From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: (qmail 83241 invoked by alias); 27 Jan 2016 11:46:53 -0000 Mailing-List: contact cygwin-help@cygwin.com; run by ezmlm Precedence: bulk List-Id: List-Subscribe: List-Archive: List-Post: List-Help: , Sender: cygwin-owner@cygwin.com Mail-Followup-To: cygwin@cygwin.com Received: (qmail 83224 invoked by uid 89); 27 Jan 2016 11:46:52 -0000 Authentication-Results: sourceware.org; auth=none X-Virus-Found: No X-Spam-SWARE-Status: No, score=-2.6 required=5.0 tests=BAYES_00,FREEMAIL_FROM,RCVD_IN_DNSWL_LOW,SPF_PASS autolearn=ham version=3.3.2 spammy=exeext, EXEEXT, dear, HContent-Transfer-Encoding:8bit X-HELO: mail-qg0-f50.google.com Received: from mail-qg0-f50.google.com (HELO mail-qg0-f50.google.com) (209.85.192.50) by sourceware.org (qpsmtpd/0.93/v0.84-503-g423c35a) with (AES128-GCM-SHA256 encrypted) ESMTPS; Wed, 27 Jan 2016 11:46:50 +0000 Received: by mail-qg0-f50.google.com with SMTP id b35so4103196qge.0 for ; Wed, 27 Jan 2016 03:46:50 -0800 (PST) X-Google-DKIM-Signature: v=1; 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WOW64; rv:38.0) Gecko/20100101 Thunderbird/38.5.1 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit X-IsSubscribed: yes X-SW-Source: 2016-01/txt/msg00385.txt.bz2 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 ppuzzle.c:905:3: warning: ‘MPI_Address’ is deprecated (declared at /usr/include/mpi.h:1183): MPI_Address is superseded by MPI_Get_address in MPI-2.0 [-Wdeprecated-declarations] 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 > : 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 -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple