From AEtzold at gmx.de Sat Dec 1 10:47:14 2007 From: AEtzold at gmx.de (Axel Etzold) Date: Sat, 01 Dec 2007 16:47:14 +0100 Subject: [Tioga-users] Compiling problems for 64-bit linux architecture Message-ID: <20071201154714.62740@gmx.net> Dear all, when installing tioga http://www.kitp.ucsb.edu/~paxton/tioga.html, I get a cannot read symbol, bad value error (see below). I tried the gem and QUICK_INSTALL and HOME_INSTALL variants. Has somebody else had this problem ? How did they solve it - change compilation flags for -fPIC ? Best regards, Axel ------------------------------------- dhcppc0:/home/axel # gem install tioga Need to update 15 gems from http://gems.rubyforge.org ............... complete Building native extensions. This could take a while... ERROR: While executing gem ... (Gem::Installer::ExtensionBuildError) ERROR: Failed to build gem native extension. ruby extconf.rb install tioga checking for zlib.h... yes checking for compress() in -lz... yes creating Makefile make gcc -I. -I. -I/usr/local/lib/ruby/1.8/x86_64-linux -I. -DHAVE_ZLIB_H -fPIC -g -O2 -c flate.c gcc -shared -o Flate.so flate.o -L'.' -L'/usr/local/lib' -Wl,-R'/usr/local/lib' -L. -rdynamic -Wl,-export-dynamic -lz -ldl -lcrypt -lm -lc /usr/lib64/gcc/x86_64-suse-linux/4.1.2/../../../../x86_64-suse-linux/bin/ld: /usr/local/lib/libz.a(compress.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libz.a: could not read symbols: Bad value collect2: ld returned 1 exit status make: *** [Flate.so] Error 1 Gem files will remain installed in /usr/local/lib/ruby/gems/1.8/gems/tioga-1.6 for inspection. Results logged to /usr/local/lib/ruby/gems/1.8/gems/tioga-1.6/split/Flate/gem_make.out -- Psssst! Schon vom neuen GMX MultiMessenger geh?rt? Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger From fourmond at gmail.com Sat Dec 1 11:03:30 2007 From: fourmond at gmail.com (Vincent Fourmond) Date: Sat, 01 Dec 2007 17:03:30 +0100 Subject: [Tioga-users] Compiling problems for 64-bit linux architecture In-Reply-To: <20071201154714.62740@gmx.net> References: <20071201154714.62740@gmx.net> Message-ID: <475185D2.4060608@gmail.com> Hello Axel, Axel Etzold wrote: > when installing tioga > > http://www.kitp.ucsb.edu/~paxton/tioga.html, > > I get a cannot read symbol, bad value error (see below). > I tried the gem and QUICK_INSTALL and HOME_INSTALL > variants. Apparently, your system is picking up the static zlib library. You don't have any shared libz.so somewhere around (locate libz.so) ? Try to move (temporarily...) /usr/local/lib/libz.a somewhere else. If that does not work, try compiling a shared version of libz (but that really should already be the case); see http://www.zlib.net/. > Has somebody else had this problem ? How did they solve it - > change compilation flags for -fPIC ? Just for the record, it is libz that misses the -fPIC flag, not tioga (as can be seen on the line above the one failing). Cheers, Vincent From kenshen at physics.ucsb.edu Sun Dec 16 18:16:39 2007 From: kenshen at physics.ucsb.edu (Ken Shen) Date: Sun, 16 Dec 2007 15:16:39 -0800 (PST) Subject: [Tioga-users] Trouble installing Message-ID: Hi, I'm having problems installing Tioga. Running ./QUICK_INSTALL yields: ----------- checking for zlib.h... yes checking for compress() in -lz... no Error: you should have zlib (including development files) installed to build and run Tioga. You can get it there: http://www.zlib.net/ If that doesn't solve your problem, please report it on the Tioga tracker: http://rubyforge.org/tracker/?group_id=701 ----------- I reinstalled zlib-1.2.3 from zlib.net, thinking that the zlib that came with Leopard might be funny. So I have a libz.a in my /usr/local/lib. I don't know if it matters, but I don't have a libz.a in my /usr/lib, I only have libz.dylib and various versions of that (libz.1, libz.1.1.3, libz.1.2.3). Also, I have zlib.h in both /usr/include and /usr/local/include. Thanks for any help! Ken From fourmond at gmail.com Mon Dec 17 03:13:53 2007 From: fourmond at gmail.com (Vincent Fourmond) Date: Mon, 17 Dec 2007 09:13:53 +0100 Subject: [Tioga-users] Trouble installing In-Reply-To: References: Message-ID: <2e474d6f0712170013n4beea281mca973924eb5d225a@mail.gmail.com> Hello, On Dec 17, 2007 12:16 AM, Ken Shen wrote: > Hi, I'm having problems installing Tioga. Running ./QUICK_INSTALL yields: > > ----------- > checking for zlib.h... yes > checking for compress() in -lz... no > Error: you should have zlib (including development files) installed to > build and run Tioga. You can get it there: > > http://www.zlib.net/ > > If that doesn't solve your problem, please report it on the Tioga tracker: > > http://rubyforge.org/tracker/?group_id=701 > ----------- > > I reinstalled zlib-1.2.3 from zlib.net, thinking that the zlib that came > with Leopard might be funny. So I have a libz.a in my /usr/local/lib. I > don't know if it matters, but I don't have a libz.a in my /usr/lib, I only > have libz.dylib and various versions of that (libz.1, libz.1.1.3, > libz.1.2.3). Also, I have zlib.h in both /usr/include and > /usr/local/include. Funny... There should be a file split/mkmf2.log produced during the build process. Could you post it here, so we can get a better idea ? Cheers, Vincent From kenshen at physics.ucsb.edu Mon Dec 17 10:29:50 2007 From: kenshen at physics.ucsb.edu (Ken Shen) Date: Mon, 17 Dec 2007 07:29:50 -0800 (PST) Subject: [Tioga-users] Trouble installing In-Reply-To: <2e474d6f0712170013n4beea281mca973924eb5d225a@mail.gmail.com> References: <2e474d6f0712170013n4beea281mca973924eb5d225a@mail.gmail.com> Message-ID: Here is what my mkmf2.log says: have_header: checking for zlib.h... -------------------- yes "gcc -E -I/usr/local/lib/ruby/1.8 -I/usr/local/lib/ruby/1.8/universal-darwin8.0 -I. -I./include -IDvector -IDvector/include -IDtable -IDtable/include -IFlate -IFlate/include -IFunction -IFunction/include -g -O2 -fno-common -pipe -fno-common conftest.c -o conftest.i" checked program was: /* begin */ #include /* end */ -------------------- have_library: checking for compress() in -lz... -------------------- no "gcc -o conftest $INCFLAGS conftest.c -I$hdrdir -g -O2 -fno-common -pipe -fno-common $src $LIBPATH -arch i386 -lpthread -ldl -lobjc -lz" cc1: error: unrecognized command line option "-arch" checked program was: /* begin */ #include /*top*/ int main() { return 0; } int t() { compress(); return 0; } /* end */ "gcc -o conftest $INCFLAGS conftest.c -I$hdrdir -g -O2 -fno-common -pipe -fno-common $src $LIBPATH -arch i386 -lpthread -ldl -lobjc -lz" cc1: error: unrecognized command line option "-arch" checked program was: /* begin */ #include /*top*/ int main() { return 0; } int t() { void ((*volatile p)()); p = (void ((*)()))compress; return 0; } /* end */ -------------------- -Ken On Mon, 17 Dec 2007, Vincent Fourmond wrote: > Hello, > > On Dec 17, 2007 12:16 AM, Ken Shen wrote: > > Hi, I'm having problems installing Tioga. Running ./QUICK_INSTALL yields: > > > > ----------- > > checking for zlib.h... yes > > checking for compress() in -lz... no > > Error: you should have zlib (including development files) installed to > > build and run Tioga. You can get it there: > > > > http://www.zlib.net/ > > > > If that doesn't solve your problem, please report it on the Tioga tracker: > > > > http://rubyforge.org/tracker/?group_id=701 > > ----------- > > > > I reinstalled zlib-1.2.3 from zlib.net, thinking that the zlib that came > > with Leopard might be funny. So I have a libz.a in my /usr/local/lib. I > > don't know if it matters, but I don't have a libz.a in my /usr/lib, I only > > have libz.dylib and various versions of that (libz.1, libz.1.1.3, > > libz.1.2.3). Also, I have zlib.h in both /usr/include and > > /usr/local/include. > > Funny... There should be a file split/mkmf2.log produced during the > build process. Could you post it here, so we can get a better idea ? > > Cheers, > > Vincent > From fourmond at gmail.com Mon Dec 17 10:34:45 2007 From: fourmond at gmail.com (Vincent Fourmond) Date: Mon, 17 Dec 2007 16:34:45 +0100 Subject: [Tioga-users] Trouble installing In-Reply-To: References: <2e474d6f0712170013n4beea281mca973924eb5d225a@mail.gmail.com> Message-ID: <2e474d6f0712170734s314cf504ubea4b39d4fc4fb43@mail.gmail.com> Hello, On Dec 17, 2007 4:29 PM, Ken Shen wrote: > "gcc -o conftest $INCFLAGS conftest.c -I$hdrdir -g -O2 -fno-common > -pipe -fno-common $src $LIBPATH -arch i386 -lpthread -ldl -lobjc > -lz" > cc1: error: unrecognized command line option "-arch" Argh ! And you said it is building fine when you install with rubygems ? If that is the case, it is a bug in my mkmf2.rb... Could you post your rbconfig.rb (locate it, it should be in (prefix)/lib/ruby/(version)/(arch)). Cheers, Vincent From kenshen at physics.ucsb.edu Mon Dec 17 11:24:21 2007 From: kenshen at physics.ucsb.edu (Ken Shen) Date: Mon, 17 Dec 2007 08:24:21 -0800 (PST) Subject: [Tioga-users] Trouble installing In-Reply-To: <2e474d6f0712170734s314cf504ubea4b39d4fc4fb43@mail.gmail.com> References: <2e474d6f0712170013n4beea281mca973924eb5d225a@mail.gmail.com> <2e474d6f0712170734s314cf504ubea4b39d4fc4fb43@mail.gmail.com> Message-ID: Sorry, you might be confusing me with my officemate Ken Henisey! I've never installed with rubygems; I'm not even sure what that means because I am basically computer illiterate. I am running Leopard, and was informed by Bill that