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From: James M. <jm...@me...> - 2002-11-13 15:34:10
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Maybe that is part of their privacy policy... Jim James W. MacDonald UMCCC Microarray Core Facility 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> ca...@th... 11/13/02 10:26AM >>> Locedie Mansueto writes: > Do you Yahoo!? Nah, their privacy policy is quite disturbing, so I cancelled my account there a while back. Seriously, though, I think your message body (and the subject) got lost somehow. :-o //Carl --=20 Carl Troein - ca...@th...=20 http://www.thep.lu.se/~carl/=20 BASE developer - http://base.thep.lu.se=20 ------------------------------------------------------- This sf.net email is sponsored by: Are you worried about=20 your web server security? Click here for a FREE Thawte=20 Apache SSL Guide and answer your Apache SSL security=20 needs: http://www.gothawte.com/rd523.html=20 _______________________________________________ basedb-users mailing list bas...@li...=20 https://lists.sourceforge.net/lists/listinfo/basedb-users |
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From: Carl T. <ca...@th...> - 2002-11-13 15:26:15
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Locedie Mansueto writes: > Do you Yahoo!? Nah, their privacy policy is quite disturbing, so I cancelled my account there a while back. Seriously, though, I think your message body (and the subject) got lost somehow. :-o //Carl -- Carl Troein - ca...@th... http://www.thep.lu.se/~carl/ BASE developer - http://base.thep.lu.se |
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From: James M. <jm...@me...> - 2002-11-13 15:14:33
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I couldn't ever get the local-infile option to work either. I ended up = having to compile from source (which is much more fun anyway ;-D). If you = take this option, remember to add --enable-local-infile to your configure = statement. Jim James W. MacDonald UMCCC Microarray Core Facility 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> abi...@na... 11/12/02 12:41PM >>> Hello, I used RPM to install Mysql (v 3.23.53a) and apparently, the local-infile option is disable. so I can't use LOAD DATA LOCAL. I try to add the line "local-infile=3D1" in the my.cnf file as indicated = in the BASE README file, but it doesn't work. How can I get through it ? Thanks. *-----------------------* Audrey Bihouee INSERM U533 Facult=E9 de m=E9decine, 1, rue Gaston Veil 44035 Nantes Cedex 1 Tel : 02.40.41.29.86 *-----------------------* ------------------------------------------------------- This sf.net email is sponsored by: Are you worried about your web server security? Click here for a FREE Thawte Apache SSL Guide and answer your Apache SSL security needs: http://www.gothawte.com/rd523.html=20 _______________________________________________ basedb-users mailing list bas...@li...=20 https://lists.sourceforge.net/lists/listinfo/basedb-users |
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From: Carl T. <ca...@th...> - 2002-11-13 14:12:23
|
Shaoqing Yu writes: > Some of our users suggest that when uploading result file, we should n >ot include the Median value as required field. So I am wondering what's > the purpose that the developer add Median as required field. Thank you The columns in RawBioAssay correspond to (most of) the fields found in the files GenePix produces. This is clearly not what many (or most) users want, and in version 1.2 the admin will be able to define the columns of that table. //Carl -- Carl Troein - ca...@th... http://www.thep.lu.se/~carl/ BASE developer - http://base.thep.lu.se |
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From: Carl T. <ca...@th...> - 2002-11-13 14:09:04
|
Cao, Xiaohong (Sherry) writes: > Our company's mail server is screwed up lately so it sends duplicate mails. > They said it's been fixed but apparently not. I think you probably have > pretty good idea of dealing with mis. So I can only say sorry to you even > though it's not really my fault. As I said, give the server a good hard kick. Or in this case I think the threat was enough, as it seems to behave better now. But considering how fun it is to kick around expensive hardware, I think I'd let it taste my boot anyway just to be sure. //Carl -- Carl Troein - ca...@th... http://www.thep.lu.se/~carl/ BASE developer - http://base.thep.lu.se |
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From: Carl T. <ca...@th...> - 2002-11-13 14:06:15
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Cao, Xiaohong (Sherry) writes: > Hi, > > I can't seem to delete any of the hybridizations that I created. Kept on > getting this error message: > Error: Unable to delete hybridization - it may be in use > > Checked both Apache and PHP error_logs, nothing was written about this. > > Does anyone know why? Do the hybridizations have image sets attached to them? If so, they're considered to be in use. If nothing at all references them, it might be that the useCount (which will be completely removed in version 1.2) is wrong. If you're sure there are no references to the hybridizations, you can set the useCount column to 0 for those rows in the database, and then you should be able to delete them from BASE. //Carl -- Carl Troein - ca...@th... http://www.thep.lu.se/~carl/ BASE developer - http://base.thep.lu.se |
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From: Carl T. <ca...@th...> - 2002-11-13 13:58:09
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Shaoqing Yu writes: > Will the new sample annotation system still be shared to everybody? Some of > our users seems like to have private annotation. Annotation types will use the new access control system with group/world privileges. In fact, pretty much everything will, including Experiments. //Carl -- Carl Troein - ca...@th... http://www.thep.lu.se/~carl/ BASE developer - http://base.thep.lu.se |
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From: Carl T. <ca...@th...> - 2002-11-13 13:50:38
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Patrick Cahan writes: > General question: In the TODO list Affy-friendliness is listed. What is the > progress on that now? Raw data sets with more or less than 2 channels is in the CVS. The corresponding changes need to be made downstream (BioAssay etc.), and I'm working on it. And we need to look at the Affy formats and how they work. //Carl -- Carl Troein - ca...@th... http://www.thep.lu.se/~carl/ BASE developer - http://base.thep.lu.se |
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From: Carl T. <ca...@th...> - 2002-11-13 13:46:18
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Cao, Xiaohong (Sherry) writes: > I have a similar question to Zhilin about data analysis. I was able to > start the job to normalize the dataset using LOWESS but the job was not > finished. I have never got a result file but I did get an error message in > the apache error_log saying > > sh: ~/base/exec/jobController.php: not found > > the "exec" directory is in the PATH so I am not quite sure what went wrong. > Also, there is no job id listed in the data/jobs directory. It sounds like $config["execDir"] is not correct. Make sure that it really points to the 'exec' directory, and note that you should NOT use ~ to denote the path to your home directory - tilde expansion is something the shell does, not a feature of the file system itself, so although tilde expansion might work sometimes (e.g. when PHP's exec() function is used), it's not reliable. //Carl -- Carl Troein - ca...@th... http://www.thep.lu.se/~carl/ BASE developer - http://base.thep.lu.se |
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From: Carl T. <ca...@th...> - 2002-11-13 11:45:33
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Andrea Splendiani writes: > Is it possible in BASE retrieve entire data sets, or single genes, by > filtering on the Sample description value ? > How ? If by retrieve you mean get all the gene expression values (as from the export page), you'll have to first get all the raw data sets into a single experiment. The raw data set list doesn't let you do filtering on the sample descriptions, but only because it's not in the list of things you can filter on. Some rather minor changes to raw.inc.php is all that should be needed. Genes and samples are as good as orthagonal, so I'm not sure what it would mean to search for a single gene based on anything that has to do with samples. But at least you can get a list of all genes that appear on arrays which have been used with a set of samples, if you can get the corresponding raw data sets into an experiment. //Carl -- Carl Troein - ca...@th... http://www.thep.lu.se/~carl/ BASE developer - http://base.thep.lu.se |
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From: Audrey b. <abi...@na...> - 2002-11-13 10:04:47
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Dear Philippe, Yes, I try to restart the daemon with /usr/bin/safe_mysqld and /usr/share/mysql/mysql.server start But it doesn't work. *-----------------------* Audrey Bihouee INSERM U533 Facult=E9 de m=E9decine, 1, rue Gaston Veil 44035 Nantes Cedex 1 Tel : 02.40.41.29.86 *-----------------------* |
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From: Philippe A. <phi...@ge...> - 2002-11-13 09:54:24
