tree puzzle error running Configure after installing update 2.4.1.1 to Cygwin64
Marco Atzeri
marco.atzeri@gmail.com
Wed Jan 27 13:30:00 GMT 2016
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 ppuzzle.c:905:3: warning: ‘MPI_Address’ is deprecated (declared at /usr/include/mpi.h:1183): MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]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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