[Rd] Possible POSIXlt / wday glitch bugs.r-project.org status

2013-10-04 Thread Imanuel Costigan
Wanted to raise two questions: 1. Is bugs.r-project.org down? I haven't been able to reach it for two or three days: ``` ping bugs.r-project.org PING rbugs.research.att.com (207.140.168.137): 56 data bytes Request timeout for icmp_seq 0 Request timeout for icmp_seq 1 Request timeout for

[Rd] read.table() with quoted integers

2013-10-04 Thread Jens Oehlschlägel
I agree that quoted integer columns are not the most efficient way of delivering csv-files. However, the sad reality is that one receives such formats and still needs to read the data. Therefore it is not helpful to state that one should 'consider character to be the correct colClass in case

Re: [Rd] check warning with .onLoad() and setClass()

2013-10-04 Thread Rainer M Krug
Thanks John that is likely the solution to my problem, but I don't understand how I can use it and I can't find the example in the Rcpp package (I did grep for setLoadAtion on the whole source package of Rcpp, but nothing came up with ). Could you please provide me a link (or the filename) where

Re: [Rd] read.table() with quoted integers

2013-10-04 Thread Joshua Ulrich
On Tue, Oct 1, 2013 at 11:29 AM, David Winsemius dwinsem...@comcast.net wrote: On Sep 30, 2013, at 6:38 AM, Joshua Ulrich wrote: On Mon, Sep 30, 2013 at 7:33 AM, Milan Bouchet-Valat nalimi...@club.fr wrote: Hi! It seems that read.table() in R 3.0.1 (Linux 64-bit) does not consider

Re: [Rd] check warning with .onLoad() and setClass()

2013-10-04 Thread Dirk Eddelbuettel
On 4 October 2013 at 12:59, Rainer M Krug wrote: | Thanks John | | that is likely the solution to my problem, but I don't understand how I | can use it and I can't find the example in the Rcpp package (I did grep | for setLoadAtion on the whole source package of Rcpp, but nothing came up with

Re: [Rd] read.table() with quoted integers

2013-10-04 Thread Duncan Murdoch
On 13-10-04 7:31 AM, Joshua Ulrich wrote: On Tue, Oct 1, 2013 at 11:29 AM, David Winsemius dwinsem...@comcast.net wrote: On Sep 30, 2013, at 6:38 AM, Joshua Ulrich wrote: On Mon, Sep 30, 2013 at 7:33 AM, Milan Bouchet-Valat nalimi...@club.fr wrote: Hi! It seems that read.table() in R

Re: [Rd] check warning with .onLoad() and setClass()

2013-10-04 Thread Rainer M Krug
Dirk Eddelbuettel e...@debian.org writes: On 4 October 2013 at 12:59, Rainer M Krug wrote: | Thanks John | | that is likely the solution to my problem, but I don't understand | how I | can use it and I can't find the example in the Rcpp package (I did | grep | for setLoadAtion on the

[Rd] bug/infelicity in citation(base)

2013-10-04 Thread Michael Friendly
utils::citation() offers the option auto=(NULL|TRUE) to obtain the citations for a package from the package DESCRIPTION file or a CITATION file, as described below: |auto| a logical indicating whether the default citation auto-generated from the package 'DESCRIPTION' metadata should be used or

Re: [Rd] read.table() with quoted integers

2013-10-04 Thread Joshua Ulrich
On Thu, Oct 3, 2013 at 9:44 AM, Jens Oehlschlägel jens.oehlschlae...@truecluster.com wrote: I agree that quoted integer columns are not the most efficient way of delivering csv-files. However, the sad reality is that one receives such formats and still needs to read the data. Therefore it is

Re: [Rd] Possible POSIXlt / wday glitch bugs.r-project.org status

2013-10-04 Thread Joshua Ulrich
Quoting from ?timezone: Note that except on Windows, the operation of time zones is an OS service, and even on Windows a third-party database is used and can be updated (see the section on ‘Time zone names’). Incorrect results will never be an R issue, so please ensure that

Re: [Rd] check warning with .onLoad() and setClass()

2013-10-04 Thread Dirk Eddelbuettel
On 4 October 2013 at 14:15, Rainer M Krug wrote: | Hm. loadModule is Rcpp function, but I am only interested in using the | setClass() function, which has nothing to do with Rcpp. I don't even use | Rcpp in the package, only in one which is imported. Sorry, assumed Reference Class created via

Re: [Rd] read.table() with quoted integers

2013-10-04 Thread Milan Bouchet-Valat
Le vendredi 04 octobre 2013 à 07:34 -0500, Joshua Ulrich a écrit : On Thu, Oct 3, 2013 at 9:44 AM, Jens Oehlschlägel jens.oehlschlae...@truecluster.com wrote: I agree that quoted integer columns are not the most efficient way of delivering csv-files. However, the sad reality is that one

Re: [Rd] read.table() with quoted integers

2013-10-04 Thread Milan Bouchet-Valat
Le vendredi 04 octobre 2013 à 07:55 -0400, Duncan Murdoch a écrit : On 13-10-04 7:31 AM, Joshua Ulrich wrote: On Tue, Oct 1, 2013 at 11:29 AM, David Winsemius dwinsem...@comcast.net wrote: On Sep 30, 2013, at 6:38 AM, Joshua Ulrich wrote: On Mon, Sep 30, 2013 at 7:33 AM, Milan

Re: [Rd] check warning with .onLoad() and setClass()

2013-10-04 Thread Rainer M Krug
Dirk Eddelbuettel e...@debian.org writes: On 4 October 2013 at 14:15, Rainer M Krug wrote: | Hm. loadModule is Rcpp function, but I am only interested in using the | setClass() function, which has nothing to do with Rcpp. I don't even use | Rcpp in the package, only in one which is imported.

