[package - main-arm64-default][biology/velvet] Failed for velvet-1.2.10_2 in build
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Date: Thu, 09 Jul 2026 13:11:46 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: mzaki@m.u-tokyo.ac.jp
Log URL: https://pkg-status.freebsd.org/ampere2/data/main-arm64-default/p4503d4fcebc4_s830f690eb67/logs/velvet-1.2.10_2.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p4503d4fcebc4_s830f690eb67
Log:
=>> Building biology/velvet
build started at Thu Jul 9 13:11:30 UTC 2026
port directory: /usr/ports/biology/velvet
package name: velvet-1.2.10_2
building for: FreeBSD main-arm64-default-job-01 16.0-CURRENT FreeBSD 16.0-CURRENT 1600019 arm64
maintained by: mzaki@m.u-tokyo.ac.jp
Makefile datestamp: -rw-r--r-- 1 root wheel 2559 Sep 10 2022 /usr/ports/biology/velvet/Makefile
Ports top last git commit: 4503d4fcebc45912c083a9b07c2753e55137f07d
Ports top unclean checkout: no
Port dir last git commit: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.8
Host OSVERSION: 1600018
Jail OSVERSION: 1600019
Job Id: 01
!!! Jail is newer than host. (Jail: 1600019, Host: 1600018) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1600019
UNAME_v=FreeBSD 16.0-CURRENT 1600019
UNAME_r=16.0-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=3.4.8
MASTERMNT=/usr/local/poudriere/data/.m/main-arm64-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-arm64-default/01/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-arm64-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.8
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---
===> The following configuration options are available for velvet-1.2.10_2:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
mzaki@m.u-tokyo.ac.jp
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 MAKE=/usr/local/bin/gmake PYTHON="/usr/local/bin/python3.12" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/velvet/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/velvet/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/velvet/work/.cache HOME=/wrkdirs/usr/ports/biology/velvet/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/velvet/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/velvet/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--
MAXKMERLENGTH=31 CATEGORIES=2 PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/velvet/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/velvet/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/velvet/work/.cache HOME=/wrkdirs/usr/ports/biology/velvet/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/velvet/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/velvet/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=" " 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_DAT
A="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
PORTDOCS="" PYTHON_INCLUDEDIR=include/python3.12 PYTHON_LIBDIR=lib/python3.12 PYTHON_PLATFORM=freebsd16 PYTHON_SITELIBDIR=lib/python3.12/site-packages PYTHON_SUFFIX=312 PYTHON_BASESUFFIX=312 PYTHON_TAG=.cpython-312 PYTHON_SOABI=.cpython-312 PYTHON_VER=3.12 PYTHON_BASEVER=3.12 PYTHON_VERSION=python3.12 PYTHON2="@comment " PYTHON3="" OSREL=16.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.2 PERL_VER=5.42 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/5.42 DOCSDIR="share/doc/velvet" EXAMPLESDIR="share/examples/velvet" DATADIR="share/velvet" WWWDIR="www/velvet" ETCDIR="etc/velvet"
--End PLIST_SUB--
--SUB_LIST--
PYTHON_INCLUDEDIR=/usr/local/include/python3.12 PYTHON_LIBDIR=/usr/local/lib/python3.12 PYTHON_PLATFORM=freebsd16 PYTHON_SITELIBDIR=/usr/local/lib/python3.12/site-packages PYTHON_SUFFIX=312 PYTHON_BASESUFFIX=312 PYTHON_TAG=.cpython-312 PYTHON_SOABI=.cpython-312 PYTHON_VER=3.12 PYTHON_BASEVER=3.12 PYTHON_VERSION=python3.12 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/velvet DOCSDIR=/usr/local/share/doc/velvet EXAMPLESDIR=/usr/local/share/examples/velvet WWWDIR=/usr/local/www/velvet ETCDIR=/usr/local/etc/velvet
--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
#### ####
# 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) 1048576
stack size (kbytes, -s) 1048576
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 (kbytes, -y) unlimited
virtual machines (-V) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> velvet-1.2.10_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.7.5.pkg
[main-arm64-default-job-01] Installing pkg-2.7.5...
