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Date:      Thu, 2 Aug 2018 15:29:52 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - head-armv6-default][biology/primer3] Failed for primer3-2.3.6 in build
Message-ID:  <201808021529.w72FTqGX007081@beefy8.nyi.freebsd.org>

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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:     ports@FreeBSD.org
Last committer: tijl@FreeBSD.org
Ident:          $FreeBSD: head/biology/primer3/Makefile 354670 2014-05-20 19:32:39Z tijl $
Log URL:        http://beefy8.nyi.freebsd.org/data/head-armv6-default/p476207_s337063/logs/primer3-2.3.6.log
Build URL:      http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p476207_s337063
Log:

=>> Building biology/primer3
build started at Thu Aug  2 15:29:31 UTC 2018
port directory: /usr/ports/biology/primer3
package name: primer3-2.3.6
building for: FreeBSD head-armv6-default-job-13 12.0-CURRENT FreeBSD 12.0-CURRENT 1200076 arm
maintained by: ports@FreeBSD.org
Makefile ident:      $FreeBSD: head/biology/primer3/Makefile 354670 2014-05-20 19:32:39Z tijl $
Poudriere version: 3.2.7-2-g1cf194be
Host OSVERSION: 1200069
Jail OSVERSION: 1200076
Job Id: 13




!!! Jail is newer than host. (Jail: 1200076, Host: 1200069) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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---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--
ports@FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/primer3/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/primer3/work  HOME=/wrkdirs/usr/ports/biology/primer3/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/primer3/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/primer3/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/primer3/work  HOME=/wrkdirs/usr/ports/biology/primer3/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/primer3/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  -fno-strict-aliasing"  CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS=""  LDFLAGS="" LIBS=""  CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -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--
PORTDOCS="" PORTEXAMPLES="" OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/primer3"  EXAMPLESDIR="share/examples/primer3"  DATADIR="share/primer3"  WWWDIR="www/primer3"  ETCDIR="etc/primer3"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/primer3 DOCSDIR=/usr/local/share/doc/primer3 EXAMPLESDIR=/usr/local/share/examples/primer3  WWWDIR=/usr/local/www/primer3 ETCDIR=/usr/local/etc/primer3
--End SUB_LIST--

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USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
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MACHINE=arm
MACHINE_ARCH=armv6
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

# stable/10 includes src.conf too late but make.conf is in sys.mk
.if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*}
# Disable build of llib now that head no longer has lint(1)
LINT=	true
.endif
#### /usr/ports/Mk/Scripts/ports_env.sh ####
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CC_OUTPUT_9d218390_58173849=yes
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CC_OUTPUT_9d218390_67d20829=yes
CC_OUTPUT_9d218390_bfa62e83=yes
CC_OUTPUT_9d218390_f0b4d593=yes
CC_OUTPUT_9d218390_308abb44=yes
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CC_OUTPUT_9d218390_65ad290d=yes
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CC_OUTPUT_9d218390_380987f7=yes
CC_OUTPUT_9d218390_160933ec=yes
CC_OUTPUT_9d218390_fb62803b=yes
_OBJC_CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv6-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin
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#### Misc Poudriere ####
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CC=/nxb-bin/usr/bin/cc
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core file size      (512-blocks, -c)  unlimited
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--End resource limits--
=======================<phase: check-sanity   >============================
===>   NOTICE:

