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:     y...@freebsd.org
Last committer: y...@freebsd.org
Ident:          $FreeBSD: branches/2019Q4/biology/gatk/Makefile 507364 
2019-07-26 18:03:08Z yuri $
Log URL:        
http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/514178/logs/gatk-4.1.2.0.43.log
Build URL:      
http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=514178
Log:

=>> Building biology/gatk
build started at Thu Oct 10 11:10:11 UTC 2019
port directory: /usr/ports/biology/gatk
package name: gatk-4.1.2.0.43
building for: FreeBSD 120armv7-quarterly-job-04 12.0-RELEASE-p10 FreeBSD 
12.0-RELEASE-p10 1200086 arm
maintained by: y...@freebsd.org
Makefile ident:      $FreeBSD: branches/2019Q4/biology/gatk/Makefile 507364 
2019-07-26 18:03:08Z yuri $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300040
Jail OSVERSION: 1200086
Job Id: 04

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UNAME_r=12.0-RELEASE-p10
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---End Environment---

---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---

---Begin OPTIONS List---
---End OPTIONS List---

--MAINTAINER--
y...@freebsd.org
--End MAINTAINER--

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gatk/work  
XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gatk/work  
HOME=/wrkdirs/usr/ports/biology/gatk/work TMPDIR="/tmp" 
PATH=/wrkdirs/usr/ports/biology/gatk/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
 SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--

--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gatk/work  
XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gatk/work  
HOME=/wrkdirs/usr/ports/biology/gatk/work TMPDIR="/tmp" 
PATH=/wrkdirs/usr/ports/biology/gatk/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
 NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES 
PREFIX=/usr/local  LOCALBASE=/usr/local  CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 
-pipe  -fstack-protector-strong -fno-strict-aliasing "  
CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS=""  LDFLAGS=" -fstack-protector-strong " 
LIBS=""  CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe 
-fstack-protector-strong -fno-strict-aliasing  "  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--
JAVASHAREDIR="share/java"  JAVAJARDIR="share/java/classes" OSREL=12.0 PREFIX=%D 
LOCALBASE=/usr/local  RESETPREFIX=/usr/local LIB32DIR=lib 
DOCSDIR="share/doc/gatk"  EXAMPLESDIR="share/examples/gatk"  
DATADIR="share/gatk"  WWWDIR="www/gatk"  ETCDIR="etc/gatk"
--End PLIST_SUB--

--SUB_LIST--
PORTVERSION=4.1.2.0.43 JAVA=/usr/local/openjdk8/bin/java 
JAVASHAREDIR="/usr/local/share/java"  
JAVAJARDIR="/usr/local/share/java/classes"  
JAVALIBDIR="/usr/local/share/java/classes" PREFIX=/usr/local 
LOCALBASE=/usr/local  DATADIR=/usr/local/share/gatk 
DOCSDIR=/usr/local/share/doc/gatk EXAMPLESDIR=/usr/local/share/examples/gatk  
WWWDIR=/usr/local/www/gatk ETCDIR=/usr/local/etc/gatk
--End SUB_LIST--