the Ruby that comes pre-installed on Macs is weird, so I installed a clean version from http://rubyosx.rubyforge.org/. When I type "ruby -v" at the prompt, I get "ruby 1.8.6 (2007-03-13 patchlevel 0) [universal-darwin8.0]", and "which ruby" gives "/usr/local/bin/ruby". "locate rbconfig.rb" shows 2 rbconfg.rb's, one at /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/universal-darwin9.0/rbconfig.rb and one at /usr/local/lib/ruby/1.8/universal-darwin8.0/rbconfig.rb. Since I'm using the ruby in /usr/local, here are the contents of /usr/local/lib/ruby/1.8/universal-darwin8.0/rbconfig.rb: # This file was created by mkconfig.rb when ruby was built. Any # changes made to this file will be lost the next time ruby is built. module Config RUBY_VERSION == "1.8.6" or raise "ruby lib version (1.8.6) doesn't match executable version (#{RUBY_VERSION})" TOPDIR = File.dirname(__FILE__).chomp!("/lib/ruby/1.8/universal-darwin8.0") DESTDIR = '' unless defined? DESTDIR CONFIG = {} CONFIG["DESTDIR"] = DESTDIR CONFIG["INSTALL"] = "/usr/bin/install -c" CONFIG["prefix"] = (TOPDIR || DESTDIR + "/usr/local") CONFIG["EXEEXT"] = "" CONFIG["ruby_install_name"] = "ruby" CONFIG["RUBY_INSTALL_NAME"] = "ruby" CONFIG["RUBY_SO_NAME"] = "ruby" CONFIG["SHELL"] = "/bin/sh" CONFIG["PATH_SEPARATOR"] = ":" CONFIG["PACKAGE_NAME"] = "" CONFIG["PACKAGE_TARNAME"] = "" CONFIG["PACKAGE_VERSION"] = "" CONFIG["PACKAGE_STRING"] = "" CONFIG["PACKAGE_BUGREPORT"] = "" CONFIG["exec_prefix"] = "$(prefix)" CONFIG["bindir"] = "$(exec_prefix)/bin" CONFIG["sbindir"] = "$(exec_prefix)/sbin" CONFIG["libexecdir"] = "$(exec_prefix)/libexec" CONFIG["datadir"] = "$(prefix)/share" CONFIG["sysconfdir"] = "$(prefix)/etc" CONFIG["sharedstatedir"] = "$(prefix)/com" CONFIG["localstatedir"] = "$(prefix)/var" CONFIG["libdir"] = "$(exec_prefix)/lib" CONFIG["includedir"] = "$(prefix)/include" CONFIG["oldincludedir"] = "/usr/include" CONFIG["infodir"] = "$(prefix)/info" CONFIG["mandir"] = "$(prefix)/man" CONFIG["build_alias"] = "" CONFIG["host_alias"] = "" CONFIG["target_alias"] = "" CONFIG["ECHO_C"] = "" CONFIG["ECHO_N"] = "-n" CONFIG["ECHO_T"] = "" CONFIG["LIBS"] = "-lpthread -ldl -lobjc " CONFIG["MAJOR"] = "1" CONFIG["MINOR"] = "8" CONFIG["TEENY"] = "6" CONFIG["build"] = "i686-apple-darwin8.10.1" CONFIG["build_cpu"] = "i686" CONFIG["build_vendor"] = "apple" CONFIG["build_os"] = "darwin8.10.1" CONFIG["host"] = "i686-apple-darwin8.10.1" CONFIG["host_cpu"] = "i686" CONFIG["host_vendor"] = "apple" CONFIG["host_os"] = "darwin8.10.1" CONFIG["target"] = "i686-apple-darwin8.10.1" CONFIG["target_cpu"] = "i686" CONFIG["target_vendor"] = "apple" CONFIG["target_os"] = "darwin8.10.1" CONFIG["CC"] = "gcc" CONFIG["CFLAGS"] = "-g -O2 -fno-common -pipe -fno-common" CONFIG["LDFLAGS"] = "" CONFIG["CPPFLAGS"] = "" CONFIG["OBJEXT"] = "o" CONFIG["CPP"] = "gcc -E" CONFIG["EGREP"] = "grep -E" CONFIG["GNU_LD"] = "no" CONFIG["CPPOUTFILE"] = "-o conftest.i" CONFIG["OUTFLAG"] = "-o " CONFIG["YACC"] = "bison -y" CONFIG["RANLIB"] = "ranlib" CONFIG["AR"] = "ar" CONFIG["AS"] = "as" CONFIG["ASFLAGS"] = "" CONFIG["NM"] = "" CONFIG["WINDRES"] = "" CONFIG["DLLWRAP"] = "" CONFIG["OBJDUMP"] = "" CONFIG["LN_S"] = "ln -s" CONFIG["SET_MAKE"] = "" CONFIG["INSTALL_PROGRAM"] = "$(INSTALL)" CONFIG["INSTALL_SCRIPT"] = "$(INSTALL)" CONFIG["INSTALL_DATA"] = "$(INSTALL) -m 644" CONFIG["RM"] = "rm -f" CONFIG["CP"] = "cp" CONFIG["MAKEDIRS"] = "mkdir -p" CONFIG["ALLOCA"] = "" CONFIG["DLDFLAGS"] = "" CONFIG["ARCH_FLAG"] = " -arch i386" CONFIG["STATIC"] = "" CONFIG["CCDLFLAGS"] = " -fno-common" CONFIG["LDSHARED"] = "cc -dynamic -bundle -undefined suppress -flat_namespace" CONFIG["DLEXT"] = "bundle" CONFIG["DLEXT2"] = "" CONFIG["LIBEXT"] = "a" CONFIG["LINK_SO"] = "" CONFIG["LIBPATHFLAG"] = " -L\"%s\"" CONFIG["RPATHFLAG"] = "" CONFIG["LIBPATHENV"] = "DYLD_LIBRARY_PATH" CONFIG["TRY_LINK"] = "" CONFIG["STRIP"] = "strip -A -n" CONFIG["EXTSTATIC"] = "" CONFIG["setup"] = "Setup" CONFIG["MINIRUBY"] = "./miniruby$(EXEEXT)" CONFIG["PREP"] = "miniruby$(EXEEXT)" CONFIG["RUNRUBY"] = "$(MINIRUBY) $(srcdir)/runruby.rb --extout=$(EXTOUT) --" CONFIG["EXTOUT"] = ".ext" CONFIG["ARCHFILE"] = "" CONFIG["RDOCTARGET"] = "install-doc" CONFIG["XCFLAGS"] = " -DRUBY_EXPORT" CONFIG["XLDFLAGS"] = " -L." CONFIG["LIBRUBY_LDSHARED"] = "cc -dynamiclib -undefined suppress -flat_namespace" CONFIG["LIBRUBY_DLDFLAGS"] = "-install_name $(libdir)/lib$(RUBY_SO_NAME).dylib -current_version $(MAJOR).$(MINOR).$(TEENY) -compatibility_version $(MAJOR).$(MINOR)" CONFIG["rubyw_install_name"] = "" CONFIG["RUBYW_INSTALL_NAME"] = "" CONFIG["LIBRUBY_A"] = "lib$(RUBY_SO_NAME)-static.a" CONFIG["LIBRUBY_SO"] = "lib$(RUBY_SO_NAME).$(MAJOR).$(MINOR).