Re: [Rd] news.Rd format

the version format should be x.y 'Changes in version 2.36' should work... benilton On 22 January 2011 15:58, Terry Therneau thern...@mayo.edu wrote:  I'm converting the Changelog files that I have used in the survival package (since the 1980s) to the inst/NEWS.Rd format and a couple of things

[Rd] changes in recent R-devel revisions?

Hi, I have a BioC infra-structure package that works fine (I can build, check and load it successfully) on revision r53950. The very same package fails on r54591 with the error below: Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source) : cyclic name space

Re: [Rd] changes in recent R-devel revisions?

Martin and Professor Ripley, Thank you very much for your attention and time on this. I've fixed the package accordingly. benilton On 2 March 2011 06:39, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On Tue, 1 Mar 2011, Martin Morgan wrote: On 03/01/2011 03:19 PM, Benilton Carvalho wrote

Re: [Rd] diag() has a bug (PR#13702)

My understanding is that providing nrow and ncol, you want to create a diagonal matrix with those dimensions. diag(pi, 6, 6) and that by diag(foo, 2, 2) you really meant diag(foo)[2] Apologies if I misunderstood. b On May 14, 2009, at 10:45 AM, michael.m.spie...@gmail.com wrote:

[Rd] problem with plot.lm?

I'm bringing this issue to r-devel as my idea of sending it to r-help appears to be wrong. The following is reproducible in R-patched and R-devel (also in older versions). An outlier is inserted in group E and the last plot by plot.lm suggests that the point belongs to D. It appears to

Re: [Rd] Surprising length() of POSIXlt vector (PR#14073)

Check the documentation and the archives. Not a bug. b On Nov 19, 2009, at 8:30 PM, m...@celos.net wrote: Arrays of POSIXlt dates always return a length of 9. This is correct (they're really lists of vectors of seconds, hours, and so forth), but other methods disguise them as flat vectors,

Re: [Rd] Surprising length() of POSIXlt vector (PR#14073)

need to return a length of 9? Thanks Steve McKinney -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r- project.org] On Behalf Of Benilton Carvalho Sent: Thursday, November 19, 2009 4:29 PM To: m...@celos.net Cc: r-de...@stat.math.ethz.ch Subject: Re: [Rd

[Rd] Display list redraw incomplete

Hi, I'm observing the following warning with R-2.10.0 on a machine I have remote access to. Like what happened to Roger ( http://www.mail-archive.com/r-devel@r-project.org/msg08669.html ), two extra instances of X11 are open after dev.off(). Although I'm reporting this on R-2.10.0, it's

Re: [Rd] Surprising length() of POSIXlt vector (PR#14073)

Thank you Martin, for putting this together. Cheers, b On Nov 30, 2009, at 11:10 AM, maech...@stat.math.ethz.ch wrote: Tony Plate tpl...@acm.org on Sun, 22 Nov 2009 10:21:33 -0600 writes: maech...@stat.math.ethz.ch wrote: PD == Peter Dalgaard p.dalga...@biostat.ku.dk on Fri, 20 Nov 2009

Re: [Rd] optional package dependency

How about using: Enhances: Rmpi ? b On Fri, Jan 15, 2010 at 6:00 AM, Ross Boylan r...@biostat.ucsf.edu wrote: I have a package that can use rmpi, but works fine without it. None of the automatic test code invokes rmpi functionality. (One test file illustrates how to use it, but has quit()

[Rd] Failing to install R-2.4.0 on FC4

:// tolstoy.newcastle.edu.au/R/devel/06/01/3699.html) but the proposed solution did not work for me. Any suggestion? Thank you very much, Benilton Carvalho PhD Candidate Department of Biostatistics Johns Hopkins University __ R-devel@r-project.org mailing list

[Rd] Building R from the source

Hi Everyone, when building (say) R-2.4.0 from the source, is it still the recommendation to use GCC 3.4? Thank you very much, Benilton Carvalho PhD Candidate Department of Biostatistics Johns Hopkins University __ R-devel@r-project.org mailing list

Re: [Rd] Building R from the source

Professor Ripley, thank you very much for your reply. I'm currently trying to build R-2.4.0 from the source on a system (Xeon) running Fedora Core 4. As for the available compilers: gcc/g++/gfortran/f95 (version 4.0.0-8) Thank you very much, Benilton Carvalho PhD Candidate Department

Re: [Rd] inconsistency or bug in coef() (PR#9358)

it doesn't appear to be a bug for me, given that one of your coefficients is NA due to linear dependencies on your design matrix. i prefer to think of it as a feature :-) (show only the coefficients for the variables that do not show linear dependencies). x=1:5 y=c(1:3, 7, 6) fit=lm(y~x)

Re: [Rd] Missing install libraries for R on OpenSuse 10.2 (PR#9425)

Hi Matjaz, I don't see that as a bug. Instead, you don't have the requirements, as you already noticed. Isn't it simpler just to install the requirements? See: http://download.opensuse.org/distribution/10.2/repo/oss/suse/i586/ best, benilton On Dec 20, 2006, at 2:04 PM, [EMAIL PROTECTED]

Re: [Rd] Trailing message on R CMD BATCH

I do find that info to be useful and would very much appreciate if it is kept. b Brian Ripley wrote: Unix versions of R CMD BATCH have reported proc.time() unless the script ends in q(). E.g. if the input is 'search()' the output is invisible(options(echo = TRUE)) search() [1] .GlobalEnv

