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From: Diane T. <di...@ca...> - 2004-09-27 17:31:02
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Hi, I think the subversion daemon is currently stopped. Thanks, diane |
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From: Hrishikesh D. <hde...@gm...> - 2004-09-27 15:20:39
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Hi Jason, Here is the error which i get when i try to use GUI for QT-dim file. Here also a relation doesn't get dropped. As i understand qt-dim and AD files are to loaded once and then there is no need, since here we are testing GUI also, it would help us if we can get simple scripts to drop tables and relations,so that we can continue testing. Thanks, Hrishi Genex Job Status Page Your job is finished. The status is: ERROR The error status is: 6400 Output of the program: NOTICE: CREATE TABLE / UNIQUE will create implicit index "quantarray_3_0_mba_fk_key" for table "quantarray_3_0" DBD::Pg::db do failed: ERROR: relation "quantarray_3_0" already exists at /usr/local/share/perl/5.8.4/Bio/Genex/Connect.pm line 898. main:/usr/local/genex/bin/qtdim-insert.pl:197:Bio::Genex::Connect::insert_mba_data_table: Creating table QUANTARRAY_3_0, SQL=[[CREATE TABLE QUANTARRAY_3_0 ( "feature_fk" int4 NOT NULL, "mba_fk" int4 NOT NULL, "i_ch1_intensity" int4 NOT NULL, "i_ch1_background" int4 NOT NULL, "i_ch1_intensity_std_dev" int4 NOT NULL, "i_ch1_background_std_dev" int4 NOT NULL, "i_ch1_signal_noise_ratio" int4 NOT NULL, "i_ch2_intensity" int4 NOT NULL, "i_ch2_background" int4 NOT NULL, "i_ch2_intensity_std_dev" int4 NOT NULL, "i_ch2_background_std_dev" int4 NOT NULL, "i_ch2_signal_noise_ratio" int4 NOT NULL, UNIQUE (mba_fk, feature_fk) ) ; ]], DBI=[[ERROR: relation "quantarray_3_0" already exists]] Jason E. Stewart wrote: > Hey Harry, Hrishi, Jennifer, Andrew, et. al. > > I think the new version is fairly stable. Can you give it a day or two > of testing on genex2 and then you can decide to update matrix. It will > require DB changes for the new applications to work properly. > > As I wrote in a private email to Jennifer, this release contains all > the needed schema changes that I am aware of. Only testing will reveal > where it needs more work. > > *Please* do read the new Data Processing Protocol HOWTO, and test out > the examples. It is designed to be an Admin/Curator level document > explaining how to set up protocols to allow users to process their > data. I need feedback on: > * how understandable it is > * how much detail is needed (more/less) > * whether the examples work > * whether the whole system makes sense - i.e. will real people be able > to use it - both curators and users. > > Cheers, > jas. > > > ------------------------------------------------------- > This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170 > Project Admins to receive an Apple iPod Mini FREE for your judgement on > who ports your project to Linux PPC the best. Sponsored by IBM. > Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php > _______________________________________________ > Genex-dev mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genex-dev |
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From: Hrishikesh D. <hde...@gm...> - 2004-09-27 14:58:30
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Hi Jason, I want to load QT-dim files but documentation needs some examples for every step for QT-dim. Can you give me input values for say /DB/curated_data/quantarray.xml file, so that i can try loading this,i am a little confused and i think i am using wrong input values for the GUI, so thats the reason i am seeing errors. Waiting for the input values. Hrishi Jason E. Stewart wrote: > Hey Harry, Hrishi, Jennifer, Andrew, et. al. > > I think the new version is fairly stable. Can you give it a day or two > of testing on genex2 and then you can decide to update matrix. It will > require DB changes for the new applications to work properly. > > As I wrote in a private email to Jennifer, this release contains all > the needed schema changes that I am aware of. Only testing will reveal > where it needs more work. > > *Please* do read the new Data Processing Protocol HOWTO, and test out > the examples. It is designed to be an Admin/Curator level document > explaining how to set up protocols to allow users to process their > data. I need feedback on: > * how understandable it is > * how much detail is needed (more/less) > * whether the examples work > * whether the whole system makes sense - i.e. will real people be able > to use it - both curators and users. > > Cheers, > jas. > > > ------------------------------------------------------- > This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170 > Project Admins to receive an Apple iPod Mini FREE for your judgement on > who ports your project to Linux PPC the best. Sponsored by IBM. > Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php > _______________________________________________ > Genex-dev mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genex-dev |
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From: SourceForge.net <no...@so...> - 2004-09-25 08:36:32
