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tutorial problem to view database
by Kie Kyon Huang
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hi all,
i had recently install gbrowse on windows and is trying to follow the tutorial below http://cpansearch.perl.org/src/LDS/GBrowse-1.9971/htdocs/tutorial/tutorial.html#basics however, i was not able to view the volvox example or even the default yeast chr 1 & 2 with the following error An internal error has occurred Could not open database. Can't locate DB_File.pm in @INC (@INC contains: C:/Perl/site/lib C:/Perl/lib .) at C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. BEGIN failed--compilation aborted at C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. Compilation failed in require at C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. BEGIN failed--compilation aborted at C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. Compilation failed in require at C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. BEGIN failed--compilation aborted at C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. Compilation failed in require at (eval 89) line 3. at C:/Perl/site/lib/Bio/Graphics/Browser/Util.pm line 187 i am also atttaching the error log as instructed in the tutorial. pls advice me on this. thanks a lot huang ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: tutorial problem to view database
by Sheldon McKay-3
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It looks like you do not have the required DB_File.pm perl module
installed. You will have to install it from CPAN. >From your error message. it looks like you are working on a Windows machine. If you are using ActiveState Perl, you can use these instructions for installing DB_File: http://www.rcbowen.com/imho/perl/modules.html#Installing_modules_on_Windows_NT Sheldon On Thu, Nov 5, 2009 at 8:43 AM, Kie Kyon Huang <kiekyon.huang@...> wrote: > hi all, > > i had recently install gbrowse on windows and is trying to follow the > tutorial below > > http://cpansearch.perl.org/src/LDS/GBrowse-1.9971/htdocs/tutorial/tutorial.html#basics > > however, i was not able to view the volvox example or even the default > yeast chr 1 & 2 with the following error > > An internal error has occurred > > Could not open database. > > Can't locate DB_File.pm in @INC (@INC contains: C:/Perl/site/lib > C:/Perl/lib .) at > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. > BEGIN failed--compilation aborted at > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. > Compilation failed in require at > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. > BEGIN failed--compilation aborted at > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. > Compilation failed in require at > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. > BEGIN failed--compilation aborted at > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. > Compilation failed in require at (eval 89) line 3. > at C:/Perl/site/lib/Bio/Graphics/Browser/Util.pm line 187 > > i am also atttaching the error log as instructed in the tutorial. > pls advice me on this. > > thanks a lot > > huang > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > -- Sheldon McKay, PhD Cold Spring Harbor Laboratory New! Google Voice: (203) 701-9204 Sent from Milford, Connecticut, United States ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: tutorial problem to view database
by Chris Fields-5
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If you're using ActivePerl 5.10.0 or higher, the DB_File module is a
stub (it doesn't work). The Trouchelle repo has a working one; see the bioperl installation instructions for more: http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows chris On Nov 5, 2009, at 7:53 AM, Sheldon McKay wrote: > It looks like you do not have the required DB_File.pm perl module > installed. You will have to install it from CPAN. > >> From your error message. it looks like you are working on a Windows > machine. If you are using ActiveState Perl, you can use these > instructions for installing DB_File: > > http://www.rcbowen.com/imho/perl/modules.html#Installing_modules_on_Windows_NT > > Sheldon > > On Thu, Nov 5, 2009 at 8:43 AM, Kie Kyon Huang <kiekyon.huang@... > > wrote: >> hi all, >> >> i had recently install gbrowse on windows and is trying to follow the >> tutorial below >> >> http://cpansearch.perl.org/src/LDS/GBrowse-1.9971/htdocs/tutorial/tutorial.html#basics >> >> however, i was not able to view the volvox example or even the >> default >> yeast chr 1 & 2 with the following error >> >> An internal error has occurred >> >> Could not open database. >> >> Can't locate DB_File.pm in @INC (@INC contains: C:/Perl/site/lib >> C:/Perl/lib .) at >> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. >> BEGIN failed--compilation aborted at >> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. >> Compilation failed in require at >> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. >> BEGIN failed--compilation aborted at >> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. >> Compilation failed in require at >> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. >> BEGIN failed--compilation aborted at >> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. >> Compilation failed in require at (eval 89) line 3. >> at C:/Perl/site/lib/Bio/Graphics/Browser/Util.pm line 187 >> >> i am also atttaching the error log as instructed in the tutorial. >> pls advice me on this. >> >> thanks a lot >> >> huang >> >> ------------------------------------------------------------------------------ >> Let Crystal Reports handle the reporting - Free Crystal Reports >> 2008 30-Day >> trial. Simplify your report design, integration and deployment - >> and focus on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> > > > > -- > Sheldon McKay, PhD > Cold Spring Harbor Laboratory > New! Google Voice: (203) 701-9204 > > Sent from Milford, Connecticut, United States > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: tutorial problem to view database
by Kie Kyon Huang
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ok, i had downloaded the version 1.817 version of DB_File from trouchelle.
