[package - main-amd64-default][biology/primer3] Failed for primer3-2.3.6 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Sat, 24 Jun 2023 21:29:22 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:     ports@FreeBSD.org
Log URL:        https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/p4785b313b958_se8efee297c/logs/primer3-2.3.6.log
Build URL:      https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p4785b313b958_se8efee297c
Log:

=>> Building biology/primer3
build started at Sat Jun 24 21:29:15 UTC 2023
port directory: /usr/ports/biology/primer3
package name: primer3-2.3.6
building for: FreeBSD main-amd64-default-job-09 14.0-CURRENT FreeBSD 14.0-CURRENT 1400091 amd64
maintained by: ports@FreeBSD.org
Makefile ident: 
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400089
Jail OSVERSION: 1400091
Job Id: 09




!!! Jail is newer than host. (Jail: 1400091, Host: 1400089) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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=======================<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://docs.freebsd.org/en/articles/contributing/#ports-contributing

===>  License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   primer3-2.3.6 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.19.1_1.pkg
[main-amd64-default-job-09] Installing pkg-1.19.1_1...
[main-amd64-default-job-09] Extracting pkg-1.19.1_1: .......... done
===>   primer3-2.3.6 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of primer3-2.3.6
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>   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://docs.freebsd.org/en/articles/contributing/#ports-contributing

===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by primer3-2.3.6 for building
===========================================================================
=======================<phase: checksum       >============================
===>   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://docs.freebsd.org/en/articles/contributing/#ports-contributing

===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by primer3-2.3.6 for building
=> SHA256 Checksum OK for primer3-src-2.3.6.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>   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://docs.freebsd.org/en/articles/contributing/#ports-contributing

===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by primer3-2.3.6 for building
===>  Extracting for primer3-2.3.6
=> SHA256 Checksum OK for primer3-src-2.3.6.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for primer3-2.3.6
===>  Applying FreeBSD patches for primer3-2.3.6 from /usr/ports/biology/primer3/files
===========================================================================
=======================<phase: build-depends  >============================
===>   primer3-2.3.6 depends on package: gmake>=4.3 - not found
===>   Installing existing package /packages/All/gmake-4.3_2.pkg
[main-amd64-default-job-09] Installing gmake-4.3_2...
[main-amd64-default-job-09] `-- Installing gettext-runtime-0.21.1...
[main-amd64-default-job-09] |   `-- Installing indexinfo-0.3.1...
[main-amd64-default-job-09] |   `-- Extracting indexinfo-0.3.1: .... done
[main-amd64-default-job-09] `-- Extracting gettext-runtime-0.21.1: .......... done
[main-amd64-default-job-09] Extracting gmake-4.3_2: .......... done
===>   primer3-2.3.6 depends on package: gmake>=4.3 - 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'
c++ -c -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -g -Wall -D__USE_FIXED_PROTOTYPES__  primer3_boulder_main.c
c++ -c -O2 -pipe  -fstack-protector-strong -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]
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 )
                                   ~~~~~~~~^~~    ~~~~
c++ -c -O2 -pipe  -fstack-protector-strong -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]
8 warnings generated.
c++ -c -O2 -pipe  -fstack-protector-strong -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]
c++ -c -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -g -Wall -D__USE_FIXED_PROTOTYPES__ -Wno-deprecated  -o libprimer3.o libprimer3.c
c++ -c -O2 -pipe  -fstack-protector-strong -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]
c++ -c -O2 -pipe  -fstack-protector-strong -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: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int i, j, k, mg, c;
    ^~~~~~~~~
dpal.c:368:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int i, j, k, mg, c;
    ^~~~~~~~~
dpal.c:368:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int i, j, k, mg, c;
    ^~~~~~~~~
dpal.c:368:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int i, j, k, mg, c;
    ^~~~~~~~~
dpal.c:368:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int i, j, k, mg, c;
    ^~~~~~~~~
dpal.c:369:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
    ^~~~~~~~~
dpal.c:369:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
    ^~~~~~~~~
dpal.c:369:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
    ^~~~~~~~~
dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int i, j, k, mg, mgy, c;
    ^~~~~~~~~
dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int i, j, k, mg, mgy, c;
    ^~~~~~~~~
dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int i, j, k, mg, mgy, c;
    ^~~~~~~~~
dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int i, j, k, mg, mgy, c;
    ^~~~~~~~~
dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int i, j, k, mg, mgy, c;
    ^~~~~~~~~
dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int i, j, k, mg, mgy, c;
    ^~~~~~~~~
dpal.c:595:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
    ^~~~~~~~~
dpal.c:595:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
    ^~~~~~~~~
dpal.c:595:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap;
    ^~~~~~~~~
dpal.c:760:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int i, j;
    ^~~~~~~~~
dpal.c:760:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
    register int i, j;
    ^~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
gmake[1]: *** [Makefile:189: dpal_primer.o] Error 1
gmake[1]: *** Waiting for unfinished jobs....
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/primer3/work/primer3-2.3.6/src'
===> 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/primer3