[package - 131i386-default][biology/kallisto] Failed for kallisto-0.50.0,1 in build
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Date: Fri, 14 Jul 2023 06:14:06 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: jwb@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy15/data/131i386-default/8fb94260154e/logs/kallisto-0.50.0,1.log
Build URL: https://pkg-status.freebsd.org/beefy15/build.html?mastername=131i386-default&build=8fb94260154e
Log:
=>> Building biology/kallisto
build started at Fri Jul 14 06:13:40 UTC 2023
port directory: /usr/ports/biology/kallisto
package name: kallisto-0.50.0,1
building for: FreeBSD 131i386-default-job-09 13.1-RELEASE-p8 FreeBSD 13.1-RELEASE-p8 i386
maintained by: jwb@FreeBSD.org
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===> The following configuration options are available for kallisto-0.50.0,1:
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===> Use 'make config' to modify these settings
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--End PLIST_SUB--
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=======================<phase: check-sanity >============================
===> License BSD2CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> kallisto-0.50.0,1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.4.pkg
[131i386-default-job-09] Installing pkg-1.20.4...
[131i386-default-job-09] Extracting pkg-1.20.4: .......... done
===> kallisto-0.50.0,1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of kallisto-0.50.0,1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD2CLAUSE accepted by the user
=> pachterlab-kallisto-v0.50.0_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.50.0?dummy=/pachterlab-kallisto-v0.50.0_GH0.tar.gz
fetch: https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.50.0?dummy=/pachterlab-kallisto-v0.50.0_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.50.0?dummy=/pachterlab-kallisto-v0.50.0_GH0.tar.gz: size of remote file is not known
pachterlab-kallisto-v0.50.0_GH0.tar.gz 5799 kB 5366 kBps 01s
===> Fetching all distfiles required by kallisto-0.50.0,1 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by kallisto-0.50.0,1 for building
=> SHA256 Checksum OK for pachterlab-kallisto-v0.50.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by kallisto-0.50.0,1 for building
===> Extracting for kallisto-0.50.0,1
=> SHA256 Checksum OK for pachterlab-kallisto-v0.50.0_GH0.tar.gz.
/bin/rm -f -rf /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/htslib
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for kallisto-0.50.0,1
===> Applying FreeBSD patches for kallisto-0.50.0,1 from /usr/ports/biology/kallisto/files
===========================================================================
=======================<phase: build-depends >============================
===> kallisto-0.50.0,1 depends on file: /usr/local/bin/cmake - not found
<snip>
CMAKE_C_FLAGS_RELEASE
CMAKE_MODULE_LINKER_FLAGS
CMAKE_SHARED_LINKER_FLAGS
FETCHCONTENT_FULLY_DISCONNECTED
-- Build files have been written to: /wrkdirs/usr/ports/biology/kallisto/work/.build
===========================================================================
=======================<phase: build >============================
===> Building for kallisto-0.50.0,1
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
/usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0 -B/wrkdirs/usr/ports/biology/kallisto/work/.build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/kallisto/work/.build/CMakeFiles /wrkdirs/usr/ports/biology/kallisto/work/.build//CMakeFiles/progress.marks
gmake -f CMakeFiles/Makefile2 all
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
gmake -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/depend
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
cd /wrkdirs/usr/ports/biology/kallisto/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0 /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0 /wrkdirs/usr/ports/biology/kallisto/work/.build /wrkdirs/usr/ports/biology/kallisto/work/.build /wrkdirs/usr/ports/biology/kallisto/work/.build/CMakeFiles/bifrost.dir/DependInfo.cmake
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
gmake -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/build
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
[ 3%] Creating directories for 'bifrost'
/usr/local/bin/cmake -Dcfgdir= -P /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/tmp/bifrost-mkdirs.cmake
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/bifrost-stamp/bifrost-mkdir
[ 7%] No download step for 'bifrost'
/usr/local/bin/cmake -E echo_append
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/bifrost-stamp/bifrost-download
[ 11%] No update step for 'bifrost'
/usr/local/bin/cmake -E echo_append
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/bifrost-stamp/bifrost-update
[ 15%] No patch step for 'bifrost'
/usr/local/bin/cmake -E echo_append
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/bifrost-stamp/bifrost-patch
[ 19%] Performing configure step for 'bifrost'
cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost && mkdir -p build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX= "-DCMAKE_CXX_FLAGS=-Wno-subobject-linkage -Wno-return-type"
-- The C compiler identification is Clang 13.0.0
-- The CXX compiler identification is Clang 13.0.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
Compilation architecture: native
Build type: Release
Maximum k-mer size: 31
Maximum g-mer size: 31
-- Found ZLIB: /usr/lib/libz.so (found version "1.2.12")
-- Configuring done (0.8s)
-- Generating done (0.0s)
-- Build files have been written to: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build
cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/bifrost-stamp/bifrost-configure
[ 23%] Performing build step for 'bifrost'
cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost && cd build && gmake
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
[ 3%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o
warning: unknown warning option '-Wno-subobject-linkage' [-Wunknown-warning-option]