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Bugs item #985186, was opened at 2004-07-04 23:05 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=985186&group_id=16453 Category: Mason GUI Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 8 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: comp for running external applications should grab STDERR Initial Comment: instead of needing to check the apache error logs all the time, we should grab STDERR and display it directly in the browser when there is an error from an external application ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=985186&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-09-25 08:36:32
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Bugs item #981103, was opened at 2004-06-28 02:53 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=981103&group_id=16453 Category: DB Schema Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: QuantitationType Table needs OntologyEntries not strings Initial Comment: The QT table was never converted to use OntologyEntry's, it is still using strings. When entering QT Dimensions we need to convert from MAGE OE entries to Genex OE entries. I'm afraid this is going to require a table drop and reload. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=981103&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-09-25 08:36:32
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Bugs item #981106, was opened at 2004-06-28 02:55 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=981106&group_id=16453 Category: DB Schema Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: QT Tables want to be curator tables Initial Comment: Since it looks like the QT table is going to be heavily modified, I might as well make this change, too. It makes no sense to track security for these objects, they want to be curator controlled. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=981106&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-09-25 08:36:32
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Bugs item #953954, was opened at 2004-05-14 07:15 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=953954&group_id=16453 Category: Mason GUI Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 8 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: analyze-experiment.html cannot export data Initial Comment: mason error: Error during compilation of /var/www/genex/mason/login/workspace/comps/export-bad-tab-file.mason: Global symbol "$data_table" requires explicit package name at /var/www/genex/mason/login/workspace/comps/export-bad-tab-file.mason line 47. ---------------------------------------------------------------------- Comment By: Jason E. Stewart (jason_e_stewart) Date: 2004-05-16 00:29 Message: Logged In: YES user_id=85550 export of MBA data is now working, but exporting of DBA data is still broken ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=953954&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-09-25 08:36:32
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Bugs item #953804, was opened at 2004-05-14 02:19 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=953804&group_id=16453 Category: Bio::Genex Perl API Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Scratch table: inserting float fields into int colums Initial Comment: create_scratch_view_sql() is doing the wrong transformation. it is placing all the i_ columns into int fields and not float fields ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=953804&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-09-25 08:36:31
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Bugs item #848076, was opened at 2003-11-24 00:29 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848076&group_id=16453 Category: Bio::Genex Perl API Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Nobody/Anonymous (nobody) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Set identifier in insert_db() Initial Comment: since we don't let the user set identifier from Mason, we'd better set it in insert_db() ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848076&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-09-25 08:36:31
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Bugs item #945353, was opened at 2004-04-30 09:02 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945353&group_id=16453 Category: Mason GUI Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 6 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: 'no child processes' error in copy-to-scratch.html Initial Comment: When copying an MBA to a Scratch view, an error is caught after copy-to-scratch.pl is called even though the process exits normally. ---------------------------------------------------------------------- Comment By: Jason E. Stewart (jason_e_stewart) Date: 2004-05-10 07:46 Message: Logged In: YES user_id=85550 This bug is back but I've commented out the error checking code for now so I'm setting this as a low priority. ---------------------------------------------------------------------- Comment By: Jason E. Stewart (jason_e_stewart) Date: 2004-04-30 09:48 Message: Logged In: YES user_id=85550 It was a valid error. Due to a switch in the CGI parameter name, the hidden variable was no longer being store if the page was called from the old application route through exp-analyze.mason. This old route has been disabled. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945353&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-09-25 08:36:31