i am still having problem though An internal error has occurred Could not open database. Can't load 'C:/Perl/site/lib/auto/DB_File/DB_File.dll' for module DB_File: load_file:The specified module could not be found at C:/Perl/lib/XSLoader.pm line 70. at C:/Perl/site/lib/DB_File.pm line 252 Compilation failed in require at C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. BEGIN failed--compilation aborted at C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. Compilation failed in require at C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. BEGIN failed--compilation aborted at C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. Compilation failed in require at C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. BEGIN failed--compilation aborted at C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. Compilation failed in require at (eval 89) line 3. at C:/Perl/site/lib/Bio/Graphics/Browser/Util.pm line 187 On Thu, Nov 5, 2009 at 10:31 PM, Chris Fields <cjfields@...> wrote: > If you're using ActivePerl 5.10.0 or higher, the DB_File module is a stub > (it doesn't work). The Trouchelle repo has a working one; see the bioperl > installation instructions for more: > > http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > chris > > On Nov 5, 2009, at 7:53 AM, Sheldon McKay wrote: > >> It looks like you do not have the required DB_File.pm perl module >> installed. You will have to install it from CPAN. >> >>> From your error message. it looks like you are working on a Windows >> >> machine. If you are using ActiveState Perl, you can use these >> instructions for installing DB_File: >> >> >> http://www.rcbowen.com/imho/perl/modules.html#Installing_modules_on_Windows_NT >> >> Sheldon >> >> On Thu, Nov 5, 2009 at 8:43 AM, Kie Kyon Huang <kiekyon.huang@...> >> wrote: >>> >>> hi all, >>> >>> i had recently install gbrowse on windows and is trying to follow the >>> tutorial below >>> >>> >>> http://cpansearch.perl.org/src/LDS/GBrowse-1.9971/htdocs/tutorial/tutorial.html#basics >>> >>> however, i was not able to view the volvox example or even the default >>> yeast chr 1 & 2 with the following error >>> >>> An internal error has occurred >>> >>> Could not open database. >>> >>> Can't locate DB_File.pm in @INC (@INC contains: C:/Perl/site/lib >>> C:/Perl/lib .) at >>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. >>> BEGIN failed--compilation aborted at >>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. >>> Compilation failed in require at >>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. >>> BEGIN failed--compilation aborted at >>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. >>> Compilation failed in require at >>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. >>> BEGIN failed--compilation aborted at >>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. >>> Compilation failed in require at (eval 89) line 3. >>> at C:/Perl/site/lib/Bio/Graphics/Browser/Util.pm line 187 >>> >>> i am also atttaching the error log as instructed in the tutorial. >>> pls advice me on this. >>> >>> thanks a lot >>> >>> huang >>> >>> >>> ------------------------------------------------------------------------------ >>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >>> 30-Day >>> trial. Simplify your report design, integration and deployment - and >>> focus on >>> what you do best, core application coding. Discover what's new with >>> Crystal Reports now. http://p.sf.net/sfu/bobj-july >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmod-gbrowse@... >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >>> >> >> >> >> -- >> Sheldon McKay, PhD >> Cold Spring Harbor Laboratory >> New! Google Voice: (203) 701-9204 >> >> Sent from Milford, Connecticut, United States >> >> >> ------------------------------------------------------------------------------ >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >> 30-Day >> trial. Simplify your report design, integration and deployment - and focus >> on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: tutorial problem to view database
by Scott Cain-4
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Hi Kie,
When you say you downloaded it, did you use ppm to install it? My suggestion would actually be to use ActiveState perl 5.8. Scott On Thu, Nov 5, 2009 at 10:45 AM, Kie Kyon Huang <kiekyon.huang@...> wrote: > ok, i had downloaded the version 1.817 version of DB_File from trouchelle. > > i am still having problem though > > An internal error has occurred > > Could not open database. > > Can't load 'C:/Perl/site/lib/auto/DB_File/DB_File.dll' for module > DB_File: load_file:The specified module could not be found at > C:/Perl/lib/XSLoader.pm line 70. > at C:/Perl/site/lib/DB_File.pm line 252 > Compilation failed in require at > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. > BEGIN failed--compilation aborted at > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. > Compilation failed in require at > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. > BEGIN failed--compilation aborted at > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. > Compilation failed in require at > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. > BEGIN failed--compilation aborted at > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. > Compilation failed in require at (eval 89) line 3. > at C:/Perl/site/lib/Bio/Graphics/Browser/Util.pm line 187 > > On Thu, Nov 5, 2009 at 10:31 PM, Chris Fields <cjfields@...> wrote: >> If you're using ActivePerl 5.10.0 or higher, the DB_File module is a stub >> (it doesn't work). The Trouchelle repo has a working one; see the bioperl >> installation instructions for more: >> >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >> >> chris >> >> On Nov 5, 2009, at 7:53 AM, Sheldon McKay wrote: >> >>> It looks like you do not have the required DB_File.pm perl module >>> installed. You will have to install it from CPAN. >>> >>>> From your error message. it looks like you are working on a Windows >>> >>> machine. If you are using ActiveState Perl, you can use these >>> instructions for installing DB_File: >>> >>> >>> http://www.rcbowen.com/imho/perl/modules.html#Installing_modules_on_Windows_NT >>> >>> Sheldon >>> >>> On Thu, Nov 5, 2009 at 8:43 AM, Kie Kyon Huang <kiekyon.huang@...> >>> wrote: >>>> >>>> hi all, >>>> >>>> i had recently install gbrowse on windows and is trying to follow the >>>> tutorial below >>>> >>>> >>>> http://cpansearch.perl.org/src/LDS/GBrowse-1.9971/htdocs/tutorial/tutorial.html#basics >>>> >>>> however, i was not able to view the volvox example or even the default >>>> yeast chr 1 & 2 with the following error >>>> >>>> An internal error has occurred >>>> >>>> Could not open database. >>>> >>>> Can't locate DB_File.pm in @INC (@INC contains: C:/Perl/site/lib >>>> C:/Perl/lib .) at >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. >>>> BEGIN failed--compilation aborted at >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. >>>> Compilation failed in require at >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. >>>> BEGIN failed--compilation aborted at >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. >>>> Compilation failed in require at >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. >>>> BEGIN failed--compilation aborted at >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. >>>> Compilation failed in require at (eval 89) line 3. >>>> at C:/Perl/site/lib/Bio/Graphics/Browser/Util.pm line 187 >>>> >>>> i am also atttaching the error log as instructed in the tutorial. >>>> pls advice me on this. >>>> >>>> thanks a lot >>>> >>>> huang >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >>>> 30-Day >>>> trial. Simplify your report design, integration and deployment - and >>>> focus on >>>> what you do best, core application coding. Discover what's new with >>>> Crystal Reports now. http://p.sf.net/sfu/bobj-july >>>> _______________________________________________ >>>> Gmod-gbrowse mailing list >>>> Gmod-gbrowse@... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>> >>>> >>> >>> >>> >>> -- >>> Sheldon McKay, PhD >>> Cold Spring Harbor Laboratory >>> New! Google Voice: (203) 701-9204 >>> >>> Sent from Milford, Connecticut, United States >>> >>> >>> ------------------------------------------------------------------------------ >>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >>> 30-Day >>> trial. Simplify your report design, integration and deployment - and focus >>> on >>> what you do best, core application coding. Discover what's new with >>> Crystal Reports now. http://p.sf.net/sfu/bobj-july >>> _______________________________________________ >>> Gmod-gbrowse mailing list >>> Gmod-gbrowse@... >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: tutorial problem to view database
by Kie Kyon Huang
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yes, i install with ppm.
does that mean i have to uninstall the previous perl 5.10? On Nov 5, 2009 11:56pm, Scott Cain <scott@...> wrote: > Hi Kie, > > > > When you say you downloaded it, did you use ppm to install it? > > > > My suggestion would actually be to use ActiveState perl 5.8. > > > > Scott > > > > > > On Thu, Nov 5, 2009 at 10:45 AM, Kie Kyon Huang kiekyon.huang@...> wrote: > > > ok, i had downloaded the version 1.817 version of DB_File from trouchelle. > > > > > > i am still having problem though > > > > > > An internal error has occurred > > > > > > Could not open database. > > > > > > Can't load 'C:/Perl/site/lib/auto/DB_File/DB_File.dll' for module > > > DB_File: load_file:The specified module could not be found at > > > C:/Perl/lib/XSLoader.pm line 70. > > > at C:/Perl/site/lib/DB_File.pm line 252 > > > Compilation failed in require at > > > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. > > > BEGIN failed--compilation aborted at > > > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. > > > Compilation failed in require at > > > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. > > > BEGIN failed--compilation aborted at > > > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. > > > Compilation failed in require at > > > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. > > > BEGIN failed--compilation aborted at > > > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. > > > Compilation failed in require at (eval 89) line 3. > > > at C:/Perl/site/lib/Bio/Graphics/Browser/Util.pm line 187 > > > > > > On Thu, Nov 5, 2009 at 10:31 PM, Chris Fields cjfields@...> wrote: > > >> If you're using ActivePerl 5.10.0 or higher, the DB_File module is a stub > > >> (it doesn't work). The Trouchelle repo has a working one; see the bioperl > > >> installation instructions for more: > > >> > > >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows > > >> > > >> chris > > >> > > >> On Nov 5, 2009, at 7:53 AM, Sheldon McKay wrote: > > >> > > >>> It looks like you do not have the required DB_File.pm perl module > > >>> installed. You will have to install it from CPAN. > > >>> > > >>>> From your error message. it looks like you are working on a Windows > > >>> > > >>> machine. If you are using ActiveState Perl, you can use these > > >>> instructions for installing DB_File: > > >>> > > >>> > > >>> http://www.rcbowen.com/imho/perl/modules.html#Installing_modules_on_Windows_NT > > >>> > > >>> Sheldon > > >>> > > >>> On Thu, Nov 5, 2009 at 8:43 AM, Kie Kyon Huang kiekyon.huang@...> > > >>> wrote: > > >>>> > > >>>> hi all, > > >>>> > > >>>> i had recently install gbrowse on windows and is trying to follow the > > >>>> tutorial below > > >>>> > > >>>> > > >>>> http://cpansearch.perl.org/src/LDS/GBrowse-1.9971/htdocs/tutorial/tutorial.html#basics > > >>>> > > >>>> however, i was not able to view the volvox example or even the default > > >>>> yeast chr 1 & 2 with the following error > > >>>> > > >>>> An internal error has occurred > > >>>> > > >>>> Could not open database. > > >>>> > > >>>> Can't locate DB_File.pm in @INC (@INC contains: C:/Perl/site/lib > > >>>> C:/Perl/lib .) at > > >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. > > >>>> BEGIN failed--compilation aborted at > > >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. > > >>>> Compilation failed in require at > > >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. > > >>>> BEGIN failed--compilation aborted at > > >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. > > >>>> Compilation failed in require at > > >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. > > >>>> BEGIN failed--compilation aborted at > > >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. > > >>>> Compilation failed in require at (eval 89) line 3. > > >>>> at C:/Perl/site/lib/Bio/Graphics/Browser/Util.pm line 187 > > >>>> > > >>>> i am also atttaching the error log as instructed in the tutorial. > > >>>> pls advice me on this. > > >>>> > > >>>> thanks a lot > > >>>> > > >>>> huang > > >>>> > > >>>> > > >>>> ------------------------------------------------------------------------------ > > >>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > > >>>> 30-Day > > >>>> trial. Simplify your report design, integration