[package - 133i386-default][biology/fermi-lite] Failed for fermi-lite-0.1.13 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Tue, 03 Sep 2024 13:09:52 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/beefy15/data/133i386-default/94b089c7ad30/logs/fermi-lite-0.1.13.log
Build URL:      https://pkg-status.freebsd.org/beefy15/build.html?mastername=133i386-default&build=94b089c7ad30
Log:

=>> Building biology/fermi-lite
build started at Tue Sep  3 13:09:46 UTC 2024
port directory: /usr/ports/biology/fermi-lite
package name: fermi-lite-0.1.13
building for: FreeBSD 133i386-default-job-11 13.3-RELEASE-p5 FreeBSD 13.3-RELEASE-p5 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: 94b089c7ad3
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: 1303001
Job Id: 11

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--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--

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--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
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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
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--PLIST_SUB--
OSREL=13.3 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--

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=======================<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
[133i386-default-job-11] Installing pkg-1.21.3...
[133i386-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
[133i386-default-job-11] Installing gmake-4.4.1...
[133i386-default-job-11] `-- Installing gettext-runtime-0.22.5...
[133i386-default-job-11] |   `-- Installing indexinfo-0.3.1...
[133i386-default-job-11] |   `-- Extracting indexinfo-0.3.1: .... done
[133i386-default-job-11] `-- Extracting gettext-runtime-0.22.5: .......... done
[133i386-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;
      |                                                                ^
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    bubble.c -o bubble.o
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/17/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 in /usr/ports/biology/fermi-lite