---Begin make.conf---
.sinclude "/etc/make.nxb.conf"
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=arm
MACHINE_ARCH=armv7
ARCH=${MACHINE_ARCH}
#### /usr/local/etc/poudriere.d/make.conf ####
# 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 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) 
(based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: 
posix InstalledDir: /nxb-bin/usr/bin
_ALTCCVERSION_9d218390=none
_CXXINTERNAL_9c45a5b1=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 
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"--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" 
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"/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" 
"--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" 
"--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_9d218390_58173849=yes
CC_OUTPUT_9d218390_9bdba57c=yes
CC_OUTPUT_9d218390_6a4fe7f5=yes
CC_OUTPUT_9d218390_6bcac02b=yes
CC_OUTPUT_9d218390_67d20829=yes
CC_OUTPUT_9d218390_bfa62e83=yes
CC_OUTPUT_9d218390_f0b4d593=yes
CC_OUTPUT_9d218390_308abb44=yes
CC_OUTPUT_9d218390_f00456e5=yes
CC_OUTPUT_9d218390_65ad290d=yes
CC_OUTPUT_9d218390_f2776b26=yes
CC_OUTPUT_9d218390_b2657cc3=yes
CC_OUTPUT_9d218390_380987f7=yes
CC_OUTPUT_9d218390_160933ec=yes
CC_OUTPUT_9d218390_fb62803b=yes
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ARCH=armv7
OPSYS=FreeBSD
_OSRELEASE=12.0-RELEASE-p10
OSREL=12.0
OSVERSION=1200086
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=262144
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
---Begin make.nxb.conf---
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
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AS=/nxb-bin/usr/bin/as
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LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
---End make.nxb.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)  2048
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   >============================
===>  License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   gatk-4.1.2.0.43 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.12.0.txz
[120armv7-quarterly-job-04] Installing pkg-1.12.0...
[120armv7-quarterly-job-04] Extracting pkg-1.12.0: .......... done
===>   gatk-4.1.2.0.43 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of gatk-4.1.2.0.43
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.1.2.0.43 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.1.2.0.43 for building
=> SHA256 Checksum OK for gatk-4.1.2.0-43-deps.tar.gz.
=> SHA256 Checksum OK for broadinstitute-gatk-4.1.2.0-43-g1f31a805b_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by gatk-4.1.2.0.43 for building
===>  Extracting for gatk-4.1.2.0.43
=> SHA256 Checksum OK for gatk-4.1.2.0-43-deps.tar.gz.
=> SHA256 Checksum OK for broadinstitute-gatk-4.1.2.0-43-g1f31a805b_GH0.tar.gz.
<snip>
=======================<phase: patch          >============================
===>  Patching for gatk-4.1.2.0.43
===>  Applying FreeBSD patches for gatk-4.1.2.0.43
===========================================================================
=======================<phase: build-depends  >============================
===>   gatk-4.1.2.0.43 depends on executable: gradle - not found
===>   Installing existing package /packages/All/gradle-5.0.txz
[120armv7-quarterly-job-04] Installing gradle-5.0...
[120armv7-quarterly-job-04] `-- Installing openjdk8-8.222.10.1_2...
[120armv7-quarterly-job-04] |   `-- Installing alsa-lib-1.1.2_2...
[120armv7-quarterly-job-04] |   `-- Extracting alsa-lib-1.1.2_2: .......... done
[120armv7-quarterly-job-04] |   `-- Installing dejavu-2.37_1...
[120armv7-quarterly-job-04] |   | `-- Installing fontconfig-2.12.6,1...
[120armv7-quarterly-job-04] |   |   `-- Installing expat-2.2.8...
[120armv7-quarterly-job-04] |   |   `-- Extracting expat-2.2.8: .......... done
[120armv7-quarterly-job-04] |   |   `-- Installing freetype2-2.10.1...
[120armv7-quarterly-job-04] |   |   `-- Extracting freetype2-2.10.1: .......... 