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:27:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Common.hpp:47:47: error: constant expression evaluates to 4504192333906058 which cannot be narrowed to type 'size_t' (aka 'unsigned int') [-Wc++11-narrowing]
static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL};
^~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Common.hpp:47:47: note: insert an explicit cast to silence this issue
static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL};
^~~~~~~~~~~~~~~~~~~
static_cast<size_t>( )
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Common.hpp:47:47: warning: implicit conversion from 'unsigned long long' to 'const size_t' (aka 'const unsigned int') changes value from 4504192333906058 to 1048714 [-Wconstant-conversion]
static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL};
~ ^~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Common.hpp:180:12: warning: shift count >= width of type [-Wshift-count-overflow]
v |= v >> 32;
^ ~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Common.hpp:186:21: error: redefinition of 'rndup'
BFG_INLINE uint32_t rndup(uint32_t v) {
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Common.hpp:172:19: note: previous definition is here
BFG_INLINE size_t rndup(size_t v) {
^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:28:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/File_Parser.hpp:230:64: warning: shift count >= width of type [-Wshift-count-overflow]
else if ((reinterpret_cast<size_t*>(buffer)[0] >> 32) == BFG_GRAPHBIN_FORMAT_HEADER) ret_v = 3; // BFG
^ ~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/File_Parser.hpp:231:64: warning: shift count >= width of type [-Wshift-count-overflow]
else if ((reinterpret_cast<size_t*>(buffer)[0] >> 32) == BFG_METABIN_FORMAT_HEADER) ret_v = 4; // BFI
^ ~~
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:32:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/KmerCovIndex.hpp:7:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/BitContainer.hpp:4:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.hh:1:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:215:18: error: use of undeclared identifier '_mm_popcnt_u64'; did you mean '_mm_popcnt_u32'?
return (int) _mm_popcnt_u64(x);
^~~~~~~~~~~~~~
_mm_popcnt_u32
/usr/lib/clang/13.0.0/include/popcntintrin.h:33:1: note: '_mm_popcnt_u32' declared here
_mm_popcnt_u32(unsigned int __A)
^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:32:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/KmerCovIndex.hpp:7:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/BitContainer.hpp:4:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.hh:1:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:959:23: error: use of undeclared identifier '_mm256_extract_epi64'
return (uint64_t)(_mm256_extract_epi64(total, 0)) +
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:960:23: error: use of undeclared identifier '_mm256_extract_epi64'
(uint64_t)(_mm256_extract_epi64(total, 1)) +
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:961:23: error: use of undeclared identifier '_mm256_extract_epi64'
(uint64_t)(_mm256_extract_epi64(total, 2)) +
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:962:23: error: use of undeclared identifier '_mm256_extract_epi64'
(uint64_t)(_mm256_extract_epi64(total, 3));
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
AVXPOPCNTFNC(or, _mm256_or_si256)
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1041:27: note: expanded from macro 'AVXPOPCNTFNC'
return (uint64_t)(_mm256_extract_epi64(total, 0)) + \
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1042:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 1)) + \
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1043:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 2)) + \
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1044:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 3)); \
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1139:27: note: expanded from macro 'AVXPOPCNTFNC'
return (uint64_t)(_mm256_extract_epi64(total, 0)) + \
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1140:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 1)) + \
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1141:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 2)) + \
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1142:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 3)); \
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1146:1: error: use of undeclared identifier '_mm256_extract_epi64'
AVXPOPCNTFNC(union, _mm256_or_si256)
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1041:27: note: expanded from macro 'AVXPOPCNTFNC'
return (uint64_t)(_mm256_extract_epi64(total, 0)) + \
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1146:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1042:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 1)) + \
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1146:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1043:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 2)) + \
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1146:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/roaring.h:1044:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 3)); \
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
5 warnings and 20 errors generated.
gmake[6]: *** [src/CMakeFiles/bifrost_static.dir/build.make:76: src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o] Error 1
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
gmake[5]: *** [CMakeFiles/Makefile2:102: src/CMakeFiles/bifrost_static.dir/all] Error 2
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
gmake[4]: *** [Makefile:136: all] Error 2
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
gmake[3]: *** [CMakeFiles/bifrost.dir/build.make:89: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/bifrost-stamp/bifrost-build] Error 2
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
gmake[2]: *** [CMakeFiles/Makefile2:105: CMakeFiles/bifrost.dir/all] Error 2
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
gmake[1]: *** [Makefile:139: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/kallisto