The primer3 port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port

===>  License GPLv2 accepted by the user
===========================================================================
<snip>
[head-armv6-default-job-13] `-- Installing gettext-runtime-0.19.8.1_1...
[head-armv6-default-job-13] |   `-- Installing indexinfo-0.3.1...
[head-armv6-default-job-13] |   `-- Extracting indexinfo-0.3.1: .... done
[head-armv6-default-job-13] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done
[head-armv6-default-job-13] Extracting gmake-4.2.1_2: .......... done
===>   primer3-2.3.6 depends on executable: gmake - found
===>   Returning to build of primer3-2.3.6
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for primer3-2.3.6
===========================================================================
=======================<phase: build          >============================
===>  Building for primer3-2.3.6
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/primer3/work/primer3-2.3.6/src'
/nxb-bin/usr/bin/c++ -c -O2 -pipe  -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__  primer3_boulder_main.c
c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
/nxb-bin/usr/bin/c++ -c -O2 -pipe  -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__  -o format_output.o format_output.c
c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
format_output.c:418:48: warning: comparison of address of 'retval->rev' not equal to a null pointer is always true [-Wtautological-pointer-compare]
            if (pa->pick_right_primer && &retval->rev != NULL 
                                          ~~~~~~~~^~~    ~~~~
format_output.c:429:47: warning: comparison of address of 'retval->fwd' not equal to a null pointer is always true [-Wtautological-pointer-compare]
            if (pa->pick_left_primer && &retval->fwd != NULL 
                                         ~~~~~~~~^~~    ~~~~
format_output.c:851:45: warning: comparison of address of 'retval->fwd' not equal to a null pointer is always true [-Wtautological-pointer-compare]
    if ((pa->pick_left_primer) && (&retval->fwd != NULL )
                                    ~~~~~~~~^~~    ~~~~
format_output.c:858:48: warning: comparison of address of 'retval->intl' not equal to a null pointer is always true [-Wtautological-pointer-compare]
    if ((pa->pick_internal_oligo) && (&retval->intl != NULL )
                                       ~~~~~~~~^~~~    ~~~~
format_output.c:865:46: warning: comparison of address of 'retval->rev' not equal to a null pointer is always true [-Wtautological-pointer-compare]
    if ((pa->pick_right_primer) && (&retval->rev != NULL )
                                     ~~~~~~~~^~~    ~~~~
format_output.c:888:43: warning: comparison of address of 'retval->fwd' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  if ((pa->pick_left_primer) && (&retval->fwd != NULL )
                                  ~~~~~~~~^~~    ~~~~
format_output.c:907:46: warning: comparison of address of 'retval->intl' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  if ((pa->pick_internal_oligo) && (&retval->intl != NULL )
                                     ~~~~~~~~^~~~    ~~~~
format_output.c:926:44: warning: comparison of address of 'retval->rev' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  if ((pa->pick_right_primer) && (&retval->rev != NULL )
                                   ~~~~~~~~^~~    ~~~~
8 warnings generated.
/nxb-bin/usr/bin/c++ -c -O2 -pipe  -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__  -o read_boulder.o read_boulder.c
c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
/nxb-bin/usr/bin/c++ -c -O2 -pipe  -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__  -o print_boulder.o print_boulder.c
c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
/nxb-bin/usr/bin/c++ -c -O2 -pipe  -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -Wno-deprecated  -o libprimer3.o libprimer3.c
/nxb-bin/usr/bin/c++ -c -O2 -pipe  -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o p3_seq_lib.o p3_seq_lib.c
c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
ar rv libprimer3.a libprimer3.o p3_seq_lib.o
ar: warning: creating libprimer3.a
a - libprimer3.o
a - p3_seq_lib.o
ranlib libprimer3.a
/nxb-bin/usr/bin/c++ -c -O2 -pipe  -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__  -o dpal_primer.o dpal.c
c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
dpal.c:368:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i, j, k, mg, c;
    ^~~~~~~~~
dpal.c:368:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i, j, k, mg, c;
    ^~~~~~~~~
dpal.c:368:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i, j, k, mg, c;
    ^~~~~~~~~
dpal.c:368:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i, j, k, mg, c;
    ^~~~~~~~~
dpal.c:368:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i, j, k, mg, c;
    ^~~~~~~~~
dpal.c:369:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
    ^~~~~~~~~
dpal.c:369:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
    ^~~~~~~~~
dpal.c:369:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
    ^~~~~~~~~
dpal.c:594:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i, j, k, mg, mgy, c;
    ^~~~~~~~~
dpal.c:594:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i, j, k, mg, mgy, c;
    ^~~~~~~~~
dpal.c:594:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i, j, k, mg, mgy, c;
    ^~~~~~~~~
dpal.c:594:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i, j, k, mg, mgy, c;
    ^~~~~~~~~
dpal.c:594:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i, j, k, mg, mgy, c;
    ^~~~~~~~~
dpal.c:594:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i, j, k, mg, mgy, c;
    ^~~~~~~~~
dpal.c:595:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
    ^~~~~~~~~
dpal.c:595:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
    ^~~~~~~~~
dpal.c:595:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
    ^~~~~~~~~
dpal.c:760:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i, j;
    ^~~~~~~~~
dpal.c:760:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int i, j;
    ^~~~~~~~~
dpal.c:761:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int gap = in->gap;
    ^~~~~~~~~
dpal.c:762:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int smax;           /* The optimum score. */
    ^~~~~~~~~
dpal.c:763:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int score;          /* Current score. */
    ^~~~~~~~~
dpal.c:764:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
    register int a;
    ^~~~~~~~~
dpal.c:852:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int i, j, k;
  ^~~~~~~~~
dpal.c:852:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int i, j, k;
  ^~~~~~~~~
dpal.c:852:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int i, j, k;
  ^~~~~~~~~
dpal.c:853:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int gap = in->gap;
  ^~~~~~~~~
dpal.c:854:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int smax;           /* The optimum score. */
  ^~~~~~~~~
dpal.c:855:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int score;          /* Current score. */
  ^~~~~~~~~
dpal.c:856:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int a, t;
  ^~~~~~~~~
dpal.c:856:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int a, t;
  ^~~~~~~~~
dpal.c:1049:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register const unsigned char *p;
  ^~~~~~~~~
dpal.c:1072:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int i, j;
  ^~~~~~~~~
dpal.c:1072:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int i, j;
  ^~~~~~~~~
dpal.c:1073:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int gap = in->gap;
  ^~~~~~~~~
dpal.c:1074:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int smax;           /* The optimum score. */
  ^~~~~~~~~
dpal.c:1075:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int score;          /* Current score. */
  ^~~~~~~~~
dpal.c:1076:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  register int a;
  ^~~~~~~~~
38 warnings generated.
ar rv libdpal.a dpal_primer.o
ar: warning: creating libdpal.a
a - dpal_primer.o
ranlib libdpal.a
/nxb-bin/usr/bin/c++ -c -O2 -pipe  -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -ffloat-store  -o thal_primer.o thal.c
c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
c++: warning: optimization flag '-ffloat-store' is not supported [-Wignored-optimization-argument]
thal.c:426:13: error: comparison between pointer and integer ('int' and 'const unsigned char *')
   if ('\0' == oligo_f) {
       ~~~~ ^  ~~~~~~~
thal.c:431:13: error: comparison between pointer and integer ('int' and 'const unsigned char *')
   if ('\0' == oligo_r) {
       ~~~~ ^  ~~~~~~~
thal.c:2407:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
   register char s;
   ^~~~~~~~~
thal.c:2408:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
   register char e;
   ^~~~~~~~~
2 warnings and 2 errors generated.
gmake[1]: *** [Makefile:192: thal_primer.o] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/primer3/work/primer3-2.3.6/src'
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/primer3



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