Oh well, I posted the following months ago. Today I downloaded the trunk again and all of the old fixes are still needed to build TPP.sln under MS VC++ 2005. Perhaps it will help some folks.
Dmitrii (0)==================================== To avoid making changes to the original files downloaded from https://sashimi.svn.sourceforge.net/svnroot/sashimi/trunk copy the following folders to a separate folder: qualscore trans_proteomic_pipeline and optionally run in that folder this command: for /r %a in (.svn) do rd /S /Q "%a" to remove SVN stuff (1)==================================== In the file trans_proteomic_pipeline\extern\build_boost_vc8.bat (a) replace the line bjam --toolset=msvc "-sNO_ZLIB=0" <...> with ..\bjam --toolset=msvc-8.0 "-sNO_ZLIB=0" <...> [this is a must if you have MS VS 2008 installed] (b) replace line UnxUtils\usr\local\wbin\rm.exe -rf bin.v2 with ..\UnxUtils\usr\local\wbin\rm.exe -rf bin.v2 -- non-critical optional changes: (c) replace the 1st line, cd %1 with pushd %1 (d) remove line cd %1 above :DONE at the bottom (e) add last line: popd (2)=================================== Manually expand trans_proteomic_pipeline\extern\UnxUtils.tar.bz2 preserving directory structure to trans_proteomic_pipeline\extern\ (3)=================================== Manually expand trans_proteomic_pipeline\extern\expat-2.0.1.tar.gz preserving directory structure to trans_proteomic_pipeline\extern\ (4)=================================== In trans_proteomic_pipeline\extern\: copy file bsdtar-1_2_38.exe to bsdtar.exe (5)=====Installer Case Sensitivity Issues====== (a) Manually create folder trans_proteomic_pipeline\src\Release (b) In batchcoverage project, trans_proteomic_pipeline\COVERAGE\batchcoverage.vcproj Change output name from batchcoverage.exe to BatchCoverage.exe (6)=================================== Start MS VC++ 2005. In the dialog Tools/Options/Projects and Solutions/Build and Run/ make sure that 1=maximum number of parallel project buils, otherwise you get errors due to concurrently running builds. (7)============================== In MSVC Project/Project Dependencies dialog select project msvc_makeinstall check two more items in the "Depends on:" list: indexmzXML batchcoverage (8)====project paths fixes================= (a) Right-click runperl project, select Properties, select Debug configuration at the top of the runperl Property Pages. - Select Configuration Properties/Browse Information/General - In the Output File field, replace \..\..\Debug/runperl.bsc with .\Debug/runperl.bsc - Click OK to save the changes (b) Right-click InterProphetParser project, select Properties, select Debug configuration at the top of the runperl Property Pages. - Select Configuration Properties/Browse Information/General - In the Output File field, replace \trans_proteomic_pipeline\Debug/InterProphetParser.bsc with $(SolutionDir)$(ConfigurationName)/InterProphetParser.bsc - Click OK to save the changes (c) Right-click ProteinProphet project, select Properties, select Debug configuration at the top of the runperl Property Pages. - Select Configuration Properties/Browse Information/General - In the Output File field, replace \trans_proteomic_pipeline\Debug/ProteinProphet.bsc with .\Debug/ProteinProphet.bsc - Select Configuration Properties/Linker/Debugging - In theGenerate Program Database File, replace \trans_proteomic_pipeline\Debug/ProteinProphet.pdb with .