quarterly][biology/iqtree] Failed for iqtree-2.0.6_4 in build
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Date: Thu, 05 Jan 2023 00:26:43 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: jrm@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/foul1/data/131powerpc-quarterly/fa196a207467/logs/iqtree-2.0.6_4.log
Build URL: https://pkg-status.freebsd.org/foul1/build.html?mastername=131powerpc-quarterly&build=fa196a207467
Log:
=>> Building biology/iqtree
build started at Thu Jan 5 00:25:36 UTC 2023
port directory: /usr/ports/biology/iqtree
package name: iqtree-2.0.6_4
building for: FreeBSD 131powerpc-quarterly-job-07 13.1-RELEASE FreeBSD 13.1-RELEASE powerpc
maintained by: jrm@FreeBSD.org
Makefile ident:
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=======================<phase: check-sanity >============================
===> License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> iqtree-2.0.6_4 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.18.4.pkg
[131powerpc-quarterly-job-07] Installing pkg-1.18.4...
[131powerpc-quarterly-job-07] Extracting pkg-1.18.4: .......... done
===> iqtree-2.0.6_4 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of iqtree-2.0.6_4
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by iqtree-2.0.6_4 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by iqtree-2.0.6_4 for building
=> SHA256 Checksum OK for Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by iqtree-2.0.6_4 for building
===> Extracting for iqtree-2.0.6_4
=> SHA256 Checksum OK for Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for iqtree-2.0.6_4
===> Applying FreeBSD patches for iqtree-2.0.6_4 from /usr/ports/biology/iqtree/files
===========================================================================
=======================<phase: build-depends >============================
===> iqtree-2.0.6_4 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.24.0.pkg
[131powerpc-quarterly-job-07] Installing cmake-core-3.24.0...
[131powerpc-quarterly-job-07] `-- Installing curl-7.86.0...
[131powerpc-quarterly-job-07] | `-- Installing ca_root_nss-3.83...
[131powerpc-quarterly-job-07] | `-- Extracting ca_root_nss-3.83: .......... done
[131powerpc-quarterly-job-07] | `-- Installing libnghttp2-1.48.0...
<snip>
Compiler : Clang
Target binary : 32-bit
OpenMP : Yes
MPI : NONE
Vectorization : SSE3/AVX/AVX2
C flags : -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -m32 -O3 -ffunction-sections -fdata-sections
CXX flags : -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fopenmp -pthread -m32 -O3 -ffunction-sections -fdata-sections
LINKER flags : -fstack-protector-strong -rdynamic -Wl,--gc-sections
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for getrusage
-- Looking for getrusage - found
-- Looking for GlobalMemoryStatusEx
-- Looking for GlobalMemoryStatusEx - not found
-- Looking for strndup
-- Looking for strndup - found
-- Looking for strtok_r
-- Looking for strtok_r - found
-- Looking for backtrace
-- Looking for backtrace - not found
-- Found Backtrace: /usr/lib/libexecinfo.so
-- Found ZLIB: /usr/lib/libz.so (found version "1.2.12")
Using system zlib
-- Performing Test FLAG_WEXTRA
-- Performing Test FLAG_WEXTRA - Failed
-- clang-tidy not found.
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_COLOR_MAKEFILE
CMAKE_MODULE_LINKER_FLAGS
CMAKE_SHARED_LINKER_FLAGS
CMAKE_VERBOSE_MAKEFILE
THREADS_HAVE_PTHREAD_ARG
-- Build files have been written to: /wrkdirs/usr/ports/biology/iqtree/work/.build
===========================================================================
=======================<phase: build >============================
===> Building for iqtree-2.0.6_4
[ 0% 2/237] /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6 -I/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/yaml-cpp/include -I/wrkdirs/usr/ports/biology/iqtree/work/.build -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fopenmp -pthread -m32 -O3 -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/tree/phylokernelsse.cpp
FAILED: CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o
/usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6 -I/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/yaml-cpp/include -I/wrkdirs/usr/ports/biology/iqtree/work/.build -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fopenmp -pthread -m32 -O3 -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/tree/phylokernelsse.cpp
c++: warning: argument unused during compilation: '-msse3' [-Wunused-command-line-argument]
In file included from /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/tree/phylokernelsse.cpp:9:
In file included from /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_exp.h:38:
In file included from /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_common.h:35:
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectorclass.h:38:4: error: Please compile for the SSE2 instruction set or higher
#error Please compile for the SSE2 instruction set or higher
^
In file included from /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/tree/phylokernelsse.cpp:9:
In file included from /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_exp.h:38:
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_common.h:65:8: error: unknown type name 'Vec2d'
inline Vec2d infinite_vec<Vec2d>() {
^
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_common.h:65:27: error: use of undeclared identifier 'Vec2d'
inline Vec2d infinite_vec<Vec2d>() {
^
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_common.h:108:8: error: unknown type name 'Vec2d'
inline Vec2d nan_vec<Vec2d>(int n) {
^
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_common.h:108:22: error: use of undeclared identifier 'Vec2d'
inline Vec2d nan_vec<Vec2d>(int n) {
^
In file included from /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/tree/phylokernelsse.cpp:9:
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_exp.h:674:15: error: unknown type name 'Vec4f'
static inline Vec4f exponent_f(Vec4f const & x) {
^
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_exp.h:674:32: error: unknown type name 'Vec4f'
static inline Vec4f exponent_f(Vec4f const & x) {
^
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_exp.h:681:11: error: unknown type name 'vm_ufi'; did you mean 'vm_udi'?
