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Re: [AMOS-help] amos-short-0.9.3: overlap-align.cc:273: error: ‘printf’ was not declared in this scope
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From: Martin M. <mmo...@fo...> - 2010-11-29 15:00:13
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Daniel Sommer wrote: > Martin, The newest version of Bambus in now fully integrated into AMOS > (the old version didn't use the AMOS libraries). All files needed for > Bambus are now part on the AMOS cvs tree. I recommend uninstalling the > version of Bambus that came in a separate tarball and that should fix > the conflict with duplicate Perl modules. Just for completeness, these three in addition to those four reported earlier would conflict: * /usr/bin/printScaff * /usr/bin/untangle * /usr/lib/TIGR/AsmLib.pm But, I got your point and will uninstall bambus-2.33. > > After uninstalling the old Bambus, a clean cvs checkout should give you > the latest AMOS files and not the files included in the tarballs > (amos-2.0.8 or amos-short) which are very, very old. Not sure why you > are not seeing goBambus but hopefully one of the Bambus developers can > help you with that. I have included them on this email. I see Bundler and Chainer, maybe I have to use some other cvs MODULE name? Again, here is what I do: cvs -q -f -z1 -d ":pserver:ano...@am...:/cvsroot/amos" checkout -rHEAD AMOS > > I am currently working on updating the tarball releases for AMOS so that > they include the latest and greatest code and trying to fix any make > problems in the process. Thanks and please let me know when you want me to re-test something. Martin > > Dan > > > On Mon, Nov 29, 2010 at 8:26 AM, Martin Mokrejs > <mmo...@fo... <mailto:mmo...@fo...>> wrote: > > Florent Angly wrote: > > Hi Martin, > > It was a short answer, because I am unsure about the answer to your > > other questions. As far as I know, there is a single development > > repository that has all the AMOS programs (Bambus, Hawkeye, etc). I > > don't know what packages released contain what part of AMOS. Like I > > said, try the development version because I think that it has it all. > > Nope. I fetched > cvs -z3 -d:pserver:ano...@am...:/cvsroot/amos > co -P AMOS > and after compilation, I do not have e.g. goBambus in the tree. It seems > it is really having same contents as amos-2.0.8 before. > > The four *.pm files mentioned earlier exist in the cvs HEAD as well so > I still believe they will conflict with those distributed through > bambus. > > Martin > > > Florent > > > > > > On 29/11/10 10:21, Martin Mokrejs wrote: > >> Hi Florent, > >> but how about the overlaps between the packages, in which order I > >> should install > >> what? This is just a way too short answer, sorry^H^H^H^H^H^please. ;) > >> Martin > >> > >> > >> Florent Angly wrote: > >>> Hi Martin, > >>> > >>> Most of these errors are fixed in the development version of AMOS. > >>> Please refer to the wiki for installation. I think that a new > version of > >>> AMOS is going to be released soon, so let us know if you encounter > >>> problems so that we can fix them before the release. > >>> > >>> Best, > >>> > >>> Florent > >>> > >>> > >>> > >>> On 29/11/10 08:49, Martin Mokrejs wrote: > >>>> Hi, > >>>> I am trying to compile amos-short but it fails for me with this > >>>> message: > >>>> > >>>> i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. > >>>> -I../../src/CelMsg -I../../src/Slice -I../../src/Common > >>>> -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 > >>>> -march=pentium4 -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb > >>>> -MT overlap-align.o -MD -MP -MF .deps/overlap-align.Tpo -c -o > >>>> overlap-align.o overlap-align.cc > >>>> overlap-align.cc: In function ‘void align(const std::string&, const > >>>> std::string&, int, int, int, int)’: > >>>> overlap-align.cc:273: error: ‘printf’ was not declared in this > scope > >>>> make[3]: *** [overlap-align.o] Error 1 > >>>> make[3]: Leaving directory > >>>> `/var/tmp/amos-short-0.9.3/work/AMOS/src/Align' > >>>> > >>>> > >>>> BTW, for compilation I needed this patch from Gentoo linux > >>>> (attached) > >>>> which applies also to both amos-2.0.8 and amos-short-0.9.3 sources > >>>> (I suspect to many other "packages on your sourceforge pages as > well, > >>>> read below). > >>>> > >>>> I have also some questions and comments. On the page > >>>> http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS > >>>> there is Bambus and Bambus2. The page for Bambus2 is empty and I > >>>> guess the > >>>> file bambus-2.33.tar.gz hosted on source is the Bambus version one, > >>>> right? > >>>> If that is so, I think it is bad numbering. If you are going to > rewrite > >>>> Bambus into Bambus2 and you already have bambus-2.33.tar.gz, please > >>>> pick up > >>>> a different name for the project (and do not release > >>>> bambus2-0.1.tar.gz). > >>>> ;-) > >>>> > >>>> I am somehow lost in the namings of all the > utilities/assemblers/etc > >>>> listed in that mediawiki page. Please tag clearly which of > those tools > >>>> are in the AMOS bundle (amos-2.0.8) and which are not. For example, > >>>> I do > >>>> not understand why amos-short-0.9.3 seems to be a repackaged > version of > >>>> amos-2.0.8, seems one has to compile same code with unclear > differences > >>>> to me. I bet some of the resulting binaries will be just same as > >>>> from the > >>>> amos-2.0.8 package. AMOScmp is in amos-2.0.8 while AMOS-short-reads > >>>> is not, > >>>> why? > >>>> > >>>> That makes me uncertain because in the very same listing of > >>>> tools/programs > >>>> there is hawkeye which seems NOT to be included in the amos-2.0.8 > >>>> bundle. > >>>> If I got it right, the configure warning from amos-2.0.8 stating > >>>> > >>>> <quote> > >>>> -- AMOS Assembler 2.0.8 Configuration Results -- > >>>> C compiler: i686-pc-linux-gnu-gcc -O2 -march=pentium4 > >>>> -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb > >>>> C++ compiler: i686-pc-linux-gnu-g++ -O2 -march=pentium4 > >>>> -mmmx -msse -msse2 -pipe -fno-strict-aliasing -ggdb > >>>> GCC version: i686-pc-linux-gnu-gcc (Gentoo 4.4.5 p1.0, > >>>> pie-0.4.5) 4.4.5 > >>>> Host System type: i686-pc-linux-gnu > >>>> Install prefix: /usr > >>>> Install eprefix: ${prefix} > >>>> > >>>> See config.h for further configuration information. > >>>> Email<amo...@li... > <mailto:amo...@li...>> with questions and bug > >>>> reports. > >>>> > >>>> WARNING! Qt3 toolkit was not found but is required to run AMOS GUIs > >>>> install Qt3 or locate Qt3 with configure to build GUIs > >>>> see config.log for more information on what went wrong > >>>> </quote> > >>>> > >>>> is just misleading, because nothing really needs qt3. If you just > >>>> recycle same > >>>> configure for each package, just drop those tests which are not > >>>> relevant. > >>>> > >>>> Please give a me a list of all packages I need to download and > >>>> tell me > >>>> about their overlaps. Or better, drp the overlaps and just document > >>>> their dependencies and in which order I have to go the process > of their > >>>> installation. I would be very happy to give some feedback > afterwards. > >>>> > >>>> Is there a chance qt4 is supported instead of qt3? ;) > >>>> > >>>> Many thanks for your answer, > >>>> Martin > > > > > > ------------------------------------------------------------------------------ > Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! > Tap into the largest installed PC base & get more eyes on your game by > optimizing for Intel(R) Graphics Technology. Get started today with the > Intel(R) Software Partner Program. Five $500 cash prizes are up for > grabs. > http://p.sf.net/sfu/intelisp-dev2dev > _______________________________________________ > AMOS-help mailing list > AMO...@li... <mailto:AMO...@li...> > https://lists.sourceforge.net/lists/listinfo/amos-help > > |