[package - 140releng-armv7-quarterly][biology/mashmap] Failed for mashmap-3.1.1 in build
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Date: Sun, 03 Dec 2023 16:49:01 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: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/ampere1/data/140releng-armv7-quarterly/1121637d9005/logs/mashmap-3.1.1.log
Build URL: https://pkg-status.freebsd.org/ampere1/build.html?mastername=140releng-armv7-quarterly&build=1121637d9005
Log:
=>> Building biology/mashmap
build started at Sun Dec 3 16:48:47 UTC 2023
port directory: /usr/ports/biology/mashmap
package name: mashmap-3.1.1
building for: FreeBSD 140releng-armv7-quarterly-job-05 14.0-RELEASE FreeBSD 14.0-RELEASE 1400097 arm
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 637 Oct 5 01:01 /usr/ports/biology/mashmap/Makefile
Ports top last git commit: 1121637d9
Ports top unclean checkout: no
Port dir last git commit: 46c5200e9
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.3.0-1258-gbc38e2e6
Host OSVERSION: 1500000
Jail OSVERSION: 1400097
Job Id: 05
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1400097
UNAME_v=FreeBSD 14.0-RELEASE 1400097
UNAME_r=14.0-RELEASE
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MAIL=/var/mail/root
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LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
LOCALBASE=/usr/local
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
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MASTERMNT=/usr/local/poudriere/data/.m/140releng-armv7-quarterly/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
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PWD=/usr/local/poudriere/data/.m/140releng-armv7-quarterly/05/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=140releng-armv7-quarterly
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POUDRIERE_PKGNAME=poudriere-git-3.3.0-1258-gbc38e2e6
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 mashmap-3.1.1:
NATIVE=off: Use native optimization (-march=native)
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mashmap/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mashmap/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/mashmap/work/.cache HOME=/wrkdirs/usr/ports/biology/mashmap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mashmap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/mashmap/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--
NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mashmap/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mashmap/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/mashmap/work/.cache HOME=/wrkdirs/usr/ports/biology/mashmap/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mashmap/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/mashmap/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 DESTDIR=/wrkdirs/usr/ports/biology/mashmap/work/stage 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 -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include
-fno-strict-aliasing -isystem /usr/local/include " MANPREFIX="/usr/local" 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--
CMAKE_BUILD_TYPE="release" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/mashmap" EXAMPLESDIR="share/examples/mashmap" DATADIR="share/mashmap" WWWDIR="www/mashmap" ETCDIR="etc/mashmap"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/mashmap DOCSDIR=/usr/local/share/doc/mashmap EXAMPLESDIR=/usr/local/share/examples/mashmap WWWDIR=/usr/local/www/mashmap ETCDIR=/usr/local/etc/mashmap
--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
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License PD accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> mashmap-3.1.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.8.pkg
[140releng-armv7-quarterly-job-05] Installing pkg-1.20.8...
[140releng-armv7-quarterly-job-05] Extracting pkg-1.20.8: .......... done
===> mashmap-3.1.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of mashmap-3.1.1
===========================================================================
=======================<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 PD accepted by the user
===> Fetching all distfiles required by mashmap-3.1.1 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License PD accepted by the user
===> Fetching all distfiles required by mashmap-3.1.1 for building
=> SHA256 Checksum OK for marbl-MashMap-v3.1.1_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 PD accepted by the user
===> Fetching all distfiles required by mashmap-3.1.1 for building
===> Extracting for mashmap-3.1.1
=> SHA256 Checksum OK for marbl-MashMap-v3.1.1_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 mashmap-3.1.1
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> mashmap-3.1.1 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.26.1_3.pkg
[140releng-armv7-quarterly-job-05] Installing cmake-core-3.26.1_3...
[140releng-armv7-quarterly-job-05] `-- Installing expat-2.5.0...
[140releng-armv7-quarterly-job-05] `-- Extracting expat-2.5.0: .......... done
[140releng-armv7-quarterly-job-05] `-- Installing jsoncpp-1.9.5...
[140releng-armv7-quarterly-job-05] `-- Extracting jsoncpp-1.9.5: .......... done
[140releng-armv7-quarterly-job-05] `-- Installing libuv-1.46.0...
[140releng-armv7-quarterly-job-05] `-- Extracting libuv-1.46.0: .......... done
[140releng-armv7-quarterly-job-05] `-- Installing rhash-1.4.4...
[140releng-armv7-quarterly-job-05] | `-- Installing gettext-runtime-0.22_1...
[140releng-armv7-quarterly-job-05] | | `-- Installing indexinfo-0.3.1...
[140releng-armv7-quarterly-job-05] | | `-- Extracting indexinfo-0.3.1: .... done
[140releng-armv7-quarterly-job-05] | `-- Extracting gettext-runtime-0.22_1: .......... done
[140releng-armv7-quarterly-job-05] `-- Extracting rhash-1.4.4: .......... done
[140releng-armv7-quarterly-job-05] Extracting cmake-core-3.26.1_3: .......... done
===> mashmap-3.1.1 depends on file: /usr/local/bin/cmake - found
===> Returning to build of mashmap-3.1.1
===> mashmap-3.1.1 depends on executable: ninja - not found
===> Installing existing package /packages/All/ninja-1.11.1,2.pkg
[140releng-armv7-quarterly-job-05] Installing ninja-1.11.1,2...
[140releng-armv7-quarterly-job-05] `-- Installing python39-3.9.18...
[140releng-armv7-quarterly-job-05] | `-- Installing libffi-3.4.4...
[140releng-armv7-quarterly-job-05] | `-- Extracting libffi-3.4.4: .......... done
[140releng-armv7-quarterly-job-05] | `-- Installing mpdecimal-2.5.1...
