[package - 144arm64-default][biology/muscle] Failed for muscle-5.1_1 in build
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Date: Mon, 27 Jul 2026 20:20:37 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@e-mail.ne.jp
Log URL: https://pkg-status.freebsd.org/ampere3/data/144arm64-default/7c53142d6b1d/logs/muscle-5.1_1.log
Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=144arm64-default&build=7c53142d6b1d
Log:
=>> Building biology/muscle
build started at Mon Jul 27 20:17:36 UTC 2026
port directory: /usr/ports/biology/muscle
package name: muscle-5.1_1
building for: FreeBSD 144arm64-default-job-07 14.4-RELEASE-p7 FreeBSD 14.4-RELEASE-p7 arm64
maintained by: mzaki@e-mail.ne.jp
Makefile datestamp: -rw-r--r-- 1 root wheel 470 Jul 25 01:03 /usr/ports/biology/muscle/Makefile
Ports top last git commit: 7c53142d6b1d65fc3b37c1ce6ee6b703206261e2
Ports top unclean checkout: no
Port dir last git commit: 96b335dd87f538c5907a7c29d9a1ebd5318be863
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.8
Host OSVERSION: 1600019
Jail OSVERSION: 1404000
Job Id: 07
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1404000
UNAME_v=FreeBSD 14.4-RELEASE-p7
UNAME_r=14.4-RELEASE-p7
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/144arm64-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/144arm64-default/07/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=144arm64-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/144arm64-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---
---End OPTIONS List---
--MAINTAINER--
mzaki@e-mail.ne.jp
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/muscle/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/muscle/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/muscle/work/.cache HOME=/wrkdirs/usr/ports/biology/muscle/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/muscle/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/muscle/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--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/muscle/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/muscle/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/muscle/work/.cache HOME=/wrkdirs/usr/ports/biology/muscle/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/muscle/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/muscle/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_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
OSREL=14.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/muscle" EXAMPLESDIR="share/examples/muscle" DATADIR="share/muscle" WWWDIR="www/muscle" ETCDIR="etc/muscle"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/muscle DOCSDIR=/usr/local/share/doc/muscle EXAMPLESDIR=/usr/local/share/examples/muscle WWWDIR=/usr/local/www/muscle ETCDIR=/usr/local/etc/muscle
--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 (-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
===> muscle-5.1_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.8.0_1.pkg
[144arm64-default-job-07] Installing pkg-2.8.0_1...
[144arm64-default-job-07] Extracting pkg-2.8.0_1: .......... done
===> muscle-5.1_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of muscle-5.1_1
===========================================================================
=======================<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
=> rcedgar-muscle-v5.1_GH0.tar.gz doesn't seem to exist in /portdistfiles.
=> Attempting to fetch https://codeload.github.com/rcedgar/muscle/tar.gz/v5.1?dummy=/rcedgar-muscle-v5.1_GH0.tar.gz
fetch: https://codeload.github.com/rcedgar/muscle/tar.gz/v5.1?dummy=/rcedgar-muscle-v5.1_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/rcedgar/muscle/tar.gz/v5.1?dummy=/rcedgar-muscle-v5.1_GH0.tar.gz: size of remote file is not known
rcedgar-muscle-v5.1_GH0.tar.gz 179 kB 18 MBps 00s
===> Fetching all distfiles required by muscle-5.1_1 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 muscle-5.1_1 for building
=> SHA256 Checksum OK for rcedgar-muscle-v5.1_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 muscle-5.1_1 for building
===> Extracting for muscle-5.1_1
=> SHA256 Checksum OK for rcedgar-muscle-v5.1_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 muscle-5.1_1
===> Applying FreeBSD patches for muscle-5.1_1 from /usr/ports/biology/muscle/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> muscle-5.1_1 depends on package: gmake>=4.4.1 - not found
===> Installing existing package /packages/All/gmake-4.4.1.pkg
[144arm64-default-job-07] Installing gmake-4.4.1...
[144arm64-default-job-07] `-- Installing gettext-runtime-1.0_1...
[144arm64-default-job-07] | `-- Installing indexinfo-0.3.1_1...
