From minc-development@bic.mni.mcgill.ca Fri Nov 7 18:38:21 2003 From: minc-development@bic.mni.mcgill.ca (Vicka Corey) Date: Fri, 7 Nov 2003 13:38:21 -0500 Subject: [MINC-development] can't find netcdf...? Message-ID: <200311071838.hA7IcLI8029078@gate.nmr.mgh.harvard.edu> i am having a rather frustrating time with (yet another!) attempt to build 1.1 under os x. my current grievance is: i'm in: /private/homes/6/vicka/mni/src/minc-1.1 i run configure it fails at: checking for library netcdf... no configure: error: cannot find required library netcdf thing is...i just *built* a new shiny netcdf. it is in: ocelot:vicka[462] ls -lL /usr/pubsw/lib/libnetcdf.a -rw-rw-r-- 1 pubsw pubsw 238212 Nov 7 12:52 /usr/pubsw/lib/libnetcdf.a and i have set LDFLAGS: ocelot:vicka[463] env |grep LD LDFLAGS=-L/usr/pubsw/lib ...even more incredibly, putting a copy into /usr/lib or /lib still fails: ocelot:vicka[464] ls -l /usr/lib/libnetcdf* -rw-r--r-- 1 root wheel 238212 Nov 7 13:10 /usr/lib/libnetcdf.a ...anyone have any ideas? this is driving me *mad*. fwiw, using --build-prefix worked around this for a part of the package that supported that, but this one doesn't recognize it. thanks, --vicka From minc-development@bic.mni.mcgill.ca Fri Nov 7 18:53:01 2003 From: minc-development@bic.mni.mcgill.ca (Andrew Janke) Date: Fri, 7 Nov 2003 13:53:01 -0500 Subject: [MINC-development] can't find netcdf...? In-Reply-To: <200311071838.hA7IcLI8029078@gate.nmr.mgh.harvard.edu> Message-ID: On Fri, 7 Nov 2003, Vicka Corey wrote: > i am having a rather frustrating time with (yet another!) attempt > to build 1.1 under os x. > > my current grievance is: > > i'm in: /private/homes/6/vicka/mni/src/minc-1.1 > i run configure > it fails at: > checking for library netcdf... no > configure: error: cannot find required library netcdf > > thing is...i just *built* a new shiny netcdf. it is in: > ocelot:vicka[462] ls -lL /usr/pubsw/lib/libnetcdf.a > -rw-rw-r-- 1 pubsw pubsw 238212 Nov 7 12:52 /usr/pubsw/lib/libnetcdf.a > > ocelot:vicka[464] ls -l /usr/lib/libnetcdf* > -rw-r--r-- 1 root wheel 238212 Nov 7 13:10 /usr/lib/libnetcdf.a the configure script is most likely also looking for netcdf.h. > fwiw, using --build-prefix worked around this for a part of the package > that supported that, but this one doesn't recognize it. --build-prefix or --with-build-prefix? (configure --help) I'm guessing: $ ./configure --with-build-prefix=/usr/pubsw will work. -- Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From minc-development@bic.mni.mcgill.ca Fri Nov 7 19:24:13 2003 From: minc-development@bic.mni.mcgill.ca (Vicka Corey) Date: Fri, 7 Nov 2003 14:24:13 -0500 Subject: [MINC-development] can't find netcdf...? In-Reply-To: ; from rotor@bic.mni.mcgill.ca on Fri, Nov 07, 2003 at 01:53:01PM -0500 References: <200311071838.hA7IcLI8029078@gate.nmr.mgh.harvard.edu> Message-ID: <20031107142413.M29521@gate.nmr.mgh.harvard.edu> On Fri, Nov 07, 2003 at 01:53:01PM -0500, Andrew Janke wrote: > I'm guessing: > > $ ./configure --with-build-prefix=/usr/pubsw > > will work. alas, no luck with that, either. the .h file is there: ocelot:vicka[475] ls -lL /usr/pubsw/include/netcdf.h -rw-rw-r-- 1 pubsw pubsw 26587 Nov 7 12:52 /usr/pubsw/include/netcdf.h ocelot:vicka[476] ...and i have set all the flags i could think of: ocelot:vicka[473] env |grep FLAG LDFLAGS=-L/usr/pubsw/lib CCFLAGS=-I/usr/pubsw/include CFLAGS=-I/usr/pubsw/include CPPFLAGS=-I/usr/pubsw/include ...but it still dies with the same error. any other ideas, or anyone see anything i'm doing wrong here? thanks again, --vicka From minc-development@bic.mni.mcgill.ca Fri Nov 7 19:34:46 2003 From: minc-development@bic.mni.mcgill.ca (Andrew Janke) Date: Fri, 7 Nov 2003 14:34:46 -0500 Subject: [MINC-development] can't find netcdf...? In-Reply-To: <20031107142413.M29521@gate.nmr.mgh.harvard.edu> Message-ID: On Fri, 7 Nov 2003, Vicka Corey wrote: > > $ ./configure --with-build-prefix=/usr/pubsw > > > > will work. > > alas, no luck with that, either. Bah! I'm going crazy too it would appear. Make that: $ ./configure --with-build-path=/usr/pubsw !! Either way configure --help should show this option a From minc-development@bic.mni.mcgill.ca Fri Nov 7 20:43:25 2003 From: minc-development@bic.mni.mcgill.ca (Vicka Corey) Date: Fri, 7 Nov 2003 15:43:25 -0500 Subject: [MINC-development] can't find netcdf...? In-Reply-To: ; from rotor@bic.mni.mcgill.ca on Fri, Nov 07, 2003 at 02:34:46PM -0500 References: <20031107142413.M29521@gate.nmr.mgh.harvard.edu> Message-ID: <20031107154325.Q29521@gate.nmr.mgh.harvard.edu> --fdj2RfSjLxBAspz7 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline ok, umm, the option would seem to be --with-build-path. but it still doesn't work. here is my command: ./configure --prefix=/usr/pubsw/packages/minc/1.1-vicka --with-build-path=/usr/pubsw ...and here is the error: configure: error: cannot find required library netcdf ...anybody else? i will attach config.log in case that would help.... thanks again, --vicka On Fri, Nov 07, 2003 at 02:34:46PM -0500, Andrew Janke wrote: > On Fri, 7 Nov 2003, Vicka Corey wrote: > > > > $ ./configure --with-build-prefix=/usr/pubsw > > > > > > will work. > > > > alas, no luck with that, either. > > Bah! I'm going crazy too it would appear. > > Make that: > > $ ./configure --with-build-path=/usr/pubsw > > !! > > Either way configure --help should show this option > > a > > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development --fdj2RfSjLxBAspz7 Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename="config.log" This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by configure, which was generated by GNU Autoconf 2.57. Invocation command line was $ ./configure --prefix=/usr/pubsw/packages/minc/1.1-vicka --with-build-path=/usr/pubsw ## --------- ## ## Platform. ## ## --------- ## hostname = ocelot.nmr.mgh.harvard.edu uname -m = Power Macintosh uname -r = 6.8 uname -s = Darwin uname -v = Darwin Kernel Version 6.8: Wed Sep 10 15:20:55 PDT 2003; root:xnu/xnu-344.49.obj~2/RELEASE_PPC /usr/bin/uname -p = powerpc /bin/uname -X = unknown /bin/arch = unknown /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown hostinfo = Mach kernel version: Darwin Kernel Version 6.8: Wed Sep 10 15:20:55 PDT 2003; root:xnu/xnu-344.49.obj~2/RELEASE_PPC Kernel configured for up to 2 processors. 2 processors are physically available. Processor type: ppc7450 (PowerPC 7450) Processors active: 0 1 Primary memory available: 2048.00 megabytes. Default processor set: 71 tasks, 149 threads, 2 processors Load average: 1.86, Mach factor: 0.24 unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /homes/6/vicka/cvs/progs/Darwin PATH: /space/lyon/1/home/inverse/freesurfer_alpha/local/bin/Darwin PATH: /space/lyon/1/home/inverse/freesurfer_alpha/mni_tools/bin PATH: /space/lyon/1/home/inverse/freesurfer_alpha/bin/Darwin PATH: /space/lyon/1/home/inverse/freesurfer_alpha/bin/noarch PATH: /space/lyon/1/fsdev/freesurfer_dev/local/bin/Darwin PATH: /space/lyon/1/fsdev/freesurfer_dev/mni_tools/bin PATH: /space/lyon/1/fsdev/freesurfer_dev/bin/Darwin PATH: /space/lyon/1/fsdev/freesurfer_dev/bin/noarch PATH: /homes/6/vicka/bin PATH: /usr/pubsw/bin PATH: /bin PATH: /sbin PATH: /usr/bin PATH: /usr/sbin PATH: /space/lyon/1/home/inverse/bin PATH: /private/homes/6/vicka/mni/1.1/bin ## ----------- ## ## Core tests. ## ## ----------- ## configure:1489: checking for a BSD-compatible install configure:1543: result: /usr/bin/install -c configure:1554: checking whether build environment is sane configure:1597: result: yes configure:1630: checking for gawk configure:1659: result: no configure:1630: checking for mawk configure:1659: result: no configure:1630: checking for nawk configure:1659: result: no configure:1630: checking for awk configure:1646: found /usr/bin/awk configure:1656: result: awk configure:1666: checking whether make sets $(MAKE) configure:1686: result: yes configure:1858: checking for a BSD-compatible install configure:1912: result: /usr/bin/install -c configure:1923: checking whether ln -s works configure:1927: result: yes configure:1934: checking whether make sets $(MAKE) configure:1954: result: yes configure:1984: checking for style of include used by make configure:2012: result: GNU configure:2083: checking for gcc configure:2099: found /usr/bin/gcc configure:2109: result: gcc configure:2353: checking for C compiler version configure:2356: gcc --version &5 gcc (GCC) 3.1 20020420 (prerelease) Copyright (C) 2002 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. configure:2359: $? = 0 configure:2361: gcc -v &5 Reading specs from /usr/libexec/gcc/darwin/ppc/3.1/specs Thread model: posix Apple Computer, Inc. GCC version 1161, based on gcc version 3.1 20020420 (prerelease) configure:2364: $? = 0 configure:2366: gcc -V &5 gcc: argument to `-V' is missing configure:2369: $? = 1 configure:2393: checking for C compiler default output configure:2396: gcc -I/usr/pubsw/include -I/usr/pubsw/include -L/usr/pubsw/lib conftest.c >&5 configure:2399: $? = 0 configure:2445: result: a.out configure:2450: checking whether the C compiler works configure:2456: ./a.out configure:2459: $? = 0 configure:2476: result: yes configure:2483: checking whether we are cross compiling configure:2485: result: no configure:2488: checking for suffix of executables configure:2490: gcc -o conftest -I/usr/pubsw/include -I/usr/pubsw/include -L/usr/pubsw/lib conftest.c >&5 configure:2493: $? = 0 configure:2518: result: configure:2524: checking for suffix of object files configure:2546: gcc -c -I/usr/pubsw/include -I/usr/pubsw/include conftest.c >&5 configure:2549: $? = 0 configure:2571: result: o configure:2575: checking whether we are using the GNU C compiler configure:2600: gcc -c -I/usr/pubsw/include -I/usr/pubsw/include conftest.c >&5 configure:2603: $? = 0 configure:2606: test -s conftest.o configure:2609: $? = 0 configure:2622: result: yes configure:2628: checking whether gcc accepts -g configure:2650: gcc -c -g -I/usr/pubsw/include conftest.c >&5 configure:2653: $? = 0 configure:2656: test -s conftest.o configure:2659: $? = 0 configure:2670: result: yes configure:2687: checking for gcc option to accept ANSI C configure:2748: gcc -c -I/usr/pubsw/include -I/usr/pubsw/include conftest.c >&5 configure:2751: $? = 0 configure:2754: test -s conftest.o configure:2757: $? = 0 configure:2775: result: none needed configure:2793: gcc -c -I/usr/pubsw/include -I/usr/pubsw/include conftest.c >&5 conftest.c:2: undefined type, found `choke' conftest.c:2: illegal external declaration, missing `;' after `me' cpp-precomp: warning: errors during smart preprocessing, retrying in basic mode conftest.c:2: parse error before "me" configure:2796: $? = 1 configure: failed program was: | #ifndef __cplusplus | choke me | #endif configure:2907: checking dependency style of gcc configure:2969: result: gcc configure:2987: checking whether gcc and cc understand -c and -o together configure:3018: gcc -c conftest.c -o conftest.o >&5 configure:3021: $? = 0 configure:3023: gcc -c conftest.c -o conftest.o >&5 configure:3026: $? = 0 configure:3033: cc -c conftest.c >&5 configure:3036: $? = 0 configure:3039: cc -c conftest.c -o conftest.o >&5 configure:3042: $? = 0 configure:3044: cc -c conftest.c -o conftest.o >&5 configure:3047: $? = 0 configure:3065: result: yes configure:3131: checking for ranlib configure:3147: found /usr/bin/ranlib configure:3158: result: ranlib configure:3221: checking for g77 configure:3250: result: no configure:3221: checking for f77 configure:3250: result: no configure:3221: checking for xlf configure:3250: result: no configure:3221: checking for frt configure:3250: result: no configure:3221: checking for pgf77 configure:3250: result: no configure:3221: checking for fl32 configure:3250: result: no configure:3221: checking for af77 configure:3250: result: no configure:3221: checking for fort77 configure:3250: result: no configure:3221: checking for f90 configure:3250: result: no configure:3221: checking for xlf90 configure:3250: result: no configure:3221: checking for pgf90 configure:3250: result: no configure:3221: checking for epcf90 configure:3250: result: no configure:3221: checking for f95 configure:3250: result: no configure:3221: checking for fort configure:3250: result: no configure:3221: checking for xlf95 configure:3250: result: no configure:3221: checking for lf95 configure:3250: result: no configure:3221: checking for g95 configure:3250: result: no configure:3262: checking for Fortran 77 compiler version configure:3265: --version &5 ./configure: --version: command not found configure:3268: $? = 127 configure:3270: -v &5 ./configure: -v: command not found configure:3273: $? = 127 configure:3275: -V &5 ./configure: -V: command not found configure:3278: $? = 127 configure:3285: checking whether we are using the GNU Fortran 77 compiler configure:3299: -c conftest.F >&5 ./configure: -c: command not found configure:3302: $? = 127 configure: failed program was: | program main | #ifndef __GNUC__ | choke me | #endif | | end configure:3321: result: no configure:3328: checking whether accepts -g configure:3340: -c -g conftest.f >&5 ./configure: -c: command not found configure:3343: $? = 127 configure: failed program was: | program main | | end configure:3361: result: no configure:3389: checking for flex configure:3405: found /usr/bin/flex configure:3415: result: flex configure:3428: checking for yywrap in -lfl configure:3459: gcc -o conftest -I/usr/pubsw/include -I/usr/pubsw/include -L/usr/pubsw/lib conftest.c -lfl >&5 configure:3462: $? = 0 configure:3465: test -s conftest configure:3468: $? = 0 configure:3480: result: yes configure:3548: checking lex output file root configure:3559: flex conftest.l configure:3562: $? = 0 configure:3574: result: lex.yy configure:3579: checking whether yytext is a pointer configure:3595: gcc -o conftest -I/usr/pubsw/include -I/usr/pubsw/include -L/usr/pubsw/lib conftest.c -lfl >&5 configure:3598: $? = 0 configure:3601: test -s conftest configure:3604: $? = 0 configure:3617: result: yes configure:3635: checking for bison configure:3651: found /usr/bin/bison configure:3661: result: bison -y configure:3745: checking build system type configure:3763: result: powerpc-apple-darwin6.8 configure:3771: checking host system type configure:3785: result: powerpc-apple-darwin6.8 configure:3815: checking for ld used by GCC configure:3878: result: /usr/bin/ld configure:3887: checking if the linker (/usr/bin/ld) is GNU ld configure:3899: result: no configure:3904: checking for /usr/bin/ld option to reload object files configure:3911: result: -r configure:3916: checking for BSD-compatible nm configure:3952: result: /usr/bin/nm -p configure:3955: checking for a sed that does not truncate output configure:4037: result: /usr/bin/sed configure:4040: checking how to recognise dependent libraries configure:4221: result: file_magic Mach-O dynamically linked shared library configure:4233: checking command to parse /usr/bin/nm -p output configure:4317: gcc -c -I/usr/pubsw/include -I/usr/pubsw/include conftest.c >&5 configure:4320: $? = 0 configure:4324: /usr/bin/nm -p conftest.o \| sed -n -e 's/^.*[ ]\([BCDEGRST][BCDEGRST]*\)[ ][ ]*\(\)\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2\3 \3/p' \> conftest.nm configure:4327: $? = 0 cannot find nm_test_var in conftest.nm configure:4317: gcc -c -I/usr/pubsw/include -I/usr/pubsw/include conftest.c >&5 configure:4320: $? = 0 configure:4324: /usr/bin/nm -p conftest.o \| sed -n -e 's/^.*[ ]\([BCDEGRST][BCDEGRST]*\)[ ][ ]*\(_\)\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2\3 \3/p' \> conftest.nm configure:4327: $? = 0 configure:4379: gcc -o conftest -I/usr/pubsw/include -I/usr/pubsw/include -L/usr/pubsw/lib conftest.c conftstm.o >&5 configure:4382: $? = 0 configure:4426: result: ok configure:4435: checking how to run the C preprocessor configure:4471: gcc -E -I/usr/pubsw/include conftest.c configure:4473: undefined type, found `Syntax' configure:4473: illegal external declaration, missing `;' after `error' cpp-precomp: warning: errors during smart preprocessing, retrying in basic mode configure:4477: $? = 0 configure:4509: gcc -E -I/usr/pubsw/include conftest.c configure:4511: header file 'ac_nonexistent.h' not found cpp-precomp: warning: errors during smart preprocessing, retrying in basic mode configure:4515: $? = 1 configure: failed program was: | #line 4500 "configure" | /* confdefs.h. */ | | #define PACKAGE_NAME "" | #define PACKAGE_TARNAME "" | #define PACKAGE_VERSION "" | #define PACKAGE_STRING "" | #define PACKAGE_BUGREPORT "" | #define PACKAGE "minc" | #define VERSION "1.1" | #define YYTEXT_POINTER 1 | /* end confdefs.h. */ | #include configure:4553: result: gcc -E configure:4578: gcc -E -I/usr/pubsw/include conftest.c configure:4580: undefined type, found `Syntax' configure:4580: illegal external declaration, missing `;' after `error' cpp-precomp: warning: errors during smart preprocessing, retrying in basic mode configure:4584: $? = 0 configure:4616: gcc -E -I/usr/pubsw/include conftest.c configure:4618: header file 'ac_nonexistent.h' not found cpp-precomp: warning: errors during smart preprocessing, retrying in basic mode configure:4622: $? = 1 configure: failed program was: | #line 4607 "configure" | /* confdefs.h. */ | | #define PACKAGE_NAME "" | #define PACKAGE_TARNAME "" | #define PACKAGE_VERSION "" | #define PACKAGE_STRING "" | #define PACKAGE_BUGREPORT "" | #define PACKAGE "minc" | #define VERSION "1.1" | #define YYTEXT_POINTER 1 | /* end confdefs.h. */ | #include configure:4665: checking for egrep configure:4675: result: grep -E configure:4680: checking for ANSI C header files configure:4706: gcc -c -I/usr/pubsw/include -I/usr/pubsw/include conftest.c >&5 configure:4709: $? = 0 configure:4712: test -s conftest.o configure:4715: $? = 0 configure:4804: gcc -o conftest -I/usr/pubsw/include -I/usr/pubsw/include -L/usr/pubsw/lib conftest.c >&5 configure:4807: $? = 0 configure:4809: ./conftest configure:4812: $? = 0 configure:4827: result: yes configure:4851: checking for sys/types.h configure:4868: gcc -c -I/usr/pubsw/include -I/usr/pubsw/include conftest.c >&5 configure:4871: $? = 0 configure:4874: test -s conftest.o configure:4877: $? = 0 configure:4888: result: yes configure:4851: checking for sys/stat.h configure:4868: gcc -c -I/usr/pubsw/include -I/usr/pubsw/include conftest.c >&5 configure:4871: $? = 0 configure:4874: test -s conftest.o configure:4877: $? = 0 configure:4888: result: yes configure:4851: checking for stdlib.h configure:4868: gcc -c -I/usr/pubsw/include -I/usr/pubsw/include conftest.c >&5 configure:4871: $? = 0 configure:4874: test -s conftest.o configure:4877: $? = 0 configure:4888: result: yes configure:4851: checking for string.h configure:4868: gcc -c -I/usr/pubsw/include -I/usr/pubsw/include conftest.c >&5 configure:4871: $? = 0 configure:4874: test -s conftest.o configure:4877: $? = 0 configure:4888: result: yes configure:4851: checking for memory.h configure:4868: gcc -c -I/usr/pubsw/include -I/usr/pubsw/include conftest.c >&5 configure:4871: $? = 0 configure:4874: test -s conftest.o configure:4877: $? = 0 configure:4888: result: yes configure:4851: checking for strings.h configure:4868: gcc -c -I/usr/pubsw/include -I/usr/pubsw/include conftest.c >&5 configure:4871: $? = 0 configure:4874: test -s conftest.o configure:4877: $? = 0 configure:4888: result: yes configure:4851: checking for inttypes.h configure:4868: gcc -c -I/usr/pubsw/include -I/usr/pubsw/include conftest.c >&5 configure:4871: $? = 0 configure:4874: test -s conftest.o configure:4877: $? = 0 configure:4888: result: yes configure:4851: checking for stdint.h configure:4868: gcc -c -I/usr/pubsw/include -I/usr/pubsw/include conftest.c >&5 configure:4871: $? = 0 configure:4874: test -s conftest.o configure:4877: $? = 0 configure:4888: result: yes configure:4851: checking for unistd.h configure:4868: gcc -c -I/usr/pubsw/include -I/usr/pubsw/include conftest.c >&5 configure:4871: $? = 0 configure:4874: test -s conftest.o configure:4877: $? = 0 configure:4888: result: yes configure:4914: checking dlfcn.h usability configure:4927: gcc -c -I/usr/pubsw/include -I/usr/pubsw/include conftest.c >&5 configure:4930: $? = 0 configure:4933: test -s conftest.o configure:4936: $? = 0 configure:4946: result: yes configure:4950: checking dlfcn.h presence configure:4961: gcc -E -I/usr/pubsw/include conftest.c configure:4967: $? = 0 configure:4986: result: yes configure:5022: checking for dlfcn.h configure:5029: result: yes configure:5227: checking for ranlib configure:5254: result: ranlib configure:5307: checking for strip configure:5323: found /usr/bin/strip configure:5334: result: strip configure:5544: checking for objdir configure:5555: result: .libs configure:5572: checking for gcc option to produce PIC configure:5718: result: -fno-common configure:5722: checking if gcc PIC flag -fno-common works configure:5746: gcc -c -I/usr/pubsw/include -fno-common -DPIC -I/usr/pubsw/include conftest.c >&5 configure:5749: $? = 0 configure:5752: test -s conftest.o configure:5755: $? = 0 configure:5793: result: yes configure:5809: checking if gcc static flag -static works configure:5834: gcc -o conftest -I/usr/pubsw/include -I/usr/pubsw/include -L/usr/pubsw/lib -static conftest.c >&5 ld: can't locate file for: -lcrt0.o configure:5837: $? = 1 configure: failed program was: | #line 5817 "configure" | /* confdefs.h. */ | | #define PACKAGE_NAME "" | #define PACKAGE_TARNAME "" | #define PACKAGE_VERSION "" | #define PACKAGE_STRING "" | #define PACKAGE_BUGREPORT "" | #define PACKAGE "minc" | #define VERSION "1.1" | #define YYTEXT_POINTER 1 | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | /* end confdefs.h. */ | | int | main () | { | | ; | return 0; | } configure:5859: result: no configure:5871: checking if gcc supports -c -o file.o configure:5894: gcc -c -I/usr/pubsw/include -o out/conftest2.o -I/usr/pubsw/include conftest.c >&5 configure:5915: result: yes configure:5920: checking if gcc supports -c -o file.lo configure:5948: gcc -c -I/usr/pubsw/include -c -o conftest.lo -I/usr/pubsw/include conftest.c >&5 configure:5951: $? = 0 configure:5954: test -s conftest.lo configure:5957: $? = 0 configure:5979: result: yes configure:6010: checking if gcc supports -fno-rtti -fno-exceptions configure:6033: gcc -c -I/usr/pubsw/include -fno-rtti -fno-exceptions -c conftest.c -I/usr/pubsw/include conftest.c >&5 configure:6036: $? = 0 configure:6039: test -s conftest.o configure:6042: $? = 0 configure:6059: result: yes configure:6070: checking whether the linker (/usr/bin/ld) supports shared libraries configure:6765: result: yes configure:6770: checking how to hardcode library paths into programs configure:6794: result: unsupported configure:6799: checking whether stripping libraries is possible configure:6807: result: no configure:6815: checking dynamic linker characteristics configure:7235: result: darwin6.8 dyld configure:7240: checking if libtool supports shared libraries configure:7242: result: yes configure:7245: checking whether to build shared libraries configure:7266: result: no