[140releng-armv7-quarterly-job-05] | `-- Extracting mpdecimal-2.5.1: .......... done
[140releng-armv7-quarterly-job-05] | `-- Installing readline-8.2.1...
[140releng-armv7-quarterly-job-05] | `-- Extracting readline-8.2.1: .......... done
[140releng-armv7-quarterly-job-05] `-- Extracting python39-3.9.18: .......... done
[140releng-armv7-quarterly-job-05] Extracting ninja-1.11.1,2: ........ done
=====
Message from python39-3.9.18:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py39-gdbm databases/py-gdbm@py39
py39-sqlite3 databases/py-sqlite3@py39
py39-tkinter x11-toolkits/py-tkinter@py39
===> mashmap-3.1.1 depends on executable: ninja - found
===> Returning to build of mashmap-3.1.1
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> mashmap-3.1.1 depends on shared library: libgsl.so - not found
===> Installing existing package /packages/All/gsl-2.7.1.pkg
[140releng-armv7-quarterly-job-05] Installing gsl-2.7.1...
[140releng-armv7-quarterly-job-05] Extracting gsl-2.7.1: .......... done
===> mashmap-3.1.1 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so)
===> Returning to build of mashmap-3.1.1
===> mashmap-3.1.1 depends on shared library: libhts.so - not found
===> Installing existing package /packages/All/htslib-1.17.pkg
[140releng-armv7-quarterly-job-05] Installing htslib-1.17...
[140releng-armv7-quarterly-job-05] `-- Installing curl-8.4.0...
[140releng-armv7-quarterly-job-05] | `-- Installing libnghttp2-1.57.0...
[140releng-armv7-quarterly-job-05] | `-- Extracting libnghttp2-1.57.0: .......... done
[140releng-armv7-quarterly-job-05] | `-- Installing libpsl-0.21.2_3...
[140releng-armv7-quarterly-job-05] | | `-- Installing libidn2-2.3.4...
[140releng-armv7-quarterly-job-05] | | `-- Installing libunistring-1.1...
[140releng-armv7-quarterly-job-05] | | `-- Extracting libunistring-1.1: .......... done
[140releng-armv7-quarterly-job-05] | | `-- Extracting libidn2-2.3.4: .......... done
[140releng-armv7-quarterly-job-05] | `-- Extracting libpsl-0.21.2_3: .......... done
[140releng-armv7-quarterly-job-05] | `-- Installing libssh2-1.11.0,3...
[140releng-armv7-quarterly-job-05] | `-- Extracting libssh2-1.11.0,3: .......... done
[140releng-armv7-quarterly-job-05] `-- Extracting curl-8.4.0: .......... done
[140releng-armv7-quarterly-job-05] `-- Installing libdeflate-1.19...
[140releng-armv7-quarterly-job-05] `-- Extracting libdeflate-1.19: .......... done
[140releng-armv7-quarterly-job-05] Extracting htslib-1.17: .......... done
===> mashmap-3.1.1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
===> Returning to build of mashmap-3.1.1
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for mashmap-3.1.1
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/mashmap/work/.build
-- The C compiler identification is Clang 16.0.6
-- The CXX compiler identification is Clang 16.0.6
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- CMAKE_BUILD_TYPE: Release
-- Configuring done (0.9s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_COLOR_MAKEFILE
CMAKE_C_FLAGS_RELEASE
CMAKE_MODULE_LINKER_FLAGS
CMAKE_SHARED_LINKER_FLAGS
CMAKE_VERBOSE_MAKEFILE
FETCHCONTENT_FULLY_DISCONNECTED
THREADS_HAVE_PTHREAD_ARG
-- Build files have been written to: /wrkdirs/usr/ports/biology/mashmap/work/.build
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for mashmap-3.1.1
[ 16% 3/6] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap.dir/src/common/utils.cpp.o -MF CMakeFiles/mashmap.dir/src/common/utils.cpp.o.d -o CMakeFiles/mashmap.dir/src/common/utils.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common/utils.cpp
[ 33% 4/6] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap-align.dir/src/common/utils.cpp.o -MF CMakeFiles/mashmap-align.dir/src/common/utils.cpp.o.d -o CMakeFiles/mashmap-align.dir/src/common/utils.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common/utils.cpp
[ 50% 4/6] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o -MF CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o.d -o CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/map/mash_map.cpp
FAILED: CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o
/usr/bin/c++ -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o -MF CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o.d -o CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/map/mash_map.cpp
In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/map/mash_map.cpp:13:
In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/map/include/map_parameters.hpp:14:
/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common/ALeS.hpp:294:11: fatal error: unknown type name '__uint128_t'
typedef __uint128_t uint128_t;
^
1 error generated.
[ 66% 4/6] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap-align.dir/src/align/align.cpp.o -MF CMakeFiles/mashmap-align.dir/src/align/align.cpp.o.d -o CMakeFiles/mashmap-align.dir/src/align/align.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/align/align.cpp
FAILED: CMakeFiles/mashmap-align.dir/src/align/align.cpp.o
/usr/bin/c++ -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap-align.dir/src/align/align.cpp.o -MF CMakeFiles/mashmap-align.dir/src/align/align.cpp.o.d -o CMakeFiles/mashmap-align.dir/src/align/align.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/align/align.cpp
In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/align/align.cpp:18:
In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/align/include/parseCmdArgs.hpp:16:
In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/map/include/parseCmdArgs.hpp:16:
In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/map/include/map_parameters.hpp:14:
/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common/ALeS.hpp:294:11: fatal error: unknown type name '__uint128_t'
typedef __uint128_t uint128_t;
^
1 error generated.
ninja: build stopped: subcommand failed.
===> 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 in /usr/ports/biology/mashmap