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Dear Julien, I got the same problem with RedHat 8. I downloaded the package gd and copied the file gd.h in the directory /usr/include (where all the *.h files are in RedHat, I don't know whrere you have to copy the file in Mandrake). Philippe fa...@po... wrote: > Hello everybody, > > I'm writing because I have a problem to compile source code in exec/source > directory > > i want to compile code in clustering's directory...but i need gd.h and i don't > where is this file ?? > > Could you help ? How do you compile this code ? > > I'm on Mandrake 8.1 > > Thanks in advance and I apologyse for my english > > Julien Faurie > > --------------------------------------------- > This message was sent using Endymion MailMan. > http://www.endymion.com/products/mailman/ > > ------------------------------------------------------- > This sf.net email is sponsored by: Are you worried about > your web server security? Click here for a FREE Thawte > Apache SSL Guide and answer your Apache SSL security > needs: http://www.gothawte.com/rd523.html > _______________________________________________ > basedb-users mailing list > bas...@li... > https://lists.sourceforge.net/lists/listinfo/basedb-users -- ================================================================== Philippe Alard Tel:32 (0)9 2645001 Department of Plant Systems Biology Fax:32 (0)9 2645349 Ghent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium Vlaams Instituut voor Biotechnologie VIB mailto:ph...@ge... http://www.psb.rug.ac.be ================================================================== |
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From: Carl T. <ca...@th...> - 2002-11-13 09:24:03
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Hey all. As you've hopefully already noticed, the BASE mailing list is up again, now on SourceForge. The address to post to is now bas...@li..., although the old ba...@th... will still work. And, since most of you are likely to be reading this email, just a few brief words about emails in general: Please respect the netiquette RFC by: breaking lines around 70-some characters, not sending those icky HTML mails that LookOut likes to send, not quoting old messages in weird ways that make it look like someone said something he/she didn't, and not sending excessively huge mails. Thank you. :-) //Carl -- Carl Troein - ca...@th... http://www.thep.lu.se/~carl/ BASE developer - http://base.thep.lu.se |
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From: Philippe A. <phi...@ge...> - 2002-11-13 09:04:16
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Dear Audrey, Did you restart the daemon ? The following command will do that: service mysqld restart Philippe Audrey bihouee wrote: > Hello, > > I used RPM to install Mysql (v 3.23.53a) and apparently, the local-infile > option is disable. so I can't use LOAD DATA LOCAL. > I try to add the line "local-infile=1" in the my.cnf file as indicated in the > BASE README file, but it doesn't work. > > How can I get through it ? > Thanks. > > *-----------------------* > Audrey Bihouee > INSERM U533 > Faculté de médecine, > 1, rue Gaston Veil > 44035 Nantes Cedex 1 > Tel : 02.40.41.29.86 > *-----------------------* > > ------------------------------------------------------- > This sf.net email is sponsored by: Are you worried about > your web server security? Click here for a FREE Thawte > Apache SSL Guide and answer your Apache SSL security > needs: http://www.gothawte.com/rd523.html > _______________________________________________ > basedb-users mailing list > bas...@li... > https://lists.sourceforge.net/lists/listinfo/basedb-users -- ================================================================== Philippe Alard Tel:32 (0)9 2645001 Department of Plant Systems Biology Fax:32 (0)9 2645349 Ghent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium Vlaams Instituut voor Biotechnologie VIB mailto:ph...@ge... http://www.psb.rug.ac.be ================================================================== |
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From: Audrey b. <abi...@na...> - 2002-11-13 08:35:51
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Hello, I used RPM to install Mysql (v 3.23.53a) and apparently, the local-infile option is disable. so I can't use LOAD DATA LOCAL. I try to add the line "local-infile=3D1" in the my.cnf file as indicated i= n the BASE README file, but it doesn't work. How can I get through it ? Thanks. *-----------------------* Audrey Bihouee INSERM U533 Facult=E9 de m=E9decine, 1, rue Gaston Veil 44035 Nantes Cedex 1 Tel : 02.40.41.29.86 *-----------------------* |
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From: Locedie M. <lma...@ya...> - 2002-11-13 01:37:54
|
__________________________________________________ Do you Yahoo!? U2 on LAUNCH - Exclusive greatest hits videos http://launch.yahoo.com/u2 |
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From: Audrey b. <abi...@na...> - 2002-11-12 17:42:00
|