configure:7269: checking whether to build static libraries configure:7273: result: yes configure:8578: checking for library m configure:8598: gcc -o conftest -I/usr/pubsw/include -I/usr/pubsw/include -I/usr/pubsw/include -L/usr/pubsw/lib -L/usr/pubsw/lib conftest.c -lm >&5 configure:8601: $? = 0 configure:8604: test -s conftest configure:8607: $? = 0 configure:8617: result: yes configure:8626: checking for library netcdf configure:8646: gcc -o conftest -I/usr/pubsw/include -I/usr/pubsw/include -I/usr/pubsw/include -L/usr/pubsw/lib -L/usr/pubsw/lib conftest.c -L/usr/pubsw/lib -lnetcdf -lm >&5 ld: table of contents for archive: /usr/pubsw/lib/libnetcdf.a is out of date; rerun ranlib(1) (can't load from it) configure:8649: $? = 1 configure: failed program was: | #line 8629 "configure" | /* confdefs.h. */ | | #define PACKAGE_NAME "" | #define PACKAGE_TARNAME "" | #define PACKAGE_VERSION "" | #define PACKAGE_STRING "" | #define PACKAGE_BUGREPORT "" | #define PACKAGE "minc" | #define VERSION "1.1" | #define YYTEXT_POINTER 1 | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | /* end confdefs.h. */ | #include | int | main () | { | int i = ncopen("",0); | ; | return 0; | } configure:8665: result: no configure:8668: error: cannot find required library netcdf ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_build=powerpc-apple-darwin6.8 ac_cv_build_alias=powerpc-apple-darwin6.8 ac_cv_c_compiler_gnu=yes ac_cv_env_CC_set= ac_cv_env_CC_value= ac_cv_env_CFLAGS_set=set ac_cv_env_CFLAGS_value=-I/usr/pubsw/include ac_cv_env_CPPFLAGS_set=set ac_cv_env_CPPFLAGS_value=-I/usr/pubsw/include ac_cv_env_CPP_set= ac_cv_env_CPP_value= ac_cv_env_F77_set= ac_cv_env_F77_value= ac_cv_env_FFLAGS_set= ac_cv_env_FFLAGS_value= ac_cv_env_LDFLAGS_set=set ac_cv_env_LDFLAGS_value=-L/usr/pubsw/lib ac_cv_env_build_alias_set= ac_cv_env_build_alias_value= ac_cv_env_host_alias_set= ac_cv_env_host_alias_value= ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ac_cv_exeext= ac_cv_f77_compiler_gnu=no ac_cv_header_dlfcn_h=yes ac_cv_header_inttypes_h=yes ac_cv_header_memory_h=yes ac_cv_header_stdc=yes ac_cv_header_stdint_h=yes ac_cv_header_stdlib_h=yes ac_cv_header_string_h=yes ac_cv_header_strings_h=yes ac_cv_header_sys_stat_h=yes ac_cv_header_sys_types_h=yes ac_cv_header_unistd_h=yes ac_cv_host=powerpc-apple-darwin6.8 ac_cv_host_alias=powerpc-apple-darwin6.8 ac_cv_lib_fl_yywrap=yes ac_cv_objext=o ac_cv_path_install='/usr/bin/install -c' ac_cv_prog_AWK=awk ac_cv_prog_CPP='gcc -E' ac_cv_prog_LEX=flex ac_cv_prog_YACC='bison -y' ac_cv_prog_ac_ct_CC=gcc ac_cv_prog_ac_ct_RANLIB=ranlib ac_cv_prog_ac_ct_STRIP=strip ac_cv_prog_cc_g=yes ac_cv_prog_cc_gcc_c_o=yes ac_cv_prog_cc_stdc= ac_cv_prog_egrep='grep -E' ac_cv_prog_f77_g=no ac_cv_prog_lex_root=lex.yy ac_cv_prog_lex_yytext_pointer=yes ac_cv_prog_make_make_set=yes am_cv_CC_dependencies_compiler_type=gcc lt_cv_compiler_c_o=yes lt_cv_compiler_o_lo=yes lt_cv_deplibs_check_method='file_magic Mach-O dynamically linked shared library' lt_cv_file_magic_cmd='/usr/bin/file -L' lt_cv_file_magic_test_file=/usr/lib/libSystem.dylib lt_cv_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (lt_ptr) 0},/p'\'' -e '\''s/^[BCDEGRST] \([^ ]*\) \([^ ]*\)$/ {"\2", (lt_ptr) \&\2},/p'\''' lt_cv_global_symbol_to_cdecl='sed -n -e '\''s/^. .* \(.*\)$/extern char \1;/p'\''' lt_cv_ld_reload_flag=-r lt_cv_path_LD=/usr/bin/ld lt_cv_path_NM='/usr/bin/nm -p' lt_cv_path_SED=/usr/bin/sed lt_cv_prog_cc_can_build_shared=yes lt_cv_prog_cc_no_builtin= lt_cv_prog_cc_pic=' -fno-common' lt_cv_prog_cc_pic_works=yes lt_cv_prog_cc_shlib= lt_cv_prog_cc_static= lt_cv_prog_cc_static_works=no lt_cv_prog_cc_wl=-Wl, lt_cv_prog_gnu_ld=no lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([BCDEGRST][BCDEGRST]*\)[ ][ ]*\(_\)\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2\3 \3/p'\''' ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} /homes/6/vicka/mni/src/minc-1.1/ac_config_aux/missing --run aclocal-1.7' AMDEPBACKSLASH='\' AMDEP_FALSE='#' AMDEP_TRUE='' AMTAR='${SHELL} /homes/6/vicka/mni/src/minc-1.1/ac_config_aux/missing --run tar' AUTOCONF='${SHELL} /homes/6/vicka/mni/src/minc-1.1/ac_config_aux/missing --run autoconf' AUTOHEADER='${SHELL} /homes/6/vicka/mni/src/minc-1.1/ac_config_aux/missing --run autoheader' AUTOMAKE='${SHELL} /homes/6/vicka/mni/src/minc-1.1/ac_config_aux/missing --run automake-1.7' AWK='awk' CC='gcc' CCDEPMODE='depmode=gcc' CFLAGS='-I/usr/pubsw/include' CPP='gcc -E' CPPFLAGS='-I/usr/pubsw/include -I/usr/pubsw/include' CYGPATH_W='echo' DEFS='' DEPDIR='.deps' ECHO='echo' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='grep -E' EXEEXT='' F77='' FFLAGS='' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s' LDFLAGS='-L/usr/pubsw/lib -L/usr/pubsw/lib' LEX='flex' LEXLIB='-lfl' LEX_OUTPUT_ROOT='lex.yy' LIBOBJS='' LIBS='-L/usr/pubsw/lib -lnetcdf -lm ' LIBTOOL='$(SHELL) $(top_builddir)/libtool' LN_S='ln -s' LTLIBOBJS='' MAKEINFO='${SHELL} /homes/6/vicka/mni/src/minc-1.1/ac_config_aux/missing --run makeinfo' OBJEXT='o' PACKAGE='minc' PACKAGE_BUGREPORT='' PACKAGE_NAME='' PACKAGE_STRING='' PACKAGE_TARNAME='' PACKAGE_VERSION='' PATH_SEPARATOR=':' RANLIB='ranlib' SET_MAKE='' SHELL='/bin/sh' STRIP='strip' VERSION='1.1' YACC='bison -y' ac_ct_CC='gcc' ac_ct_F77='' ac_ct_RANLIB='ranlib' ac_ct_STRIP='strip' am__fastdepCC_FALSE='' am__fastdepCC_TRUE='#' am__include='include' am__quote='' bindir='${exec_prefix}/bin' build='powerpc-apple-darwin6.8' build_alias='' build_cpu='powerpc' build_os='darwin6.8' build_vendor='apple' datadir='${prefix}/share' exec_prefix='NONE' host='powerpc-apple-darwin6.8' host_alias='' host_cpu='powerpc' host_os='darwin6.8' host_vendor='apple' includedir='${prefix}/include' infodir='${prefix}/info' install_sh='/homes/6/vicka/mni/src/minc-1.1/ac_config_aux/install-sh' libdir='${exec_prefix}/lib' libexecdir='${exec_prefix}/libexec' localstatedir='${prefix}/var' mandir='${prefix}/man' oldincludedir='/usr/include' prefix='/usr/pubsw/packages/minc/1.1-vicka' program_transform_name='s,x,x,' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='${prefix}/etc' target_alias='' ## ----------- ## ## confdefs.h. ## ## ----------- ## #define HAVE_DLFCN_H 1 #define HAVE_INTTYPES_H 1 #define HAVE_MEMORY_H 1 #define HAVE_STDINT_H 1 #define HAVE_STDLIB_H 1 #define HAVE_STRINGS_H 1 #define HAVE_STRING_H 1 #define HAVE_SYS_STAT_H 1 #define HAVE_SYS_TYPES_H 1 #define HAVE_UNISTD_H 1 #define PACKAGE "minc" #define PACKAGE_BUGREPORT "" #define PACKAGE_NAME "" #define PACKAGE_STRING "" #define PACKAGE_TARNAME "" #define PACKAGE_VERSION "" #define STDC_HEADERS 1 #define VERSION "1.1" #define YYTEXT_POINTER 1 configure: exit 1 --fdj2RfSjLxBAspz7-- From minc-development@bic.mni.mcgill.ca Fri Nov 7 20:49:34 2003 From: minc-development@bic.mni.mcgill.ca (Robert VINCENT) Date: Fri, 7 Nov 2003 15:49:34 -0500 Subject: [MINC-development] can't find netcdf...? In-Reply-To: <20031107154325.Q29521@gate.nmr.mgh.harvard.edu> Message-ID: Vicka, The error you're getting isn't one I've seen before - "ld" is reporting that the "table of contents for archive: /usr/pubsw/lib/libnetcdf.a is out of date; rerun ranlib(1)" I'm not certain how "ld" determines this, but my guess is that something is wrong with the netCDF build. It might be worth trying to run ranlib against the libnetcdf.a file as an experiment. -bert On Fri, 7 Nov 2003, Vicka Corey wrote: > ok, umm, the option would seem to be --with-build-path. but it still > doesn't work. > > here is my command: > ./configure --prefix=/usr/pubsw/packages/minc/1.1-vicka --with-build-path=/usr/pubsw > > ...and here is the error: > configure: error: cannot find required library netcdf > > ...anybody else? > > i will attach config.log in case that would help.... > > thanks again, > --vicka > > On Fri, Nov 07, 2003 at 02:34:46PM -0500, Andrew Janke wrote: > > On Fri, 7 Nov 2003, Vicka Corey wrote: > > > > > > $ ./configure --with-build-prefix=/usr/pubsw > > > > > > > > will work. > > > > > > alas, no luck with that, either. > > > > Bah! I'm going crazy too it would appear. > > > > Make that: > > > > $ ./configure --with-build-path=/usr/pubsw > > > > !! > > > > Either way configure --help should show this option > > > > a > > > > _______________________________________________ > > MINC-development mailing list > > MINC-development@bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development > From minc-development@bic.mni.mcgill.ca Fri Nov 7 21:08:00 2003 From: minc-development@bic.mni.mcgill.ca (Vicka Corey) Date: Fri, 7 Nov 2003 16:08:00 -0500 Subject: [MINC-development] can't find netcdf...? In-Reply-To: ; from bert@bic.mni.mcgill.ca on Fri, Nov 07, 2003 at 03:49:34PM -0500 References: <20031107154325.Q29521@gate.nmr.mgh.harvard.edu> Message-ID: <20031107160800.S29521@gate.nmr.mgh.harvard.edu> that worked. i swoon with gratitude and delight :) next...."make"! thank you *very* much! --vicka ps. this is a brand-new, just-built libnetcdf.a -- i am now somewhat concerned about *its* build process, if the output is unusuable without this additional step. but at least i'm moving on.... On Fri, Nov 07, 2003 at 03:49:34PM -0500, Robert VINCENT wrote: > Vicka, > > The error you're getting isn't one I've seen before - "ld" is reporting > that the "table of contents for archive: /usr/pubsw/lib/libnetcdf.a is out > of date; rerun ranlib(1)" > > I'm not certain how "ld" determines this, but my guess is that something > is wrong with the netCDF build. It might be worth trying to run ranlib > against the libnetcdf.a file as an experiment. > > -bert > > On Fri, 7 Nov 2003, Vicka Corey wrote: > > > ok, umm, the option would seem to be --with-build-path. but it still > > doesn't work. > > > > here is my command: > > ./configure --prefix=/usr/pubsw/packages/minc/1.1-vicka --with-build-path=/usr/pubsw > > > > ...and here is the error: > > configure: error: cannot find required library netcdf > > > > ...anybody else? > > > > i will attach config.log in case that would help.... > > > > thanks again, > > --vicka > > > > On Fri, Nov 07, 2003 at 02:34:46PM -0500, Andrew Janke wrote: > > > On Fri, 7 Nov 2003, Vicka Corey wrote: > > > > > > > > $ ./configure --with-build-prefix=/usr/pubsw > > > > > > > > > > will work. > > > > > > > > alas, no luck with that, either. > > > > > > Bah! I'm going crazy too it would appear. > > > > > > Make that: > > > > > > $ ./configure --with-build-path=/usr/pubsw > > > > > > !! > > > > > > Either way configure --help should show this option > > > > > > a > > > > > > _______________________________________________ > > > MINC-development mailing list > > > MINC-development@bic.mni.mcgill.ca > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development > > > > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development From minc-development@bic.mni.mcgill.ca Fri Nov 7 21:13:27 2003 From: minc-development@bic.mni.mcgill.ca (Vicka Corey) Date: Fri, 7 Nov 2003 16:13:27 -0500 Subject: [MINC-development] can't find netcdf...? In-Reply-To: <20031107160800.S29521@gate.nmr.mgh.harvard.edu>; from vicka@nmr.mgh.harvard.edu on Fri, Nov 07, 2003 at 04:08:00PM -0500 References: <20031107154325.Q29521@gate.nmr.mgh.harvard.edu> <20031107160800.S29521@gate.nmr.mgh.harvard.edu> Message-ID: <20031107161327.T29521@gate.nmr.mgh.harvard.edu> depressingly, minc fails to make. ld: Undefined symbols: _minc_call_depth _minc_trash_var _minc_callers_ncopts _minc_routine_name make[2]: *** [voxeltoworld] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2 ...anyone know where these are supposed to come from? or is it hair-rippin' time