-------------------------------------------------------------------------------
-- Phase: setup
-------------------------------------------------------------------------------

Installing /packages/All/indexinfo-0.3.1.txz
Installing /packages/All/gettext-runtime-0.21.txz
Installing /packages/All/gmake-4.3_2.txz

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- 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


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: pkg-depends
-------------------------------------------------------------------------------

===>   primer3-2.3.6 depends on file: /usr/local/sbin/pkg - found

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: fetch-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

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

===>   primer3-2.3.6 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by primer3-2.3.6 for building

SUCCEEDED 00:00:00

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

===>   primer3-2.3.6 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by primer3-2.3.6 for building
=> SHA256 Checksum OK for primer3-src-2.3.6.tar.gz.

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: extract-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

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

===>   primer3-2.3.6 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by primer3-2.3.6 for building
===>  Extracting for primer3-2.3.6
===>   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

===>   primer3-2.3.6 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by primer3-2.3.6 for building
=> SHA256 Checksum OK for primer3-src-2.3.6.tar.gz.

Extracted Memory Use:  12.11M
SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: patch-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: patch
-------------------------------------------------------------------------------

===>  Patching for primer3-2.3.6
===>  Applying ports patches for primer3-2.3.6 from /xports/biology/primer3/files

SUCCEEDED 00:00:01

-------------------------------------------------------------------------------
-- Phase: build-depends
-------------------------------------------------------------------------------

===>   primer3-2.3.6 depends on package: gmake>=4.3 - found

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: lib-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: configure
-------------------------------------------------------------------------------

===>   primer3-2.3.6 depends on package: gmake>=4.3 - found
===>  Configuring for primer3-2.3.6

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: build
-------------------------------------------------------------------------------

===>  Building for primer3-2.3.6
gmake[2]: Entering directory '/construction/biology/primer3/primer3-2.3.6/src'
c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing  -g -Wall -D__USE_FIXED_PROTOTYPES__  primer3_boulder_main.c
c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing  -g -Wall -D__USE_FIXED_PROTOTYPES__  -o format_output.o format_output.c
c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing  -g -Wall -D__USE_FIXED_PROTOTYPES__  -o read_boulder.o read_boulder.c
c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing  -g -Wall -D__USE_FIXED_PROTOTYPES__  -o print_boulder.o print_boulder.c
c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing  -g -Wall -D__USE_FIXED_PROTOTYPES__ -Wno-deprecated  -o libprimer3.o libprimer3.c
c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing  -g -Wall -D__USE_FIXED_PROTOTYPES__ -o p3_seq_lib.o p3_seq_lib.c
c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing  -g -Wall -D__USE_FIXED_PROTOTYPES__  -o dpal_primer.o dpal.c
c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing  -g -Wall -D__USE_FIXED_PROTOTYPES__ -ffloat-store  -o thal_primer.o thal.c
cc -pipe -fpermissive -O2 -fno-strict-aliasing  -g -Wall -D__USE_FIXED_PROTOTYPES__   -c -o oligotm.o oligotm.c
c++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -o ntdpal_main.o ntdpal_main.c
cc1: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C
oligotm.c: In function 'oligotm':
oligotm.c:424:44: warning: comparison between pointer and zero character constant [-Wpointer-compare]
      for(i = 0; i <= len && d != NULL && d != '\0';) {
                                            ^~
oligotm.c:424:42: note: did you mean to dereference the pointer?
      for(i = 0; i <= len && d != NULL && d != '\0';) {
                                          ^
ntdpal_main.c: In function 'int main(int, const char**)':
ntdpal_main.c:49:9: warning: variable 'tmp_ret' set but not used [-Wunused-but-set-variable]
     int tmp_ret;
         ^~~~~~~
dpal.c: In function 'void print_align(const unsigned char*, const unsigned char*, int (*)[1600][3], int, int, const dpal_args*)':
dpal.c:1036:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
     for(i=j;i<j+70;i++) fprintf(stderr, "%c",sy[i]); fprintf(stderr,"\n");
     ^~~
dpal.c:1036:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
     for(i=j;i<j+70;i++) fprintf(stderr, "%c",sy[i]); fprintf(stderr,"\n");
                                                      ^~~~~~~
c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing  -g -Wall -D__USE_FIXED_PROTOTYPES__ -o dpal.o dpal.c
thal.c: In function 'void tableStartATS(double, double (*)[5])':
thal.c:1198:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
    for (i = 0; i < 5; ++i)
    ^~~
thal.c:1201:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
      atpS[0][3] = atpS[3][0] = atp_value;
      ^~~~
thal.c: In function 'void tableStartATH(double, double (*)[5])':
thal.c:1210:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
    for (i = 0; i < 5; ++i)
    ^~~
thal.c:1214:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
      atpH[0][3] = atpH[3][0] = atp_value;
      ^~~~
c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing  -g -Wall -D__USE_FIXED_PROTOTYPES__ -o thal_main.o thal_main.c
dpal.c: In function 'void print_align(const unsigned char*, const unsigned char*, int (*)[1600][3], int, int, const dpal_args*)':
dpal.c:1036:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
     for(i=j;i<j+70;i++) fprintf(stderr, "%c",sy[i]); fprintf(stderr,"\n");
     ^~~
dpal.c:1036:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
     for(i=j;i<j+70;i++) fprintf(stderr, "%c",sy[i]); fprintf(stderr,"\n");
                                                      ^~~~~~~
c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing  -g -Wall -D__USE_FIXED_PROTOTYPES__ -ffloat-store -o thal.o thal.c
thal.c: In function 'void tableStartATS(double, double (*)[5])':
thal.c:1198:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
    for (i = 0; i < 5; ++i)
    ^~~
thal.c:1201:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
      atpS[0][3] = atpS[3][0] = atp_value;
      ^~~~
thal.c: In function 'void tableStartATH(double, double (*)[5])':
thal.c:1210:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
    for (i = 0; i < 5; ++i)
    ^~~
thal.c:1214:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
      atpH[0][3] = atpH[3][0] = atp_value;
      ^~~~
ar rv liboligotm.a oligotm.o
c++ -pipe -fpermissive -O2 -fno-strict-aliasing  -g -Wall -D__USE_FIXED_PROTOTYPES__ -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o  -lm
/usr/libexec/binutils227/elf/ar: creating liboligotm.a
a - oligotm.o
ranlib liboligotm.a
c++ -pipe -fpermissive -O2 -fno-strict-aliasing  -g -Wall -D__USE_FIXED_PROTOTYPES__ -o oligotm oligotm_main.c liboligotm.a  -lm
ar rv libdpal.a dpal_primer.o
/usr/libexec/binutils227/elf/ar: creating libdpal.a
a - dpal_primer.o
ranlib libdpal.a
c++   -o ntdpal ntdpal_main.o dpal.o
c++   -o ntthal thal_main.o thal.o -lm
ar rv libthal.a thal_primer.o
/usr/libexec/binutils227/elf/ar: creating libthal.a
a - thal_primer.o
ranlib libthal.a
ar rv libprimer3.a libprimer3.o p3_seq_lib.o
/usr/libexec/binutils227/elf/ar: creating libprimer3.a
a - libprimer3.o
a - p3_seq_lib.o
ranlib libprimer3.a
c++   -o primer3_core primer3_boulder_main.o format_output.o read_boulder.o print_boulder.o  libprimer3.a libdpal.a libthal.a liboligotm.a   -lm
gmake[2]: Leaving directory '/construction/biology/primer3/primer3-2.3.6/src'

SUCCEEDED 00:00:12

-------------------------------------------------------------------------------
-- Phase: run-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: stage
-------------------------------------------------------------------------------

===>  Staging for primer3-2.3.6
===>   Generating temporary packing list
install  -s -m 555 /construction/biology/primer3/primer3-2.3.6/src/primer3_core  /construction/biology/primer3/stage/usr/local/bin/primer3
====> Compressing man pages (compress-man)
====> Running Q/A tests (stage-qa)
Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks

SUCCEEDED 00:00:01

-------------------------------------------------------------------------------
-- Phase: check-plist
-------------------------------------------------------------------------------

====> Checking for pkg-plist issues (check-plist)
===> Parsing plist
===> Checking for items in STAGEDIR missing from pkg-plist
===> Checking for items in pkg-plist which are not in STAGEDIR
===> No pkg-plist issues found (check-plist)

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: package
-------------------------------------------------------------------------------

===>  Building package for primer3-2.3.6
file sizes/checksums     [1]:   0%
file sizes/checksums     [1]: 100%
packing files            [1]:   0%
packing files            [1]: 100%
packing directories      [0]:   0%
packing directories      [0]: 100%

SUCCEEDED 00:00:01
TOTAL TIME 00:00:17