[package - main-i386-default][biology/fermi-lite] Failed for fermi-lite-0.1.13 in build
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Date: Sun, 08 Sep 2024 00:03:06 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: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy17/data/main-i386-default/p13f486017d78_s3df987c99d1/logs/fermi-lite-0.1.13.log
Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=p13f486017d78_s3df987c99d1
Log:
=>> Building biology/fermi-lite
build started at Sun Sep 8 00:03:02 UTC 2024
port directory: /usr/ports/biology/fermi-lite
package name: fermi-lite-0.1.13
building for: FreeBSD main-i386-default-job-11 15.0-CURRENT FreeBSD 15.0-CURRENT 1500023 i386
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 967 Aug 15 01:01 /usr/ports/biology/fermi-lite/Makefile
Ports top last git commit: 13f486017d7
Ports top unclean checkout: no
Port dir last git commit: 80a04a9595d
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2
Host OSVERSION: 1500023
Jail OSVERSION: 1500023
Job Id: 11
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PORT_FLAGS=
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---Begin OPTIONS List---
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fermi-lite/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fermi-lite/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fermi-lite/work/.cache HOME=/wrkdirs/usr/ports/biology/fermi-lite/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fermi-lite/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fermi-lite/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fermi-lite/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fermi-lite/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fermi-lite/work/.cache HOME=/wrkdirs/usr/ports/biology/fermi-lite/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fermi-lite/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fermi-lite/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="i
nstall -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/fermi-lite" EXAMPLESDIR="share/examples/fermi-lite" DATADIR="share/fermi-lite" WWWDIR="www/fermi-lite" ETCDIR="etc/fermi-lite"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/fermi-lite DOCSDIR=/usr/local/share/doc/fermi-lite EXAMPLESDIR=/usr/local/share/examples/fermi-lite WWWDIR=/usr/local/www/fermi-lite ETCDIR=/usr/local/etc/fermi-lite
--End SUB_LIST--
---Begin make.conf---
# XXX: We really need this but cannot use it while 'make checksum' does not
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# failed mirror and then fails rather then trying another. It *does*
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MAKE_JOBS_NUMBER=3
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PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
#### ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
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.include "/etc/make.conf.ports_env"
GID=0
UID=0
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max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 8192
virtual mem size (kbytes, -v) unlimited
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socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> fermi-lite-0.1.13 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.3.pkg
[main-i386-default-job-11] Installing pkg-1.21.3...
[main-i386-default-job-11] Extracting pkg-1.21.3: .......... done
===> fermi-lite-0.1.13 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of fermi-lite-0.1.13
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===> Fetching all distfiles required by fermi-lite-0.1.13 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===> Fetching all distfiles required by fermi-lite-0.1.13 for building
=> SHA256 Checksum OK for lh3-fermi-lite-v0.1-13-g85f159e_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===> Fetching all distfiles required by fermi-lite-0.1.13 for building
===> Extracting for fermi-lite-0.1.13
=> SHA256 Checksum OK for lh3-fermi-lite-v0.1-13-g85f159e_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for fermi-lite-0.1.13
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> fermi-lite-0.1.13 depends on package: gmake>=4.4.1 - not found
===> Installing existing package /packages/All/gmake-4.4.1.pkg
[main-i386-default-job-11] Installing gmake-4.4.1...
[main-i386-default-job-11] `-- Installing gettext-runtime-0.22.5...
[main-i386-default-job-11] | `-- Installing indexinfo-0.3.1...
