[exp - 140amd64-default-build-as-user][biology/minimap2] Failed for minimap2-2.28 in package

From: <pkg-fallout_at_FreeBSD.org>
Date: Tue, 16 Apr 2024 07:38:45 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/package19/data/140amd64-default-build-as-user/68eb816d1485/logs/minimap2-2.28.log
Build URL:      https://pkg-status.freebsd.org/package19/build.html?mastername=140amd64-default-build-as-user&build=68eb816d1485
Log:

=>> Building biology/minimap2
build started at Tue Apr 16 07:38:37 UTC 2024
port directory: /usr/ports/biology/minimap2
package name: minimap2-2.28
building for: FreeBSD 140amd64-default-build-as-user-job-02 14.0-RELEASE-p6 FreeBSD 14.0-RELEASE-p6 amd64
maintained by: jwb@FreeBSD.org
Makefile datestamp: -rw-r--r--  1 root wheel 461 Apr 15 00:02 /usr/ports/biology/minimap2/Makefile
Ports top last git commit: 68eb816d148
Ports top unclean checkout: no
Port dir last git commit: 8efa6a22830
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-1-g1e9f97d6
Host OSVERSION: 1500006
Jail OSVERSION: 1400097
Job Id: 02

---Begin Environment---
SHELL=/bin/sh
OSVERSION=1400097
UNAME_v=FreeBSD 14.0-RELEASE-p6
UNAME_r=14.0-RELEASE-p6
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=3.4.1-1-g1e9f97d6
MASTERMNT=/poudriere/data/.m/140amd64-default-build-as-user/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
GID=0
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
UID=0
PWD=/poudriere/data/.m/140amd64-default-build-as-user/02/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=140amd64-default-build-as-user
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/poudriere/data/.m/140amd64-default-build-as-user/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.1-1-g1e9f97d6
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
FORCE_PACKAGE=yes
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
####  ####
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
---End make.conf---
--Resource limits--
cpu time               (seconds, -t)  unlimited
file size           (512-blocks, -f)  unlimited
data seg size           (kbytes, -d)  33554432
stack size              (kbytes, -s)  524288
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=nobody UID=65534 GID=65534
===>  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
[140amd64-default-build-as-user-job-02] Installing pkg-1.21.1...
[140amd64-default-build-as-user-job-02] 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 5775 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=nobody UID=65534 GID=65534
===>  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=nobody UID=65534 GID=65534
===>  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
[140amd64-default-build-as-user-job-02] Installing simde-0.8.0...
[140amd64-default-build-as-user-job-02] 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
[140amd64-default-build-as-user-job-02] Installing gmake-4.4.1...
[140amd64-default-build-as-user-job-02] `-- Installing gettext-runtime-0.22.5...
[140amd64-default-build-as-user-job-02] |   `-- Installing indexinfo-0.3.1...
[140amd64-default-build-as-user-job-02] |   `-- Extracting indexinfo-0.3.1: .... done
[140amd64-default-build-as-user-job-02] `-- Extracting gettext-runtime-0.22.5: .......... done
[140amd64-default-build-as-user-job-02] 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=nobody UID=65534 GID=65534
===>  Configuring for minimap2-2.28
===========================================================================
=======================<phase: build          >============================
===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534
===>  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
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
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
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
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=nobody UID=65534 GID=65534
===>  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=2024-04-16T07:38:37+0000' 'PKG_NOTE_ports_top_git_hash=68eb816d148' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=8efa6a22830' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.1-1-g1e9f97d6' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534
===>  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