const vm_ufi upow2_23 = {pow2_23};
^~~~~~
vm_udi
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_exp.h:667:7: note: 'vm_udi' declared here
union vm_udi {
^
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_exp.h:682:5: error: unknown type name 'Vec4ui'
Vec4ui a = reinterpret_i(x); // bit-cast x to integer
^
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_exp.h:683:5: error: unknown type name 'Vec4ui'
Vec4ui b = a >> 23; // shift down exponent to low bits
^
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_exp.h:684:5: error: unknown type name 'Vec4ui'
Vec4ui c = b | Vec4ui(upow2_23.i); // insert new exponent
^
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_exp.h:684:20: error: use of undeclared identifier 'Vec4ui'
Vec4ui c = b | Vec4ui(upow2_23.i); // insert new exponent
^
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_exp.h:685:5: error: unknown type name 'Vec4f'
Vec4f d = reinterpret_f(c); // bit-cast back to double
^
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_exp.h:686:5: error: unknown type name 'Vec4f'
Vec4f e = d - (pow2_23 + bias); // subtract magic number and bias
^
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_exp.h:691:15: error: unknown type name 'Vec2d'
static inline Vec2d exponent_f(Vec2d const & x) {
^
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_exp.h:691:32: error: unknown type name 'Vec2d'
static inline Vec2d exponent_f(Vec2d const & x) {
^
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_exp.h:700:5: error: unknown type name 'Vec2uq'
Vec2uq a = reinterpret_i(x); // bit-cast x to integer
^
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_exp.h:701:5: error: unknown type name 'Vec2uq'
Vec2uq b = a >> 52; // shift down exponent to low bits
^
/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/vectorclass/vectormath_exp.h:702:5: error: unknown type name 'Vec2uq'
Vec2uq c = b | Vec2uq(upow2_52.i); // insert new exponent
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
[ 0% 2/237] /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6 -I/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/yaml-cpp/include -I/wrkdirs/usr/ports/biology/iqtree/work/.build -I/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/terraphast/include -I/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fopenmp -pthread -m32 -O3 -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/obsolete/parsmultistate.cpp
FAILED: CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o
/usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6 -I/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/yaml-cpp/include -I/wrkdirs/usr/ports/biology/iqtree/work/.build -I/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/terraphast/include -I/wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -fopenmp -pthread -m32 -O3 -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/obsolete/parsmultistate.cpp
c++: warning: argument unused during compilation: '-msse3' [-Wunused-command-line-argument]
In file included from /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/obsolete/parsmultistate.cpp:21:
In file included from /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/tree/phylotree.h:44:
In file included from /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/pll/pll.h:78:
In file included from /usr/lib/clang/13.0.0/include/xmmintrin.h:13:
/usr/lib/clang/13.0.0/include/mmintrin.h:33:5: error: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'?
__builtin_ia32_emms();
^
/usr/include/c++/v1/math.h:670:12: note: '__builtin_isless' declared here
return isless(__lcpp_x, __lcpp_y);
^
/usr/include/math.h:119:23: note: expanded from macro 'isless'
#define isless(x, y) __builtin_isless((x), (y))
^
In file included from /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/obsolete/parsmultistate.cpp:21:
In file included from /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/tree/phylotree.h:44:
In file included from /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-2.0.6/pll/pll.h:78:
In file included from /usr/lib/clang/13.0.0/include/xmmintrin.h:13:
/usr/lib/clang/13.0.0/include/mmintrin.h:33:25: error: too few arguments to function call, expected 2, have 0
__builtin_ia32_emms();
~~~~~~~~~~~~~~~~~~~~^
/usr/lib/clang/13.0.0/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/13.0.0/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/13.0.0/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/13.0.0/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/13.0.0/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/13.0.0/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/13.0.0/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/13.0.0/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/13.0.0/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/13.0.0/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/13.0.0/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/13.0.0/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/13.0.0/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/13.0.0/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/13.0.0/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/13.0.0/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/13.0.0/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.
ninja: build stopped: subcommand failed.
===> 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/iqtree