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From: Robert May <tpibob AT gmail DOT com>
To: "cygwin AT cygwin DOT com" <cygwin AT cygwin DOT com>
Subject: Re: tree puzzle error running Configure after installing update 2.4.1.1 to Cygwin64
Date: Wed, 27 Jan 2016 16:45:12 +1000
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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ppuzzle.c:905:3: warning: ‘MPI_Address’ is deprecated (declared at /usr/include/mpi.h:1183): MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]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

 Bob May
DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surname and ISOGG YTree 		 	   		  
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