$(TEENY).dylib" CONFIG["LIBRUBY_ALIASES"] = "lib$(RUBY_SO_NAME).$(MAJOR).$(MINOR).dylib lib$(RUBY_SO_NAME).dylib" CONFIG["LIBRUBY"] = "$(LIBRUBY_SO)" CONFIG["LIBRUBYARG"] = "$(LIBRUBYARG_SHARED)" CONFIG["LIBRUBYARG_STATIC"] = "-l$(RUBY_SO_NAME)-static" CONFIG["LIBRUBYARG_SHARED"] = "-l$(RUBY_SO_NAME)" CONFIG["SOLIBS"] = "" CONFIG["DLDLIBS"] = "" CONFIG["ENABLE_SHARED"] = "yes" CONFIG["MAINLIBS"] = "" CONFIG["COMMON_LIBS"] = "" CONFIG["COMMON_MACROS"] = "" CONFIG["COMMON_HEADERS"] = "" CONFIG["EXPORT_PREFIX"] = "" CONFIG["MAKEFILES"] = "Makefile" CONFIG["arch"] = "universal-darwin8.0" CONFIG["sitearch"] = "universal-darwin8.0" CONFIG["sitedir"] = "$(prefix)/lib/ruby/site_ruby" CONFIG["configure_args"] = "'--prefix=/usr/local' '--enable-shared' '--enable-pthread' '--enable-fat-binary=i386' '--enable-install-doc' '--without-tk' '--with-readline-dir=/usr/local'" CONFIG["NROFF"] = "/usr/bin/nroff" CONFIG["MANTYPE"] = "doc" CONFIG["ruby_version"] = "$(MAJOR).$(MINOR)" CONFIG["rubylibdir"] = "$(libdir)/ruby/$(ruby_version)" CONFIG["archdir"] = "$(rubylibdir)/$(arch)" CONFIG["sitelibdir"] = "$(sitedir)/$(ruby_version)" CONFIG["sitearchdir"] = "$(sitelibdir)/$(sitearch)" CONFIG["topdir"] = File.dirname(__FILE__) MAKEFILE_CONFIG = {} CONFIG.each{|k,v| MAKEFILE_CONFIG[k] = v.dup} def Config::expand(val, config = CONFIG) val.gsub!(/\$\$|\$\(([^()]+)\)|\$\{([^{}]+)\}/) do |var| if !(v = $1 || $2) '$' elsif key = config[v = v[/\A[^:]+(?=(?::(.*?)=(.*))?\z)/]] pat, sub = $1, $2 config[v] = false Config::expand(key, config) config[v] = key key = key.gsub(/#{Regexp.quote(pat)}(?=\s|\z)/n) {sub} if pat key else var end end val end CONFIG.each_value do |val| Config::expand(val) end end RbConfig = Config # compatibility for ruby-1.9 CROSS_COMPILING = nil unless defined? CROSS_COMPILING On Mon, 17 Dec 2007, Vincent Fourmond wrote: > Hello, > > On Dec 17, 2007 4:29 PM, Ken Shen wrote: > > "gcc -o conftest $INCFLAGS conftest.c -I$hdrdir -g -O2 -fno-common > > -pipe -fno-common $src $LIBPATH -arch i386 -lpthread -ldl -lobjc > > -lz" > > cc1: error: unrecognized command line option "-arch" > > Argh ! And you said it is building fine when you install with > rubygems ? If that is the case, it is a bug in my mkmf2.rb... Could > you post your rbconfig.rb (locate it, it should be in > (prefix)/lib/ruby/(version)/(arch)). > > Cheers, > > Vincent > From fourmond at gmail.com Mon Dec 17 12:35:04 2007 From: fourmond at gmail.com (Vincent Fourmond) Date: Mon, 17 Dec 2007 18:35:04 +0100 Subject: [Tioga-users] Trouble installing In-Reply-To: References: <2e474d6f0712170013n4beea281mca973924eb5d225a@mail.gmail.com> <2e474d6f0712170734s314cf504ubea4b39d4fc4fb43@mail.gmail.com> Message-ID: <4766B348.4060507@gmail.com> Ken Shen wrote: > Sorry, you might be confusing me with my officemate Ken Henisey! Sorry... I must admit I didn't go further than the first name... > I am running Leopard, and was informed by Bill that the Ruby that comes > pre-installed on Macs is weird, so I installed a clean version from > http://rubyosx.rubyforge.org/. When I type "ruby -v" at the prompt, I get > "ruby 1.8.6 (2007-03-13 patchlevel 0) [universal-darwin8.0]", and "which > ruby" gives "/usr/local/bin/ruby". > > "locate rbconfig.rb" shows 2 rbconfg.rb's, one at > /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/universal-darwin9.0/rbconfig.rb > and one at /usr/local/lib/ruby/1.8/universal-darwin8.0/rbconfig.rb. > Since I'm using the ruby in /usr/local, here are the contents of > /usr/local/lib/ruby/1.8/universal-darwin8.0/rbconfig.rb: > > > # This file was created by mkconfig.rb when ruby was built. Any > # changes made to this file will be lost the next time ruby is built. > > module Config > RUBY_VERSION == "1.8.6" or > raise "ruby lib version (1.8.6) doesn't match executable version > (#{RUBY_VERSION})" > [...] > CONFIG["ARCH_FLAG"] = " -arch i386" Could you comment out that line and replace it with CONFIG["ARCH_FLAG"] = "" That should let you build correctly - or, at least, let you run to the next problem ;-). It might actually be a bug in your ruby installation rather than in mkfm2.rb, which would be a great relief to me. Hope it helps, Vincent From kenshen at physics.ucsb.edu Mon Dec 17 16:21:04 2007 From: kenshen at physics.ucsb.edu (Ken Shen) Date: Mon, 17 Dec 2007 13:21:04 -0800 (PST) Subject: [Tioga-users] Weird memory leaking? In-Reply-To: <4766B348.4060507@gmail.com> References: <2e474d6f0712170013n4beea281mca973924eb5d225a@mail.gmail.com> <2e474d6f0712170734s314cf504ubea4b39d4fc4fb43@mail.gmail.com> <4766B348.4060507@gmail.com> Message-ID: Okay, thanks to Vincent, tioga reinstalls mostly fine, with only these problems: --------- checking for ieee754.h... no