[main-i386-default-job-11] | `-- Extracting indexinfo-0.3.1: .... done
[main-i386-default-job-11] `-- Extracting gettext-runtime-0.22.5: .......... done
[main-i386-default-job-11] Extracting gmake-4.4.1: .......... done
===> fermi-lite-0.1.13 depends on package: gmake>=4.4.1 - found
===> Returning to build of fermi-lite-0.1.13
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for fermi-lite-0.1.13
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for fermi-lite-0.1.13
gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing kthread.c -o kthread.o
gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing misc.c -o misc.o
gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing bseq.c -o bseq.o
gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing htab.c -o htab.o
gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing bfc.c -o bfc.o
gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing rle.c -o rle.o
gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing rope.c -o rope.o
gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing mrope.c -o mrope.o
gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing rld0.c -o rld0.o
gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing unitig.c -o unitig.o
gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing mag.c -o mag.o
unitig.c:74:2: warning: __sync builtin operation MUST have natural alignment (consider using __atomic). [-Wsync-alignment]
74 | __sync_fetch_and_or(p, z);
| ^
unitig.c:392:8: warning: __sync builtin operation MUST have natural alignment (consider using __atomic). [-Wsync-alignment]
392 | if ((__sync_fetch_and_or(p[0], x[0])&x[0]) || (__sync_fetch_and_or(p[1], x[1])&x[1])) return;
| ^
unitig.c:392:50: warning: __sync builtin operation MUST have natural alignment (consider using __atomic). [-Wsync-alignment]
392 | if ((__sync_fetch_and_or(p[0], x[0])&x[0]) || (__sync_fetch_and_or(p[1], x[1])&x[1])) return;
| ^
gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing bubble.c -o bubble.o
mag.c:418:84: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
418 | fprintf(stderr, "[M::%s] removed %ld tips (min_len=%d, min_nsr=%d)\n", __func__, a.n, min_len, min_nsr);
| ~~~ ^~~
| %zu
mag.c:436:97: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
436 | fprintf(stderr, "[M::%s] removed %ld internal vertices (min_len=%d, min_nsr=%d)\n", __func__, a.n, min_len, min_nsr);
| ~~~ ^~~
| %zu
gcc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing ksw.c -o ksw.o
ksw.c:126:9: error: always_inline function '_mm_set1_epi32' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
126 | zero = _mm_set1_epi32(0);
| ^
ksw.c:127:10: error: always_inline function '_mm_set1_epi8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
127 | gapoe = _mm_set1_epi8(_gapo + _gape);
| ^
ksw.c:128:9: error: always_inline function '_mm_set1_epi8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
128 | gape = _mm_set1_epi8(_gape);
| ^
ksw.c:129:10: error: always_inline function '_mm_set1_epi8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
129 | shift = _mm_set1_epi8(q->shift);
| ^
ksw.c:133:3: error: always_inline function '_mm_store_si128' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
133 | _mm_store_si128(E + i, zero);
| ^
ksw.c:134:3: error: always_inline function '_mm_store_si128' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
134 | _mm_store_si128(H0 + i, zero);
| ^
ksw.c:135:3: error: always_inline function '_mm_store_si128' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
135 | _mm_store_si128(Hmax + i, zero);
| ^
ksw.c:141:7: error: always_inline function '_mm_load_si128' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
141 | h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example
| ^
ksw.c:142:7: error: '__builtin_ia32_pslldqi128_byteshift' needs target feature sse2
142 | h = _mm_slli_si128(h, 1); // h=H(i-1,-1); << instead of >> because x64 is little-endian
| ^
/usr/lib/clang/18/include/emmintrin.h:2686:13: note: expanded from macro '_mm_slli_si128'
2686 | ((__m128i)__builtin_ia32_pslldqi128_byteshift((__v2di)(__m128i)(a), \
| ^
ksw.c:150:25: error: always_inline function '_mm_load_si128' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
150 | h = _mm_adds_epu8(h, _mm_load_si128(S + j));
| ^
ksw.c:150:8: error: always_inline function '_mm_adds_epu8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
150 | h = _mm_adds_epu8(h, _mm_load_si128(S + j));
| ^
ksw.c:151:8: error: always_inline function '_mm_subs_epu8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
151 | h = _mm_subs_epu8(h, shift); // h=H'(i-1,j-1)+S(i,j)
| ^
ksw.c:152:8: error: always_inline function '_mm_load_si128' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
152 | e = _mm_load_si128(E + j); // e=E'(i,j)
| ^
ksw.c:153:8: error: always_inline function '_mm_max_epu8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
153 | h = _mm_max_epu8(h, e);
| ^
ksw.c:154:8: error: always_inline function '_mm_max_epu8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
154 | h = _mm_max_epu8(h, f); // h=H'(i,j)
| ^
ksw.c:155:10: error: always_inline function '_mm_max_epu8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
155 | max = _mm_max_epu8(max, h); // set max
| ^
ksw.c:156:4: error: always_inline function '_mm_store_si128' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
156 | _mm_store_si128(H1 + j, h); // save to H'(i,j)
| ^
ksw.c:158:8: error: always_inline function '_mm_subs_epu8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
158 | h = _mm_subs_epu8(h, gapoe); // h=H'(i,j)-gapo
| ^
ksw.c:159:8: error: always_inline function '_mm_subs_epu8' requires target feature 'sse2', but would be inlined into function 'ksw_u8' that is compiled without support for 'sse2'
159 | e = _mm_subs_epu8(e, gape); // e=E'(i,j)-gape
| ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
gmake: *** [Makefile:15: ksw.o] Error 1
gmake: *** Waiting for unfinished jobs....
3 warnings generated.
2 warnings generated.
===> 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 making "build" in /usr/ports/biology/fermi-lite