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Bugs item #956693, was opened at 2004-05-19 06:56 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=956693&group_id=16453 Category: DB Schema Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: using oid for pkey is breaking DB insertion code Initial Comment: the change to make oid act as pkey is attempting to make bogus insert statements. SQL=[[INSERT INTO GENEX_ROLE (role_name_ont_fk,oid,other_table_fk,other_fk) VALUES ('305','641','161','637')]], DBI=[[ERROR: column "oid" of relation "genex_role" does not exist]] ---------------------------------------------------------------------- Comment By: Jason E. Stewart (jason_e_stewart) Date: 2004-06-18 01:43 Message: Logged In: YES user_id=85550 This is a test comment, please ignore ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=956693&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-09-25 08:36:31
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Bugs item #985176, was opened at 2004-07-04 22:41 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=985176&group_id=16453 Category: Mason GUI Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: analyze-experiment.html must handle ProtocolApplication's Initial Comment: Currently this app is not inserting ProtocolApplication, ProtocolStepApplication, or ParameterValue's when running a protocol. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=985176&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-09-25 08:36:31
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Bugs item #980298, was opened at 2004-06-26 09:01 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=980298&group_id=16453 Category: DB Schema Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Procedure needs extra columns Initial Comment: In order to make data processing procedures work we need extra information: * parameter call style (order, long option names, short options names) * path (can't overload name for this) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=980298&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-09-25 08:36:31
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Bugs item #848083, was opened at 2003-11-24 00:29 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848083&group_id=16453 Category: Mason GUI Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Nobody/Anonymous (nobody) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: fix the job status page to run inside the workspace Initial Comment: fix the job status page to run inside the workspace ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848083&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-09-25 08:36:29
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Bugs item #980297, was opened at 2004-06-26 08:57 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=980297&group_id=16453 Category: DB Schema Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Parameter needs extra columns Initial Comment: In order to make data processing procedures work we need extra information: * parameter order * data type * is_required ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=980297&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-09-25 08:33:03
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Bugs item #1015474, was opened at 2004-08-24 12:41 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=1015474&group_id=16453 Category: Mason GUI Group: None >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Hrishikesh Deshmukh (hdeshmuk) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Must specify --abbrev_name for QTD files Initial Comment: Hrishikesh Deshmukh <gen...@ya...> writes: > Now loading the array design file was successful, i > have selected dataset 4 (one of your emails dated: 27 > April,04 has the details). What did you do to fix it? > Second thing which i wanted to do was loading QTD > file, i selected the quantarray.xml file, the data set > file is 1200-mangle-.txt, the values used were: > Must specify --abbrev_name Ok. This is a bug. Could you file a bug report so this doesn't get lost. Cheers, jas. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=1015474&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-09-25 08:33:03
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Bugs item #1031756, was opened at 2004-09-21 03:03 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=1031756&group_id=16453 Category: Installer Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Nobody/Anonymous (nobody) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: test Array and ArrayManufacture must have name Initial Comment: The test data is inserting nameless Array and ArrayManufacture which make them dificult to select from the drop-down menus ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=1031756&group_id=16453 |
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From: <ja...@op...> - 2004-09-25 04:42:59
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Hey Harry, Hrishi, Jennifer, Andrew, et. al. I think the new version is fairly stable. Can you give it a day or two of testing on genex2 and then you can decide to update matrix. It will require DB changes for the new applications to work properly. As I wrote in a private email to Jennifer, this release contains all the needed schema changes that I am aware of. Only testing will reveal where it needs more work. *Please* do read the new Data Processing Protocol HOWTO, and test out the examples. It is designed to be an Admin/Curator level document explaining how to set up protocols to allow users to process their data. I need feedback on: * how understandable it is * how much detail is needed (more/less) * whether the examples work * whether the whole system makes sense - i.e. will real people be able to use it - both curators and users. Cheers, jas. |
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From: <ja...@op...> - 2004-09-25 04:37:40
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Harry J Mangalam <hj...@ta...> writes: > OK - just tried version 1554 - installed fine with the exception of: > > !! System Error: No such file or directory @ line: 249 (cp > Mason/nologin/docs/data-processing-protocol.html /var/www/genex/mason/nologin/docs) > > another MANIFEST error? I'll correct and svn it ifyou want.. Thanks for catching that one Harry. Actually, it was fixed locally but not committed. It is now in 1555. Cheers, jas. |
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From: <ja...@op...> - 2004-09-25 04:35:41
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Hrishikesh Deshmukh <hde...@gm...> writes: > Jason the awesome, Flattery will get you everywhere... > I have tried commandline QT dim loading, works like a charm. > Used GUI for loading experiment and array design and works like a charm. > Trying QT dim, i will give update once i am done with this part > today/on monday. Good! Glad that we're being able to communicate, and that things are progressing. Cheers, jas. |
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From: Hrishikesh D. <hde...@gm...> - 2004-09-24 20:35:17
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Jason the awesome, I have tried commandline QT dim loading, works like a charm. Used GUI for loading experiment and array design and works like a charm. Trying QT dim, i will give update once i am done with this part today/on monday. Thanks, Hrishi Jason E. Stewart wrote: > Harry Mangalam <hj...@ta...> writes: > > >>I agree - it looks like it's broken - missing all the files that are >>supposed to go with it. I copied over my installed copy into >>the /usr/local/lib/perl/5.8.4/Apache/SubProcess.pm, so things should >>go OK from there - give it a try. > > > Hey, > > Looking at this it seems that apache-dev and mod_perl-dev are not > installed. Without these you can't get Apache::SubProcess to run. > > Cheers, > jas. > > > ------------------------------------------------------- > This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170 > Project Admins to receive an Apple iPod Mini FREE for your judgement on > who ports your project to Linux PPC the best. Sponsored by IBM. > Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php > _______________________________________________ > Genex-dev mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genex-dev |
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From: Hrishikesh D. <hde...@gm...> - 2004-09-24 20:23:02
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Sure, if i get the latest one then i can take a shot of data loading,first thing monday morning and then email bugs if any! Thanks, Hrishi Harry J Mangalam wrote: > OK - just tried version 1554 - installed fine with the exception of: > > !! System Error: No such file or directory @ line: 249 (cp > Mason/nologin/docs/data-processing-protocol.html /var/www/genex/mason/nologin/docs) > > another MANIFEST error? I'll correct and svn it ifyou want.. |
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From: Harry J M. <hj...@ta...> - 2004-09-24 19:59:12
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OK - just tried version 1554 - installed fine with the exception of:
!! System Error: No such file or directory @ line: 249 (cp
Mason/nologin/docs/data-processing-protocol.html /var/www/genex/mason/nologin/docs)
another MANIFEST error? I'll correct and svn it ifyou want..
--
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta...
<<plain text preferred>>
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From: <ja...@op...> - 2004-09-24 15:00:35
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Harry Mangalam <hj...@ta...> writes: > I agree - it looks like it's broken - missing all the files that are > supposed to go with it. I copied over my installed copy into > the /usr/local/lib/perl/5.8.4/Apache/SubProcess.pm, so things should > go OK from there - give it a try. Hey, Looking at this it seems that apache-dev and mod_perl-dev are not installed. Without these you can't get Apache::SubProcess to run. Cheers, jas. |
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From: <ja...@op...> - 2004-09-24 14:58:12
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Harry Mangalam <hj...@ta...> writes: > I agree - it looks like it's broken - missing all the files that are > supposed to go with it. I copied over my installed copy into the > /usr/local/lib/perl/5.8.4/Apache/SubProcess.pm, so things should go > OK from there - give it a try. Hmmmm.... I really don't have a clue what is going on here. Over my head. Cheers, jas. |
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