You lack the ieee754.h header file, which might mean lower reliability when Marshalling Dvectors and Dtables checking for isnan() ... no --------- But the installation proceeds and finishes with 0 failures and 0 errors. Now I'm back to the main problem I had, which caused me to want to reinstall tioga in the first place, which is the memory leaking. When I tioga a .rb file, I get a bunch of these outputs while the .pdf is being made: ---------------- 2007-12-17 13:16:34.903 osascript[6865:10b] *** _NSAutoreleaseNoPool(): Object 0x128890 of class NSPathStore2 autoreleased with no pool in place - just leaking Stack: (0x91f3e27f 0x91e4cb67 0x91e545bf 0x91e540be 0x91e58b6b 0xc58e6 0xc5b5b 0x946c4f97 0x946c52f6 0x925a6c74 0x92598668 0x925a17de 0x925a45ab 0x952c002f 0x2241be 0x227e41 0x228004 0x20fc81 0x20ff4b 0x20ffe9 0x207a71 0x92c75ef5 0x946c3168 0x223708 0x223826 0x222bfd 0x222fc1 0x22390d 0x92c75ef5 0x946d4312 0x946cc0d8 0x946cc85d 0x2088) ---------------- But then the .pdf that is made seems to be fine and display normally. So I could just ignore these errors, but it is a little disconcerting to see all those memory leaks! Any ideas? -Ken From fourmond at gmail.com Mon Dec 17 17:48:40 2007 From: fourmond at gmail.com (Vincent Fourmond) Date: Mon, 17 Dec 2007 23:48:40 +0100 Subject: [Tioga-users] Weird memory leaking? In-Reply-To: References: <2e474d6f0712170013n4beea281mca973924eb5d225a@mail.gmail.com> <2e474d6f0712170734s314cf504ubea4b39d4fc4fb43@mail.gmail.com> <4766B348.4060507@gmail.com> Message-ID: <4766FCC8.4030605@gmail.com> Ken Shen wrote: > Okay, thanks to Vincent, tioga reinstalls mostly fine, with only these > problems: > > --------- > checking for ieee754.h... no > You lack the ieee754.h header file, which might mean lower reliability > when Marshalling Dvectors and Dtables > checking for isnan() ... no > --------- This is nothing to worry about, unless you care about marshalling Dvectors across different architectures - and even then. > But the installation proceeds and finishes with 0 failures and 0 errors. Great ! > Now I'm back to the main problem I had, which caused me to want to > reinstall tioga in the first place, which is the memory leaking. When I > tioga a .rb file, I get a bunch of these outputs while the .pdf is being > made: > > ---------------- > 2007-12-17 13:16:34.903 osascript[6865:10b] *** _NSAutoreleaseNoPool(): > Object 0x128890 of class NSPathStore2 autoreleased with no pool in place - > just leaking > Stack: (0x91f3e27f 0x91e4cb67 0x91e545bf 0x91e540be 0x91e58b6b 0xc58e6 > 0xc5b5b 0x946c4f97 0x946c52f6 0x925a6c74 0x92598668 0x925a17de 0x925a45ab > 0x952c002f 0x2241be 0x227e41 0x228004 0x20fc81 0x20ff4b 0x20ffe9 0x207a71 > 0x92c75ef5 0x946c3168 0x223708 0x223826 0x222bfd 0x222fc1 0x22390d > 0x92c75ef5 0x946d4312 0x946cc0d8 0x946cc85d 0x2088) > ---------------- I'm not quite sure I understand this. When does osascript get involved ? This might not have anything to do with Tioga after all ? I'm afraid I don't know much about OSX architecture... Bill ? Cheers, Vincent From paxton at kitp.ucsb.edu Mon Dec 17 18:34:15 2007 From: paxton at kitp.ucsb.edu (Bill Paxton) Date: Mon, 17 Dec 2007 15:34:15 -0800 Subject: [Tioga-users] Weird memory leaking? In-Reply-To: <4766FCC8.4030605@gmail.com> References: <2e474d6f0712170013n4beea281mca973924eb5d225a@mail.gmail.com> <2e474d6f0712170734s314cf504ubea4b39d4fc4fb43@mail.gmail.com> <4766B348.4060507@gmail.com> <4766FCC8.4030605@gmail.com> Message-ID: <20BA2DEE-DC92-42EA-8CB0-2CB49C6C3989@kitp.ucsb.edu> Hi Ken, On Dec 17, 2007, at 1:21 PM, Ken Shen wrote: > 2007-12-17 13:16:34.903 osascript[6865:10b] *** _NSAutoreleaseNoPool > (): > Object 0x128890 of class NSPathStore2 autoreleased with no pool in > place - > just leaking > Stack: (0x91f3e27f 0x91e4cb67 0x91e545bf 0x91e540be 0x91e58b6b 0xc58e6 > 0xc5b5b 0x946c4f97 0x946c52f6 0x925a6c74 0x92598668 0x925a17de > 0x925a45ab > 0x952c002f 0x2241be 0x227e41 0x228004 0x20fc81 0x20ff4b 0x20ffe9 > 0x207a71 > 0x92c75ef5 0x946c3168 0x223708 0x223826 0x222bfd 0x222fc1 0x22390d > 0x92c75ef5 0x946d4312 0x946cc0d8 0x946cc85d 0x2088) > This is a leak from the Apple Scripting program -- on the mac, the default pdf viewer, called Preview, has the nasty feature of not refreshing the image of an already-open file when it is called from the shell to (re)open it. To get around that, we have a script that gets Preview to do a "Revert" along with the open. The script seems to have triggered a bug in the new OSX version of AppleScripts. Two possible "solutions" -- (1) disable the script and do "Revert" by hand as necessary, or (2) ignore the error messages and wait for Apple to fix the bug. To disable the