[R] String substitution on package install?
Hello ...
I was working with some older code today that started throwing errors I'd
never seen before. The source appears to be some sort of substition of
the text of the code on install time, I was hoping that someone might be
able to point me to what I'm doing wrong.
If I take the following function:
foo <- function() {
test <- "This is a test"
grep("^FOO_\\w+_OK$", test)
}
and put it in some file (say foo.R). If I source() that file, the
function appears properly. However, if I put that file in a package, and
do a R CMD INSTALL on that package, it appears as such:
function ()
{
test <- "This is a test"
grep("^FOO_\\", test)
}
The switcharoo on the text in the grep() call was the source of the
errors, btw.
I originally saw this today on a cut of R-devel from late last week, but
then did a svn up from just now and saw it again (I realize that neither
are officially R-2.3.0 but the time window was less than a few days). I
tried it on R-2.1.1 (the only older version I had sitting around for
whatever reason) and did not see this happening.
Is this something that others can even replicate, or is it particular to
something about my setup. And even if so, is this a case where I was
doing something wrong all along which now has gotten fixed and made my
wrong thing a Really Wrong Thing?
Thanks
-J
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Re: [R] Taking code from packages
On Fri, 13 Jan 2006, Ales Ziberna wrote: > I am currently in the process of creating (my first) package, which (when > ready) I intend to publish to CRAN. In the process of creating this package > I have taken some code form existing packages. I have actually copied parts > of functions in to new functions. This code is usually something very basic > such as Rand index. What is the proper procedure for this? Why not simply specify that their package is a dependency and use their code directly? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] using paste and "\" to create a valid filename
> Sometimes even the easy stuff is difficult (for me)... I want to get > input from different places to paste together an excel filename (so > you know I'm using windows) that I can open with RODBC. I know about Using file.path() might be an easier solution for this (and it will allow your code to work in a cross-platform manner) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Digest reading is tedious
> Like many, I am sure, I get R-Help in digest form. Its easy enough to > browse the > subject lines, but then if an entry interests you, you have to embark > on this tedious search or scroll to find it. > It would be great to have a "clickable" digest, where the topics list > is a set of pointers, and clicking on a topic > takes you to that entry. I can think of at least one way to do this via > web pages, but I bet those with > more web skills than me can come up with an elegant solution. I sincerely hope you don't mean that you wish HTML enabled content in the actual emails coming through the mailing list. People who send HTML in email text should be taken out back and shot :) You could always look through the archives at: https://stat.ethz.ch/pipermail/r-help/ And simply sort by date or whatever else suits your fancy. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] reading from posgresql
> I don't know how to read data from posgresql to R. The RdbiPgSQL package will read from Postgres. Its current incarnation is available via Bioconductor (www.bioconductor.org). __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Output a dataframe from R to excel
> I am trying to output an dataframe from R to Excel file. Can anyone > tell me how to do it? Thanks a lot. write.csv() might get you where you want to go. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Help with R and Bioconductor
> seemed successful. Then while attempting to getBioC() I had to force > quit the R application since I had to attend to something else > urgently. When i returned and tried to getBioC, I am getting errors Why not just let it run? > indicating that there is a lock on some files. So i would like to The directory will likely be /library/00LOCK (I say likely because the '/library' part could be something else if you specified an alternate installation directory or your default .libPaths is different then standard), and removing that directory will solve your issues. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] deleting a file
> In Linux I would issue the command
> system('rm paste(path,'filename',sep='')')
> and this works just fine. It does not however work for windows, and I have
> no idea whether it would work on a mac.
> Is there a single command thay escapes me?