\Debug/ProteinProphet.pdb -Click OK to save the changes (9)=====Additional notes on TPP installer creation ================ The following executables required in the msvc_makeinstall project file trans_proteomic_pipeline\installer_win32\TPP_files.nsh are not created because there are no vcproj project files for that: digestdb.exe subsetdb.exe pep_dbcount.exe translateDNA2AA-FASTA.exe calculate_pi.exe add_mz.exe Under gcc, these files are built with trans_proteomic_pipeline\src\util\Makefile Bill Nelson wrote: > So, is that an error in the code or is my compiler special, that is, > do I change my local copy or has the trunk been updated? > Thanks, > Bill > > On Nov 17, 5:14 pm, Brian Pratt <[email protected]> wrote: > >> Oops, I wasn't up to date after all, sorry. >> >> Just add an (int) cast in front of that strlen call and drive on... >> >> >> >> On Tue, Nov 17, 2009 at 12:56 PM, Bill Nelson <[email protected]> wrote: >> >>> Must be the time difference. Does Seattle observe daylight savings >>> time? >>> >>> My SVN root is :https://sashimi.svn.sourceforge.net/svnroot/sashimi/ >>> trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML >>> I'm at version 4775 >>> >>> At line 752 in out2xml.cxx I have: for (i=2; i <strlen(szPep)-2; i++) >>> >>> i is defined as: int (signed) and strlen returns size_t an Unsigned >>> integral >>> I think C++ might be a little OCD. >>> >>> Thanks, >>> Bill >>> >>> On Nov 17, 2:42 pm, Brian Pratt <[email protected]> wrote: >>> >>>> Glad it's coming along. >>>> >>>> There is some weirdness here, though - my copy of out2xml.cxx doesn't >>>> >>> have a >>> >>>> comparison operator at line 752, and it's current with SVN. >>>> >>>> Brian >>>> >>> > On Tue, Nov 17, 2009 at 8:24 AM, Bill Nelson <[email protected]> >>> wrote: >>> >>>>> Hi Brian, >>>>> Well, here's a guess to what is happening. The C:\sashimi\trunk >>>>> \trans_proteomic_pipeline\extern>bsdtar-1_2_38.exe -xjf >>>>> boost_1_39_0.tar.bz2 command takes about five minutes. It takes so >>>>> long because it prints " Can't set permissions: Function not >>>>> implemented" for every file. When the build is started with VS8 the >>>>> extraction is running in the background but the build keeps running. >>>>> After the build completes, with a lot of missing boost library >>>>> errors, boost_1_39_0.tar.bz2 still has not finished extracting but the >>>>> extraction process is killed when the build script ends leaving a >>>>> corrupted boost_1_39_0 directory. >>>>> So, if I do a clean, manually run bsdtar-1_2_38.exe -xjf >>>>> boost_1_39_0.tar.bz2, and then do a build everything works except for >>>>> two errors. I do have BioworksBrowser 3.3.1 SP1 installed on this PC: >>>>> >>>>> 24>------ Build started: Project: Out2XML, Configuration: Release >>>>> Win32 ------ >>>>> 24>Compiling... >>>>> 23>Compiling... >>>>> 24>SequestOut.cxx >>>>> 23>StdAfx.cpp >>>>> 24>SequestHit.cxx >>>>> 24>Out2XMLMain.cxx >>>>> 23>Compiling... >>>>> 23>ThermoInterface.cpp >>>>> 24>Out2XML.cxx >>>>> 24>.\Out2XML.cxx(752) : error C2220: warning treated as error - no >>>>> 'object' file generated >>>>> 24>.\Out2XML.cxx(752) : warning C4018: '<' : signed/unsigned mismatch >>>>> 24>Generating Code... >>>>> 23>SimpleXMLWriter.cpp >>>>> 24>Build log was saved at "file://c:\sashimi\trunk >>>>> \trans_proteomic_pipeline\src\Parsers\Algorithm2XML\Sequest2XML\Release >>>>> \BuildLog.htm" >>>>> 24>Out2XML - 1 error(s), 1 warning(s) >>>>> >>>>> 37>------ Build started: Project: CombineOut, Configuration: Release >>>>> Win32 ------ >>>>> 37>Compiling... >>>>> 37>SequestOut.cxx >>>>> 37>SequestHit.cxx >>>>> 37>Out2XML.cxx >>>>> 37>.\Out2XML.cxx(752) : error C2220: warning treated as error - no >>>>> 'object' file generated >>>>> 37>.