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• Plone: Creating new Page fails "AttributeError: 'str' object has no attribute 'dates'"

  - by paskster

  I just installed Plone on my Centos 5.5. I was able login via the admin-account and create new users. But when I try to create a new page I get the following error message: Traceback (innermost last): Module ZPublisher.Publish, line 127, in publish Module ZPublisher.mapply, line 77, in mapply Module ZPublisher.Publish, line 47, in call_object Module Products.CMFPlone.FactoryTool, line 446, in __call__ Module ZPublisher.mapply, line 77, in mapply Module ZPublisher.Publish, line 47, in call_object Module Products.CMFFormController.FSControllerPageTemplate, line 91, in __call__ Module Products.CMFFormController.BaseControllerPageTemplate, line 31, in _call Module Shared.DC.Scripts.Bindings, line 324, in __call__ Module Shared.DC.Scripts.Bindings, line 361, in _bindAndExec Module Products.CMFCore.FSPageTemplate, line 240, in _exec Module Products.CMFCore.FSPageTemplate, line 180, in pt_render Module Products.PageTemplates.PageTemplate, line 80, in pt_render Module zope.pagetemplate.pagetemplate, line 113, in pt_render Warning: Macro expansion failed Warning: <type 'exceptions.KeyError'>: 'macro' Module zope.tal.talinterpreter, line 271, in __call__ Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 888, in do_useMacro Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 533, in do_optTag_tal Module zope.tal.talinterpreter, line 518, in do_optTag Module zope.tal.talinterpreter, line 513, in no_tag Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 888, in do_useMacro Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 533, in do_optTag_tal Module zope.tal.talinterpreter, line 518, in do_optTag Module zope.tal.talinterpreter, line 513, in no_tag Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 954, in do_defineSlot Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 533, in do_optTag_tal Module zope.tal.talinterpreter, line 518, in do_optTag Module zope.tal.talinterpreter, line 513, in no_tag Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 858, in do_defineMacro Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 954, in do_defineSlot Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 533, in do_optTag_tal Module zope.tal.talinterpreter, line 518, in do_optTag Module zope.tal.talinterpreter, line 513, in no_tag Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 946, in do_defineSlot Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 533, in do_optTag_tal Module zope.tal.talinterpreter, line 518, in do_optTag Module zope.tal.talinterpreter, line 513, in no_tag Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 858, in do_defineMacro Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 533, in do_optTag_tal Module zope.tal.talinterpreter, line 518, in do_optTag Module zope.tal.talinterpreter, line 513, in no_tag Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 888, in do_useMacro Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 852, in do_condition Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 954, in do_defineSlot Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 533, in do_optTag_tal Module zope.tal.talinterpreter, line 518, in do_optTag Module zope.tal.talinterpreter, line 513, in no_tag Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 852, in do_condition Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 533, in do_optTag_tal Module zope.tal.talinterpreter, line 518, in do_optTag Module zope.tal.talinterpreter, line 513, in no_tag Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 821, in do_loop_tal Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 533, in