[144arm64-default-job-07] | `-- Extracting indexinfo-0.3.1_1: .... done
[144arm64-default-job-07] `-- Extracting gettext-runtime-1.0_1: .......... done
[144arm64-default-job-07] Extracting gmake-4.4.1: .......... done
===> muscle-5.1_1 depends on package: gmake>=4.4.1 - found
===> Returning to build of muscle-5.1_1
===========================================================================
=======================<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 muscle-5.1_1
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for muscle-5.1_1
sh ./gitver.bash
mkdir -p FreeBSD/
./gitver.bash: git: not found
sed: 1: "gitver.tmp
": extra characters at the end of g command
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/addconfseq.o addconfseq.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/align.o align.cpp
""
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/alignpairflat.o alignpairflat.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/allocflat.o allocflat.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/alnalnsflat.o alnalnsflat.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/alnmsasflat.o alnmsasflat.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/alnmsasflat3.o alnmsasflat3.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/alpha.o alpha.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/alpha3.o alpha3.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/assertsameseqs.o assertsameseqs.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/buildposterior3flat.o buildposterior3flat.cpp
alpha.cpp:83:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
83 | switch (Alpha)
| ^~~~~
1 warning generated.
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/buildpostflat.o buildpostflat.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/bwdflat3.o bwdflat3.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/calcalnflat.o calcalnflat.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/calcalnscoreflat.o calcalnscoreflat.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/calcalnscoresparse.o calcalnscoresparse.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/calcposteriorflat.o calcposteriorflat.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/colscoreefa.o colscoreefa.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/consflat.o consflat.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/conspairflat.o conspairflat.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/defaulthmmparams.o defaulthmmparams.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/derep.o derep.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/diagbox.o diagbox.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/disperse.o disperse.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/dividetree.o dividetree.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/eacluster.o eacluster.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/eadistmx.o eadistmx.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/eadistmxmsas.o eadistmxmsas.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/eesort.o eesort.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/efabestcols.o efabestcols.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/efabestconf.o efabestconf.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/efaexplode.o efaexplode.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/efastats.o efastats.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/ensemble.o ensemble.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/fa2efa.o fa2efa.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/fasta.o fasta.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/fasta2.o fasta2.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/fwdflat3.o fwdflat3.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/getconsseq.o getconsseq.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/getpairs.o getpairs.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/getpostpairsalignedflat.o getpostpairsalignedflat.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/globalinputms.o globalinputms.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/guidetreejoinorder.o guidetreejoinorder.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/heatmapcolors.o heatmapcolors.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/help.o help.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/hmmdump.o hmmdump.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/hmmparams.o hmmparams.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/jalview.o jalview.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/jointrees.o jointrees.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/letterconf.o letterconf.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/letterconfhtml.o letterconfhtml.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/logaln.o logaln.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/logdistmx.o logdistmx.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/logmx.o logmx.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/main.o main.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/make_a2m.o make_a2m.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/maxcc.o maxcc.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/mpcflat.o mpcflat.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/msa.o msa.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/msa2.o msa2.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/msastats.o msastats.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/multisequence.o multisequence.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/mysparsemx.o mysparsemx.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/myutils.o myutils.cpp
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/pairhmm.o pairhmm.cpp
myutils.cpp:554:15: warning: result of comparison of constant -1 with expression of type 'uint32' (aka 'unsigned int') is always false [-Wtautological-constant-out-of-range-compare]
554 | if (FileSize == (off_t) (-1))
| ~~~~~~~~ ^ ~~~~~~~~~~~~
c++ -DNDEBUG -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O3 -fopenmp -ffast-math -c -o FreeBSD/permutetree.o permutetree.cpp
myutils.cpp:1099:22: error: use of undeclared identifier 'physmem'; did you mean 'physmem32'?
1099 | size_t len = sizeof(physmem);
| ^~~~~~~
| physmem32
myutils.cpp:1094:15: note: 'physmem32' declared here
1094 | unsigned int physmem32 = 0;
| ^
myutils.cpp:1102:22: error: use of undeclared identifier 'physmem'; did you mean 'physmem32'?
1102 | if (sysctl(mib, 2, &physmem, &len, NULL, 0) == -1)
| ^~~~~~~
| physmem32
myutils.cpp:1094:15: note: 'physmem32' declared here
1094 | unsigned int physmem32 = 0;
| ^
myutils.cpp:1105:17: error: use of undeclared identifier 'physmem'
1105 | return (double)physmem;
| ^
1 warning and 3 errors generated.
gmake: *** [Makefile:53: FreeBSD/myutils.o] Error 1
gmake: *** Waiting for unfinished jobs....
===> 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/muscle