[main-arm64-default-job-01] Extracting pkg-2.7.5: .......... done
===> velvet-1.2.10_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of velvet-1.2.10_2
===========================================================================
=======================<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
===> Fetching all distfiles required by velvet-1.2.10_2 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Fetching all distfiles required by velvet-1.2.10_2 for building
=> SHA256 Checksum OK for velvet_1.2.10.tgz.
===========================================================================
=======================<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
===> Fetching all distfiles required by velvet-1.2.10_2 for building
===> Extracting for velvet-1.2.10_2
=> SHA256 Checksum OK for velvet_1.2.10.tgz.
===========================================================================
=======================<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 velvet-1.2.10_2
===> Applying FreeBSD patches for velvet-1.2.10_2 from /usr/ports/biology/velvet/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> velvet-1.2.10_2 depends on package: gmake>=4.4.1 - not found
===> Installing existing package /packages/All/gmake-4.4.1.pkg
[main-arm64-default-job-01] Installing gmake-4.4.1...
[main-arm64-default-job-01] `-- Installing gettext-runtime-1.0_1...
[main-arm64-default-job-01] | `-- Installing indexinfo-0.3.1_1...
[main-arm64-default-job-01] | `-- Extracting indexinfo-0.3.1_1: .... done
[main-arm64-default-job-01] `-- Extracting gettext-runtime-1.0_1: .......... done
[main-arm64-default-job-01] Extracting gmake-4.4.1: .......... done
===> velvet-1.2.10_2 depends on package: gmake>=4.4.1 - found
===> Returning to build of velvet-1.2.10_2
===> velvet-1.2.10_2 depends on file: /usr/local/bin/python3.12 - not found
===> Installing existing package /packages/All/python312-3.12.13_3.pkg
[main-arm64-default-job-01] Installing python312-3.12.13_3...
[main-arm64-default-job-01] `-- Installing expat-2.8.2...
[main-arm64-default-job-01] `-- Extracting expat-2.8.2: .......... done
[main-arm64-default-job-01] `-- Installing libffi-3.6.0...
[main-arm64-default-job-01] `-- Extracting libffi-3.6.0: .......... done
[main-arm64-default-job-01] `-- Installing mpdecimal-4.0.1...
[main-arm64-default-job-01] `-- Extracting mpdecimal-4.0.1: .......... done
[main-arm64-default-job-01] `-- Installing readline-8.3.3...
[main-arm64-default-job-01] `-- Extracting readline-8.3.3: .......... done
[main-arm64-default-job-01] Extracting python312-3.12.13_3: .......... done
=====
Message from python312-3.12.13_3:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py312-gdbm databases/py-gdbm@py312
py312-sqlite3 databases/py-sqlite3@py312
py312-tkinter x11-toolkits/py-tkinter@py312
===> velvet-1.2.10_2 depends on file: /usr/local/bin/python3.12 - found
===> Returning to build of velvet-1.2.10_2
===========================================================================
=======================<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 velvet-1.2.10_2
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for velvet-1.2.10_2
rm obj/*.o obj/dbg/*.o
rm: obj/*.o: No such file or directory
rm: obj/dbg/*.o: No such file or directory
gmake: [Makefile:51: cleanobj] Error 1 (ignored)
mkdir -p obj
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o
In file included from src/run.c:31:
In file included from src/run.h:35:
src/scaffold.h:21:9: warning: '_SSCAFFOLD_H_' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
21 | #ifndef _SSCAFFOLD_H_
| ^~~~~~~~~~~~~
src/scaffold.h:22:9: note: '_SCAFFOLD_H_' is defined here; did you mean '_SSCAFFOLD_H_'?
22 | #define _SCAFFOLD_H_
| ^~~~~~~~~~~~
| _SSCAFFOLD_H_
1 warning generated.