Re: [Rd] can't plot a line

you don't see the line b/c you're squaring both pi and -pi compare that with lines(c(0,0), c(-1,1)*(2*pi)^2) b On Jan 23, 2007, at 10:41 AM, Spencer Graves wrote: Consider the following: plot(0, 0, xlim=c(-10, 10), ylim=c(-50, 50)) lines(c(0,0), (2*c(-pi, pi))^2) I

Re: [Rd] Problems with package containing S4 classes

your namespace probably contains: useDynLib(testS4) but you don't have any compiled code... remove that line and everything will be fine. btw, if you're playing with S4, you must import 'methods' b On Mar 16, 2007, at 4:55 PM, cstrato wrote: Dear all, Currently, I am trying to create a

Re: [Rd] Problems with package containing S4 classes

Christian Benilton Carvalho wrote: do you have a generic for 'export'? On Mar 16, 2007, at 5:38 PM, cstrato wrote: Dear Benilton Thank you, now my package works. Do you have an explanation for my second problem: * Installing *source* package 'mytest' ... ** R ** save image Error

Re: [Rd] Problems with package containing S4 classes

Biobase itself does. b On Mar 16, 2007, at 7:43 PM, cstrato wrote: Thank you, I have already read the R-exts manual, but the collate field is optional. Do you know a package which uses the Collate field so that I can study it? Best regards Christian Benilton Carvalho wrote

Re: [Rd] how to use debug.mypkg

debug.affy123 is not a function... it's just a logical flag set in ProgressBarText.R. b On Mar 22, 2007, at 6:22 PM, cstrato wrote: Dear all, The package affy has the following statement in file AffyBatch.R: if (debug.affy123) cat(--initAffyBatch\n) This is great and I would also like

Re: [Rd] how to use debug.mypkg

this flag. When I set the flag debug.mypkg-T in the R session, everything works, but the problem is that if I do not set it, it is undefined. So I need to set it initially in my package, but where? Christian Benilton Carvalho wrote: debug.affy123 is not a function... it's just a logical

Re: [Rd] how to use debug.mypkg

Great tip Seth... thanks a bunch... b On Mar 22, 2007, at 9:54 PM, Seth Falcon wrote: Benilton Carvalho [EMAIL PROTECTED] writes: it doesn't matter where.. just pick one of your files and set it... of course, your file should be listed in the Collate field (in case you changed your

Re: [Rd] X11() dies in remote background

Won't ServerAliveInterval 60 in /etc/ssh_config do the job of keeping your connection alive? And wouldn't it be more appropriate if bitmap() was used instead? b On Jul 21, 2007, at 12:23 PM, Vincent Carey 525-2265 wrote: Vincent Carey 525-2265 [EMAIL PROTECTED] writes: this is not a

[Rd] length-0 list as dimnames

Hi, I'm working on a package and observed a behaviour that was suggested to be incompatible with the documentation. The code below: x - matrix(1:4, 2) dimnames(x) - list() works just fine. But checking the documentation for dimnames(), it states that if value is a list its components are

Re: [Rd] length-0 list as dimnames

Thank you very much for pointing me to the correct part of the documentation (and apologies for that), Simon. Very much appreciated, b On 6 June 2012 00:43, Simon Urbanek simon.urba...@r-project.org wrote: On Jun 5, 2012, at 7:37 PM, Benilton Carvalho wrote: Hi, I'm working on a package

[Rd] creating a '[' method for an S4 class

Hi, I'm working on an S4 class that is expected to behave like an array. I have some difficulties when defining '[' and I wonder if someone could point me to the right direction: 1) Call the S4 object obj 2) Assume dim(obj) = c(10, 4, 2) 3) Suppose someone calls: obj[1:3,] , which is a mistake,

Re: [Rd] Vector binding on harddisk

also, take a look at the ff package. b On Feb 14, 2008, at 11:43 AM, Greg Snow wrote: You may want to look at the SQLiteDF package, this allows you to put your data into an SQLite database and treat that like a normal vector or data frame inside of R. Hope this helps, -- Gregory (Greg) L.

[Bioc-devel] Subsetting eSet-like objects with duplicated indices

Hi, I'm trying to understand why FeatureSet objects behave slightly different than eSet objects. Here's the one example I'm trying to work out: if (!require(pd.hugene.1.0.st.v1)){ library(BiocInstaller) biocLite('pd.hugene.1.0.st.v1') } library(oligoData) data(affyGeneFS) affyGeneFS

Re: [Bioc-devel] SummarizedExperiment with alternate back end

A long time ago, I created this (on top of rhdf5), which I often use when I need to use hdf5 files: https://github.com/benilton/rhdf5utils On Sat, Sep 19, 2015, 07:12 Morgan, Martin wrote: > Two less baked ideas are > > https://github.com/PaulPyl/h5array > >

Re: [Bioc-devel] Problem of circular depedencies in package

My understanding is that plasFIA should be in the Suggests field (and not in Depends). On Mon, Sep 19, 2016 at 11:31 AM DELABRIÈRE Alexis wrote: > Hi, > > I hope that it is the good place to ask this, as it is related to > Bioconductor guidelines. > > I have an issue

Re: [Bioc-devel] Question about external algorithms to Bioconductor package

Maybe gmapR? 2017-11-24 16:25 GMT-02:00 Ioannis Vardaxis : > Hei, > > Both kalliston and salmon er for RNA data, I have DNA data. Is there any > other solution rather than Rsubread which is extremely slow? > I am making an algorithm where one of its steps should be to