\Out2XML.cxx(752) : warning C4018: '<' : signed/unsigned mismatch >>>>> 37>CombineOutMain.cxx >>>>> 37>CombineOut.cxx >>>>> 37>Build log was saved at "file://c:\sashimi\trunk >>>>> \trans_proteomic_pipeline\src\Parsers\Algorithm2XML\Sequest2XML\Release >>>>> \BuildLog.htm" >>>>> 37>CombineOut - 1 error(s), 1 warning(s) >>>>> >>>>> The Centos build worked well. The pre-install scripts are very >>>>> helpful. >>>>> >>>>> Thanks for your help. >>>>> Bill >>>>> >>>>> On Nov 16, 5:40 pm, Brian Pratt <[email protected]> wrote: >>>>> >>>>>> Try opening a command window, cd to the extern directory, and run >>>>>> build_boost_vc8.bat >>>>>> >>>>>> Should have happened automatically, I wonder what's up. >>>>>> >>>>>> Brian >>>>>> >>>>> > On Mon, Nov 16, 2009 at 12:27 PM, Bill Nelson <[email protected]> >>>>> wrote: >>>>> >>>>>>> Can you tell me how to extract the external libs manually or how to >>>>>>> troubleshoot the makefile? >>>>>>> Thanks, >>>>>>> Bill >>>>>>> >>>>>>> On Nov 16, 1:34 pm, Brian Pratt <[email protected]> wrote: >>>>>>> >>>>>>>> Bill, >>>>>>>> >>>>>>>> Agreed, it's bad when the docs get stale. I'll update that >>>>>>>> >>> windows >>> >>>>>>> readme. >>>>>>> >>>>>>>> As to the IDE, I'm with you but the bulk of the TPP developers >>>>>>>> >>> are >>> >>>>> linux >>>>> >>>>>>>> folk. >>>>>>>> >>>>>>>> Brian >>>>>>>> >>>>>>> > On Mon, Nov 16, 2009 at 9:13 AM, Bill Nelson < >>>>>>> >>> [email protected]> >>> >>>>>>> wrote: >>>>>>> >>>>>>>>> Okay, I got a little side tracked but I'm back. I'm not a C++ >>>>>>>>> programmer so I don't think I'll be much help maintaining the >>>>>>>>> >>> VS8 >>> >>>>>>>>> build. I'm using VS8 because in the past this was the easiest >>>>>>>>> >>> way >>> >>>>> for >>>>> >>>>>>>>> me to build the TPP on windows and from the perspective of a >>>>>>>>> >>> Java >>> >>>>>>>>> programmer it is difficult for me to understand how one could >>>>>>>>> sacrifice the productivity of an IDE on such a large project. >>>>>>>>> >>>>>>>>> I did check out the trunk and did a clean release build. Boost >>>>>>>>> >>> did >>> >>>>> not >>>>> >>>>>>>>> extract. I'm very grateful for open source contribution of the >>>>>>>>> >>> TPP >>> >>>>> and >>>>> >>>>>>>>> I do understand how difficult it is to maintain documentation >>>>>>>>> >>> but >>> >>>>> it >>>>> >>>>>>>>> would have saved me a lot of time if, at least, the README file >>>>>>>>> >>> had >>> >>>>>>>>> been updated when the build procedure was changed. >>>>>>>>> Thanks, >>>>>>>>> Bill >>>>>>>>> >>>>>>>>> On Nov 9, 11:59 am, Brian Pratt <[email protected]> >>>>>>>>> >>> wrote: >>> >>>>>>>>>>>> Can you please guide me to the correct win_lib folder for >>>>>>>>>>>> >>> the >>> >>>>> trunk >>>>> >>>>>>> or >>>>>>> >>>>>>>>>> is it no longer needed? >>>>>>>>>> No longer needed. Instead, things are extracted as needed >>>>>>>>>> >>> from >>> >>>>>>>>> compressed >>>>>>>>> >>>>>>>>>> files in extern. Ordinarily that happens seamlessly as part >>>>>>>>>> >>> of >>> >>>>> the >>>>> >>>>>>> build >>>>>>> >>>>>>>>>> process (but as we have seen, in the case of VC you need to >>>>>>>>>> >>> do a >>> >>>>>>> release >>>>>>> >>>>>>>>>> buld first to trigger the uncompressing). >>>>>>>>>> >>>>>>>>>> Such is life in trunk. >>>>>>>>>> >>>>>>>>>> Brian >>>>>>>>>> >>>>>>>>> > On Mon, Nov 9, 2009 at 7:27 AM, Bill Nelson < >>>>>>>>> >>>>> [email protected]> >>>>> >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>>> The newer releases don't extract the external libraries. >>>>>>>>>>> I was using the XML_only solution. I switched to the plain >>>>>>>>>>> >>>>> vanilla >>>>> >>>>>>> TPP >>>>>>> >>>>>>>>>>> solution, rebuilt ziplib , and everything works now. >>>>>>>>>>> I would like to use the trunk but it does not match the >>>>>>>>>>> >>>>>>> documentation: >>>>>>> >>>>>>>>>>> I can't find the win_lib folder in the trunk. >>>>>>>>>>> Can you please