and deployment - and > > >>>> focus on > > >>>> what you do best, core application coding. Discover what's new with > > >>>> Crystal Reports now. http://p.sf.net/sfu/bobj-july > > >>>> _______________________________________________ > > >>>> Gmod-gbrowse mailing list > > >>>> Gmod-gbrowse@... > > >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > >>>> > > >>>> > > >>> > > >>> > > >>> > > >>> -- > > >>> Sheldon McKay, PhD > > >>> Cold Spring Harbor Laboratory > > >>> New! Google Voice: (203) 701-9204 > > >>> > > >>> Sent from Milford, Connecticut, United States > > >>> > > >>> > > >>> ------------------------------------------------------------------------------ > > >>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > > >>> 30-Day > > >>> trial. Simplify your report design, integration and deployment - and focus > > >>> on > > >>> what you do best, core application coding. Discover what's new with > > >>> Crystal Reports now. http://p.sf.net/sfu/bobj-july > > >>> _______________________________________________ > > >>> Gmod-gbrowse mailing list > > >>> Gmod-gbrowse@... > > >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > >> > > >> > > > > > > ------------------------------------------------------------------------------ > > > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > > > trial. Simplify your report design, integration and deployment - and focus on > > > what you do best, core application coding. Discover what's new with > > > Crystal Reports now. http://p.sf.net/sfu/bobj-july > > > _______________________________________________ > > > Gmod-gbrowse mailing list > > > Gmod-gbrowse@... > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > > > > > > > > > -- > > ------------------------------------------------------------------------ > > Scott Cain, Ph. D. scott at scottcain dot net > > GMOD Coordinator (http://gmod.org/) 216-392-3087 > > Ontario Institute for Cancer Research > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: tutorial problem to view database
by Scott Cain-4
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Hi Kie,
If you go down the route of trying 5.8, yes, you should completely uninstall 5.10 (which means using the "add/remove" thing, plus also removing the perl folder (probably C:\perl)). Before you do that, perhaps Chris or somebody else has a suggestion for getting 5.10 to work. I just know I've had more success with 5.8 (but that was before the DB_File module was released for 5.10). Scott On Thu, Nov 5, 2009 at 8:49 PM, <kiekyon.huang@...> wrote: > yes, i install with ppm. > > does that mean i have to uninstall the previous perl 5.10? > > On Nov 5, 2009 11:56pm, Scott Cain <scott@...> wrote: >> Hi Kie, >> >> >> >> When you say you downloaded it, did you use ppm to install it? >> >> >> >> My suggestion would actually be to use ActiveState perl 5.8. >> >> >> >> Scott >> >> >> >> >> >> On Thu, Nov 5, 2009 at 10:45 AM, Kie Kyon Huang kiekyon.huang@...> >> wrote: >> >> > ok, i had downloaded the version 1.817 version of DB_File from >> > trouchelle. >> >> > >> >> > i am still having problem though >> >> > >> >> > An internal error has occurred >> >> > >> >> > Could not open database. >> >> > >> >> > Can't load 'C:/Perl/site/lib/auto/DB_File/DB_File.dll' for module >> >> > DB_File: load_file:The specified module could not be found at >> >> > C:/Perl/lib/XSLoader.pm line 70. >> >> > at C:/Perl/site/lib/DB_File.pm line 252 >> >> > Compilation failed in require at >> >> > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. >> >> > BEGIN failed--compilation aborted at >> >> > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. >> >> > Compilation failed in require at >> >> > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. >> >> > BEGIN failed--compilation aborted at >> >> > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. >> >> > Compilation failed in require at >> >> > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. >> >> > BEGIN failed--compilation aborted at >> >> > C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. >> >> > Compilation failed in require at (eval 89) line 3. >> >> > at C:/Perl/site/lib/Bio/Graphics/Browser/Util.pm line 187 >> >> > >> >> > On Thu, Nov 5, 2009 at 10:31 PM, Chris Fields cjfields@...