Re: [Rd] Possible POSIXlt / wday glitch bugs.r-project.org status

2013-10-04 Thread Scott Kostyshak
On Fri, Oct 4, 2013 at 6:11 AM, Imanuel Costigan i.costi...@me.com wrote: Wanted to raise two questions: 1. Is bugs.r-project.org down? I haven't been able to reach it for two or three days: Yes. Quote from Duncan: ... the server is currently down. The volunteer who runs the server is

Re: [Rd] read.table() with quoted integers

2013-10-04 Thread Henrik Bengtsson
On Fri, Oct 4, 2013 at 4:55 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-10-04 7:31 AM, Joshua Ulrich wrote: On Tue, Oct 1, 2013 at 11:29 AM, David Winsemius dwinsem...@comcast.net wrote: On Sep 30, 2013, at 6:38 AM, Joshua Ulrich wrote: On Mon, Sep 30, 2013 at 7:33 AM, Milan

Re: [Rd] read.table() with quoted integers

2013-10-04 Thread peter dalgaard
On Oct 4, 2013, at 17:10 , Henrik Bengtsson wrote: On Fri, Oct 4, 2013 at 4:55 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-10-04 7:31 AM, Joshua Ulrich wrote: On Tue, Oct 1, 2013 at 11:29 AM, David Winsemius dwinsem...@comcast.net wrote: On Sep 30, 2013, at 6:38 AM,

Re: [Rd] read.table() with quoted integers

2013-10-04 Thread Peter Meilstrup
I think this is not the right approach -- quoting is a transport-layer feature of the CSV format, not part of the application layer. Quotes should always be interpreted away from column data before any data is handed to the application layer. (CSV does not _have_ any application layer; type

Re: [Rd] read.table() with quoted integers

2013-10-04 Thread Henrik Bengtsson
On Fri, Oct 4, 2013 at 9:15 AM, peter dalgaard pda...@gmail.com wrote: On Oct 4, 2013, at 17:10 , Henrik Bengtsson wrote: On Fri, Oct 4, 2013 at 4:55 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-10-04 7:31 AM, Joshua Ulrich wrote: On Tue, Oct 1, 2013 at 11:29 AM, David

Re: [Rd] read.table() with quoted integers

2013-10-04 Thread Peter Meilstrup
On Fri, Oct 4, 2013 at 9:20 AM, Peter Meilstrup peter.meilst...@gmail.com wrote: I think this is not the right approach -- quoting is a transport-layer feature of the CSV format, not part of the application layer. Quotes should always be interpreted away from column data before any data is

Re: [Rd] check warning with .onLoad() and setClass()

2013-10-04 Thread John Chambers
The basic tool is setLoadActions(), which takes a function definition, with the package's namespace as its argument. Read ?setLoadActions There is no such thing as setLoadFunction, as far as the standard code in R. While you haven't defined didn't work, an off-the-top-of-the-head idea would

[Rd] Allow semantic versioning for packages

2013-10-04 Thread Gábor Csárdi
Dear R developers, (http://bugs.r-project.org/ seems to be down, so I am writing a feature request here.) It would be great to allow semantic version numbers for packages. See http://semver.org/ for details. The problem I am having is that I am setting up a nightly build server, and there is no

Re: [Rd] C++ debugging help needed

2013-10-04 Thread Duncan Murdoch
I have now got two solutions to this. The rgl version currently on CRAN does a simple rename to avoid the name clash. A later version, still only on R-forge, puts most objects into a namespace called rgl. (The old code had two small namespaces gui and lib; they are gone now.) I am not yet

Re: [Rd] Possible POSIXlt / wday glitch bugs.r-project.org status

2013-10-04 Thread Imanuel Costigan
Thanks for the responses and quoting the timezone help file. I am assuming that in order to determine the wday element of POSIXlt, R does the necessary calculations in Julian time (via POSIXct). Based on this excerpt from ?DateTimeClasses, it looks like R is responsible for determining time

Re: [Rd] Possible POSIXlt / wday glitch bugs.r-project.org status

2013-10-04 Thread Joshua Ulrich
On Fri, Oct 4, 2013 at 8:02 PM, Imanuel Costigan i.costi...@me.com wrote: Thanks for the responses and quoting the timezone help file. I am assuming that in order to determine the wday element of POSIXlt, R does the necessary calculations in Julian time (via POSIXct). Based on this excerpt

Re: [Rd] Possible POSIXlt / wday glitch bugs.r-project.org status

2013-10-04 Thread Imanuel Costigan
Ok thanks for that explanation. That's bad news for me. I need to generate dates out past that limit regularly. It means that many operations past that limit are unreliable. Any suggested work arounds / alternatives? On 05/10/2013, at 11:37 AM, Joshua Ulrich josh.m.ulr...@gmail.com wrote: On

[Bioc-devel] Reminder: Warning deadline approaching

2013-10-04 Thread Dan Tenenbaum
Just a reminder. Next Wednesday, October 9, is the Deadline for packages passing R CMD build and check without warning. Some warnings will be accepted, clarification on the bioc-devel mailing list. Thanks, Dan ___ Bioc-devel@r-project.org mailing

[Bioc-devel] Courtesy message about the upcoming release

2013-10-04 Thread Marc Carlson
Hello everyone, This is a courtesy message to remind all package developers that next Wednesday the 9th of October is the deadline for all packages to pass the build system without any errors or warnings. Please have a look at our build system for the development branch and make sure that