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

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

[Robert May]

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ppuzzle.c:905:3: warning: ‘MPI_Address’ is deprecated (declared at /usr/include/mpi.h:1183): MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations]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

 Bob May
DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surname and ISOGG YTree 		 	   		  
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Re: tree puzzle error running Configure after installing update 2.4.1.1 to Cygwin64

[Marco Atzeri]

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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tree puzzle error running Configure after installing update 2.4.1.1 to Cygwin64

[Robert May]

Robert@DESKTOP-14EL82S /usr/local/bin/tree-puzzle-5.3.rc16-windows
$ ./configure
checking build system type... ./config.guess: unable to guess system type

This script, last modified 2004-08-11, has failed to recognize
the operating system you are using. It is advised that you
download the most up to date version of the config scripts from

    ftp://ftp.gnu.org/pub/gnu/config/

If the version you run (./config.guess) is already up to date, please
send the following data and any information you think might be
pertinent to <config-patches@gnu.org> in order to provide the needed
information to handle your system.

config.guess timestamp = 2004-08-11

uname -m = x86_64
uname -r = 2.4.0(0.293/5/3)
uname -s = CYGWIN_NT-10.0
uname -v = 2016-01-15 16:16

/usr/bin/uname -p = unknown
/bin/uname -X     =

hostinfo               =
/bin/universe          =
/usr/bin/arch -k       =
/bin/arch              = x86_64
/usr/bin/oslevel       =
/usr/convex/getsysinfo =

UNAME_MACHINE = x86_64
UNAME_RELEASE = 2.4.0(0.293/5/3)
UNAME_SYSTEM  = CYGWIN_NT-10.0
UNAME_VERSION = 2016-01-15 16:16
configure: error: cannot guess build type; you must specify one
onfig.guess timestamp = 2004-08-11

uname -m = x86_64
uname -r = 2.4.0(0.293/5/3)
uname -s = CYGWIN_NT-10.0
uname -v = 2016-01-15 16:16

/usr/bin/uname -p = unknown
/bin/uname -X     =

hostinfo               =
/bin/universe          =
/usr/bin/arch -k       =
/bin/arch              = x86_64
/usr/bin/oslevel       =
/usr/convex/getsysinfo =

UNAME_MACHINE = x86_64
UNAME_RELEASE = 2.4.0(0.293/5/3)
UNAME_SYSTEM  = CYGWIN_NT-10.0
UNAME_VERSION = 2016-01-15 16:16
configure: error: cannot guess build type; you must specify one
Makefile:355: recipe for target 'config.status' failed
make: *** [config.status] Error 1

 Bob May
DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surname and ISOGG YTree 		 	   		  
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Re: tree puzzle error running Configure after installing update 2.4.1.1 to Cygwin64

[cyg Simple]

On 1/25/2016 4:11 PM, Robert May wrote:
> Robert@DESKTOP-14EL82S /usr/local/bin/tree-puzzle-5.3.rc16-windows
> $ ./configure
> checking build system type... ./config.guess: unable to guess system type
> 
> This script, last modified 2004-08-11, has failed to recognize
> the operating system you are using. It is advised that you
> download the most up to date version of the config scripts from
> 
>     ftp://ftp.gnu.org/pub/gnu/config/
> 

Go to the FTP site and download the latest config.guess and config.sub.

> If the version you run (./config.guess) is already up to date, please
> send the following data and any information you think might be
> pertinent to <config-patches@gnu.org> in order to provide the needed
> information to handle your system.
> 
> config.guess timestamp = 2004-08-11
> 

Then replace config.guess and config.sub with the latest.

-- 
cyg Simple

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