Yes.
help("file.remove")
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Re: [R] unable to download
> I am currently trying to install packages from BioConductor to R. Then you probably want to post to the bioconductor mailing list instead of the R mailing list. > However, I received a error stating: "unable to connect to > 'www.bioconductor.org' on port 80" May I know what is wrong and how There are lots of things that could be wrong, but since the site actually is currently active they are most likely to be related to your end. > may I correct it?? If possible give a step by step procedures on how > can I do it... Thanks alot, Amelia The first step is to see if install functionality (install.packages, download.packages, the pulldown if you're using Windows) work for non-bioconductor software. If not, then the second step is to see question 2.17 in the R for Windows FAQ. -J __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Getting the argument list within a function
> Is there a way of getting the argument list of a function from within > that function? For example, something like Would formals() work for you here? __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] [Q] Apply Function Over Multiple Array Margins
> Is there a canonical means to apply a function > over multiple arrays simultaneously? For example, Would mapply() get you what you're looking for? __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to Arrange character vector in alphabetic order
> Is there any function that can arrange a character in alphabetic order? Thanks for > answer Check out sort(). > vv <- c(letters[5:10], letters[20:11], letters[21:26], letters[4:1]) > vv [1] "e" "f" "g" "h" "i" "j" "t" "s" "r" "q" "p" "o" "n" "m" "l" "k" "u" "v" "w"[20] "x" "y" "z" "d" "c" "b" "a" > sort(vv) [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s"[20] "t" "u" "v" "w" "x" "y" "z" __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Package rmutil
> Where I can to download rmutil package?
You can use the reposTools package from Bioconductor:
install.packages2("rmutil")
There's also the website:
http://popgen0146uns50.unimaas.nl/~jlindsey/rcode.html
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[R] Re: or of a logical vector
> Is there some fast (built-in?) way to get the OR of all the elements in > a logical vector? any() and all() should give you OR and AND, respectively. Perhaps this should be in as a 'see also' for '|' and '&'. -J __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Problem in method's Makefile?
Hi there ... Not too long after the switch to using Subversion I tried to checkout & build R but encountered an error - and being short on time at that point put it off to look at later. So today I sat down again and was encountering this error every time I would attempt to build: dumping R code in package 'methods' Saving namespace image ... initializing class and method definitions now ...done usage: touch [-acfm] [-r file] [-t [[CC]YY]MMDDhhmm[.SS]] file ... *** Error code 1 I traced this down to the Makefile in methods: $(top_builddir)/library/$(pkg)/R/$(pkg).rdb: $(top_builddir)/library/$(pkg)/R/all.rda @echo "tools:::makeLazyLoading(\"$(pkg)\")" | \ R_DEFAULT_PACKAGES=NULL LC_COLLATE=C $(R_EXE) --slave > /dev/null @cat /dev/null > $(top_builddir)/library/$(pkg)/R/all.rda @touch $^ I'm not sure what it is about that touch call, but commenting it out causes things to build normally. When I try to echo '$^', it appears to be an empty string. This is all on a FreeBSD machine - I'm assuming it is somehow OS specific as this would have come up a bunch of times if it wasn't. -J __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] bad restore file magic number
> I'm running R 1.9.1 and trying to load a macro I've written. It gives the e > Error: bad restore file magic number (file may be corrupted)-- no data > loaded You probably want to use source() here, if you have the code in a file. The load() command is for use with stuff saved via the save() command. -J __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Files and classes in a package?
> Surely, there may be elegant solutions for this somewhat trivial issue. But, > I cant find it. Can you help me? Thanks. The 'Collate' field for DESCRIPTION. Section 1.1.1 of the R Extensions manual should describe it for you. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] MacOS X binaries won't install
Sorry, I missed the original message, so piggybacking off of a reply. > On Tue, 29 Jun 2004, Ruben Solis wrote: > > I've tried installing the MacOS X binaries for R available at: > > http://www.bioconductor.org/CRAN/ > > I'm running MacOS X version 10.2.8. Since this is coming out of our mirror (bioconductor), I'm curious if the same problem occurs with the packages available at the other mirrors, or if this is specific to the BioC mirror? Thanks -J __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] (no subject)
> implemented in MS-DOS to. The question for you is if you know about > the existence of an R function that allows me to run -in Windows- > executable files in MS-DOS from the R command window. Does system() do what you're looking for? __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] (no subject)
> Hello! Please!How do I download R from the internet? http://cran.r-project.org/doc/FAQ/R-FAQ.html#How%20can%20R%20be%20obtained%3f __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] replacing backslashes with slashes using gsub
> gsub("","/","D:\Prog\R\rw1090\library\cluster\libs")
> [1] "D:ProgR\rw1090libraryclusterlibs"
Probably not the best way, but what about escaping all the backslashes in
the original string?
