[package - 131i386-default][biology/bifrost] Failed for bifrost-1.2.1 in build
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Date: Sun, 16 Jul 2023 06:21:24 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/1987fa591b3a/logs/bifrost-1.2.1.log
Build URL: https://pkg-status.freebsd.org/beefy15/build.html?mastername=131i386-default&build=1987fa591b3a
Log:
=>> Building biology/bifrost
build started at Sun Jul 16 06:21:14 UTC 2023
port directory: /usr/ports/biology/bifrost
package name: bifrost-1.2.1
building for: FreeBSD 131i386-default-job-05 13.1-RELEASE-p8 FreeBSD 13.1-RELEASE-p8 i386
maintained by: jwb@FreeBSD.org
Makefile ident:
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=======================<phase: check-sanity >============================
===> License BSD2CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> bifrost-1.2.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.4.pkg
[131i386-default-job-05] Installing pkg-1.20.4...
[131i386-default-job-05] Extracting pkg-1.20.4: .......... done
===> bifrost-1.2.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of bifrost-1.2.1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by bifrost-1.2.1 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by bifrost-1.2.1 for building
=> SHA256 Checksum OK for pmelsted-bifrost-v1.2.1_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by bifrost-1.2.1 for building
===> Extracting for bifrost-1.2.1
=> SHA256 Checksum OK for pmelsted-bifrost-v1.2.1_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for bifrost-1.2.1
===> Applying FreeBSD patches for bifrost-1.2.1 from /usr/ports/biology/bifrost/files
===========================================================================
=======================<phase: build-depends >============================
===> bifrost-1.2.1 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.26.1_1.pkg
[131i386-default-job-05] Installing cmake-core-3.26.1_1...
[131i386-default-job-05] `-- Installing expat-2.5.0...
[131i386-default-job-05] `-- Extracting expat-2.5.0: .......... done
[131i386-default-job-05] `-- Installing jsoncpp-1.9.5...
[131i386-default-job-05] `-- Extracting jsoncpp-1.9.5: .......... done
[131i386-default-job-05] `-- Installing libuv-1.46.0...
[131i386-default-job-05] `-- Extracting libuv-1.46.0: .......... done
[131i386-default-job-05] `-- Installing rhash-1.4.3...
<snip>
(uint64_t)(_mm256_extract_epi64(total, 1)) + \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1141:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 2)) + \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1142:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 3)); \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1146:1: error: use of undeclared identifier '_mm256_extract_epi64'
AVXPOPCNTFNC(union, _mm256_or_si256)
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1041:27: note: expanded from macro 'AVXPOPCNTFNC'
return (uint64_t)(_mm256_extract_epi64(total, 0)) + \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1146:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1042:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 1)) + \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1146:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1043:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 2)) + \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1146:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1044:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 3)); \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1146:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1139:27: note: expanded from macro 'AVXPOPCNTFNC'
return (uint64_t)(_mm256_extract_epi64(total, 0)) + \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1146:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1140:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 1)) + \
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
[ 6% 2/32] /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -march=native -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -MF src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o.d -o src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -c /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp
FAILED: src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o
/usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++11 -march=native -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -MF src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o.d -o src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -c /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp
In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.hpp:27:
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/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/bifrost/work/bifrost-1.2.1/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/bifrost/work/bifrost-1.2.1/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/bifrost/work/bifrost-1.2.1/src/Common.hpp:180:12: warning: shift count >= width of type [-Wshift-count-overflow]
v |= v >> 32;
^ ~~
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Common.hpp:186:21: error: redefinition of 'rndup'
BFG_INLINE uint32_t rndup(uint32_t v) {
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/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/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.hpp:28:
In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/File_Parser.hpp:10:
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/FASTX_Parser.hpp:18:1: warning: shift count >= width of type [-Wshift-count-overflow]
KSEQ_INIT(gzFile, gzread);
^~~~~~~~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/kseq.h:239:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/kseq.h:234:2: note: expanded from macro 'KSEQ_INIT2'
KSTREAM_INIT(type_t, __read, 16384) \
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/kseq.h:157:2: note: expanded from macro 'KSTREAM_INIT'
__KS_GETUNTIL(__read, __bufsize)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/kseq.h:130:5: note: expanded from macro '__KS_GETUNTIL'
kroundup64(str->m); \
^~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/kseq.h:95:105: note: expanded from macro 'kroundup64'
#define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x))
^ ~~
In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.hpp:28:
In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/File_Parser.hpp:10:
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/FASTX_Parser.hpp:18:1: warning: shift count >= width of type [-Wshift-count-overflow]
KSEQ_INIT(gzFile, gzread);
^~~~~~~~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/kseq.h:239:35: note: expanded from macro 'KSEQ_INIT'
#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/kseq.h:237:2: note: expanded from macro 'KSEQ_INIT2'
__KSEQ_READ(SCOPE)
^~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/kseq.h:207:4: note: expanded from macro '__KSEQ_READ'
kroundup64(seq->seq.m); /* rounded to the next closest 2^k */ \
^~~~~~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/kseq.h:95:105: note: expanded from macro 'kroundup64'
#define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x))
^ ~~
In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.hpp:28:
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/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/bifrost/work/bifrost-1.2.1/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/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.hpp:32:
In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/KmerCovIndex.hpp:7:
In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/BitContainer.hpp:4:
In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.hh:1:
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/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/bifrost/work/bifrost-1.2.1/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/CompactedDBG.hpp:32:
In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/KmerCovIndex.hpp:7:
In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/BitContainer.hpp:4:
In file included from /wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.hh:1:
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/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/bifrost/work/bifrost-1.2.1/src/roaring.h:960:23: error: use of undeclared identifier '_mm256_extract_epi64'
(uint64_t)(_mm256_extract_epi64(total, 1)) +
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:961:23: error: use of undeclared identifier '_mm256_extract_epi64'
(uint64_t)(_mm256_extract_epi64(total, 2)) +
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:962:23: error: use of undeclared identifier '_mm256_extract_epi64'
(uint64_t)(_mm256_extract_epi64(total, 3));
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
AVXPOPCNTFNC(or, _mm256_or_si256)
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1041:27: note: expanded from macro 'AVXPOPCNTFNC'
return (uint64_t)(_mm256_extract_epi64(total, 0)) + \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1042:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 1)) + \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1043:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 2)) + \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1044:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 3)); \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1139:27: note: expanded from macro 'AVXPOPCNTFNC'
return (uint64_t)(_mm256_extract_epi64(total, 0)) + \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1140:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 1)) + \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1141:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 2)) + \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1145:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1142:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 3)); \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1146:1: error: use of undeclared identifier '_mm256_extract_epi64'
AVXPOPCNTFNC(union, _mm256_or_si256)
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1041:27: note: expanded from macro 'AVXPOPCNTFNC'
return (uint64_t)(_mm256_extract_epi64(total, 0)) + \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1146:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1042:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 1)) + \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1146:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1043:27: note: expanded from macro 'AVXPOPCNTFNC'
(uint64_t)(_mm256_extract_epi64(total, 2)) + \
^
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/src/roaring.h:1146:1: error: use of undeclared identifier '_mm256_extract_epi64'
/wrkdirs/usr/ports/biology/bifrost/work/bifrost-1.2.1/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=]
6 warnings and 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/bifrost