do_optTag_tal Module zope.tal.talinterpreter, line 518, in do_optTag Module zope.tal.talinterpreter, line 513, in no_tag Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 533, in do_optTag_tal Module zope.tal.talinterpreter, line 522, in do_optTag Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 821, in do_loop_tal Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 533, in do_optTag_tal Module zope.tal.talinterpreter, line 518, in do_optTag Module zope.tal.talinterpreter, line 513, in no_tag Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 888, in do_useMacro Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 533, in do_optTag_tal Module zope.tal.talinterpreter, line 518, in do_optTag Module zope.tal.talinterpreter, line 513, in no_tag Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 888, in do_useMacro Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 533, in do_optTag_tal Module zope.tal.talinterpreter, line 518, in do_optTag Module zope.tal.talinterpreter, line 513, in no_tag Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 852, in do_condition Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 533, in do_optTag_tal Module zope.tal.talinterpreter, line 518, in do_optTag Module zope.tal.talinterpreter, line 513, in no_tag Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 852, in do_condition Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 946, in do_defineSlot Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 533, in do_optTag_tal Module zope.tal.talinterpreter, line 518, in do_optTag Module zope.tal.talinterpreter, line 513, in no_tag Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 533, in do_optTag_tal Module zope.tal.talinterpreter, line 518, in do_optTag Module zope.tal.talinterpreter, line 513, in no_tag Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 888, in do_useMacro Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 583, in do_setLocal_tal Module zope.tales.tales, line 696, in evaluate URL: file:/usr/local/Plone/buildout-cache/eggs/Plone-4.0.2-py2.6.egg/Products/CMFPlone/skins/plone_templates/calendar_macros.pt Line 12, Column 4 Expression: <PythonExpr date_components_support_view.result(inputvalue, 0, starting_year, ending_year, future_years)> Names: {'container': <PloneSite at /reeple>, 'context': <ATDocument at /reeple/portal_factory/Document/document.2010-12-24.9331499294 used for /reeple>, 'default': <object object at 0x2ad1b9a18ae0>, 'here': <ATDocument at /reeple/portal_factory/Document/document.2010-12-24.9331499294 used for /reeple>, 'loop': {u'field': <Products.PageTemplates.Expressions.PathIterator object at 0x1bc9b9d0>, u'fieldset': <Products.PageTemplates.Expressions.PathIterator object at 0x1d396c90>}, 'nothing': None, 'options': {'args': (), 'state': <Products.CMFFormController.ControllerState.ControllerState object at 0x1ccdb2d0>}, 'repeat': <Products.PageTemplates.Expressions.SafeMapping object at 0x1d452ec0>, 'request': <HTTPRequest, URL=http://82.165.145.121:8081/reeple/portal_factory/Document/document.2010-12-24.9331499294/atct_edit>, 'root': <Application at >, 'template': <FSControllerPageTemplate at /reeple/atct_edit used for /reeple/portal_factory/Document/document.2010-12-24.9331499294>, 'traverse_subpath': [], 'user': <PloneUser 'pascalklein'>} Module Products.PageTemplates.ZRPythonExpr, line 49, in __call__ __traceback_info__: date_components_support_view.result(inputvalue, 0, starting_year, ending_year, future_years) Module PythonExpr, line 1, in <expression> Module plone.app.form.widgets.datecomponents, line 50, in result AttributeError: 'str' object has no attribute 'dates' Any suggestions? CentOS 5.5 has the Python Version 2.4. So I'm not sure if that causes the issue.

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• Tal condition always evaluates to false

  - by Ander2

  I'm using plone and trying to display a form result in a page template. I'm trying to filter some database results using tal:condition with a python expression but it always evaluates to false. The code looks like this: <tr tal:repeat="result view/results"> <td> <span tal:condition="python:view.teams[0]==result.team_id" tal:replace="result/position">Position</span></td> <td> <span tal:condition="python:view.teams[1]==result.team_id" tal:replace="result/position">Position</span></td> </tr> I want the table cells to be filled with the team position when the team id is matched in the result, but the cells always are empty. If I remove the tal:condition from the span and replace the tal:replace="result/position" with tal:replace=python:view.teams[0]==result.team_id it prints True or False so I can check that the result is correct. Can anyone help me about this issue? Why does tal:condition allways evaluate false?

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• SQL Quey slow in .NET application but instantaneous in SQL Server Management Studio

  - by user203882

  Here is the SQL SELECT tal.TrustAccountValue FROM TrustAccountLog AS tal INNER JOIN TrustAccount ta ON ta.TrustAccountID = tal.TrustAccountID INNER JOIN Users usr ON usr.UserID = ta.UserID WHERE usr.UserID = 70402 AND ta.TrustAccountID = 117249 AND tal.trustaccountlogid = ( SELECT MAX (tal.trustaccountlogid) FROM TrustAccountLog AS tal INNER JOIN TrustAccount ta ON ta.TrustAccountID = tal.TrustAccountID INNER JOIN Users usr ON usr.UserID = ta.UserID WHERE usr.UserID = 70402 AND ta.TrustAccountID = 117249 AND tal.TrustAccountLogDate < '3/1/2010 12:00:00 AM' ) Basicaly there is a Users table a TrustAccount table and a TrustAccountLog table. Users: Contains users and their details TrustAccount: A User can have multiple TrustAccounts. TrustAccountLog: Contains an audit of all TrustAccount "movements". A TrustAccount is associated with multiple TrustAccountLog entries. Now this query executes in milliseconds inside SQL Server Management Studio, but for some strange reason it takes forever in my C# app and even timesout (120s) sometimes. Here is the code in a nutshell. It gets called multiple times in a loop and the statement gets prepared. cmd.CommandTimeout = Configuration.DBTimeout; cmd.CommandText = "SELECT tal.TrustAccountValue FROM TrustAccountLog AS tal INNER JOIN TrustAccount ta ON ta.TrustAccountID = tal.TrustAccountID INNER JOIN Users usr ON usr.UserID = ta.UserID WHERE usr.UserID = @UserID1 AND ta.TrustAccountID = @TrustAccountID1 AND tal.trustaccountlogid = (SELECT MAX (tal.trustaccountlogid) FROM TrustAccountLog AS tal INNER JOIN TrustAccount ta ON ta.TrustAccountID = tal.TrustAccountID INNER JOIN Users usr ON usr.UserID = ta.UserID WHERE usr.UserID = @UserID2 AND ta.TrustAccountID = @TrustAccountID2 AND tal.TrustAccountLogDate < @TrustAccountLogDate2 ))"; cmd.Parameters.Add("@TrustAccountID1", SqlDbType.Int).Value = trustAccountId; cmd.Parameters.Add("@UserID1", SqlDbType.Int).Value = userId; cmd.Parameters.Add("@TrustAccountID2", SqlDbType.Int).Value = trustAccountId; cmd.Parameters.Add("@UserID2", SqlDbType.Int).Value = userId; cmd.Parameters.Add("@TrustAccountLogDate2", SqlDbType.DateTime).Value =TrustAccountLogDate; // And then... reader = cmd.ExecuteReader(); if (reader.Read()) { double value = (double)reader.GetValue(0); if (System.Double.IsNaN(value)) return 0; else return value; } else return 0;

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• SQL Query slow in .NET application but instantaneous in SQL Server Management Studio