gsub("","/","D:\\Prog\\R\\rw1090\\library\\cluster\\libs")
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Re: Windows versus Unix packages in CRAN (Was Re: [R] Rmetrics)
> Yes, I agree with Ajay Shah's comments. The Rmetrics website makes a > virtue of open source yet the Rmetrics people do not make available > their package for the open source platform, Linux. It wouldn't be difficult to create a source tarball and submit it to them __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to free memory space ??
> I thought that 'rm' function would free the memory used for the > deleted object, but it doesn't seem to be the case, as I don't observe > any change in the allocated memory for R in the windows task manager. > I ask this question because sometimes I have encounter a '... ran out > of memory' error - for a calculation that previously worked fine - I > did notice that this error often occurs when other objects are using a > lot of memory. Closing/relaunching R and redoing the calculation helps > under these circumstances. gc() will reclaim memory from objects which are no longer being used. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] availability of version 1.9.0?
> When will version 1.9 (for Windows) be ready, please? You can download the beta version at http://cran.r-project.org/bin/windows/base/rdevel.html > My reason for asking: there is an interesting library from > Bioconductor called tkWidgets. However, it will only > work with version 1.9.0 or higher. Note that the version of tkWidgets that is available as part of the 1.3 release of Bioconductor works with 1.8.x versions of R. I'm not sure if you're looking for functionality specifically found in the devel version of tkWidgets or not though. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] loop through files in a dir
> I have data in many files in a directory, how can I
> loop through the files in a given dir in-order-to
> build a data.frame?
Just use something like 'x <- dir(YOUR_ARGS_HERE)', and then you can do a
loop like:
for (i in x) {
do something
do something else
etc ...
}
-J
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Re: [R] R-business case
> Some web sites have "hit counters". It should be possible to get > a counts of the numbers of times different parts of R are downloaded. > Do the CRAN web sites include any such? But how would CRAN know what sort of activity its mirrors is receiving? And what does a 'download' mean in an environment like this - I could download R 10 times, or 10 people could download it ... or even one person could download it and then give it to 50 people. The numbers don't necessarily reflect usage patterns, IMO. -J __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Different missing links on Windows in 'check' vs. 'install'
Hello ... Using R-1.9.0 alpha, I'm having some problem getting a few packages to pass check under Windows - specifically with the 'missing link(s)' section of the package install phase. I started trying to track down how the missing link was showing up as in some cases I could not see why the link was considered missing. For instance, in one package it was looking for 'makeViewers' although when the packages is loaded in R, 'makeViewers' is even in the search path (by way of a dependent package which was loaded initially). In trying to figure out how these things are determiend, I noticed that in Windows there was a difference in the reported missing links when one does 'Rcmd check' vs 'Rcmd install' (or 'Rcmd install --build'). In the example above, using either of the 'install' methods results in that link not being reported as missing (and if I put in an intentionally missing link it gets picked up as such), but 'check' reports it as missing. I'm wondering what the difference in environment is between check & install on Windows as that might help me to figure out why check reports these as missing links. Thanks -Jeff __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] my own function given to lapply
> treshold <- function(pred) {
> Error in match.fun(FUN) : Object "threshold" not found
^
If this is a direct cut & paste, you have a typo as you've defined the
function as "treshold".
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Re: [R] Test for pre-existing Win menu or item
> Before using winMenuAdd(), is it possible to test whether the menu already > exists? One could use try(winMenuAddItem()) with appropriate arguments, but > is there anything more elegant? winMenuNames() and winMenuItems() should give you the sort of information you're looking for, tho they're in R-devel and not R-1.8.x. -J __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to detect whether a file exists or not?