done
[120armv7-quarterly-job-04] |   | `-- Extracting fontconfig-2.12.6,1: 
.......... done
Running fc-cache to build fontconfig cache...
/usr/local/share/fonts: skipping, no such directory
/usr/local/lib/X11/fonts: skipping, no such directory
/var/db/fontconfig: cleaning cache directory
fc-cache: succeeded
[120armv7-quarterly-job-04] |   | `-- Installing mkfontscale-1.2.1...
[120armv7-quarterly-job-04] |   |   `-- Installing libfontenc-1.1.4...
[120armv7-quarterly-job-04] |   |   `-- Extracting libfontenc-1.1.4: ......... 
done
[120armv7-quarterly-job-04] |   | `-- Extracting mkfontscale-1.2.1: ....... done
[120armv7-quarterly-job-04] |   `-- Extracting dejavu-2.37_1: .......... done
[120armv7-quarterly-job-04] |   `-- Installing giflib-5.1.9...
[120armv7-quarterly-job-04] |   `-- Extracting giflib-5.1.9: .......... done
[120armv7-quarterly-job-04] |   `-- Installing java-zoneinfo-2019.b...
[120armv7-quarterly-job-04] |   `-- Extracting java-zoneinfo-2019.b: .......... 
done
[120armv7-quarterly-job-04] |   `-- Installing javavmwrapper-2.7.3...
[120armv7-quarterly-job-04] |   `-- Extracting javavmwrapper-2.7.3: .......... 
done
[120armv7-quarterly-job-04] |   `-- Installing libX11-1.6.8,1...
[120armv7-quarterly-job-04] |   | `-- Installing libXau-1.0.9...
[120armv7-quarterly-job-04] |   | `-- Extracting libXau-1.0.9: .......... done
[120armv7-quarterly-job-04] |   | `-- Installing libXdmcp-1.1.3...
[120armv7-quarterly-job-04] |   |   `-- Installing xorgproto-2019.1...
[120armv7-quarterly-job-04] |   |   `-- Extracting xorgproto-2019.1: .......... 
done
[120armv7-quarterly-job-04] |   | `-- Extracting libXdmcp-1.1.3: ......... done
[120armv7-quarterly-job-04] |   | `-- Installing libxcb-1.13.1...
[120armv7-quarterly-job-04] |   |   `-- Installing libpthread-stubs-0.4...
[120armv7-quarterly-job-04] |   |   `-- Extracting libpthread-stubs-0.4: .... 
done
[120armv7-quarterly-job-04] |   |   `-- Installing libxml2-2.9.9...
[120armv7-quarterly-job-04] |   |   `-- Extracting libxml2-2.9.9: .......... 
done
[120armv7-quarterly-job-04] |   | `-- Extracting libxcb-1.13.1: .......... done
[120armv7-quarterly-job-04] |   `-- Extracting libX11-1.6.8,1: .......... done
[120armv7-quarterly-job-04] |   `-- Installing libXext-1.3.4,1...
[120armv7-quarterly-job-04] |   `-- Extracting libXext-1.3.4,1: .......... done
[120armv7-quarterly-job-04] |   `-- Installing libXi-1.7.10,1...
[120armv7-quarterly-job-04] |   | `-- Installing libXfixes-5.0.3_2...
[120armv7-quarterly-job-04] |   | `-- Extracting libXfixes-5.0.3_2: .......... 
done
[120armv7-quarterly-job-04] |   `-- Extracting libXi-1.7.10,1: .......... done
[120armv7-quarterly-job-04] |   `-- Installing libXrender-0.9.10_2...
[120armv7-quarterly-job-04] |   `-- Extracting libXrender-0.9.10_2: .......... 
done
[120armv7-quarterly-job-04] |   `-- Installing libXt-1.2.0,1...
[120armv7-quarterly-job-04] |   | `-- Installing libICE-1.0.10,1...
[120armv7-quarterly-job-04] |   | `-- Extracting libICE-1.0.10,1: .......... 
done
[120armv7-quarterly-job-04] |   | `-- Installing libSM-1.2.3,1...
[120armv7-quarterly-job-04] |   | `-- Extracting libSM-1.2.3,1: .......... done
[120armv7-quarterly-job-04] |   `-- Extracting libXt-1.2.0,1: .......... done
[120armv7-quarterly-job-04] |   `-- Installing libXtst-1.2.3_2...
[120armv7-quarterly-job-04] |   `-- Extracting libXtst-1.2.3_2: .......... done
[120armv7-quarterly-job-04] |   `-- Installing libffi-3.2.1_3...
[120armv7-quarterly-job-04] |   | `-- Installing indexinfo-0.3.1...
[120armv7-quarterly-job-04] |   | `-- Extracting indexinfo-0.3.1: .... done
[120armv7-quarterly-job-04] |   `-- Extracting libffi-3.2.1_3: .......... done
[120armv7-quarterly-job-04] |   `-- Installing libinotify-20180201_1...
[120armv7-quarterly-job-04] |   `-- Extracting libinotify-20180201_1: 
.......... done
[120armv7-quarterly-job-04] `-- Extracting openjdk8-8.222.10.1_2: .......... 
done
[120armv7-quarterly-job-04] Extracting gradle-5.0: .......... done
=====
Message from freetype2-2.10.1:

--
The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as
the default, emulating a modern version of ClearType. This change inevitably
leads to different rendering results, and you might change port's options to
adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment
variable).

The environment variable "FREETYPE_PROPERTIES" can be used to control the
driver properties. Example:

FREETYPE_PROPERTIES=truetype:interpreter-version=35 \
        cff:no-stem-darkening=1 \
        autofitter:warping=1

This allows to select, say, the subpixel hinting mode at runtime for a given
application.

If LONG_PCF_NAMES port's option was enabled, the PCF family names may include
the foundry and information whether they contain wide characters. For example,
"Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at
run time with using pcf:no-long-family-names property, if needed. Example:

FREETYPE_PROPERTIES=pcf:no-long-family-names=1

How to recreate fontconfig cache with using such environment variable,
if needed:
# env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv

The controllable properties are listed in the section "Controlling FreeType
Modules" in the reference's table of contents
(/usr/local/share/doc/freetype2/reference/site/index.html, if documentation was 
installed).
=====
Message from dejavu-2.37_1:

--
Make sure that the freetype module is loaded.  If it is not, add the following
line to the "Modules" section of your X Windows configuration file:

        Load "freetype"

Add the following line to the "Files" section of X Windows configuration file:

        FontPath "/usr/local/share/fonts/dejavu/"

Note: your X Windows configuration file is typically /etc/X11/XF86Config
if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org.
=====
Message from libinotify-20180201_1:

--
============================================================================

Libinotify functionality on FreeBSD is missing support for

  - detecting a file being moved into or out of a directory within the
    same filesystem
  - certain modifications to a symbolic link (rather than the
    file it points to.)

in addition to the known limitations on all platforms using kqueue(2)
where various open and close notifications are unimplemented.

This means the following regression tests will fail:

Directory notifications:
   IN_MOVED_FROM
   IN_MOVED_TO

Open/close notifications:
   IN_OPEN
   IN_CLOSE_NOWRITE
   IN_CLOSE_WRITE

Symbolic Link notifications:
   IN_DONT_FOLLOW
   IN_ATTRIB
   IN_MOVE_SELF
   IN_DELETE_SELF

Kernel patches to address the missing directory and symbolic link
notifications are available from:

https://github.com/libinotify-kqueue/libinotify-kqueue/tree/master/patches

=============================================================================
You might want to consider increasing the kern.maxfiles tunable if you plan
to use this library for applications that need to monitor activity of a lot
of files.
=============================================================================
=====
Message from openjdk8-8.222.10.1_2:

--
This OpenJDK implementation requires fdescfs(5) mounted on /dev/fd

If you have not done it yet, please do the following:

        mount -t fdescfs fdesc /dev/fd

To make it permanent, you need the following lines in /etc/fstab:

        fdesc   /dev/fd         fdescfs         rw      0       0
===>   gatk-4.1.2.0.43 depends on executable: gradle - found
===>   Returning to build of gatk-4.1.2.0.43
===>   gatk-4.1.2.0.43 depends on file: /usr/local/openjdk8/bin/java - found
===========================================================================
=======================<phase: lib-depends    >============================
===>   gatk-4.1.2.0.43 depends on shared library: libintl.so - not found
===>   Installing existing package /packages/All/gettext-runtime-0.20.1.txz
[120armv7-quarterly-job-04] Installing gettext-runtime-0.20.1...
[120armv7-quarterly-job-04] Extracting gettext-runtime-0.20.1: .......... done
===>   gatk-4.1.2.0.43 depends on shared library: libintl.so - found 
(/usr/local/lib/libintl.so)
===>   Returning to build of gatk-4.1.2.0.43
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for gatk-4.1.2.0.43
===========================================================================
=======================<phase: build          >============================
===>  Building for gatk-4.1.2.0.43
Starting a Gradle Daemon, 1 incompatible and 1 stopped Daemons could not be 
reused, use --status for details
> Task :compileJava
> Task :processResources
> Task :classes
> Task :shadowJar
=>> Killing runaway build after 21600 seconds with no output
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