  - by user203882

  Here is the SQL SELECT tal.TrustAccountValue FROM TrustAccountLog AS tal INNER JOIN TrustAccount ta ON ta.TrustAccountID = tal.TrustAccountID INNER JOIN Users usr ON usr.UserID = ta.UserID WHERE usr.UserID = 70402 AND ta.TrustAccountID = 117249 AND tal.trustaccountlogid = ( SELECT MAX (tal.trustaccountlogid) FROM TrustAccountLog AS tal INNER JOIN TrustAccount ta ON ta.TrustAccountID = tal.TrustAccountID INNER JOIN Users usr ON usr.UserID = ta.UserID WHERE usr.UserID = 70402 AND ta.TrustAccountID = 117249 AND tal.TrustAccountLogDate < '3/1/2010 12:00:00 AM' ) Basicaly there is a Users table a TrustAccount table and a TrustAccountLog table. Users: Contains users and their details TrustAccount: A User can have multiple TrustAccounts. TrustAccountLog: Contains an audit of all TrustAccount "movements". A TrustAccount is associated with multiple TrustAccountLog entries. Now this query executes in milliseconds inside SQL Server Management Studio, but for some strange reason it takes forever in my C# app and even timesout (120s) sometimes. Here is the code in a nutshell. It gets called multiple times in a loop and the statement gets prepared. cmd.CommandTimeout = Configuration.DBTimeout; cmd.CommandText = "SELECT tal.TrustAccountValue FROM TrustAccountLog AS tal INNER JOIN TrustAccount ta ON ta.TrustAccountID = tal.TrustAccountID INNER JOIN Users usr ON usr.UserID = ta.UserID WHERE usr.UserID = @UserID1 AND ta.TrustAccountID = @TrustAccountID1 AND tal.trustaccountlogid = (SELECT MAX (tal.trustaccountlogid) FROM TrustAccountLog AS tal INNER JOIN TrustAccount ta ON ta.TrustAccountID = tal.TrustAccountID INNER JOIN Users usr ON usr.UserID = ta.UserID WHERE usr.UserID = @UserID2 AND ta.TrustAccountID = @TrustAccountID2 AND tal.TrustAccountLogDate < @TrustAccountLogDate2 ))"; cmd.Parameters.Add("@TrustAccountID1", SqlDbType.Int).Value = trustAccountId; cmd.Parameters.Add("@UserID1", SqlDbType.Int).Value = userId; cmd.Parameters.Add("@TrustAccountID2", SqlDbType.Int).Value = trustAccountId; cmd.Parameters.Add("@UserID2", SqlDbType.Int).Value = userId; cmd.Parameters.Add("@TrustAccountLogDate2", SqlDbType.DateTime).Value =TrustAccountLogDate; // And then... reader = cmd.ExecuteReader(); if (reader.Read()) { double value = (double)reader.GetValue(0); if (System.Double.IsNaN(value)) return 0; else return value; } else return 0;

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• Change permission to mount disk at rdesktop

  - by Tal

  I have ubuntu 10.04 and have installed rdesktop 1.7. I have run these commands: sudo umount /media/Tal sudo mount -t ntfs-3g -o uid=1000,gid=1000,umask=0000 /dev/sdb1 /media/Tal rdesktop -0 -r sound:local -f -u administrator -r clipboard:PRIMARYCLIPBOARD -r disk:tal=/media/Tal myip Tal is external hard drive connecting at USB in ntfs file system. I connect to windows 7 I see the hard drive in computer and I can access to files and create new files and folders, But when I try to copy a new file to a folder he show me an error message: You need permission perform this action Your require permission from computer's administrator to make changes to this folder Tal on my computername Disk from Remote Desktop Connection. I try chmod and chown too but I read I linux forum when it ntfs is no use. Some one can help me with my problem?

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• Zenoss No space left on device Error

  - by Pastelinux

  Site Error An error was encountered while publishing this resource. Sorry, a site error occurred. Traceback (innermost last): Module ZPublisher.Publish, line 231, in publish_module_standard Module ZPublisher.Publish, line 165, in publish Module Zope2.App.startup, line 211, in __call__ Module Products.ZenUI3.browser, line 105, in __call__ Module Products.Five.browser.pagetemplatefile, line 60, in __call__ Module zope.pagetemplate.pagetemplate, line 115, in pt_render Module zope.tal.talinterpreter, line 271, in __call__ Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 858, in do_defineMacro Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 533, in do_optTag_tal Module zope.tal.talinterpreter, line 518, in do_optTag Module zope.tal.talinterpreter, line 513, in no_tag Module zope.tal.talinterpreter, line 343, in interpret Module zope.tal.talinterpreter, line 620, in do_insertText_tal Module Products.PageTemplates.Expressions, line 203, in evaluateText Module Products.PageTemplates.Expressions, line 222, in _handleText Module zope.component._api, line 174, in queryUtility Module zope.component.registry, line 165, in queryUtility Module ZODB.Connection, line 834, in setstate Module ZODB.Connection, line 884, in _setstate Module ZEO.ClientStorage, line 815, in load Module ZEO.cache, line 143, in call Module ZEO.cache, line 607, in store IOError: [Errno 28] No space left on device Went in to check my server through zenoss today and it looks like somehow my server is full. Which when i look at my server its only 85% full: unclebob:~# df -h Filesystem Size Used Avail Use% Mounted on /dev/mapper/unclebob--vg0-unclebob--root 1.9G 1.5G 335M 82% / tmpfs 471M 0 471M 0% /lib/init/rw udev 10M 820K 9.2M 9% /dev tmpfs 471M 0 471M 0% /dev/shm overflow 1.0M 1.0M 0 100% /tmp /dev/hde1 942M 36M 859M 5% /boot unclebob:/tmp# df -i Filesystem Inodes IUsed IFree IUse% Mounted on /dev/mapper/unclebob--vg0-unclebob--root 121920 54844 67076 45% / tmpfs 120489 3 120486 1% /lib/init/rw udev 120489 1520 118969 2% /dev tmpfs 120489 1 120488 1% /dev/shm overflow 120489 14 120475 1% /tmp /dev/hde1 61312 33 61279 1% /boot It looks like theres these two files: .ICE-unix/ .X11-unix/ They had been hidden. I'll remove those. Any idea upon what they maybe? Any ideas on a fix? Probably has something to do with Zenoss