> I would like my program to load variables x,y,x from a file 'myFile.r' but > if this file does not exist, I want my program to create/initialize x,y,z. > Does anyone know how to do this? ?file.exists __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Printting 'for' and 'while' indices
> How do I "print" the "i" at each step? print(i)? __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Detect the presence of an object
> Is there a function like "is.there" such that > is.there ( a ) returns TRUE is object 'a' is in the current environment and > FALSE otherwise? exists() __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] please help me!
>I'm a new user to R and I am having difficulty reading a file into the > program. Here's the error I keep getting, I bet there's a simple solution, > but I cant find any... > Error in file(file, "r") : unable to open connection > In addition: Warning message: > cannot open file `c:MikeWeather2.txt' I am guessing that you didn't escape the backslash in the filename 'c:\MikeWeather2.txt', so you would have to refer to it as 'c:\\MikeWeather2.txt' in R. But, since you didn't show what you did to spawn the error, I could be wrong __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] install.packages() for a local file
> There is a method to install a package from a local file. > From the unix command line, use >R INSTALL > possibly using >R CMD build > first. Right. I already do this within the function (I need to install the packages from inside of R), but was going through trying to find redundant code and thought this might be a place where I could replace one of my functions with a call to one of R's functions. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] install.packages() for a local file
On 13 Nov 2003, Peter Dalgaard wrote: > I suppose the theory is that you might as well just run "R CMD > INSTALL" on the file. That's what I figured here, but wanted to be sure. I had found a block of code of mine where I was basically reinventing the wheel installing local packages and was wondering why I hadn't just used install.packages() on the files. I can at least change the code for the Windows side of things. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] install.packages() for a local file
Hello ... I see that on Windows one can specify a filename as the "pkgs" argument and then set CRAN=NULL when calling install.packages() for a local file. Is there a way to do this on unix? It doesn't appear to be possible, but perhaps I am missing something here. Also, if indeed there is no method to do this on unix, is there a reason behind it or has it just never been implemented? __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] How to call R from C?
> Hi. I Would like to know if it is possible to call R from C and how can I do > it. There is any material about this or examples? You'll want to read through the "Writing R Extensions" document at: http://cran.r-project.org/manuals.html -J __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Stifling REprintf() output
In some code that I have written, use of url() is generating the output line: "cannot open: HTTP status was `404 Not Found`" The problem is that I do not want R to be outputting any error messages - I have 'internet.info' set to 3, show.error.messages set to FALSE and the url() wrapped in a try(). When the URL is not found I am already handling it in a manner consistent with the rest of the package and the 'cannot open' line is confusing some users. The problem is that I can not figure out how to turn it off, the comment in printutils says that REprintf writes to stderr and is not redirected by sink(). The call in question appears to be coming from in_R_HTTPOpen, in that if the HTTP return code is != 200 the REprintf is called. Is there any way within R to keep this output from appearing? Thanks -J __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R and pointer
> I want to write a function that modify directly variables passed as > parameters (the equivalent in C language of *ptr/&ptr) so that I don't > have to return a list and to reaffect all my variables. Is it possible > to do so in R? Thanks a lot. You can use environments as they're passed by reference. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Viewing function source
> If I want to "view source" on the rpois() function, for example, can I do > somethink like: > > source(rpois) > > To see how the function is implemented? Just type the name of the function __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Regexpr with "."
> I'm trying to use the regexpr function to locate the decimal in a character
> string. Regardless of the position of the decimal, the function returns 1.
You need to escape it.
> gsub("\\.",",","Female.Alabama")
[1] "Female,Alabama"
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RE: [R] R won't connect to the internet on SUSE Linux 8.1
> then everything works fine h, but I still have a problem as the
> command I really want to run is :
> source("http://wwwbioconductor.org/getBioC.R";)
> and source() does not accept an option 'method="wget"'
getBioC() accepts the 'method' parameter as per its documentation.