again? :) thanks, --vicka From minc-development@bic.mni.mcgill.ca Fri Nov 7 21:25:26 2003 From: minc-development@bic.mni.mcgill.ca (Robert VINCENT) Date: Fri, 7 Nov 2003 16:25:26 -0500 Subject: [MINC-development] can't find netcdf...? In-Reply-To: <20031107161327.T29521@gate.nmr.mgh.harvard.edu> Message-ID: Vicka, Those are all supposed to be defined in minc_globdef.o, which should be in your libminc.a I'm going to venture an ill-informed guess that there's something odd about 'ranlib' on OS X. Perhaps the following will work. From your MINC build directory, try running: ranlib .libs/libminc.a ranlib .libs/libvolume_io.a and see if the MINC programs build happily from there on... -bert On Fri, 7 Nov 2003, Vicka Corey wrote: > depressingly, minc fails to make. > > ld: Undefined symbols: > _minc_call_depth > _minc_trash_var > _minc_callers_ncopts > _minc_routine_name > make[2]: *** [voxeltoworld] Error 1 > make[1]: *** [all-recursive] Error 1 > make: *** [all] Error 2 > > ...anyone know where these are supposed to come from? or is it > hair-rippin' time again? :) > > thanks, > --vicka > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development > From minc-development@bic.mni.mcgill.ca Fri Nov 7 21:35:50 2003 From: minc-development@bic.mni.mcgill.ca (Vicka Corey) Date: Fri, 7 Nov 2003 16:35:50 -0500 Subject: [MINC-development] can't find netcdf...? In-Reply-To: ; from bert@bic.mni.mcgill.ca on Fri, Nov 07, 2003 at 04:25:26PM -0500 References: <20031107161327.T29521@gate.nmr.mgh.harvard.edu> Message-ID: <20031107163550.A3531@gate.nmr.mgh.harvard.edu> alas, same error. On Fri, Nov 07, 2003 at 04:25:26PM -0500, Robert VINCENT wrote: > Vicka, > > Those are all supposed to be defined in minc_globdef.o, which should be in > your libminc.a > > I'm going to venture an ill-informed guess that there's something odd > about 'ranlib' on OS X. > > Perhaps the following will work. From your MINC build directory, try > running: > > ranlib .libs/libminc.a > ranlib .libs/libvolume_io.a > > and see if the MINC programs build happily from there on... > > -bert > > On Fri, 7 Nov 2003, Vicka Corey wrote: > > > depressingly, minc fails to make. > > > > ld: Undefined symbols: > > _minc_call_depth > > _minc_trash_var > > _minc_callers_ncopts > > _minc_routine_name > > make[2]: *** [voxeltoworld] Error 1 > > make[1]: *** [all-recursive] Error 1 > > make: *** [all] Error 2 > > > > ...anyone know where these are supposed to come from? or is it > > hair-rippin' time again? :) > > > > thanks, > > --vicka > > _______________________________________________ > > MINC-development mailing list > > MINC-development@bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development > > > > > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development From minc-development@bic.mni.mcgill.ca Fri Nov 7 21:43:05 2003 From: minc-development@bic.mni.mcgill.ca (Vicka Corey) Date: Fri, 7 Nov 2003 16:43:05 -0500 Subject: [MINC-development] can't find netcdf...? In-Reply-To: ; from bert@bic.mni.mcgill.ca on Fri, Nov 07, 2003 at 04:25:26PM -0500 References: <20031107161327.T29521@gate.nmr.mgh.harvard.edu> Message-ID: <20031107164305.B3531@gate.nmr.mgh.harvard.edu> oh wait, i think maybe i see the problem: the command that's running is: gcc -I/usr/pubsw/include -o voxeltoworld progs/coordinates/voxeltoworld.o -L/usr/pubsw/lib ./.libs/libvolume_io.a ./.libs/libminc.a -lnetcdf -lm should that work? do those "./[...].a"'s need some -l-like or -L-like flag? (this gcc line is the output of "make"; it just looks weird to me) thanks, --vicka On Fri, Nov 07, 2003 at 04:25:26PM -0500, Robert VINCENT wrote: > Vicka, > > Those are all supposed to be defined in minc_globdef.o, which should be in > your libminc.a > > I'm going to venture an ill-informed guess that there's something odd > about 'ranlib' on OS X. > > Perhaps the following will work. From your MINC build directory, try > running: > > ranlib .libs/libminc.a > ranlib .libs/libvolume_io.a > > and see if the MINC programs build happily from there on... > > -bert > > On Fri, 7 Nov 2003, Vicka Corey wrote: > > > depressingly, minc fails to make. > > > > ld: Undefined symbols: > > _minc_call_depth > > _minc_trash_var > > _minc_callers_ncopts > > _minc_routine_name > > make[2]: *** [voxeltoworld] Error 1 > > make[1]: *** [all-recursive] Error 1 > > make: *** [all] Error 2 > > > > ...anyone know where these are supposed to come from? or is it > > hair-rippin' time again? :) > > > > thanks, > > --vicka > > _______________________________________________ > > MINC-development mailing list > > MINC-development@bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development > > > > > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development From minc-development@bic.mni.mcgill.ca Tue Nov 11 20:12:35 2003 From: minc-development@bic.mni.mcgill.ca (Steve ROBBINS) Date: Tue, 11 Nov 2003 15:12:35 -0500 Subject: [MINC-development] can't find netcdf...? In-Reply-To: <20031107160800.S29521@gate.nmr.mgh.harvard.edu>; from vicka@nmr.mgh.harvard.edu on Fri, Nov 07, 2003 at 04:08:00PM -0500 References: <20031107154325.Q29521@gate.nmr.mgh.harvard.edu> <20031107160800.S29521@gate.nmr.mgh.harvard.edu> Message-ID: <20031111151235.P4171602@shadow.bic.mni.mcgill.ca> On Fri, Nov 07, 2003 at 04:08:00PM -0500, Vicka Corey wrote: > ps. this is a brand-new, just-built libnetcdf.a -- i am now somewhat > concerned about *its* build process, if the output is unusuable > without this additional step. but at least i'm moving on.... Yes, it looks like the netcdf install procedure is broken. You need to run "ranlib" after copying the newly-built library, see: http://developer.apple.com/documentation/Darwin/Reference/ManPages/html/libtool.1.html (the BUGS section implies it is just a warning, but your experience suggests that it is actually a fatal error). -Steve From minc-development@bic.mni.mcgill.ca Tue Nov 11 20:18:53 2003 From: minc-development@bic.mni.mcgill.ca (Steve ROBBINS) Date: Tue, 11 Nov 2003 15:18:53 -0500 Subject: [MINC-development] can't find netcdf...? In-Reply-To: <20031107161327.T29521@gate.nmr.mgh.harvard.edu>; from vicka@nmr.mgh.harvard.edu on Fri, Nov 07, 2003 at 04:13:27PM -0500 References: <20031107154325.Q29521@gate.nmr.mgh.harvard.edu> <20031107160800.S29521@gate.nmr.mgh.harvard.edu> <20031107161327.T29521@gate.nmr.mgh.harvard.edu> Message-ID: <20031111151853.Q4171602@shadow.bic.mni.mcgill.ca> On Fri, Nov 07, 2003 at 04:13:27PM -0500, Vicka Corey wrote: > depressingly, minc fails to make. > > ld: Undefined symbols: > _minc_call_depth > _minc_trash_var > _minc_callers_ncopts > _minc_routine_name > make[2]: *** [voxeltoworld] Error 1 > make[1]: *** [all-recursive] Error 1 > make: *** [all] Error 2 > > ...anyone know where these are supposed to come from? or is it > hair-rippin' time again? :) Those should come from libsrc/minc_globdef.c. Try this: rm libminc.la make libminc.la and send the output. If you don't see a ranlib invocation, try ranlib .libs/libminc.a make Regards, -Steve From minc-development@bic.mni.mcgill.ca Fri Nov 21 20:02:30 2003 From: minc-development@bic.mni.mcgill.ca (Vicka Corey) Date: Fri, 21 Nov 2003 15:02:30 -0500 Subject: [MINC-development] mincresample error? Message-ID: <20031121150229.A9717@gate.nmr.mgh.harvard.edu> hi -- i'm trying (yet again!) to build an osx (still 10.2) tarball minc (still 1.1) tools for folks to use with freesurfer. i am trying to run a recon-all script (which is a freesurfer thing) and it dies thus: Resampling /tmp/cor-2.mnc Fri Nov 21 14:43:25 EST 2003 ncopen: filename "/tmp/cor-1.mnc": Invalid dimension id or name miopen: MINC package entry point ERROR: mincresample failed ERROR: mri_motion_correct exited with non-zero status ....anybody know what that error might mean, or how i might address it? i believe this is the first call to mincresample in the script. thanks, --vicka From minc-development@bic.mni.mcgill.ca Fri Nov 21 20:06:59 2003 From: minc-development@bic.mni.mcgill.ca (Andrew Janke) Date: Fri, 21 Nov 2003 15:06:59 -0500 Subject: [MINC-development] mincresample error? In-Reply-To: <20031121150229.A9717@gate.nmr.mgh.harvard.edu> Message-ID: On Fri, 21 Nov 2003, Vicka Corey wrote: > i'm trying (yet again!) to build an osx (still 10.2) tarball > minc (still 1.1) tools for folks to use with freesurfer. > i am trying to run a recon-all script (which is a freesurfer > thing) and it dies thus: > > Resampling /tmp/cor-2.mnc > Fri Nov 21 14:43:25 EST 2003 > ncopen: filename "/tmp/cor-1.mnc": Invalid dimension id or name > miopen: MINC package entry point > ERROR: mincresample failed > ERROR: mri_motion_correct exited with non-zero status Dig through mri_motion_correct and send the arguments that mincresample was called with. And while you are at it do a 'mincinfo on /tmp/cor-1.mnc' and send the output. -- Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From minc-development@bic.mni.mcgill.ca Fri Nov 21 20:15:46 2003 From: minc-development@bic.mni.mcgill.ca (Steve ROBBINS) Date: Fri, 21 Nov 2003 15:15:46 -0500 Subject: [MINC-development] mincresample error? In-Reply-To: ; from rotor@bic.mni.mcgill.ca on Fri, Nov 21, 2003 at 03:06:59PM -0500 References: <20031121150229.A9717@gate.nmr.mgh.harvard.edu> Message-ID: <20031121151546.D6123806@shadow.bic.mni.mcgill.ca> On Fri, Nov 21, 2003 at 03:06:59PM -0500, Andrew Janke wrote: > On Fri, 21 Nov 2003, Vicka Corey wrote: > > > i'm trying (yet again!) to build an osx (still 10.2) tarball > > minc (still 1.1) tools for folks to use with freesurfer. > > i am trying to run a recon-all script (which is a freesurfer > > thing) and it dies thus: > > > > Resampling /tmp/cor-2.mnc > > Fri Nov 21 14:43:25 EST 2003 > > ncopen: filename "/tmp/cor-1.mnc": Invalid dimension id or name > > miopen: MINC package entry point > > ERROR: mincresample failed > > ERROR: mri_motion_correct exited with non-zero status > > Dig through mri_motion_correct and send the arguments that mincresample was > called with. > > And while you are at it do a 'mincinfo on /tmp/cor-1.mnc' and send the output. In addition to what Andrew said, just double-check that you don't have a problem with disk space or permissions along the way. -Steve From minc-development@bic.mni.mcgill.ca Sun Nov 23 12:44:14 2003 From: minc-development@bic.mni.mcgill.ca (Jason Lerch) Date: Sun, 23 Nov 2003 07:44:14 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip Message-ID: --Boundary_(ID_/01n1O6gO/22SbxG0L5CYA) Content-type: text/plain; charset=US-ASCII; format=flowed Content-transfer-encoding: 7BIT Greetings folks, here's a patch (against CVS version of minc) fixing an issue on OS X - namely that, in order for gzipped minc files to be handled correctly, #define unix has to be true. I've replaced that with a configure time check for gunzip. Thanks to Sridar for pointing this out! Cheers, Jason --Boundary_(ID_/01n1O6gO/22SbxG0L5CYA) Content-type: application/octet-stream; x-unix-mode=0644; name=jpl_gunzip.patch Content-transfer-encoding: 7bit Content-disposition: attachment; filename=jpl_gunzip.patch ? jpl_gunzip.patch Index: configure.in =================================================================== RCS file: /software/source/minc/cvsroot/minc/configure.in,v retrieving revision 6.12 diff -u -b -B -r6.12 configure.in --- configure.in 14 Nov 2003 05:01:51 -0000 6.12 +++ configure.in 23 Nov 2003 12:27:48 -0000 @@ -4,7 +4,7 @@ AC_CONFIG_SRCDIR([libsrc/minc.h]) AC_CONFIG_AUX_DIR(ac_config_aux) AM_INIT_AUTOMAKE(minc, 1.2) -AC_CONFIG_HEADERS([config.h]) +AM_CONFIG_HEADER([config.h]) AC_REVISION($Revision: 6.12 $) @@ -35,6 +35,12 @@ dnl need ac 2.57 for this? AC_CONFIG_LIBOBJ_DIR(libsrc) AC_REPLACE_FUNCS(strdup) + +dnl check for gzip +AC_PATH_PROGS(GUNZIP, gunzip, no) +if test "$GUNZIP" != no; then + AC_DEFINE(HAVE_GUNZIP, 1, [Program gunzip exists]) +fi dnl Verify existence of mkstemp, tempnam, and tmpnam AC_CHECK_FUNCS(mkstemp tempnam tmpnam) Index: libsrc/netcdf_convenience.c =================================================================== RCS file: /software/source/minc/cvsroot/minc/libsrc/netcdf_convenience.c,v retrieving revision 6.8 diff -u -b -B -r6.8 netcdf_convenience.c --- libsrc/netcdf_convenience.c 17 Mar 2003 16:15:33 -0000 6.8 +++ libsrc/netcdf_convenience.c 23 Nov 2003 12:27:50 -0000 @@ -189,7 +189,7 @@ #define BYTES_PER_OPEN (1024*64) #define NUM_BUFFERS_PER_OPEN ((BYTES_PER_OPEN - 1) / sizeof(buffer) + 1) -#ifndef unix +#ifndef HAVE_GUNZIP return 1; --Boundary_(ID_/01n1O6gO/22SbxG0L5CYA)-- From minc-development@bic.mni.mcgill.ca Sun Nov 23 15:59:09 2003 From: minc-development@bic.mni.mcgill.ca (Steve ROBBINS) Date: Sun, 23 Nov 2003 10:59:09 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: ; from jason@bic.mni.mcgill.ca on Sun, Nov 23, 2003 at 07:44:14AM -0500 References: Message-ID: <20031123105909.A6472338@shadow.bic.mni.mcgill.ca> On Sun, Nov 23, 2003 at 07:44:14AM -0500, Jason Lerch wrote: > Greetings folks, > > here's a patch (against CVS version of minc) fixing an issue on OS X - > namely that, in order for gzipped minc files to be handled correctly, > #define unix has to be true. I've replaced that with a configure time > check for gunzip. Checking for gunzip rather than unix is an improvement, certainly. One then worries about the possibility that gunzip is not installed when MINC is built, but is installed later. Moreover the programs "bunzip2", "zcat" and "pcat" are also used to decompress MINC files. The function execute_decompress_command() requires the unix-like (probably POSIX is enough) functions: system(), popen(), and fork(). I'd suggest an alternate patch that checks for those three functions, rather than for "gzip". I'll post a patch later today. -S From minc-development@bic.mni.mcgill.ca Sun Nov 23 19:17:08 2003 From: minc-development@bic.mni.mcgill.ca (Steve ROBBINS) Date: Sun, 23 Nov 2003 14:17:08 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: <20031123105909.A6472338@shadow.bic.mni.mcgill.ca>; from stever@bic.mni.mcgill.ca on Sun, Nov 23, 2003 at 10:59:09AM -0500 References: <20031123105909.A6472338@shadow.bic.mni.mcgill.ca> Message-ID: <20031123141708.B6472338@shadow.bic.mni.mcgill.ca> --fdj2RfSjLxBAspz7 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline On Sun, Nov 23, 2003 at 10:59:09AM -0500, Steve ROBBINS wrote: > The function execute_decompress_command() requires the unix-like (probably > POSIX is enough) functions: system(), popen(), and fork(). I'd suggest > an alternate patch that checks for those three functions, rather than > for "gzip". I'll post a patch later today. Here's the proposed patch. -S --fdj2RfSjLxBAspz7 Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename=diff ? minc-1.3.tar.gz Index: ChangeLog =================================================================== RCS file: /software/source/minc/cvsroot/minc/ChangeLog,v retrieving revision 1.26 diff -u -b -B -r1.26 ChangeLog --- ChangeLog 23 Nov 2003 16:07:11 -0000 1.26 +++ ChangeLog 23 Nov 2003 19:14:14 -0000 @@ -1,3 +1,13 @@ +2003-11-23 Steve M. Robbins + + * configure.in: Set version to 1.3. Check for headers sys/stat.h, + sys/wait.h, unistd.h; and for functions fork, system, and popen. + + * libsrc/netcdf_convenience.c: Use above checks for conditional + inclusion of headers. + (execute_decompress_command): Use fork or system to decompress + file, if facility available. + 2003-11-21 Steve ROBBINS * volume_io/Include/basic.h: Include for M_PI definition. Index: NEWS =================================================================== RCS file: /software/source/minc/cvsroot/minc/NEWS,v retrieving revision 1.7 diff -u -b -B -r1.7 NEWS --- NEWS 14 Nov 2003 05:01:51 -0000 1.7 +++ NEWS 23 Nov 2003 19:14:15 -0000 @@ -1,3 +1,9 @@ + New in Release 1.3 + ------------------ + +* Build fixes. + + New in Release 1.2 ------------------ Index: configure.in =================================================================== RCS file: /software/source/minc/cvsroot/minc/configure.in,v retrieving revision 6.12 diff -u -b -B -r6.12 configure.in --- configure.in 14 Nov 2003 05:01:51 -0000 6.12 +++ configure.in 23 Nov 2003 19:14:15 -0000 @@ -3,7 +3,7 @@ AC_INIT AC_CONFIG_SRCDIR([libsrc/minc.h]) AC_CONFIG_AUX_DIR(ac_config_aux) -AM_INIT_AUTOMAKE(minc, 1.2) +AM_INIT_AUTOMAKE(minc, 1.3) AC_CONFIG_HEADERS([config.h]) AC_REVISION($Revision: 6.12 $) @@ -19,7 +19,7 @@ AC_PROG_YACC AC_HEADER_TIME -AC_CHECK_HEADERS(sys/time.h) +AC_CHECK_HEADERS(sys/time.h sys/stat.h sys/wait.h unistd.h) dnl Build only static libs by default AC_DISABLE_SHARED @@ -38,6 +38,10 @@ dnl Verify existence of mkstemp, tempnam, and tmpnam AC_CHECK_FUNCS(mkstemp tempnam tmpnam) + +# Functions required for execute_decompress_command(). +AC_FUNC_FORK +AC_CHECK_FUNCS(system popen) dnl This link is needed to allow style includes. AC_CONFIG_LINKS(volume_io/Include/volume_io:volume_io/Include) Index: libsrc/netcdf_convenience.c =================================================================== RCS file: /software/source/minc/cvsroot/minc/libsrc/netcdf_convenience.c,v retrieving revision 6.8 diff -u -b -B -r6.8 netcdf_convenience.c --- libsrc/netcdf_convenience.c 17 Mar 2003 16:15:33 -0000 6.8 +++ libsrc/netcdf_convenience.c 23 Nov 2003 19:14:17 -0000 @@ -141,9 +141,16 @@ #include "config.h" /* From configure */ #include -#ifdef unix + +#if HAVE_UNISTD_H #include +#endif + +#if HAVE_SYS_WAIT_H #include +#endif + +#if HAVE_SYS_STAT_H #include /* For S_IREAD, S_IWRITE */ #endif @@ -189,7 +196,7 @@ #define BYTES_PER_OPEN (1024*64) #define NUM_BUFFERS_PER_OPEN ((BYTES_PER_OPEN - 1) / sizeof(buffer) + 1) -#ifndef unix +#if !(HAVE_WORKING_FORK && HAVE_SYSTEM && HAVE_POPEN) return 1; --fdj2RfSjLxBAspz7-- From minc-development@bic.mni.mcgill.ca Mon Nov 24 15:43:04 2003 From: minc-development@bic.mni.mcgill.ca (Jason Lerch) Date: Mon, 24 Nov 2003 10:43:04 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: <20031123141708.B6472338@shadow.bic.mni.mcgill.ca> References: <20031123105909.A6472338@shadow.bic.mni.mcgill.ca> <20031123141708.B6472338@shadow.bic.mni.mcgill.ca> Message-ID: This patch appears to do the trick on OS X. I still get this warning when running autogen.sh, which I had fixed in my earlier patch (though I'm not sure how much it actually matters): configure.in:7: `automake requires `AM_CONFIG_HEADER', not `AC_CONFIG_HEADER' Thanks Steve! Jason On Nov 23, 2003, at 2:17 PM, Steve ROBBINS wrote: > On Sun, Nov 23, 2003 at 10:59:09AM -0500, Steve ROBBINS wrote: > >> The function execute_decompress_command() requires the unix-like >> (probably >> POSIX is enough) functions: system(), popen(), and fork(). I'd >> suggest >> an alternate patch that checks for those three functions, rather than >> for "gzip". I'll post a patch later today. > > Here's the proposed patch. > > -S > > > > From minc-development@bic.mni.mcgill.ca Mon Nov 24 18:03:02 2003 From: minc-development@bic.mni.mcgill.ca (Vicka Corey) Date: Mon, 24 Nov 2003 13:03:02 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip Message-ID: <200311241803.hAOI32Jr019586@gate.nmr.mgh.harvard.edu> Jason Lerch said: >This patch appears to do the trick on OS X. I still get this warning >when running autogen.sh, which I had fixed in my earlier patch (though >I'm not sure how much it actually matters): ...does this imply that there is currently a working, usable os x version? if so, can i get ahold of it? i am currently in the middle of yet another os x rebuild, and if there's already a wheel out there, i'd just as soon quit trying to reinvent it :) thanks, --vicka From minc-development@bic.mni.mcgill.ca Mon Nov 24 18:07:30 2003 From: minc-development@bic.mni.mcgill.ca (Jason Lerch) Date: Mon, 24 Nov 2003 13:07:30 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: <200311241803.hAOI32Jr019586@gate.nmr.mgh.harvard.edu> References: <200311241803.hAOI32Jr019586@gate.nmr.mgh.harvard.edu> Message-ID: <11E93682-1EA9-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> Hello Vicka, yes, I've compiled all of our tools under OS 10.3 for the MINC-workshop that we had last week. I will soon put the contents of that CD (including the Mac installer) on our web-page. (I encountered none of the problems you appeared to be having when I was doing the compiles). Cheers, Jason On Nov 24, 2003, at 1:03 PM, Vicka Corey wrote: > Jason Lerch said: >> This patch appears to do the trick on OS X. I still get this warning >> when running autogen.sh, which I had fixed in my earlier patch (though >> I'm not sure how much it actually matters): > > ...does this imply that there is currently a working, usable os x > version? > > if so, can i get ahold of it? > > i am currently in the middle of yet another os x rebuild, and if > there's > already a wheel out there, i'd just as soon quit trying to reinvent it > :) > > thanks, > --vicka > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development From minc-development@bic.mni.mcgill.ca Mon Nov 24 18:18:14 2003 From: minc-development@bic.mni.mcgill.ca (Vicka Corey) Date: Mon, 24 Nov 2003 13:18:14 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: <11E93682-1EA9-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca>; from jason@bic.mni.mcgill.ca on Mon, Nov 24, 2003 at 01:07:30PM -0500 References: <200311241803.hAOI32Jr019586@gate.nmr.mgh.harvard.edu> <11E93682-1EA9-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> Message-ID: <20031124131814.A20004@gate.nmr.mgh.harvard.edu> i'm working with os x 10.2 and minc 1.1, which may explain some of the differences. but anyway i should really try your version. if nothing else i can see if it's backwards-compatible osx-wise, and how well 1.2 works with freesurfer.... (i was at the workshop; now where did i put that cd??) thanks, --vicka On Mon, Nov 24, 2003 at 01:07:30PM -0500, Jason Lerch wrote: > Hello Vicka, > > yes, I've compiled all of our tools under OS 10.3 for the MINC-workshop > that we had last week. I will soon put the contents of that CD > (including the Mac installer) on our web-page. > > (I encountered none of the problems you appeared to be having when I > was doing the compiles). > > Cheers, > > Jason > > On Nov 24, 2003, at 1:03 PM, Vicka Corey wrote: > > > Jason Lerch said: > >> This patch appears to do the trick on OS X. I still get this warning > >> when running autogen.sh, which I had fixed in my earlier patch (though > >> I'm not sure how much it actually matters): > > > > ...does this imply that there is currently a working, usable os x > > version? > > > > if so, can i get ahold of it? > > > > i am currently in the middle of yet another os x rebuild, and if > > there's > > already a wheel out there, i'd just as soon quit trying to reinvent it > > :) > > > > thanks, > > --vicka > > _______________________________________________ > > MINC-development mailing list > > MINC-development@bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development > > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development From minc-development@bic.mni.mcgill.ca Mon Nov 24 18:24:48 2003 From: minc-development@bic.mni.mcgill.ca (Jason Lerch) Date: Mon, 24 Nov 2003 13:24:48 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: <20031124131814.A20004@gate.nmr.mgh.harvard.edu> References: <200311241803.hAOI32Jr019586@gate.nmr.mgh.harvard.edu> <11E93682-1EA9-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124131814.A20004@gate.nmr.mgh.harvard.edu> Message-ID: <7CB36F8A-1EAB-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> We've gotten it all to work under 10.2.8 from my installer. But the tests weren't all that thorough, to be honest, so there might still be incompatibilities lurking somewhere (I don't know enough about OS X yet to know what to expect in this regard). For the rest of our toolkit there were a decent number of fixes I had to make in order to get out code to compile. With a bit of time all those fixes will migrate back to CVS and future releases, so hopefully OS X will soon be fully supported for all of our stuff. Cheers, Jason P.S. There was an issue with the installer and permissions under 10.2.8 - basically, you have to create the directory /usr/local/mni first and make it owned by the user who will be running the install. That problem will be fixed for the next release of the OS X installer. (As will the gzipped minc files problem). On Nov 24, 2003, at 1:18 PM, Vicka Corey wrote: > i'm working with os x 10.2 and minc 1.1, which may explain some of the > differences. but anyway i should really try your version. if nothing > else i can see if it's backwards-compatible osx-wise, and how well 1.2 > works with freesurfer.... > > (i was at the workshop; now where did i put that cd??) > > thanks, > --vicka > > On Mon, Nov 24, 2003 at 01:07:30PM -0500, Jason Lerch wrote: >> Hello Vicka, >> >> yes, I've compiled all of our tools under OS 10.3 for the >> MINC-workshop >> that we had last week. I will soon put the contents of that CD >> (including the Mac installer) on our web-page. >> >> (I encountered none of the problems you appeared to be having when I >> was doing the compiles). >> >> Cheers, >> >> Jason >> >> On Nov 24, 2003, at 1:03 PM, Vicka Corey wrote: >> >>> Jason Lerch said: >>>> This patch appears to do the trick on OS X. I still get this warning >>>> when running autogen.sh, which I had fixed in my earlier patch >>>> (though >>>> I'm not sure how much it actually matters): >>> >>> ...does this imply that there is currently a working, usable os x >>> version? >>> >>> if so, can i get ahold of it? >>> >>> i am currently in the middle of yet another os x rebuild, and if >>> there's >>> already a wheel out there, i'd just as soon quit trying to reinvent >>> it >>> :) >>> >>> thanks, >>> --vicka >>> _______________________________________________ >>> MINC-development mailing list >>> MINC-development@bic.mni.mcgill.ca >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development >> >> _______________________________________________ >> MINC-development mailing list >> MINC-development@bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development From minc-development@bic.mni.mcgill.ca Mon Nov 24 18:31:07 2003 From: minc-development@bic.mni.mcgill.ca (Vicka Corey) Date: Mon, 24 Nov 2003 13:31:07 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: <7CB36F8A-1EAB-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca>; from jason@bic.mni.mcgill.ca on Mon, Nov 24, 2003 at 01:24:48PM -0500 References: <200311241803.hAOI32Jr019586@gate.nmr.mgh.harvard.edu> <11E93682-1EA9-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124131814.A20004@gate.nmr.mgh.harvard.edu> <7CB36F8A-1EAB-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> Message-ID: <20031124133107.B20004@gate.nmr.mgh.harvard.edu> On Mon, Nov 24, 2003 at 01:24:48PM -0500, Jason Lerch wrote: > P.S. There was an issue with the installer and permissions under 10.2.8 > - basically, you have to create the directory /usr/local/mni first and > make it owned by the user who will be running the install. ...how much hardcoded-path stuff is involved with this? that's not a directory we currently use at our site.... thanks, --vicka From minc-development@bic.mni.mcgill.ca Mon Nov 24 18:37:40 2003 From: minc-development@bic.mni.mcgill.ca (Jason Lerch) Date: Mon, 24 Nov 2003 13:37:40 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: <20031124133107.B20004@gate.nmr.mgh.harvard.edu> References: <200311241803.hAOI32Jr019586@gate.nmr.mgh.harvard.edu> <11E93682-1EA9-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124131814.A20004@gate.nmr.mgh.harvard.edu> <7CB36F8A-1EAB-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124133107.B20004@gate.nmr.mgh.harvard.edu> Message-ID: <48D414B0-1EAD-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> A small amount. If all you care about are the MINC tools then it should be relocateable. The libraries are a bit trickier, since the libtool archives remember the flags (and therefore the paths) that they were compiled with and will complain if they are relocated.There are a few other applications, such as MNI-Display, which also unfortunately still depend on a few files being in a hardcoded place (which is determined at configure time when the software is being compiled). So for the purposes of the installer I've set it to be hardcoded for now to avoid any of those issues. It is also a monolithic installer at this point (i.e. has all of our tools), which might not be ideal for your purposes. Jason On Nov 24, 2003, at 1:31 PM, Vicka Corey wrote: > On Mon, Nov 24, 2003 at 01:24:48PM -0500, Jason Lerch wrote: >> P.S. There was an issue with the installer and permissions under >> 10.2.8 >> - basically, you have to create the directory /usr/local/mni first and >> make it owned by the user who will be running the install. > > ...how much hardcoded-path stuff is involved with this? that's not a > directory we currently use at our site.... > > thanks, > --vicka > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development From minc-development@bic.mni.mcgill.ca Mon Nov 24 19:33:45 2003 From: minc-development@bic.mni.mcgill.ca (Vicka Corey) Date: Mon, 24 Nov 2003 14:33:45 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: <48D414B0-1EAD-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca>; from jason@bic.mni.mcgill.ca on Mon, Nov 24, 2003 at 01:37:40PM -0500 References: <200311241803.hAOI32Jr019586@gate.nmr.mgh.harvard.edu> <11E93682-1EA9-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124131814.A20004@gate.nmr.mgh.harvard.edu> <7CB36F8A-1EAB-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124133107.B20004@gate.nmr.mgh.harvard.edu> <48D414B0-1EAD-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> Message-ID: <20031124143345.C20004@gate.nmr.mgh.harvard.edu> On Mon, Nov 24, 2003 at 01:37:40PM -0500, Jason Lerch wrote: > A small amount. If all you care about are the MINC tools then it should > be relocateable. The libraries are a bit trickier, since the libtool > archives remember the flags (and therefore the paths) that they were > compiled with and will complain if they are relocated.There are a few > other applications, such as MNI-Display, which also unfortunately still > depend on a few files being in a hardcoded place (which is determined > at configure time when the software is being compiled). So for the > purposes of the installer I've set it to be hardcoded for now to avoid > any of those issues. It is also a monolithic installer at this point > (i.e. has all of our tools), which might not be ideal for your > purposes. hmm. well, i went ahead and installed it, and tried running it with the freesurfer recon-all script. it doesn't quite succeed though: mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc transforms/talairach.xfm defined(@array) is deprecated at /usr/local/mni/lib/mni_autoreg/Startup.pm line 231. (Maybe you should just omit the defined()?) Can't locate Getopt/Tabular.pm in @INC (@INC contains: /usr/local/mni/lib/mni_autoreg usr/local/mni/lib/Library/Perl/5.8.1 /System/Library/Perl/darwin /System/Library/Perl /Library/Perl/darwin /Library/Perl /Network/Library/Perl/darwin /Network/Library/Perl .) at /usr/local/mni/bin/mritotal line 56. BEGIN failed--compilation aborted at /usr/local/mni/bin/mritotal line 56. ERROR: mritotal failed ERROR: talairach exited with non-zero status ...is Tabular.pm one of your things, or do i need to get it from some other perl distribution source? or is there something else going wrong here? thanks, --vicka From minc-development@bic.mni.mcgill.ca Mon Nov 24 20:01:44 2003 From: minc-development@bic.mni.mcgill.ca (Vicka Corey) Date: Mon, 24 Nov 2003 15:01:44 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: <20031124143345.C20004@gate.nmr.mgh.harvard.edu>; from vicka@nmr.mgh.harvard.edu on Mon, Nov 24, 2003 at 02:33:45PM -0500 References: <200311241803.hAOI32Jr019586@gate.nmr.mgh.harvard.edu> <11E93682-1EA9-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124131814.A20004@gate.nmr.mgh.harvard.edu> <7CB36F8A-1EAB-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124133107.B20004@gate.nmr.mgh.harvard.edu> <48D414B0-1EAD-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124143345.C20004@gate.nmr.mgh.harvard.edu> Message-ID: <20031124150144.D20004@gate.nmr.mgh.harvard.edu> i said: > mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc transforms/talairach.xfm > defined(@array) is deprecated at /usr/local/mni/lib/mni_autoreg/Startup.pm line 231. > (Maybe you should just omit the defined()?) > Can't locate Getopt/Tabular.pm in @INC (@INC contains: /usr/local/mni/lib/mni_autoreg usr/local/mni/lib/Library/Perl/5.8.1 /System/Library/Perl/darwin /System/Library/Perl /Library/Perl/darwin /Library/Perl /Network/Library/Perl/darwin /Network/Library/Perl .) at /usr/local/mni/bin/mritotal line 56. > BEGIN failed--compilation aborted at /usr/local/mni/bin/mritotal line 56. > ERROR: mritotal failed > ERROR: talairach exited with non-zero status > > ...is Tabular.pm one of your things, or do i need to get it from some other > perl distribution source? or is there something else going wrong here? ...and the odd thing is, Getopt/Tabular.pm is there: ocelot:vicka[161] find /usr -name Tabular.pm -ls 1331082 56 -r--r--r-- 1 corey wheel 26892 Apr 7 1999 /usr/local/mni/lib/Library/Perl/5.8.1/Getopt/Tabular.pm ocelot:vicka[162] ...so now i am rather confused :/ --vicka From minc-development@bic.mni.mcgill.ca Mon Nov 24 20:40:58 2003 From: minc-development@bic.mni.mcgill.ca (Sylvain MILOT) Date: Mon, 24 Nov 2003 15:40:58 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: <20031124150144.D20004@gate.nmr.mgh.harvard.edu> Message-ID: Hello, I couldn't help but notice the missong "/" in the @INC definition below: usr/local/mni/lib/Library/Perl/5.8.1 I forget where this is set ... but moving the Getopt directory to /usr/local/mni/lib/mni_autoreg should fix the problem since it is part of @INC Sylvain On Mon, 24 Nov 2003, Vicka Corey wrote: > i said: > > mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc transforms/talairach.xfm > > defined(@array) is deprecated at /usr/local/mni/lib/mni_autoreg/Startup.pm line 231. > > (Maybe you should just omit the defined()?) > > Can't locate Getopt/Tabular.pm in @INC (@INC contains: /usr/local/mni/lib/mni_autoreg usr/local/mni/lib/Library/Perl/5.8.1 /System/Library/Perl/darwin /System/Library/Perl /Library/Perl/darwin /Library/Perl /Network/Library/Perl/darwin /Network/Library/Perl .) at /usr/local/mni/bin/mritotal line 56. > > BEGIN failed--compilation aborted at /usr/local/mni/bin/mritotal line 56. > > ERROR: mritotal failed > > ERROR: talairach exited with non-zero status > > > > ...is Tabular.pm one of your things, or do i need to get it from some