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Subject:	Re: tree puzzle error running Configure after installing update 2.4.1.1 to Cygwin64
To:	cygwin AT cygwin DOT com
References:	<BAY175-W38CA0B8417C1EB8BD551BEADD90 AT phx DOT gbl>
From:	Marco Atzeri <marco DOT atzeri AT gmail DOT com>
Message-ID:	<56A8AE20.30200@gmail.com>
Date:	Wed, 27 Jan 2016 12:46:40 +0100
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On 27/01/2016 07:45, Robert May wrote:
> cyg Simple
>
> OK replaced the two files config.guess and config.sub with a 2016 timestamp and ran make again.
> like samtools it has a couple of warning for terms like
>
> But it does not get the job done.
>
> the problem area seems to be in this area of make
> ppuzzle.c: In function ‘PP_Update_Rates’:
> ppuzzle.c:258:38: error: ‘PP_UPDATERATES’ undeclared (first use in this function)
>     MPI_Send(&dummy, 0, MPI_INT, dest, PP_UPDATERATES, PP_Comm);
>
> two pages later
> ppuzzle.c: In function ‘PP_RecvData’:
> ppuzzle.c:905:3: warning: ‘MPI_Address’ is deprecated (declared at /usr/include/mpi.h:1183): MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]
>     MPI_Address(&(Seqpat[0][0]), &(Dtypeaddr[0]));
>
> this continues back and forth till we get to the end with
> <builtin>: recipe for target 'ppuzzle' failed
> make[3]: *** [ppuzzle] Error 1
> make[3]: Leaving directory '/usr/local/bin/tree-puzzle-5.3.rc16-windows/src'
> Makefile:532: recipe for target 'all-recursive' failed
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory '/usr/local/bin/tree-puzzle-5.3.rc16-windows/src'
> Makefile:397: recipe for target 'all' failed
> make[1]: *** [all] Error 2
> make[1]: Leaving directory '/usr/local/bin/tree-puzzle-5.3.rc16-windows/src'
> Makefile:370: recipe for target 'all-recursive' failed
> make: *** [all-recursive] Error 1
>
> Robert AT DESKTOP-14EL82S /usr/local/bin/tree-puzzle-5.3.rc16-windows
>
> I also ran make check
> Robert AT DESKTOP-14EL82S /usr/local/bin/tree-puzzle-5.3.rc16-windows
> $ make check
> Making check in src
> make[1]: Entering directory '/usr/local/bin/tree-puzzle-5.3.rc16-windows/src'
> Making check in sprng
> make[2]: Entering directory '/usr/local/bin/tree-puzzle-5.3.rc16-windows/src/sprng'
> make[2]: Nothing to be done for 'check'.
> make[2]: Leaving directory '/usr/local/bin/tree-puzzle-5.3.rc16-windows/src/sprng'
> make[2]: Entering directory '/usr/local/bin/tree-puzzle-5.3.rc16-windows/src'
> cd sprng && make mlfg.o makeseed.o memory.o checkid.o store.o
> make[3]: Entering directory '/usr/local/bin/tree-puzzle-5.3.rc16-windows/src/sprng'
> make[3]: 'mlfg.o' is up to date.
> make[3]: 'makeseed.o' is up to date.
> make[3]: 'memory.o' is up to date.
> make[3]: 'checkid.o' is up to date.
> make[3]: 'store.o' is up to date.
> make[3]: Leaving directory '/usr/local/bin/tree-puzzle-5.3.rc16-windows/src/sprng'
> gcc  -g -O2   sgamma.o sml1.o sml2.o smlparam.o smodel1.o smodel2.o spuzzle1.o spuzzle2.o spstep.o sutil.o sconsensus.o streesort.o streetest.o  sprng/mlfg.o sprng/makeseed.o sprng/memory.o sprng/checkid.o sprng/store.o -lm  -o puzzle.exe
> gcc -g -O2    ppuzzle.c   -o ppuzzle
> ppuzzle.c: In function ‘PP_Update_Rates’:
> ppuzzle.c:258:38: error: ‘PP_UPDATERATES’ undeclared (first use in this function)
>     MPI_Send(&dummy, 0, MPI_INT, dest, PP_UPDATERATES, PP_Comm);
>
> I can send full make and make check runs if needed
>
> help
>
> Bob

Dear Bob,

"make check" is useless if "make" does not work.

to me it seems you need to work with upstream developer to solve the 
different issues.
It is not a cygwin issue that the MPI call are referring to old versions 
or that the configure/Makefile.am are wrong handling "$(EXEEXT)"

Please note that
  gcc -g -O2    ppuzzle.c   -o ppuzzle

is clearly not coming from src/Makefile.am rule:

ppuzzle_SOURCES = gamma.c ml1.c ml2.c mlparam.c model1.c model2.c 
puzzle1.c puzzle2.c pstep.c sched.c util.c consensus.c treesort.c 
treetest.c ppuzzle.c ml.h util.h puzzle.h pstep.h gamma.h ppuzzle.h 
sched.h consensus.h treesort.h treetest.h

so there is an error in the src/Makefile.am

If you change inside it in:

bin_PROGRAMS = puzzle$(EXEEXT) @PPUZZLE@$(EXEEXT)
EXTRA_PROGRAMS = ppuzzle$(EXEEXT)

and then run

autoreconf -ifv
./configure
make

it will compile

Make check will fail but it seems at first glance a rounding issue.

Regards
Marco




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