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• PHPTAL Nested Repeat

  - by 114343500565423229598

  Hello guys, I am having an problem trying to achieve a nested repeat in PHPTAL: <tr tal:repeat="business analysis_result"> <td>${business/trading_name}</td> <tal:block tal:repeat="selected_key selected_keys"> <td>HOW??????</td> <---problem </tal:block> </tr> basically I want to have the of inner repeat to get the value of $business[$selected_key], I have looked at the phptal manual which doesn't really give you a demo on how to do this... cheers guys! James

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• Is there a way to extract gmail data into R ?

  - by Tal Galili

  Like there is the rgoogledocs package and twitteR, is there a gmailR package ? Tal

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• Ripping sound from online video ?

  - by Tal Galili

  Hi all, I wish to take Hello There are a couple of videos on the Web whose soundtracks I'd like to rip so I can listen to them while walking. What webapps/applications (for Windows), free or affordable, are there that will let me record whatever is being played? (That is following this SO thread that didn't get many replies) Thanks! Tal

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• Save static version of a webpage to be available offline

  - by Tal Weiss

  Is there a way to save a webpage as static HTML, available for offline viewing, editing etc.? I want to remove all javascript files. Leave only HTML, CSS and images. For example, if this web page has a Facebook Like button, I want the image of the button to be part of the HTML as a regular image (and not be loaded as some Javascript code runs after I load the page). I'm trying to prepare a webpage for an offline demo. When I use the standard "save as HTML complete" like tools, all the Javascript is saved as well, and when viewed offline, all the dynamic content is blanks. Note- I don't expect the dynamic content to work, of course, with no Javascript. I just want the web page to LOOK as though it was just loaded from the interwebs. Thanks, Tal.

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• j2me - compare 2 dates

  - by Tal

  I am developing a J2ME application (CLDC 1.1 and MIDP 2.0) and I was wondering, What is the best way to get the time span between 2 dates? thanks, Tal.

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• Is there a Pair-Wise PostHoc Comparisons for the Chi-Square Test in R?

  - by Tal Galili

  Hi all, I am wondering if there exists in R a package/function to perform the: "Post Hoc Pair-Wise Comparisons for the Chi-Square Test of Homogeneity of Proportions" (or an equivalent of it) Which is described here: http://epm.sagepub.com/cgi/content/abstract/53/4/951 My situation is of just making a chi test, on a 2 by X matrix. I found a difference, but I want to know which of the columns is "responsible" for the difference. Thanks, Tal

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• In R: How can I know if my packages are up to date ?