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o
src/splayTable.c:881:10: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
881 | if (c == EOF || c == '>')
| ~ ^ ~~~
src/splayTable.c:945:10: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
945 | if (c == EOF || c == '>') {
| ~ ^ ~~~
src/splayTable.c:1201:42: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
1201 | while (seqFile && (c = getc(seqFile)) != EOF) {
| ~~~~~~~~~~~~~~~~~~~ ^ ~~~
3 warnings generated.
cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o
src/graph.c:2115:41: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
2115 | while ((c = fgetc(file)) != '\n' && c != EOF) {
| ~ ^ ~~~
src/graph.c:2143:41: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
2143 | while ((c = fgetc(file)) != '\n' && c != EOF) {
| ~ ^ ~~~
Assertion failed: (!KeyInfoT::isEqual(Val, EmptyKey) && !KeyInfoT::isEqual(Val, TombstoneKey) && "Empty/Tombstone value shouldn't be inserted into map!"), function LookupBucketFor, file /usr/local/poudriere/jails/main-arm64/usr/src/contrib/llvm-project/llvm/include/llvm/ADT/DenseMap.h, line 698.
PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script.
Stack dump:
0. Program arguments: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o
1. <eof> parser at end of file
2. Optimizer
3. Running pass "function<eager-inv>(float2int,lower-constant-intrinsics,loop(loop-rotate<header-duplication;no-prepare-for-lto>,loop-deletion),loop-distribute,inject-tli-mappings,loop-vectorize<no-interleave-forced-only;no-vectorize-forced-only;>,infer-alignment,loop-load-elim,instcombine<max-iterations=1;no-verify-fixpoint>,simplifycfg<bonus-inst-threshold=1;forward-switch-cond;switch-range-to-icmp;switch-to-lookup;no-keep-loops;hoist-common-insts;no-hoist-loads-stores-with-cond-faulting;sink-common-insts;speculate-blocks;simplify-cond-branch;no-speculate-unpredictables>,slp-vectorizer,vector-combine,instcombine<max-iterations=1;no-verify-fixpoint>,loop-unroll<O2>,transform-warning,sroa<preserve-cfg>,infer-alignment,instcombine<max-iterations=1;no-verify-fixpoint>,loop-mssa(licm<allowspeculation>),alignment-from-assumptions,loop-sink,instsimplify,div-rem-pairs,tailcallelim,simplifycfg<bonus-inst-threshold=1;no-forward-switch-cond;switch-range-to-icmp;no-switch-to-lookup;ke
ep-loops;no-hoist-common-insts;hoist-loads-stores-with-cond-faulting;no-sink-common-insts;speculate-blocks;simplify-cond-branch;speculate-unpredictables>)" on module "src/graph.c"
4. Running pass "slp-vectorizer" on function "createArc"
#0 0x000026522791e8d0 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/usr/lib/libprivatellvm.so.21+0x411e8d0)
#1 0x000026522791c638 llvm::sys::RunSignalHandlers() (/usr/lib/libprivatellvm.so.21+0x411c638)
#2 0x00002652278c5a38 (/usr/lib/libprivatellvm.so.21+0x40c5a38)
#3 0x000026521d0a234c (/lib/libthr.so.3+0x2b34c)
cc: error: clang frontend command failed with exit code 134 (use -v to see invocation)
FreeBSD clang version 21.1.8 (https://github.com/llvm/llvm-project.git llvmorg-21.1.8-0-g2078da43e25a)
Target: aarch64-unknown-freebsd16.0
Thread model: posix
InstalledDir: /usr/bin
Build config: +assertions
cc: note: diagnostic msg:
********************
PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
cc: note: diagnostic msg: /tmp/graph-7c8edf.c
cc: note: diagnostic msg: /tmp/graph-7c8edf.sh
cc: note: diagnostic msg:
********************
gmake: *** [Makefile:110: obj/graph.o] Error 1
*** Error code 1
Stop.
make: stopped making "build" in /usr/ports/biology/velvet