> >> > wrote: >> >> >> If you're using ActivePerl 5.10.0 or higher, the DB_File module is a >> >> stub >> >> >> (it doesn't work). The Trouchelle repo has a working one; see the >> >> bioperl >> >> >> installation instructions for more: >> >> >> >> >> >> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >> >> >> >> >> >> chris >> >> >> >> >> >> On Nov 5, 2009, at 7:53 AM, Sheldon McKay wrote: >> >> >> >> >> >>> It looks like you do not have the required DB_File.pm perl module >> >> >>> installed. You will have to install it from CPAN. >> >> >>> >> >> >>>> From your error message. it looks like you are working on a Windows >> >> >>> >> >> >>> machine. If you are using ActiveState Perl, you can use these >> >> >>> instructions for installing DB_File: >> >> >>> >> >> >>> >> >> >>> >> >>> http://www.rcbowen.com/imho/perl/modules.html#Installing_modules_on_Windows_NT >> >> >>> >> >> >>> Sheldon >> >> >>> >> >> >>> On Thu, Nov 5, 2009 at 8:43 AM, Kie Kyon Huang >> >>> kiekyon.huang@...> >> >> >>> wrote: >> >> >>>> >> >> >>>> hi all, >> >> >>>> >> >> >>>> i had recently install gbrowse on windows and is trying to follow the >> >> >>>> tutorial below >> >> >>>> >> >> >>>> >> >> >>>> >> >>>> http://cpansearch.perl.org/src/LDS/GBrowse-1.9971/htdocs/tutorial/tutorial.html#basics >> >> >>>> >> >> >>>> however, i was not able to view the volvox example or even the >> >>>> default >> >> >>>> yeast chr 1 & 2 with the following error >> >> >>>> >> >> >>>> An internal error has occurred >> >> >>>> >> >> >>>> Could not open database. >> >> >>>> >> >> >>>> Can't locate DB_File.pm in @INC (@INC contains: C:/Perl/site/lib >> >> >>>> C:/Perl/lib .) at >> >> >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. >> >> >>>> BEGIN failed--compilation aborted at >> >> >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. >> >> >>>> Compilation failed in require at >> >> >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. >> >> >>>> BEGIN failed--compilation aborted at >> >> >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. >> >> >>>> Compilation failed in require at >> >> >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. >> >> >>>> BEGIN failed--compilation aborted at >> >> >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. >> >> >>>> Compilation failed in require at (eval 89) line 3. >> >> >>>> at C:/Perl/site/lib/Bio/Graphics/Browser/Util.pm line 187 >> >> >>>> >> >> >>>> i am also atttaching the error log as instructed in the tutorial. >> >> >>>> pls advice me on this. >> >> >>>> >> >> >>>> thanks a lot >> >> >>>> >> >> >>>> huang >> >> >>>> >> >> >>>> >> >> >>>> >> >>>> ------------------------------------------------------------------------------ >> >> >>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >> >> >>>> 30-Day >> >> >>>> trial. Simplify your report design, integration and deployment - and >> >> >>>> focus on >> >> >>>> what you do best, core application coding. Discover what's new with >> >> >>>> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> >> >>>> _______________________________________________ >> >> >>>> Gmod-gbrowse mailing list >> >> >>>> Gmod-gbrowse@... >> >> >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> >>>> >> >> >>>> >> >> >>> >> >> >>> >> >> >>> >> >> >>> -- >> >> >>> Sheldon McKay, PhD >> >> >>> Cold Spring Harbor Laboratory >> >> >>> New! Google Voice: (203) 701-9204 >> >> >>> >> >> >>> Sent from Milford, Connecticut, United States >> >> >>> >> >> >>> >> >> >>> >> >>> ------------------------------------------------------------------------------ >> >> >>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >> >> >>> 30-Day >> >> >>> trial. Simplify your report design, integration and deployment - and >> >>> focus >> >> >>> on >> >> >>> what you do best, core application coding. Discover what's new with >> >> >>> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> >> >>> _______________________________________________ >> >> >>> Gmod-gbrowse mailing list >> >> >>> Gmod-gbrowse@... >> >> >>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> >> >> >> >> >> >> > >> >> > >> > ------------------------------------------------------------------------------ >> >> > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >> > 