  - by Tal Galili

  Hi all, I am looking for a function that will tell me, for a list of packages, which of them is up to date and which is not (I need it so to trace back an R crash). Thanks, Tal

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• Extracting the fitted terms in the local polynomial of a loess (in R)

  - by Tal Galili

  Hi all, How can I extract what the loess function has fitted for the polynomial function, for a particular x of my data? Thanks, Tal

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• Downloading RGoogleDocs for R (it fails)

  - by Tal Galili

  Hi all, I am trying: install.packages("RGoogleDocs", repos = "http://www.omegahat.org/R") As suggested here, but it doesn't work. I ended up manually downloading the file from here. What other ways are there for me to get to the file directly? Thanks, Tal

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• How do you compare the "similarity" between two dendrograms (in R) ?

  - by Tal Galili

  I have two dendrograms which I wish to compare to each other in order to find out how "similar" they are. But I don't know of any method to do so (let alone a code to implement it, say, in R). Any leads ? Thanks, Tal

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• How to extract e-mail data into R ?

  - by Tal Galili

  How could I export my e-mail database from Gmail (or Thunderbird) into R? Like there is the rgoogledocs package and twitteR, is there a gmailR package, or a standard format for exporting emails into stat packages ? Tal

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• Why am I getting different results from cor VS ccf ? (R)

  - by Tal Galili

  Hi all, I am getting different results from ccf and cor, Here is a simple example: set.seed(100) N <- 100 x1 <- sample(N) x2 <- x1 + rnorm(N,0,5) ccf(x1,x2)$acf[ccf(x1,x2)$lag == -1] cor(x1[-N], x2[-1]) Results: > ccf(x1,x2)$acf[ccf(x1,x2)$lag == -1] [1] -0.128027 > cor(x1[-N], x2[-1]) [1] -0.1301427 Thanks, Tal

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• URL regex search and replace on MySQL (in WordPress)

  - by Tal Galili

  Hello all, I have a WordPress blog with numerous URL's I wish to replace from this: http://www.oldwebsite.co.il/name/*.asp To this: http://www.newwebsite.com/?p=* For example, from this: http://oldwebsite.co.il/name/65971.asp To this: http://www.newwebsite.com/?p=65971 I believe the following plugin: http://urbangiraffe.com/plugins/search-regex/ will do the trick with regex, but I am looking for the correct regex to use here. I found this stackoverflow thread that has a similar task, but since I am not too apt with regex, I was hoping for help so I don't mess anything up. Thanks, Tal After searching stackoverflow, I found

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• How (and where) to get aligned tRNA sequences (and import it into R)

  - by Tal Galili

  (This is a database / R commands question) I wish (for my thesis work), to import tRNA data into R and have it aligned. My questions are: 1) What resources can I use for the data. 2) What commands might help me with the import/alignment. So far, I found two nice repositories that holds such data: http://trnadb.bioinf.uni-leipzig.de/Resulthttp://trnadb.bioinf.uni-leipzig.de/Result http://gtrnadb.ucsc.edu/download.htmlhttp://gtrnadb.ucsc.edu/download.html And also the readFASTA command from Biostrings, that does basic importing of the data into R. My problem still remains with how to handle the alignment of the tRNA. Since I am not from the field, I might be missing a very basic answer (like where I should download the data from, or what command to use). If you might be willing to advice me, that would be most helpful. Many thanks in advance, Tal

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• Polygon with different line width (in R)

  - by Tal Galili

  Hi all, I would like to use a command like this: plot(c(1,8), 1:2, type="n") polygon(1:7, c(2,1,2,NA,2,1,2), col=c("red", "blue"), # border=c("green", "yellow"), border=c(1,10), lwd=c(1:10)) To create two triangles, with different line widths. But the polygon command doesn't seem to recycle the "lwd" parameter as it does the col or the border parameters. I would like the resulting plot to look like what the following code will produce: plot(c(1,8), 1:2, type="n") polygon(1:3, c(2,1,2), col=c("red"), # border=c("green", "yellow"), border=c(1,10), lwd=c(1)) polygon(5:7, c(2,1,2), col=c( "blue"), # border=c("green", "yellow"), border=c(1,10), lwd=c(10)) So my questions are: Is there something like polygon that does what I asked for? (If not, I would do it by creating a new polygon function that will break the original x,y by their NA's, although I am not yet sure what is the smartest way to do that...) Thanks, Tal

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• What ways are there for cleaning an R environment from objects?

