[package - 140i386-default][biology/minimap2] Failed for minimap2-2.28 in package
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Date: Sat, 13 Apr 2024 18:04:15 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/beefy11/data/140i386-default/d866b4f57293/logs/minimap2-2.28.log
Build URL: https://pkg-status.freebsd.org/beefy11/build.html?mastername=140i386-default&build=d866b4f57293
Log:
=>> Building biology/minimap2
build started at Sat Apr 13 18:04:07 UTC 2024
port directory: /usr/ports/biology/minimap2
package name: minimap2-2.28
building for: FreeBSD 140i386-default-job-09 14.0-RELEASE-p6 FreeBSD 14.0-RELEASE-p6 i386
maintained by: jwb@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 461 Apr 13 01:01 /usr/ports/biology/minimap2/Makefile
Ports top last git commit: d866b4f572
Ports top unclean checkout: no
Port dir last git commit: 8efa6a2283
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-1-g1e9f97d6
Host OSVERSION: 1500006
Jail OSVERSION: 1400097
Job Id: 09
---Begin Environment---
SHELL=/bin/sh
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MAKE_OBJDIR_CHECK_WRITABLE=0
UNAME_m=i386
UNAME_p=i386
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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--
jwb@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/minimap2/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/minimap2/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/minimap2/work/.cache HOME=/wrkdirs/usr/ports/biology/minimap2/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/minimap2/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/minimap2/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--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/minimap2/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/minimap2/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/minimap2/work/.cache HOME=/wrkdirs/usr/ports/biology/minimap2/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/minimap2/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/minimap2/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 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -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_SCRIP
T="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/minimap2" EXAMPLESDIR="share/examples/minimap2" DATADIR="share/minimap2" WWWDIR="www/minimap2" ETCDIR="etc/minimap2"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/minimap2 DOCSDIR=/usr/local/share/doc/minimap2 EXAMPLESDIR=/usr/local/share/examples/minimap2 WWWDIR=/usr/local/www/minimap2 ETCDIR=/usr/local/etc/minimap2
--End SUB_LIST--
---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
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
#### 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
--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
===> minimap2-2.28 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.1.pkg
[140i386-default-job-09] Installing pkg-1.21.1...
[140i386-default-job-09] Extracting pkg-1.21.1: .......... done
===> minimap2-2.28 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of minimap2-2.28
===========================================================================
=======================<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
=> lh3-minimap2-v2.28_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/lh3/minimap2/tar.gz/v2.28?dummy=/lh3-minimap2-v2.28_GH0.tar.gz
fetch: https://codeload.github.com/lh3/minimap2/tar.gz/v2.28?dummy=/lh3-minimap2-v2.28_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/lh3/minimap2/tar.gz/v2.28?dummy=/lh3-minimap2-v2.28_GH0.tar.gz: size of remote file is not known
lh3-minimap2-v2.28_GH0.tar.gz 254 kB 6806 kBps 00s
===> Fetching all distfiles required by minimap2-2.28 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 minimap2-2.28 for building
=> SHA256 Checksum OK for lh3-minimap2-v2.28_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 minimap2-2.28 for building
===> Extracting for minimap2-2.28
=> SHA256 Checksum OK for lh3-minimap2-v2.28_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 minimap2-2.28
===> Applying FreeBSD patches for minimap2-2.28 from /usr/ports/biology/minimap2/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> minimap2-2.28 depends on package: simde>0 - not found
===> Installing existing package /packages/All/simde-0.8.0.pkg
[140i386-default-job-09] Installing simde-0.8.0...
[140i386-default-job-09] Extracting simde-0.8.0: .......... done
===> minimap2-2.28 depends on package: simde>0 - found
===> Returning to build of minimap2-2.28
===> minimap2-2.28 depends on package: gmake>=4.4.1 - not found
===> Installing existing package /packages/All/gmake-4.4.1.pkg
[140i386-default-job-09] Installing gmake-4.4.1...