30-Day >> >> > trial. Simplify your report design, integration and deployment - and >> > focus on >> >> > what you do best, core application coding. Discover what's new with >> >> > Crystal Reports now. http://p.sf.net/sfu/bobj-july >> >> > _______________________________________________ >> >> > Gmod-gbrowse mailing list >> >> > Gmod-gbrowse@... >> >> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> > >> >> >> >> >> >> >> >> -- >> >> ------------------------------------------------------------------------ >> >> Scott Cain, Ph. D. scott at scottcain >> dot net >> >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> >> Ontario Institute for Cancer Research >> -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: tutorial problem to view database
by Chris Fields-5
::
Rate this Message:
Scott,
Unfortunately, not much I can add; I've moved to OS X and Ubuntu and haven't tried Gbrowse on Windows in many years. chris On Nov 5, 2009, at 9:15 PM, Scott Cain wrote: > Hi Kie, > > If you go down the route of trying 5.8, yes, you should completely > uninstall 5.10 (which means using the "add/remove" thing, plus also > removing the perl folder (probably C:\perl)). > > Before you do that, perhaps Chris or somebody else has a suggestion > for getting 5.10 to work. I just know I've had more success with 5.8 > (but that was before the DB_File module was released for 5.10). > > Scott > > > > On Thu, Nov 5, 2009 at 8:49 PM, <kiekyon.huang@...> wrote: >> yes, i install with ppm. >> >> does that mean i have to uninstall the previous perl 5.10? >> >> On Nov 5, 2009 11:56pm, Scott Cain <scott@...> wrote: >>> Hi Kie, >>> >>> >>> >>> When you say you downloaded it, did you use ppm to install it? >>> >>> >>> >>> My suggestion would actually be to use ActiveState perl 5.8. >>> >>> >>> >>> Scott >>> >>> >>> >>> >>> >>> On Thu, Nov 5, 2009 at 10:45 AM, Kie Kyon Huang kiekyon.huang@... >>> > >>> wrote: >>> >>>> ok, i had downloaded the version 1.817 version of DB_File from >>>> trouchelle. >>> >>>> >>> >>>> i am still having problem though >>> >>>> >>> >>>> An internal error has occurred >>> >>>> >>> >>>> Could not open database. >>> >>>> >>> >>>> Can't load 'C:/Perl/site/lib/auto/DB_File/DB_File.dll' for module >>> >>>> DB_File: load_file:The specified module could not be found at >>> >>>> C:/Perl/lib/XSLoader.pm line 70. >>> >>>> at C:/Perl/site/lib/DB_File.pm line 252 >>> >>>> Compilation failed in require at >>> >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. >>> >>>> BEGIN failed--compilation aborted at >>> >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. >>> >>>> Compilation failed in require at >>> >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. >>> >>>> BEGIN failed--compilation aborted at >>> >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. >>> >>>> Compilation failed in require at >>> >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. >>> >>>> BEGIN failed--compilation aborted at >>> >>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. >>> >>>> Compilation failed in require at (eval 89) line 3. >>> >>>> at C:/Perl/site/lib/Bio/Graphics/Browser/Util.pm line 187 >>> >>>> >>> >>>> On Thu, Nov 5, 2009 at 10:31 PM, Chris Fields >>>> cjfields@...> >>>> wrote: >>> >>>>> If you're using ActivePerl 5.10.0 or higher, the DB_File module >>>>> is a >>>>> stub >>> >>>>> (it doesn't work). The Trouchelle repo has a working one; see the >>>>> bioperl >>> >>>>> installation instructions for more: >>> >>>>> >>> >>>>> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows >>> >>>>> >>> >>>>> chris >>> >>>>> >>> >>>>> On Nov 5, 2009, at 7:53 AM, Sheldon McKay wrote: >>> >>>>> >>> >>>>>> It looks like you do not have the required DB_File.pm perl module >>> >>>>>> installed. You will have to install it from CPAN. >>> >>>>>> >>> >>>>>>> From your error message. it looks like you are working on a >>>>>>> Windows >>> >>>>>> >>> >>>>>> machine. If you are using ActiveState Perl, you can use these >>> >>>>>> instructions for installing DB_File: >>> >>>>>> >>> >>>>>> >>> >>>>>> >>>>>> http://www.rcbowen.com/imho/perl/modules.html#Installing_modules_on_Windows_NT >>> >>>>>> >>> >>>>>> Sheldon >>> >>>>>> >>> >>>>>> On Thu, Nov 5, 2009 at 8:43 AM, Kie Kyon Huang >>>>>> kiekyon.huang@...> >>> >>>>>> wrote: >>> >>>>>>> >>> >>>>>>> hi all, >>> >>>>>>> >>> >>>>>>> i had recently install gbrowse on windows and is trying to >>>>>>> follow the >>> >>>>>>> tutorial below >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>>>>>> http://cpansearch.perl.org/src/LDS/GBrowse-1.9971/htdocs/tutorial/tutorial.html#basics >>> >>>>>>> >>> >>>>>>> however, i was not able to view the volvox example or even the >>>>>>> default >>> >>>>>>> yeast chr 1 & 2 with the following error >>> >>>>>>> >>> >>>>>>> An internal error has occurred >>> >>>>>>> >>> >>>>>>> Could not open database. >>> >>>>>>> >>> >>>>>>> Can't locate DB_File.pm in @INC (@INC contains: C:/Perl/site/lib >>> >>>>>>> C:/Perl/lib .) at >>> >>>>>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. >>> >>>>>>> BEGIN failed--compilation aborted at >>> >>>>>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 39. >>> >>>>>>> Compilation failed in require at >>> >>>>>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. >>> >>>>>>> BEGIN failed--compilation aborted at >>> >>>>>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/GFF3Loader.pm line 72. >>> >>>>>>> Compilation failed in require at >>> >>>>>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. >>> >>>>>>> BEGIN failed--compilation aborted at >>> >>>>>>> C:/Perl/site/lib/Bio/DB/SeqFeature/Store/memory.pm line 126. >>> >>>>>>> Compilation failed in require at (eval 89) line 3. >>> >>>>>>> at C:/Perl/site/lib/Bio/Graphics/Browser/Util.pm line 187 >>> >>>>>>> >>> >>>>>>> i am also atttaching the error log as instructed in the >>>>>>> tutorial. >>> >>>>>>> pls advice me on this. >>> >>>>>>> >>> >>>>>>> thanks a lot >>> >>>>>>> >>> >>>>>>> huang >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>> >>>>>>> Let Crystal Reports handle the reporting - Free Crystal >>>>>>> Reports 2008 >>> >>>>>>> 30-Day >>> >>>>>>> trial. Simplify your report design, integration and deployment >>>>>>> - and >>> >>>>>>> focus on >>> >>>>>>> what you do best, core application coding. Discover what's new >>>>>>> with >>> >>>>>>> Crystal Reports now. http://p.sf.net/sfu/bobj-july >>> >>>>>>> _______________________________________________ >>> >>>>>>> Gmod-gbrowse mailing list >>> >>>>>>> Gmod-gbrowse@... >>> >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >>>>>>> >>> >>>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> -- >>> >>>>>> Sheldon McKay, PhD >>> >>>>>> Cold Spring Harbor Laboratory >>> >>>>>> New! Google Voice: (203) 701-9204 >>> >>>>>> >>> >>>>>> Sent from Milford, Connecticut, United States >>> >>>>>> >>> >>>>>> >>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>> >>>>>> Let Crystal Reports handle the reporting - Free Crystal Reports >>>>>> 2008 >>> >>>>>> 30-Day >>> >>>>>> trial. Simplify your report design, integration and deployment >>>>>> - and >>>>>> focus >>> >>>>>> on >>> >>>>>> what you do best, core application coding. Discover what's new >>>>>> with >>> >>>>>> Crystal Reports now. http://p.sf.net/sfu/bobj-july >>> >>>>>> _______________________________________________ >>> >>>>>> Gmod-gbrowse mailing list >>> >>>>>> Gmod-gbrowse@... >>> >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >>>>> >>> >>>>> >>> >>>> >>> >>>> >>>> ------------------------------------------------------------------------------ >>> >>>> Let Crystal Reports handle the reporting - Free Crystal Reports >>>> 2008 >>>> 30-Day >>> >>>> trial. Simplify your report design, integration and deployment - >>>> and >>>> focus on >>> >>>> what you do best, core application coding. Discover what's new with >>> >>>> Crystal Reports now. http://p.sf.net/sfu/bobj-july >>> >>>> _______________________________________________ >>> >>>> Gmod-gbrowse mailing list >>> >>>> Gmod-gbrowse@... >>> >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >>>> >>> >>> >>> >>> >>> >>> >>> >>> -- >>> >>> ------------------------------------------------------------------------ >>> >>> Scott Cain, Ph. D. scott at >>> scottcain >>> dot net >>> >>> GMOD Coordinator (http://gmod.org/) 216-392-3087 >>> >>> Ontario Institute for Cancer Research >>> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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