other > > perl distribution source? or is there something else going wrong here? > > ...and the odd thing is, Getopt/Tabular.pm is there: > ocelot:vicka[161] find /usr -name Tabular.pm -ls > 1331082 56 -r--r--r-- 1 corey wheel 26892 Apr 7 1999 /usr/local/mni/lib/Library/Perl/5.8.1/Getopt/Tabular.pm > ocelot:vicka[162] > > ...so now i am rather confused :/ > > --vicka > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development > --- Sylvain Milot (sylvain@bic.mni.mcgill.ca) Positron Imaging Laboratories Montreal Neurological Institute Webster 2B, Room 208 Montreal, Qc., Canada, H3A 2B4 Phone: (514)-398-4965, 1996 Fax: 8948 From minc-development@bic.mni.mcgill.ca Mon Nov 24 21:03:28 2003 From: minc-development@bic.mni.mcgill.ca (Jason Lerch) Date: Mon, 24 Nov 2003 16:03:28 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: <20031124150144.D20004@gate.nmr.mgh.harvard.edu> References: <200311241803.hAOI32Jr019586@gate.nmr.mgh.harvard.edu> <11E93682-1EA9-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124131814.A20004@gate.nmr.mgh.harvard.edu> <7CB36F8A-1EAB-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124133107.B20004@gate.nmr.mgh.harvard.edu> <48D414B0-1EAD-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124143345.C20004@gate.nmr.mgh.harvard.edu> <20031124150144.D20004@gate.nmr.mgh.harvard.edu> Message-ID: The key is in setting the environment variable PERL5LIB - and, like Sylvain pointed out, ensuring that the leading slash is there for the /usr/local/mni line. Cheers, Jason On Nov 24, 2003, at 3:01 PM, Vicka Corey wrote: > i said: >> mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc >> transforms/talairach.xfm >> defined(@array) is deprecated at >> /usr/local/mni/lib/mni_autoreg/Startup.pm line 231. >> (Maybe you should just omit the defined()?) >> Can't locate Getopt/Tabular.pm in @INC (@INC contains: >> /usr/local/mni/lib/mni_autoreg usr/local/mni/lib/Library/Perl/5.8.1 >> /System/Library/Perl/darwin /System/Library/Perl /Library/Perl/darwin >> /Library/Perl /Network/Library/Perl/darwin /Network/Library/Perl .) >> at /usr/local/mni/bin/mritotal line 56. >> BEGIN failed--compilation aborted at /usr/local/mni/bin/mritotal line >> 56. >> ERROR: mritotal failed >> ERROR: talairach exited with non-zero status >> >> ...is Tabular.pm one of your things, or do i need to get it from some >> other >> perl distribution source? or is there something else going wrong >> here? > > ...and the odd thing is, Getopt/Tabular.pm is there: > ocelot:vicka[161] find /usr -name Tabular.pm -ls > 1331082 56 -r--r--r-- 1 corey wheel 26892 Apr 7 1999 > /usr/local/mni/lib/Library/Perl/5.8.1/Getopt/Tabular.pm > ocelot:vicka[162] > > ...so now i am rather confused :/ > > --vicka > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development From minc-development@bic.mni.mcgill.ca Mon Nov 24 21:16:55 2003 From: minc-development@bic.mni.mcgill.ca (Vicka Corey) Date: Mon, 24 Nov 2003 16:16:55 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: ; from jason@bic.mni.mcgill.ca on Mon, Nov 24, 2003 at 04:03:28PM -0500 References: <200311241803.hAOI32Jr019586@gate.nmr.mgh.harvard.edu> <11E93682-1EA9-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124131814.A20004@gate.nmr.mgh.harvard.edu> <7CB36F8A-1EAB-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124133107.B20004@gate.nmr.mgh.harvard.edu> <48D414B0-1EAD-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124143345.C20004@gate.nmr.mgh.harvard.edu> <20031124150144.D20004@gate.nmr.mgh.harvard.edu> Message-ID: <20031124161655.E20004@gate.nmr.mgh.harvard.edu> got it :) btw, this is wrong in the ReadMe.rtf document included on the cd, so you might want to change it there.... thanks, --vicka On Mon, Nov 24, 2003 at 04:03:28PM -0500, Jason Lerch wrote: > The key is in setting the environment variable PERL5LIB - and, like > Sylvain pointed out, ensuring that the leading slash is there for the > /usr/local/mni line. > > Cheers, > > Jason > > On Nov 24, 2003, at 3:01 PM, Vicka Corey wrote: > > > i said: > >> mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc > >> transforms/talairach.xfm > >> defined(@array) is deprecated at > >> /usr/local/mni/lib/mni_autoreg/Startup.pm line 231. > >> (Maybe you should just omit the defined()?) > >> Can't locate Getopt/Tabular.pm in @INC (@INC contains: > >> /usr/local/mni/lib/mni_autoreg usr/local/mni/lib/Library/Perl/5.8.1 > >> /System/Library/Perl/darwin /System/Library/Perl /Library/Perl/darwin > >> /Library/Perl /Network/Library/Perl/darwin /Network/Library/Perl .) > >> at /usr/local/mni/bin/mritotal line 56. > >> BEGIN failed--compilation aborted at /usr/local/mni/bin/mritotal line > >> 56. > >> ERROR: mritotal failed > >> ERROR: talairach exited with non-zero status > >> > >> ...is Tabular.pm one of your things, or do i need to get it from some > >> other > >> perl distribution source? or is there something else going wrong > >> here? > > > > ...and the odd thing is, Getopt/Tabular.pm is there: > > ocelot:vicka[161] find /usr -name Tabular.pm -ls > > 1331082 56 -r--r--r-- 1 corey wheel 26892 Apr 7 1999 > > /usr/local/mni/lib/Library/Perl/5.8.1/Getopt/Tabular.pm > > ocelot:vicka[162] > > > > ...so now i am rather confused :/ > > > > --vicka > > _______________________________________________ > > MINC-development mailing list > > MINC-development@bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development > > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development From minc-development@bic.mni.mcgill.ca Mon Nov 24 21:18:59 2003 From: minc-development@bic.mni.mcgill.ca (Vicka Corey) Date: Mon, 24 Nov 2003 16:18:59 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: ; from jason@bic.mni.mcgill.ca on Mon, Nov 24, 2003 at 04:03:28PM -0500 References: <200311241803.hAOI32Jr019586@gate.nmr.mgh.harvard.edu> <11E93682-1EA9-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124131814.A20004@gate.nmr.mgh.harvard.edu> <7CB36F8A-1EAB-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124133107.B20004@gate.nmr.mgh.harvard.edu> <48D414B0-1EAD-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124143345.C20004@gate.nmr.mgh.harvard.edu> <20031124150144.D20004@gate.nmr.mgh.harvard.edu> Message-ID: <20031124161858.F20004@gate.nmr.mgh.harvard.edu> ...and having gotten past that, we bring you the next in error messages: nu_correct -clobber nu/nu0.mnc nu/nu1.mnc [vicka@ocelot.nmr.mgh.harvard.edu:/private/space/birn/2/users/vicka/subjects/bert/mri/] [2003-11-24 16:16:04] running: /usr/local/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /var/tmp/nu_correct_2481/ nu/nu0.mnc nu/nu1.imp expected floating-point argument for "-const" but got"DEBUG: state of _s: 0 DEBUG: state of _s: 0 DEBUG: state of path: /tmp/test DEBUG: state of _s: 0 0" Usage: /usr/local/mni/bin/mincmath [options] [ ...] /usr/local/mni/bin/mincmath -help nu_estimate_np_and_em: crashed while running mincmath (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct ------------------------------------------ Filesystem 512-blocks Used Avail Capacity Mounted on birn:/local_mount/space/birn/2 131980784 8524680 123456104 6% /private/space/birn/2 ------------------------------------------ i gather that the last bit is a check for space, which looks fine. this looks to me like nu_correct not properly calling mincmath somehow? any ideas? thanks, --vicka From minc-development@bic.mni.mcgill.ca Mon Nov 24 21:55:06 2003 From: minc-development@bic.mni.mcgill.ca (Jason Lerch) Date: Mon, 24 Nov 2003 16:55:06 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: <20031124161655.E20004@gate.nmr.mgh.harvard.edu> References: <200311241803.hAOI32Jr019586@gate.nmr.mgh.harvard.edu> <11E93682-1EA9-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124131814.A20004@gate.nmr.mgh.harvard.edu> <7CB36F8A-1EAB-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124133107.B20004@gate.nmr.mgh.harvard.edu> <48D414B0-1EAD-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124143345.C20004@gate.nmr.mgh.harvard.edu> <20031124150144.D20004@gate.nmr.mgh.harvard.edu> <20031124161655.E20004@gate.nmr.mgh.harvard.edu> Message-ID: On Nov 24, 2003, at 4:16 PM, Vicka Corey wrote: > got it :) btw, this is wrong in the ReadMe.rtf document included on > the cd, so you might want to change it there.... OK, thanks! The dangers of using copy and paste from the shell, I 'spose! Jason > > thanks, > --vicka > > On Mon, Nov 24, 2003 at 04:03:28PM -0500, Jason Lerch wrote: >> The key is in setting the environment variable PERL5LIB - and, like >> Sylvain pointed out, ensuring that the leading slash is there for the >> /usr/local/mni line. >> >> Cheers, >> >> Jason >> >> On Nov 24, 2003, at 3:01 PM, Vicka Corey wrote: >> >>> i said: >>>> mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc >>>> transforms/talairach.xfm >>>> defined(@array) is deprecated at >>>> /usr/local/mni/lib/mni_autoreg/Startup.pm line 231. >>>> (Maybe you should just omit the defined()?) >>>> Can't locate Getopt/Tabular.pm in @INC (@INC contains: >>>> /usr/local/mni/lib/mni_autoreg usr/local/mni/lib/Library/Perl/5.8.1 >>>> /System/Library/Perl/darwin /System/Library/Perl >>>> /Library/Perl/darwin >>>> /Library/Perl /Network/Library/Perl/darwin /Network/Library/Perl .) >>>> at /usr/local/mni/bin/mritotal line 56. >>>> BEGIN failed--compilation aborted at /usr/local/mni/bin/mritotal >>>> line >>>> 56. >>>> ERROR: mritotal failed >>>> ERROR: talairach exited with non-zero status >>>> >>>> ...is Tabular.pm one of your things, or do i need to get it from >>>> some >>>> other >>>> perl distribution source? or is there something else going wrong >>>> here? >>> >>> ...and the odd thing is, Getopt/Tabular.pm is there: >>> ocelot:vicka[161] find /usr -name Tabular.pm -ls >>> 1331082 56 -r--r--r-- 1 corey wheel 26892 Apr 7 1999 >>> /usr/local/mni/lib/Library/Perl/5.8.1/Getopt/Tabular.pm >>> ocelot:vicka[162] >>> >>> ...so now i am rather confused :/ >>> >>> --vicka >>> _______________________________________________ >>> MINC-development mailing list >>> MINC-development@bic.mni.mcgill.ca >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development >> >> _______________________________________________ >> MINC-development mailing list >> MINC-development@bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development From minc-development@bic.mni.mcgill.ca Mon Nov 24 22:15:11 2003 From: minc-development@bic.mni.mcgill.ca (Steve ROBBINS) Date: Mon, 24 Nov 2003 17:15:11 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: <20031124161858.F20004@gate.nmr.mgh.harvard.edu>; from vicka@nmr.mgh.harvard.edu on Mon, Nov 24, 2003 at 04:18:59PM -0500 References: <200311241803.hAOI32Jr019586@gate.nmr.mgh.harvard.edu> <11E93682-1EA9-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124131814.A20004@gate.nmr.mgh.harvard.edu> <7CB36F8A-1EAB-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124133107.B20004@gate.nmr.mgh.harvard.edu> <48D414B0-1EAD-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124143345.C20004@gate.nmr.mgh.harvard.edu> <20031124150144.D20004@gate.nmr.mgh.harvard.edu> <20031124161858.F20004@gate.nmr.mgh.harvard.edu> Message-ID: <20031124171510.C6769116@shadow.bic.mni.mcgill.ca> On Mon, Nov 24, 2003 at 04:18:59PM -0500, Vicka Corey wrote: > ...and having gotten past that, we bring you the next in error messages: > > nu_correct -clobber nu/nu0.mnc nu/nu1.mnc > [vicka@ocelot.nmr.mgh.harvard.edu:/private/space/birn/2/users/vicka/subjects/bert/mri/] [2003-11-24 16:16:04] running: > /usr/local/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /var/tmp/nu_correct_2481/ nu/nu0.mnc nu/nu1.imp > > expected floating-point argument for "-const" but got"DEBUG: state of _s: 0 > DEBUG: state of _s: 0 > DEBUG: state of path: /tmp/test > DEBUG: state of _s: 0 > 0" This is a goof on our part. Apply the following diff to EBTKS, rebuild and install it, then rebuild N3. -Steve Index: ChangeLog =================================================================== RCS file: /software/source/libraries/EBTKS/ChangeLog,v retrieving revision 1.4 retrieving revision 1.5 diff -u -b -B -r1.4 -r1.5 --- ChangeLog 17 Nov 2003 04:07:51 -0000 1.4 +++ ChangeLog 21 Nov 2003 20:38:44 -0000 1.5 @@ -1,3 +1,8 @@ +2003-11-21 Steve ROBBINS + + * templates/CachedArray.cc: Remove debugging statements + erroneously left in code. + 2003-11-14 Steve ROBBINS * configure.ac: Set version to 1.0. Index: templates/CachedArray.cc =================================================================== RCS file: /software/source/libraries/EBTKS/templates/CachedArray.cc,v retrieving revision 1.5 retrieving revision 1.6 diff -u -b -B -r1.5 -r1.6 --- templates/CachedArray.cc 17 Nov 2003 04:07:52 -0000 1.5 +++ templates/CachedArray.cc 21 Nov 2003 20:38:44 -0000 1.6 @@ -12,9 +12,9 @@ express or implied warranty. ---------------------------------------------------------------------------- $RCSfile: CachedArray.cc,v $ -$Revision: 1.5 $ +$Revision: 1.6 $ $Author: stever $ -$Date: 2003/11/17 04:07:52 $ +$Date: 2003/11/21 20:38:44 $ $State: Exp $ --------------------------------------------------------------------------*/ #include @@ -478,9 +480,6 @@ { assert(_size); - cout << "DEBUG: in median of CachedArray" << endl; - cout << "DEBUG: _size = " << _size << endl; - if (_size <= _blockSize) { if (!