Hello, I used RPM to install Mysql (v 3.23.53a) and apparently, the local-infile option is disable. so I can't use LOAD DATA LOCAL. I try to add the line "local-infile=3D1" in the my.cnf file as indicated i= n the BASE README file, but it doesn't work. How can I get through it ? Thanks. *-----------------------* Audrey Bihouee INSERM U533 Facult=E9 de m=E9decine, 1, rue Gaston Veil 44035 Nantes Cedex 1 Tel : 02.40.41.29.86 *-----------------------* |
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From: <fa...@po...> - 2002-11-12 10:58:45
|
Hello everybody, I'm writing because I have a problem to compile source code in exec/source directory i want to compile code in clustering's directory...but i need gd.h and i don't where is this file ?? Could you help ? How do you compile this code ? I'm on Mandrake 8.1 Thanks in advance and I apologyse for my english Julien Faurie --------------------------------------------- This message was sent using Endymion MailMan. http://www.endymion.com/products/mailman/ |
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From: Shaoqing Y. <sh...@ae...> - 2002-11-11 21:52:49
|
Some of our users suggest that when uploading result file, we should not = include the Median value as required field. So I am wondering what's the = purpose that the developer add Median as required field. Thank you Shaoqing |
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From: Cao, X. (Sherry) <Xia...@ge...> - 2002-11-11 20:12:34
|
Hi, I can't seem to delete any of the hybridizations that I created. Kept on getting this error message: Error: Unable to delete hybridization - it may be in use Checked both Apache and PHP error_logs, nothing was written about this. Does anyone know why? Sherry |
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From: Johan Vallon-C. <Joh...@on...> - 2002-11-09 15:40:09
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As it is now you can not delete protocols through the web interface. If the protocol is not used by anyone you can 'reuse' it by changing the name and associated files to something meaningful rather than creating a new protocol. Johan >-----Original Message----- >From: joe dougherty [mailto:jo...@uc...] >Sent: den 7 november 2002 20:04 >To: ba...@th... >Subject: [base] Deleting Data > > >Hi >Sorry if this is a duplicate message. I have sent it before but >did not see >it appear on the list. My question is, how does one delete old protocols? >I put a couple in while I was testing base, and now I want to remove them. >Thanks, >joe > > >--------------------------------------------------------------------- >To unsubscribe, e-mail: bas...@th... >For additional commands, e-mail: bas...@th... > |
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From: Cao, X. (Sherry) <Xia...@ge...> - 2002-11-08 14:44:58
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Hi Carl: Our company's mail server is screwed up lately so it sends duplicate mails. They said it's been fixed but apparently not. I think you probably have pretty good idea of dealing with mis. So I can only say sorry to you even though it's not really my fault. Sherry -----Original Message----- From: Carl Troein [mailto:ca...@th...] Sent: Thursday, November 07, 2002 5:33 PM To: ba...@th... Subject: [base] Re: plot error Cao, Xiaohong (Sherry) writes: > When I chose postscript and clicked on view, I actually downloaded the ps > file onto my client computer. I was able to view it after using the pdf > distiller to convert it to pdf file. When I clicked on pdf and clicked on > view, I was able to view it in a separate explorer window. > > I guess only the preview button doesn't work. I got "error: no output from > gnuplot" on the screen. Sherry, your two latest mails to the list have arrived in two copies each. If you've resent them for the lack of immediate response: please don't, it won't help (quite the opposite, in fact). And in the case that these double postings haven't been intentional, I can only advice you to give your mail server a good hard kick and tell it not to do that again. It usually helps, or at least it makes you (well, me) feel better. Anyway, the preview thingy converts postscript to pnm (in the case that the selected format is postscript or pdf), and from the earlier mails I'm convinced that that's where the problem lies. //Carl -- Carl Troein - ca...@th... http://www.thep.lu.se/~carl/ BASE developer - http://base.thep.lu.se --------------------------------------------------------------------- To unsubscribe, e-mail: bas...@th... For additional commands, e-mail: bas...@th... |
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From: Carl T. <ca...@th...> - 2002-11-08 12:38:37
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Hi all. The BASE mailing list is down at the moment. As soon as the subscriber list is added to the new list on sourceforge, I will let you know. The new address for posting will be bas...@li... but ba...@th... should still work as well. //Carl |
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