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Re: tree puzzle error running Configure after installing update 2.4.1.1 to Cygwin64




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ppuzzle.c:905:3: warning: ‘MPI_Address’ is deprecated (declared at /usr/include/mpi.h:1183): MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]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@DESKTOP-14EL82S /usr/local/bin/tree-puzzle-5.3.rc16-windows

I also ran make check
Robert@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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