guide me to the correct win_lib folder for >>>>>>>>>>> >>> the >>> >>>>> trunk >>>>> >>>>>>> or >>>>>>> >>>>>>>>>>> is it no longer needed? >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> Bill >>>>>>>>>>> >>>>>>>>>>> On Nov 6, 6:27 pm, Brian Pratt <[email protected]> >>>>>>>>>>> >>>>> wrote: >>>>> >>>>>>>>>>>> Just about everything links against tpplib, so yes, if >>>>>>>>>>>> >>> that's >>> >>>>> not >>>>> >>>>>>>>> happy >>>>>>>>> >>>>>>>>>>>> nobody's happy. And tpplib depends on zlib, so... >>>>>>>>>>>> >>>>>>>>>>>> I think you're better off looking forward than backward, >>>>>>>>>>>> >>>>> though, >>>>> >>>>>>> and >>>>>>> >>>>>>>>> I'd >>>>>>>>> >>>>>>>>>>> say >>>>>>>>>>> >>>>>>>>>>>> go with trunk. >>>>>>>>>>>> >>>>>>>>>>> > On Fri, Nov 6, 2009 at 2:39 PM, Bill Nelson < >>>>>>>>>>> >>>>>>> [email protected]> >>>>>>> >>>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>>>> I couldn't get 4.3 to work so I went back to 4.2 >>>>>>>>>>>>> >>> (because >>> >>>>> it >>>>> >>>>>>> was >>>>>>> >>>>>>>>> the >>>>>>>>> >>>>>>>>>>>>> release used in the documentation's build example). >>>>>>>>>>>>> It definitely got better and the build was running for >>>>>>>>>>>>> >>>>> about 45 >>>>> >>>>>>>>>>>>> minutes but still no joy. I hope you've seen this one: >>>>>>>>>>>>> >>>>>>>>>>>>> LIB : fatal error LNK1181: cannot open input file >>>>>>>>>>>>> >>>>> 'C:\sashimi >>>>> >>> \release4-2-1\trans_proteomic_pipeline\src\/Debug/zlib.lib' >>> >>>>>>>>>>>>> LINK : fatal error LNK1181: cannot open input file >>>>>>>>>>>>> >>>>>>> '..\..\..\debug >>>>>>> >>>>>>>>>>>>> \tpplib.lib' *this one happens in almost every >>>>>>>>>>>>> >>> target* >>> >>>>>>>>>>>>> ========== Build: 7 succeeded, 38 failed, 0 up-to-date, >>>>>>>>>>>>> >>> 0 >>> >>>>>>> skipped >>>>>>> >>>>>>>>>>>>> ========== >>>>>>>>>>>>> >>>>>>>>>>>>> On Nov 6, 2:05 pm, Brian Pratt < >>>>>>>>>>>>> >>> [email protected]> >>> >>>>>>> wrote: >>>>>>> >>>>>>>>>>>>>> Branch should be fine - trunk build system is being >>>>>>>>>>>>>> >>>>> worked on >>>>> >>>>>>> so >>>>>>> >>>>>>>>> no >>>>>>>>> >>>>>>>>>>>>> surprise >>>>>>>>>>>>> >>>>>>>>>>>>>> to find a hiccup there. >>>>>>>>>>>>>> >>>>>>>>>>>>> > On Fri, Nov 6, 2009 at 10:41 AM, Bill Nelson < >>>>>>>>>>>>> >>>>>>>>> [email protected]> >>>>>>>>> >>>>>>>>>>>>> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Brian, >>>>>>>>>>>>>>> I am using branch 4-3. do you know the last release >>>>>>>>>>>>>>> >>>>> that >>>>> >>>>>>>>> working? >>>>>>>>> >>>>>>>>>>>>>>> Thanks for your help. >>>>>>>>>>>>>>> Bill >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Nov 6, 1:16 pm, Brian Pratt < >>>>>>>>>>>>>>> >>>>> [email protected]> >>>>> >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>>>>>>>> Try a release build first - it handles the >>>>>>>>>>>>>>>> >>>>> uncompressing >>>>> >>>>>>>>> stuff. >>>>>>>>> >>>>>>>>>>>>>>> Apparently >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> just an oversight on the debug side, I'm sure it >>>>>>>>>>>>>>>> >>> will >>> >>>>> get >>>>> >>>>>>>>> fixed >>>>>>>>> >>>>>>>>>>> soon, >>>>>>>>>>> >>>>>>>>>>>>> but >>>>>>>>>>>>> >>>>>>>>>>>>>>>> this should get you rolling. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> > On Fri, Nov 6, 2009 at 7:58 AM, Bill Nelson < >>>>>>>>>>>>>>> >>>>>>>>>>> [email protected]> >>>>>>>>>>> >>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> I'm building tpp on windows with VS8. I >>>>>>>>>>>>>>>>> >>> checked >>> >>>>> out >>>>> >>>>>>> 4.3. I >>>>>>> >>>>>>>>>>> have a >>>>>>>>>>> >>>>>>>>>>>>>>>>> couple questions. >>>>>>>>>>>>>>>>> >> ... >> >> read more ยป >> > > -- > > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