_blocks[0]) _read(0); @@ -503,7 +502,6 @@ _read(0); return (*_blocks[0])(_size).medianVolatile(); } - cout << "DEBUG: histMedian = " << _histMedian() << endl; return _histMedian(); } @@ -723,7 +721,6 @@ void CachedArray::_openStream() { - cout << "DEBUG: state of _s: " << _s.is_open() << endl; if (_s.is_open()) _self->_s.close(); @@ -734,10 +731,7 @@ _s.open(path, ios::in|ios::out); // _s.open(path, ios::in); - cout << "DEBUG: state of path: " << path << endl; unlink(path); - - cout << "DEBUG: state of _s: " << _s.is_open() << endl; //assert(_s.is_open()); // Create file at requested size From minc-development@bic.mni.mcgill.ca Mon Nov 24 22:19:55 2003 From: minc-development@bic.mni.mcgill.ca (Jason Lerch) Date: Mon, 24 Nov 2003 17:19:55 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: <20031124171510.C6769116@shadow.bic.mni.mcgill.ca> References: <200311241803.hAOI32Jr019586@gate.nmr.mgh.harvard.edu> <11E93682-1EA9-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124131814.A20004@gate.nmr.mgh.harvard.edu> <7CB36F8A-1EAB-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124133107.B20004@gate.nmr.mgh.harvard.edu> <48D414B0-1EAD-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124143345.C20004@gate.nmr.mgh.harvard.edu> <20031124150144.D20004@gate.nmr.mgh.harvard.edu> <20031124161858.F20004@gate.nmr.mgh.harvard.edu> <20031124171510.C6769116@shadow.bic.mni.mcgill.ca> Message-ID: <551E346E-1ECC-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> Or give me another few days and I'll have the updated binary dist which fixes this and some of the other problems pointed out. Sorry about all these problems, and thanks for the (perhaps unwilling) beta testing! Jason On Nov 24, 2003, at 5:15 PM, Steve ROBBINS wrote: > On Mon, Nov 24, 2003 at 04:18:59PM -0500, Vicka Corey wrote: >> ...and having gotten past that, we bring you the next in error >> messages: >> >> nu_correct -clobber nu/nu0.mnc nu/nu1.mnc >> [vicka@ocelot.nmr.mgh.harvard.edu:/private/space/birn/2/users/vicka/ >> subjects/bert/mri/] [2003-11-24 16:16:04] running: >> /usr/local/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 >> 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify >> -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir >> /var/tmp/nu_correct_2481/ nu/nu0.mnc nu/nu1.imp >> >> expected floating-point argument for "-const" but got"DEBUG: state of >> _s: 0 >> DEBUG: state of _s: 0 >> DEBUG: state of path: /tmp/test >> DEBUG: state of _s: 0 >> 0" > > This is a goof on our part. Apply the following diff to EBTKS, > rebuild and install it, > then rebuild N3. > > -Steve > > Index: ChangeLog > =================================================================== > RCS file: /software/source/libraries/EBTKS/ChangeLog,v > retrieving revision 1.4 > retrieving revision 1.5 > diff -u -b -B -r1.4 -r1.5 > --- ChangeLog 17 Nov 2003 04:07:51 -0000 1.4 > +++ ChangeLog 21 Nov 2003 20:38:44 -0000 1.5 > @@ -1,3 +1,8 @@ > +2003-11-21 Steve ROBBINS > + > + * templates/CachedArray.cc: Remove debugging statements > + erroneously left in code. > + > 2003-11-14 Steve ROBBINS > > * configure.ac: Set version to 1.0. > Index: templates/CachedArray.cc > =================================================================== > RCS file: /software/source/libraries/EBTKS/templates/CachedArray.cc,v > retrieving revision 1.5 > retrieving revision 1.6 > diff -u -b -B -r1.5 -r1.6 > --- templates/CachedArray.cc 17 Nov 2003 04:07:52 -0000 1.5 > +++ templates/CachedArray.cc 21 Nov 2003 20:38:44 -0000 1.6 > @@ -12,9 +12,9 @@ > express or implied warranty. > > ----------------------------------------------------------------------- > ----- > $RCSfile: CachedArray.cc,v $ > -$Revision: 1.5 $ > +$Revision: 1.6 $ > $Author: stever $ > -$Date: 2003/11/17 04:07:52 $ > +$Date: 2003/11/21 20:38:44 $ > $State: Exp $ > > ----------------------------------------------------------------------- > ---*/ > #include > @@ -478,9 +480,6 @@ > { > assert(_size); > > - cout << "DEBUG: in median of CachedArray" << endl; > - cout << "DEBUG: _size = " << _size << endl; > - > if (_size <= _blockSize) { > if (!_blocks[0]) > _read(0); > @@ -503,7 +502,6 @@ > _read(0); > return (*_blocks[0])(_size).medianVolatile(); > } > - cout << "DEBUG: histMedian = " << _histMedian() << endl; > return _histMedian(); > } > > @@ -723,7 +721,6 @@ > void > CachedArray::_openStream() > { > - cout << "DEBUG: state of _s: " << _s.is_open() << endl; > if (_s.is_open()) > _self->_s.close(); > > @@ -734,10 +731,7 @@ > _s.open(path, ios::in|ios::out); > // _s.open(path, ios::in); > > - cout << "DEBUG: state of path: " << path << endl; > unlink(path); > - > - cout << "DEBUG: state of _s: " << _s.is_open() << endl; > //assert(_s.is_open()); > > // Create file at requested size > > > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development From minc-development@bic.mni.mcgill.ca Tue Nov 25 16:38:51 2003 From: minc-development@bic.mni.mcgill.ca (Vicka Corey) Date: Tue, 25 Nov 2003 11:38:51 -0500 Subject: [MINC-development] minc-patch: fixing check for gunzip In-Reply-To: <551E346E-1ECC-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca>; from jason@bic.mni.mcgill.ca on Mon, Nov 24, 2003 at 05:19:55PM -0500 References: <20031124131814.A20004@gate.nmr.mgh.harvard.edu> <7CB36F8A-1EAB-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124133107.B20004@gate.nmr.mgh.harvard.edu> <48D414B0-1EAD-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> <20031124143345.C20004@gate.nmr.mgh.harvard.edu> <20031124150144.D20004@gate.nmr.mgh.harvard.edu> <20031124161858.F20004@gate.nmr.mgh.harvard.edu> <20031124171510.C6769116@shadow.bic.mni.mcgill.ca> <551E346E-1ECC-11D8-AA3B-000A95DBBFD8@bic.mni.mcgill.ca> Message-ID: <20031125113850.I20004@gate.nmr.mgh.harvard.edu> i'm actually delighted to be testing :) feel free to send me any new binaries as they get built, or let me know when the new dist is ready... thanks, --vicka On Mon, Nov 24, 2003 at 05:19:55PM -0500, Jason Lerch wrote: > Or give me another few days and I'll have the updated binary dist which > fixes this and some of the other problems pointed out. Sorry about all > these problems, and thanks for the (perhaps unwilling) beta testing! > > Jason > > On Nov 24, 2003, at 5:15 PM, Steve ROBBINS wrote: > > > On Mon, Nov 24, 2003 at 04:18:59PM -0500, Vicka Corey wrote: > >> ...and having gotten past that, we bring you the next in error > >> messages: > >> > >> nu_correct -clobber nu/nu0.mnc nu/nu1.mnc > >> [vicka@ocelot.nmr.mgh.harvard.edu:/private/space/birn/2/users/vicka/ > >> subjects/bert/mri/] [2003-11-24 16:16:04] running: > >> /usr/local/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 > >> 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify > >> -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir > >> /var/tmp/nu_correct_2481/ nu/nu0.mnc nu/nu1.imp > >> > >> expected floating-point argument for "-const" but got"DEBUG: state of > >> _s: 0 > >> DEBUG: state of _s: 0 > >> DEBUG: state of path: /tmp/test > >> DEBUG: state of _s: 0 > >> 0" > > > > This is a goof on our part. Apply the following diff to EBTKS, > > rebuild and install it, > > then rebuild N3. > > > > -Steve > > > > Index: ChangeLog > > =================================================================== > > RCS file: /software/source/libraries/EBTKS/ChangeLog,v > > retrieving revision 1.4 > > retrieving revision 1.5 > > diff -u -b -B -r1.4 -r1.5 > > --- ChangeLog 17 Nov 2003 04:07:51 -0000 1.4 > > +++ ChangeLog 21 Nov 2003 20:38:44 -0000 1.5 > > @@ -1,3 +1,8 @@ > > +2003-11-21 Steve ROBBINS > > + > > + * templates/CachedArray.cc: Remove debugging statements > > + erroneously left in code. > > + > > 2003-11-14 Steve ROBBINS > > > > * configure.ac: Set version to 1.0. > > Index: templates/CachedArray.cc > > =================================================================== > > RCS file: /software/source/libraries/EBTKS/templates/CachedArray.cc,v > > retrieving revision 1.5 > > retrieving revision 1.6 > > diff -u -b -B -r1.5 -r1.6 > > --- templates/CachedArray.cc 17 Nov 2003 04:07:52 -0000 1.5 > > +++ templates/CachedArray.cc 21 Nov 2003 20:38:44 -0000 1.6 > > @@ -12,9 +12,9 @@ > > express or implied warranty. > > > > ----------------------------------------------------------------------- > > ----- > > $RCSfile: CachedArray.cc,v $ > > -$Revision: 1.5 $ > > +$Revision: 1.6 $ > > $Author: stever $ > > -$Date: 2003/11/17 04:07:52 $ > > +$Date: 2003/11/21 20:38:44 $ > > $State: Exp $ > > > > ----------------------------------------------------------------------- > > ---*/ > > #include > > @@ -478,9 +480,6 @@ > > { > > assert(_size); > > > > - cout << "DEBUG: in median of CachedArray" << endl; > > - cout << "DEBUG: _size = " << _size << endl; > > - > > if (_size <= _blockSize) { > > if (!_blocks[0]) > > _read(0); > > @@ -503,7 +502,6 @@ > > _read(0); > > return (*_blocks[0])(_size).medianVolatile(); > > } > > - cout << "DEBUG: histMedian = " << _histMedian() << endl; > > return _histMedian(); > > } > > > > @@ -723,7 +721,6 @@ > > void > > CachedArray::_openStream() > > { > > - cout << "DEBUG: state of _s: " << _s.is_open() << endl; > > if (_s.is_open()) > > _self->_s.close(); > > > > @@ -734,10 +731,7 @@ > > _s.open(path, ios::in|ios::out); > > // _s.open(path, ios::in); > > > > - cout << "DEBUG: state of path: " << path << endl; > > unlink(path); > > - > > - cout << "DEBUG: state of _s: " << _s.is_open() << endl; > > //assert(_s.is_open()); > > > > // Create file at requested size > > > > > > _______________________________________________ > > MINC-development mailing list > > MINC-development@bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development > > _______________________________________________ > MINC-development mailing list > MINC-development@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development