script, open your ~/.tiogainit and change pdf_viewer from 'repreview' to 'open'. Good luck! BTW: you might want to be really brave and try the Mac GUI for Tioga: http://theory.kitp.ucsb.edu/~paxton/Tioga-1.5.dmg Cheers, Bill -------------- next part -------------- An HTML attachment was scrubbed... URL: http://rubyforge.org/pipermail/tioga-users/attachments/20071217/d58f3050/attachment.html From jeanjulien.fleck at gmail.com Tue Dec 18 15:04:07 2007 From: jeanjulien.fleck at gmail.com (Fleck Jean-Julien) Date: Tue, 18 Dec 2007 21:04:07 +0100 Subject: [Tioga-users] Weird memory leaking? In-Reply-To: <20BA2DEE-DC92-42EA-8CB0-2CB49C6C3989@kitp.ucsb.edu> References: <2e474d6f0712170013n4beea281mca973924eb5d225a@mail.gmail.com> <2e474d6f0712170734s314cf504ubea4b39d4fc4fb43@mail.gmail.com> <4766B348.4060507@gmail.com> <4766FCC8.4030605@gmail.com> <20BA2DEE-DC92-42EA-8CB0-2CB49C6C3989@kitp.ucsb.edu> Message-ID: Hello, > This is a leak from the Apple Scripting program -- on the mac, the default > pdf viewer, called Preview, > has the nasty feature of not refreshing the image of an already-open file > when it is called from the > shell to (re)open it. By the way, the new preview from Leopard (X.5) does the refresh part on itself, so there will be no more need for this feature anymore. Cheers, JJ From pd.yates at gmail.com Wed Dec 19 15:25:21 2007 From: pd.yates at gmail.com (Peter Yates) Date: Wed, 19 Dec 2007 20:25:21 +0000 Subject: [Tioga-users] .png output Message-ID: <1198095921.19363.9.camel@ubuntu> Hi all, I've been experimenting with Tioga for the last few hours and first impressions are fantastic. I plan to use it in a rails app for making graphs on the fly so would like to output in png rather than pdf. Is this possible? I'm using Tioga 1.6. Kind regards Peter -- Peter Yates mobile: +(44) 7733 075 395 e-mail: pd.yates at gmail.com sip: peter.yates at ekiga.net -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: This is a digitally signed message part Url : http://rubyforge.org/pipermail/tioga-users/attachments/20071219/3cc5a777/attachment.bin From fourmond at gmail.com Wed Dec 19 15:39:06 2007 From: fourmond at gmail.com (Vincent Fourmond) Date: Wed, 19 Dec 2007 21:39:06 +0100 Subject: [Tioga-users] .png output In-Reply-To: <1198095921.19363.9.camel@ubuntu> References: <1198095921.19363.9.camel@ubuntu> Message-ID: <4769816A.6070405@gmail.com> Hello Peter, Peter Yates wrote: > I've been experimenting with Tioga for the last few hours and first > impressions are fantastic. Good news ;-).. > I plan to use it in a rails app for making graphs on the fly so would > like to output in png rather than pdf. Is this possible? Well, as such, no. But it is fairly easy to use convert as a post-processing to transform to PNG. That's what I'm doing with the --png option of ctioga, you might want to have a look at the source code. Essentially, it boils down to convert -density 100 Plot.pdf -resize 400x400 Plot.png This keeps the aspect ratio, as it resizes to something included in 400x400. You might want to increase density to get a better anti-aliasing (at the expense of processing time, though). convert is coming from ImageMagick. By the way, if you don't plan to use fancy aspects of Tioga such as contour plots, you might want to try ctioga, which is a pure command-line front-end for Tioga. Enjoy ! Vincent From fourmond at gmail.com Sat Dec 22 04:18:51 2007 From: fourmond at gmail.com (Vincent Fourmond) Date: Sat, 22 Dec 2007 10:18:51 +0100 Subject: [Tioga-users] Fwd: bug tioga? In-Reply-To: <839a0b670712211410i1e659717s562e0ef442031801@mail.gmail.com> References: <839a0b670712211410i1e659717s562e0ef442031801@mail.gmail.com> Message-ID: <2e474d6f0712220118vd78aadfs479a198535a8bc59@mail.gmail.com> Hello, I've just received this message about a bug in Tioga. It is in french, but the backtrace should be clear enough ;-)... I think this bug arises because there is an undetected and non-destructive buffer overflow somewhere in the code that is detected by pointer instrumentation in the libraries linked to on this guy's machine. I won't have any chance to tackle it before next Thursday, so feel free to squash it before I'm back ;-)... Cheers, Vincent ---------- Forwarded message ---------- From: Fran?ois-Xavier Pineau Date: Dec 21, 2007 11:10 PM Subject: bug tioga? To: Vincent Fourmond Salut Vincent, Si tu n'as pas le temps de regarder ca, c'est pas grave. D?sol? de te d?ranger. Je viens d'installer ruby, tioga et ctioga sur une machine. J'ai donc r?cup?r? les derni?res versions. Sur une autre machine, j'ai un script qui fonctionne tr?s bien (ruby 1.8.5, tioga 1.6, ctioga 1.6) Le m?me script avec la nouvelle config