[140i386-default-job-09] `-- Installing gettext-runtime-0.22.5...
[140i386-default-job-09] | `-- Installing indexinfo-0.3.1...
[140i386-default-job-09] | `-- Extracting indexinfo-0.3.1: .... done
[140i386-default-job-09] `-- Extracting gettext-runtime-0.22.5: .......... done
[140i386-default-job-09] Extracting gmake-4.4.1: .......... done
===> minimap2-2.28 depends on package: gmake>=4.4.1 - found
===> Returning to build of minimap2-2.28
===========================================================================
=======================<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 minimap2-2.28
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for minimap2-2.28
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include main.c -o main.o
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include kthread.c -o kthread.o
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include kalloc.c -o kalloc.o
kalloc.c:223:4: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
^~~~~~~~~~~
kalloc.c:223:17: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
^~~~~~~~~~~~
kalloc.c:223:31: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
^~~~~~~~~~
kalloc.c:223:43: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
^~~~~~~~~~~
kalloc.c:223:56: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
st.capacity, st.available, st.largest, st.n_blocks, st.n_cores);
^~~~~~~~~~
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include misc.c -o misc.o
5 warnings generated.
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include bseq.c -o bseq.o
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include sketch.c -o sketch.o
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include sdust.c -o sdust.o
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include options.c -o options.o
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include index.c -o index.o
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include lchain.c -o lchain.o
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include align.c -o align.o
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include hit.c -o hit.o
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include map.c -o map.o
map.c:365:84: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest);
~~~ ^~~~~~~~~~~~~
%zu
map.c:365:99: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest);
~~~ ^~~~~~~~~~~~
%zu
map.c:365:113: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest);
~~~ ^~~~~~~~~~~~
%zu
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include format.c -o format.o
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include pe.c -o pe.o
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include seed.c -o seed.o
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include esterr.c -o esterr.o
3 warnings generated.
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include splitidx.c -o splitidx.o
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -msse4.1 -isystem /usr/local/include ksw2_extz2_sse.c -o ksw2_extz2_simde.o
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -msse4.1 -isystem /usr/local/include ksw2_extd2_sse.c -o ksw2_extd2_simde.o
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -msse4.1 -isystem /usr/local/include ksw2_exts2_sse.c -o ksw2_exts2_simde.o
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -msse2 -isystem /usr/local/include ksw2_ll_sse.c -o ksw2_ll_simde.o
cc -D_SDUST_MAIN -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ sdust.c kalloc.o -o sdust -lz
cc -c -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ -isystem /usr/local/include example.c -o example.o
ar -csru libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o map.o format.o pe.o seed.o esterr.o splitidx.o ksw2_extz2_simde.o ksw2_extd2_simde.o ksw2_exts2_simde.o ksw2_ll_simde.o
cc -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ main.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread
cc -O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -Wc++-compat -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D__SSE2__ example.o -o minimap2-lite -L. -lminimap2 -lm -lz -lpthread
===========================================================================
=======================<phase: run-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: stage >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Staging for minimap2-2.28
===> Generating temporary packing list
mkdir -p /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/bin
mkdir -p /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/man/man1
mkdir -p /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/share/minimap2
install -c minimap2 /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/bin
install -c minimap2-lite /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/bin
install -c sdust /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/bin
install -c minimap2.1 /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/man/man1
cp -R test /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/share/minimap2
strip /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/bin/minimap2
strip /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/bin/minimap2-lite
strip /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/bin/sdust
====> Compressing man pages (compress-man)
===========================================================================
=======================<phase: package >============================
===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2024-04-13T18:04:07+0000' 'PKG_NOTE_ports_top_git_hash=d866b4f572' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=8efa6a2283' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.1-1-g1e9f97d6' NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building packages for minimap2-2.28
===> Building minimap2-2.28
pkg-static: Unable to access file /wrkdirs/usr/ports/biology/minimap2/work/stage/usr/local/man/man1/minimap2.1.gz:No such file or directory
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/minimap2