  - by Tal Galili

  I know I can use ls() and rm() to see and remove objects that exist in my environment. However, when dealing with "old" .RData file, one needs to sometimes pick an environment a part to find what to keep and what to leave out. What I would like to do, is to have a GUI like interface to allow me to see the objects, sort them (for example, by there size), and remove the ones I don't need (for example, by a check-box interface). Since I imagine such a system is not currently implemented in R, what ways do exist? What do you use for cleaning old .RData files? Thanks, Tal

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• is there a way to get a "subtree" from hclust ? (R)

  - by Tal Galili

  Hello all, I wish to create a "subtree" from an hclust object. For example, let's say I have the following object: a <- list() # initialize empty object a$merge <- matrix(c(-1, -2, -3, -4, 1, 2, -5,-6, 3,4), nc=2, byrow=TRUE ) a$height <- c(1, 1.5, 3,4,4.5) # define merge heights a$order <- 1:6 # order of leaves(trivial if hand-entered) a$labels <- 1:6# LETTERS[1:4] # labels of leaves class(a) <- "hclust" # make it an hclust object plot(a) # look at the result Now I wish the extract from it the following subtree: a <- list() # initialize empty object a$merge <- matrix(c(-1, -2, -3, -4, 1, 2 ), nc=2, byrow=TRUE ) a$height <- c(1, 1.5, 3) # define merge heights a$order <- 1:4 # order of leaves(trivial if hand-entered) a$labels <- 1:4# LETTERS[1:4] # labels of leaves class(a) <- "hclust" # make it an hclust object plot(a) # look at the result How could I access it? (I know that cutree could get me the objects of the sub tree, but not create an actual hclust object) Thanks for any help, Tal

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• Last Observation Carried Forward In a data frame?

  - by Tal Galili

  Hi all, I wish to implement a "Last Observation Carried Forward" for a data set I am working on which has missing values at the end of it. Here is a simple code to do it (question after it): LOCF <- function(x) { # Last Observation Carried Forward (for a left to right series) LOCF <- max(which(!is.na(x))) # the location of the Last Observation to Carry Forward x[LOCF:length(x)] <- x[LOCF] return(x) } # example: LOCF(c(1,2,3,4,NA,NA)) LOCF(c(1,NA,3,4,NA,NA)) Now this works great for simple vectors. But if I where to try and use it on a data frame: a <- data.frame(rep("a",4), 1:4,1:4, c(1,NA,NA,NA)) a t(apply(a, 1, LOCF)) # will make a mess It will turn my data frame into a character matrix. Can you think of a way to do LOCF on a data.frame, without turning it into a matrix? (I could use loops and such to correct the mess, but would love for a more elegant solution) Cheers, Tal

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• Make conversion to a native type explicit in C++

  - by Tal Pressman

  I'm trying to write a class that implements 64-bit ints for a compiler that doesn't support long long, to be used in existing code. Basically, I should be able to have a typedef somewhere that selects whether I want to use long long or my class, and everything else should compile and work. So, I obviously need conversion constructors from int, long, etc., and the respective conversion operators (casts) to those types. This seems to cause errors with arithmetic operators. With native types, the compiler "knows" that when operator*(int, char) is called, it should promote the char to int and call operator*(int, int) (rather than casting the int to char, for example). In my case it gets confused between the various built-in operators and the ones I created. It seems to me like if I could flag the conversion operators as explicit somehow, that it would solve the issue, but as far as I can tell the explicit keyword is only for constructors (and I can't make constructors for built-in types). So is there any way of marking the casts as explicit? Or am I barking up the wrong tree here and there's another way of solving this? Or maybe I'm just doing something else wrong...

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