plante (ruby 1.8.6, tioga 1.6, ctioga 1.6.2) J'ai downgrad? ctioga en 1.6, m?me bug. Ca viens de la nouvelle version de ruby (1.8.6)? Voil? le msg d'erreur: *** buffer overflow detected ***: ruby terminated ======= Backtrace: ========= /lib/i686/libc.so.6(__chk_fail+0x41)[0xb7d3ae51] /lib/i686/libc.so.6[0xb7d3a658] /lib/i686/libc.so.6(_IO_default_xsputn+0xb7)[0xb7cbbaf7] /lib/i686/libc.so.6(_IO_vfprintf+0x174)[0xb7c93b54] /lib/i686/libc.so.6(__vsprintf_chk+0xad)[0xb7d3a70d] /lib/i686/libc.so.6(__sprintf_chk+0x30)[0xb7d3a640] /usr/lib/ruby/gems/1.8/gems/tioga-1.6/lib/Tioga/FigureMaker.so[0xb79181bf] /usr/lib/ruby/gems/1.8/gems/tioga-1.6/lib/Tioga/FigureMaker.so[0xb7918c87] /usr/lib/ruby/gems/1.8/gems/tioga-1.6/lib/Tioga/FigureMaker.so(FM_show_axis+0xd0)[0xb7919750] /usr/lib/libruby.so.1.8[0xb7e2aa72] /usr/lib/libruby.so.1.8[0xb7e330ec] /usr/lib/libruby.so.1.8[0xb7e333c8] /usr/lib/libruby.so.1.8[0xb7e3951b] /usr/lib/libruby.so.1.8[0xb7e33023] /usr/lib/libruby.so.1.8[0xb7e333c8] /usr/lib/libruby.so.1.8[0xb7e39564] /usr/lib/libruby.so.1.8[0xb7e33023] /usr/lib/libruby.so.1.8[0xb7e333c8] /usr/lib/libruby.so.1.8[0xb7e39564] /usr/lib/libruby.so.1.8[0xb7e3dff2] /usr/lib/libruby.so.1.8[0xb7e3ebd8] /usr/lib/libruby.so.1.8[0xb7e2aab2] /usr/lib/libruby.so.1.8[0xb7e330ec] /usr/lib/libruby.so.1.8[0xb7e333c8] /usr/lib/libruby.so.1.8[0xb7e393df] /usr/lib/libruby.so.1.8[0xb7e3a6d4] /usr/lib/libruby.so.1.8[0xb7e33023] /usr/lib/libruby.so.1.8[0xb7e333c8] /usr/lib/libruby.so.1.8[0xb7e3951b] /usr/lib/libruby.so.1.8[0xb7e3c7d7] /usr/lib/libruby.so.1.8[0xb7e33023] /usr/lib/libruby.so.1.8[0xb7e333c8] /usr/lib/libruby.so.1.8[0xb7e393df] /usr/lib/libruby.so.1.8[0xb7e3c7d7] /usr/lib/libruby.so.1.8[0xb7e3dff2] /usr/lib/libruby.so.1.8[0xb7e3ebd8] /usr/lib/libruby.so.1.8[0xb7e2aab2] /usr/lib/libruby.so.1.8[0xb7e330ec] /usr/lib/libruby.so.1.8[0xb7e333c8] /usr/lib/libruby.so.1.8[0xb7e393df] /usr/lib/libruby.so.1.8[0xb7e3dff2] /usr/lib/libruby.so.1.8[0xb7e3ebd8] /usr/lib/libruby.so.1.8[0xb7e2aab2] /usr/lib/libruby.so.1.8[0xb7e330ec] /usr/lib/libruby.so.1.8[0xb7e333c8] /usr/lib/libruby.so.1.8[0xb7e393df] /usr/lib/libruby.so.1.8[0xb7e3dff2] /usr/lib/libruby.so.1.8[0xb7e3ebd8] /usr/lib/libruby.so.1.8[0xb7e2aab2] /usr/lib/libruby.so.1.8[0xb7e330ec] /usr/lib/libruby.so.1.8[0xb7e333c8] /usr/lib/libruby.so.1.8[0xb7e393df] /usr/lib/libruby.so.1.8[0xb7e3c18f] /usr/lib/libruby.so.1.8[0xb7e33023] /usr/lib/libruby.so.1.8[0xb7e333c8] /usr/lib/libruby.so.1.8[0xb7e339cc] /usr/lib/libruby.so.1.8(rb_funcall+0x20)[0xb7e33b60] /usr/lib/ruby/gems/1.8/gems/tioga-1.6/lib/Tioga/FigureMaker.so(do_cmd+0x38)[0xb78ff4f8] /usr/lib/ruby/gems/1.8/gems/tioga-1.6/lib/Tioga/FigureMaker.so[0xb79128f8] /usr/lib/libruby.so.1.8(rb_ensure+0xde)[0xb7e2f33e] /usr/lib/ruby/gems/1.8/gems/tioga-1.6/lib/Tioga/FigureMaker.so(FM_private_context+0x72)[0xb7912822] /usr/lib/libruby.so.1.8[0xb7e2aa72] /usr/lib/libruby.so.1.8[0xb7e330ec] ======= Memory map: ======== 08048000-08049000 r-xp 00000000 03:01 1790034 /usr/bin/ruby 08049000-0804a000 rwxp 00000000 03:01 1790034 /usr/bin/ruby 0804a000-08553000 rwxp 0804a000 00:00 0 [heap] b77b4000-b78d1000 rwxp b77b4000 00:00 0 b78d1000-b78e3000 r-xp 00000000 03:01 360505 /lib/libz.so.1.2.3 b78e3000-b78e4000 rwxp 00011000 03:01 360505 /lib/libz.so.1.2.3 b78e6000-b78f1000 r-xp 00000000 03:01 360502 /lib/libgcc_s-4.2.2.so.1 b78f1000-b78f2000 rwxp 0000a000 03:01 360502 /lib/libgcc_s-4.2.2.so.1 b78f2000-b78f6000 r-xp 00000000 03:01 579522 /usr/lib/ruby/gems/1.8/gems/tioga-1.6/lib/Dobjects/Function.so b78f6000-b78f7000 rwxp 00003000 03:01 579522 /usr/lib/ruby/gems/1.8/gems/tioga-1.6/lib/Dobjects/Function.so b78f7000-b7925000 r-xp 00000000 03:01 579483 /usr/lib/ruby/gems/1.8/gems/tioga-1.6/lib/Tioga/FigureMaker.so b7925000-b7938000 rwxp 0002d000 03:01 579483 /usr/lib/ruby/gems/1.8/gems/tioga-1.6/lib/Tioga/FigureMaker.so b7938000-b79d7000 rwxp b7938000 00:00 0 b79d7000-b7b22000 r-xp 00000000 03:01 1798808 /usr/lib/libcrypto.so.0.9.8 b7b22000-b7b37000 rwxp 0014b000 03:01 1798808 /usr/lib/libcrypto.so.0.9.8 b7b37000-b7b3a000 rwxp b7b37000 00:00 0 b7b3a000-b7b79000 r-xp 00000000 03:01 1798809 /usr/lib/libssl.so.0.9.8 b7b79000-b7b7d000 r./reliabilityMC.bash: line 36: 6057 Abandon ctioga --no-ylabel --legend-pos right,0.2 --col -x '$\log_{10}(LR)$' -t "${cat} ${mag}, ${group_name_latex}" --save-dir ${dir_output} -n "${group_name}_${cat}_${mag}_Histos" -y 'Counts' -l 'Candidate' --histogram ${ filetmp}@1:2 -l 'Noise' ${filetmp}@1:3 --next -y 'Reliability' -l 'Reliability' --histogram ${filetmp}@1:4 -l 'Fitted Reliability' --no-histogram ${filetmp}@1:5 Mon fichier est clean et m?me la simple commande: ctioga ${filetmp}@1:2 produit le m?me bug! fichier: -0.625 269 182.858803670514 0.320227495648647 0.224435168326937 -0.375 285 182.858803670513 0.358390162559604 0.29693198215989 -0.125 344 182.858803670513 0.468433710260137 0.3845189409575 0.125 329 182.858803670513 0.444198165135219 0.483659213771608 0.375 390 182.858803670513 0.53113127263971 0.587374821591426 0.625 520 182.858803670513 0.648348454479783 0.686782274702473 0.875 825 182.858803670513 0.778352965247863 0.77392344262659 1.125 1208 182.858803670514 0.848626818153548 0.844166949679748 1.375 2011 182.858803670514 0.909070709263792 0.896786307667508 1.625 1994 100.642262973314 0.949527450865941 0.933884675268143 Merci beaucoup si t'a le temps de regarder, sinon tant pis. Bonne f?tes de fin d'ann?e. fx From AEtzold at gmx.de Thu Dec 27 18:12:45 2007 From: AEtzold at gmx.de (Axel Etzold) Date: Fri, 28 Dec 2007 00:12:45 +0100 Subject: [Tioga-users] Tioga on Windows ? Message-ID: <20071227231245.74230@gmx.net> Hi, I am using Tioga for some weeks now on a Linux architecture and like it so much I'd also want to use it in Windows (both XP and Vista). On the Tioga website, there is no mention of Windows though (Linux and Mac are the only supported architectures). Is it possible to compile the source code on Windows too ? If so, what approach should be used, e.g. using Mingw, to do that ? Thank you very much, Best regards, Axel -- Psssst! Schon vom neuen GMX MultiMessenger geh?rt? Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger?did=10 From paxton at kitp.ucsb.edu Thu Dec 27 18:40:48 2007 From: paxton at kitp.ucsb.edu (Bill Paxton) Date: Thu, 27 Dec 2007 15:40:48 -0800 Subject: [Tioga-users] Tioga on Windows ? In-Reply-To: <20071227231245.74230@gmx.net> References: <20071227231245.74230@gmx.net> Message-ID: Hi Axel, I'm glad to hear that you are liking Tioga! It would be great to have a version for Windows, but none of the people currently working on Tioga have the necessary background to do the task. But if you'd like to volunteer, we'll help if we can! ; - ) Cheers, Bill Paxton On Dec 27, 2007, at 3:12 PM, Axel Etzold wrote: > Hi, > > I am using Tioga for some weeks now on a Linux architecture > and like it so much I'd also want to use it in Windows (both > XP and Vista). > On the Tioga website, there is no mention of Windows though > (Linux and Mac are the only supported architectures). > > Is it possible to compile the source code on Windows too ? > > If so, what approach should be used, e.g. using Mingw, to do that ? > > Thank you very much, > > Best regards, > > Axel > > > > -- > Psssst! Schon vom neuen GMX MultiMessenger geh?rt? > Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger?did=10 > _______________________________________________ > Tioga-users mailing list > Tioga-users at rubyforge.org > http://rubyforge.org/mailman/listinfo/tioga-users > From fourmond at gmail.com Thu Dec 27 18:42:46 2007 From: fourmond at gmail.com (Vincent Fourmond) Date: Fri, 28 Dec 2007 00:42:46 +0100 Subject: [Tioga-users] Tioga on Windows ? In-Reply-To: <20071227231245.74230@gmx.net> References: <20071227231245.74230@gmx.net> Message-ID: <47743876.1080309@gmail.com> Hello Axel ! Axel Etzold wrote: > I am using Tioga for some weeks now on a Linux architecture > and like it so much I'd also want to use it in Windows (both > XP and Vista). Great ! > Is it possible to compile the source code on Windows too ? It should be, though the lack of documentation comes from the lack of tries... I got it compiled and running on Cygwin (Linux Emulation Layer for Windows), but I never tried directly. > If so, what approach should be used, e.g. using Mingw, to do that ? I guess that would be the way to go. I don't know much about Ruby for Windows, but here are a few things you must have: * a compiler (mingw should be fine) * a Unix-like make (maybe mingw comes with one, I really don't know). * a working zlib (place it somewhere where the compiler will find it and its include files) * ruby development files (that should include a file called rbconfig.rb plus many header files) Then, try to run ruby extconf.rb in the split/ directory, and make. If that fails (likely, I'd say), here's some hints (though only guesswork): * edit the rbconfig.rb file to have the CC variable point to your C compiler * try to play with CFLAGS and LDFLAGS in the same file as well. Whenever you get trouble, send it here, we might be able to sort it out. And, most importantly, if you succeed, please tell us how ! We'd put that on the website. In the worst case, you might simply want to try Cygwin - though I admit it is a rather inelegant solution. Good luck and happy hacking... Vincent, very interested about a Tioga working on Windows...