[package - main-armv7-default][biology/bwa] Failed for bwa-0.7.18 in build
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Date: Wed, 01 Jan 2025 12:07:57 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: alster@vinterdalen.se
Log URL: https://pkg-status.freebsd.org/ampere2/data/main-armv7-default/pd594ba044905_s6ea1ce222c/logs/bwa-0.7.18.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=pd594ba044905_s6ea1ce222c
Log:
=>> Building biology/bwa
build started at Wed Jan 1 12:07:42 UTC 2025
port directory: /usr/ports/biology/bwa
package name: bwa-0.7.18
building for: FreeBSD main-armv7-default-job-06 15.0-CURRENT FreeBSD 15.0-CURRENT 1500029 arm
maintained by: alster@vinterdalen.se
Makefile datestamp: -rw-r--r-- 1 root wheel 904 Nov 30 01:02 /usr/ports/biology/bwa/Makefile
Ports top last git commit: d594ba04490
Ports top unclean checkout: no
Port dir last git commit: 482229547aa
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2
Host OSVERSION: 1500028
Jail OSVERSION: 1500029
Job Id: 06
!!! Jail is newer than host. (Jail: 1500029, Host: 1500028) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1500029
UNAME_v=FreeBSD 15.0-CURRENT 1500029
UNAME_r=15.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
MAKE_OBJDIR_CHECK_WRITABLE=0
LOCALBASE=/usr/local
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.2
MASTERMNT=/usr/local/poudriere/data/.m/main-armv7-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
PWD=/usr/local/poudriere/data/.m/main-armv7-default/06/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-armv7-default
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SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-armv7-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.2
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
---End OPTIONS List---
--MAINTAINER--
alster@vinterdalen.se
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bwa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bwa/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bwa/work/.cache HOME=/wrkdirs/usr/ports/biology/bwa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bwa/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bwa/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local"
--End CONFIGURE_ENV--
--MAKE_ENV--
PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bwa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bwa/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bwa/work/.cache HOME=/wrkdirs/usr/ports/biology/bwa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bwa/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bwa/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 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " BSD_INSTALL_PROGRAM="install -
s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -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 PERL_VERSION=5.36.3 PERL_VER=5.36 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.36 DOCSDIR="share/doc/bwa" EXAMPLESDIR="share/examples/bwa" DATADIR="share/bwa" WWWDIR="www/bwa" ETCDIR="etc/bwa"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bwa DOCSDIR=/usr/local/share/doc/bwa EXAMPLESDIR=/usr/local/share/examples/bwa WWWDIR=/usr/local/www/bwa ETCDIR=/usr/local/etc/bwa
--End SUB_LIST--
---Begin make.conf---
# 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
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### ####
# 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
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
UID=0
---End make.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 524288
stack size (kbytes, -s) 65536
core file size (512-blocks, -c) unlimited
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
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
pipebuf (-y) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> bwa-0.7.18 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.3.pkg
[main-armv7-default-job-06] Installing pkg-1.21.3...
[main-armv7-default-job-06] Extracting pkg-1.21.3: .......... done
===> bwa-0.7.18 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of bwa-0.7.18
===========================================================================
=======================<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 GPLv3 accepted by the user
===> Fetching all distfiles required by bwa-0.7.18 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bwa-0.7.18 for building
=> SHA256 Checksum OK for lh3-bwa-v0.7.18_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 GPLv3 accepted by the user
===> Fetching all distfiles required by bwa-0.7.18 for building
===> Extracting for bwa-0.7.18
=> SHA256 Checksum OK for lh3-bwa-v0.7.18_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 bwa-0.7.18
===> Applying FreeBSD patches for bwa-0.7.18 from /usr/ports/biology/bwa/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> bwa-0.7.18 depends on package: simde>0 - not found
===> Installing existing package /packages/All/simde-0.8.2.pkg
[main-armv7-default-job-06] Installing simde-0.8.2...
[main-armv7-default-job-06] Extracting simde-0.8.2: .......... done
===> bwa-0.7.18 depends on package: simde>0 - found
===> Returning to build of bwa-0.7.18
===> bwa-0.7.18 depends on package: gmake>=4.4.1 - not found
===> Installing existing package /packages/All/gmake-4.4.1.pkg
[main-armv7-default-job-06] Installing gmake-4.4.1...
[main-armv7-default-job-06] `-- Installing gettext-runtime-0.22.5...
[main-armv7-default-job-06] | `-- Installing indexinfo-0.3.1...
[main-armv7-default-job-06] | `-- Extracting indexinfo-0.3.1: .... done
[main-armv7-default-job-06] `-- Extracting gettext-runtime-0.22.5: .......... done
[main-armv7-default-job-06] Extracting gmake-4.4.1: .......... done
===> bwa-0.7.18 depends on package: gmake>=4.4.1 - found
===> Returning to build of bwa-0.7.18
===========================================================================
=======================<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 bwa-0.7.18
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for bwa-0.7.18
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include utils.c -o utils.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include kthread.c -o kthread.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include kstring.c -o kstring.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include ksw.c -o ksw.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwt.c -o bwt.o
ksw.c:211:18: warning: call to undeclared function 'vmaxvq_u8'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
211 | if (UNLIKELY(allzero_16(_mm_subs_epu8(f, h)))) goto end_loop16;
| ^
ksw.c:145:25: note: expanded from macro 'allzero_16'
145 | #define allzero_16(xx) (vmaxvq_u8((xx)) == 0)
| ^
ksw.c:216:3: warning: call to undeclared function 'vmaxvq_u8'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
216 | __max_16(imax, max); // imax is the maximum number in max
| ^
ksw.c:144:35: note: expanded from macro '__max_16'
144 | #define __max_16(ret, xx) (ret) = vmaxvq_u8((xx))
| ^
ksw.c:331:17: warning: call to undeclared function 'vmaxvq_u16'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
331 | if(UNLIKELY(allzero_0f_8(_mm_cmpgt_epi16(f, h)))) goto end_loop8;
| ^
ksw.c:277:27: note: expanded from macro 'allzero_0f_8'
277 | #define allzero_0f_8(xx) (vmaxvq_u16(vreinterpretq_u16_u8((xx))) == 0)
| ^
ksw.c:335:3: warning: call to undeclared function 'vmaxvq_s16'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
335 | __max_8(imax, max);
| ^
ksw.c:276:34: note: expanded from macro '__max_8'
276 | #define __max_8(ret, xx) (ret) = vmaxvq_s16(vreinterpretq_s16_u8((xx)))
| ^
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bntseq.c -o bntseq.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwa.c -o bwa.o
4 warnings generated.
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwamem.c -o bwamem.o
bwamem.c:213:1: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
213 | KBTREE_INIT(chn, mem_chain_t, chain_cmp)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./kbtree.h:366:2: note: expanded from macro 'KBTREE_INIT'
366 | __KB_PUT(name, key_t, __cmp) \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
./kbtree.h:218:32: note: expanded from macro '__KB_PUT'
218 | b->root = s; s->is_internal = 1; s->n = 0; \
| ^ ~
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwamem_pair.c -o bwamem_pair.o
bwamem.c:1105:72: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
1105 | err_printf("* %ld chains remain after removing duplicated chains\n", regs.n);
| ~~~ ^~~~~~
| %zu
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwamem_extra.c -o bwamem_extra.o
bwamem_pair.c:91:131: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
91 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n);
| ~~~ ^~~~~~~~~~
| %zu
bwamem_pair.c:91:143: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
91 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n);
| ~~~ ^~~~~~~~~~
| %zu
bwamem_pair.c:91:155: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
91 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n);
| ~~~ ^~~~~~~~~~
| %zu
bwamem_pair.c:91:167: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
91 | if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n);
| ~~~ ^~~~~~~~~~
| %zu
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include malloc_wrap.c -o malloc_wrap.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include QSufSort.c -o QSufSort.o
4 warnings generated.
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwt_gen.c -o bwt_gen.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include rope.c -o rope.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include rle.c -o rle.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include is.c -o is.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwtindex.c -o bwtindex.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwashm.c -o bwashm.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwase.c -o bwase.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwaseqio.c -o bwaseqio.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwtgap.c -o bwtgap.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwtaln.c -o bwtaln.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bamlite.c -o bamlite.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwape.c -o bwape.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include kopen.c -o kopen.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include pemerge.c -o pemerge.o
2 warnings generated.
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include maxk.c -o maxk.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwtsw2_core.c -o bwtsw2_core.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwtsw2_main.c -o bwtsw2_main.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwtsw2_aux.c -o bwtsw2_aux.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwt_lite.c -o bwt_lite.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwtsw2_chain.c -o bwtsw2_chain.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include fastmap.c -o fastmap.o
fastmap.c:448:42: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
448 | err_printf("SQ\t%s\t%ld", seq->name.s, seq->seq.l);
| ~~~ ^~~~~~~~~~
| %zu
1 warning generated.
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include bwtsw2_pair.c -o bwtsw2_pair.o
cc -c -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS -isystem /usr/local/include main.c -o main.o
ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread
ld: error: undefined symbol: vmaxvq_u8
>>> referenced by ksw.c
>>> ksw.o:(ksw_u8) in archive ./libbwa.a
>>> referenced by ksw.c
>>> ksw.o:(ksw_u8) in archive ./libbwa.a
ld: error: undefined symbol: vmaxvq_u16
>>> referenced by ksw.c
>>> ksw.o:(ksw_i16) in archive ./libbwa.a
ld: error: undefined symbol: vmaxvq_s16
>>> referenced by ksw.c
>>> ksw.o:(ksw_i16) in archive ./libbwa.a
cc: error: linker command failed with exit code 1 (use -v to see invocation)
gmake: *** [Makefile:30: bwa] Error 1
===> 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/bwa