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Re: [R] Version Number of a Package
> I am documenting an analysis procedure in a DB and I would like to know the
> specific version number of each package that I use. Is there a standardized
> way of getting that information out from R, or should I parse it out from the
> source-code files? Ideally I would like a function like this:
> myVerNum <- Version(package.names);
There are a several ways to skin that cat.
A few that come to mind are using package.description():
> package.description("Biobase")["Version"]
Version
"1.3.27"
You can also use installed.packages():
> z <- installed.packages()
> z[1,"Version"]
[1] "1.2.28"
Also, in the Biobase package in Bioconductor (www.bioconductor.org),
there's a function package.version():
> package.version("Biobase")
[1] "1.3.27"
-J
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[R] Bioconductor 1.2 Released
The Bioconductor development team announces release 1.2 of the Bioconductor packages for the analysis of genomic data. Bioconductor is an open source bioinformatics software project based on the R language. Version 1.2 features: = * All packages from the 1.1 release are included. All current bug fixes have been applied, and most have been upgraded and provide enhanced functionality. * affy: The affy package now provides for the automatic downloads of necessary CDF packages. There is also a new function, justRMA() which will use less system resources if one just wants RMA vs. using ReadAffy() and then rma/expresso - this will solve some users' problem when they do not have enough memory for working with the full method. The package's implementation of MAS 5.0 now agrees better with Affymetrix's then in previous releases, and now includes a function mas5() to make it easier for a user to obtain these results. * affycomp: A new package that serves as a graphics toolbox for the assessment of Affymetrix expression measures. * AnnBuilder: DB support is no longer required. ABPkgBuilder now provides a signle API for building of data packages. Also, data packages built with AnnBuilder will include an evidence code and association information for GO ids. * Biobase: The exprs2excel method for the exprSet class has been added, which will create an excel friendly file from the expression component of an exprSet. * DynDoc: A new package that provides a set of functions to create and interact with dynamic documents and vignettes * limma: A new package that provides functionality to handle linear models for microarray data. * makecdfenv: A package to create hash table environments from CDF files, as well as functionality to create data packages out of these environments. * RBGL: A new package that provides an interface to the Boost libraries for graph manipulation. * Rgraphviz: A new package that provides an interface with Graphviz to plot graph objects in R. * Ruuid: A new package that provides Universally Unique ID values (UUIDs). * SAGElyzer: A new package that will store SAGE data in a database and then provide functionality to locate genes that are similar to a given SAGE tag. * tkWidgets: The importWizard functionality was added, which provides an Excel style interface for importing data into R. Also the DPExplorer is new in 1.2 - allowing users to explore a BioC data package. The argsWidget widget set will create a GUI for accepting input dynamically. * vsn: vsn can now be used as a normalization method with the affy package. The likelihood function optimization has been streamlined and is faster. There is a new function to produce a diagnostic plot for the variance-mean relationship of microarray data, meanSdPlot. The data returned by vsn is now an object of class "exprSet". * widgetTools: A new package that provides user friendly tools to create Tcl/Tk widgets in R. Software, documentation, and further details are available on the Bioconductor WWW site: http://www.bioconductor.org/ HELP AND RESOURCES: === Information on subscribing to the mailing list and viewing its archives can be found at: http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Please use that list to discuss Bioconductor specific issues, bugs, and problems. Note that every package has a vignette (a literate program which provides an annotated example of the package's use) as well as possibly some "HOWTO"s. These document the tool's usage, and are provided in the "doc" subdirectory of each package library. WHO: For the Bioconductor development team: Douglas Bates, University of Wisconsin, USA. Vince Carey, Harvard Medical School, USA. Marcel Dettling, Federal Inst. Technology, Switzerland. Sandrine Dudoit, Division of Biostatistics, University of California, Berkeley, USA. Byron Ellis, Harvard Department of Statistics, USA. Laurent Gautier, Technial University of Denmark, Denmark. Robert Gentleman, Harvard Medical School, USA. Jeff Gentry, Dana-Farber Cancer Institute, USA. Kurt Hornik, Technische Universitat Wien, Austria. Torsten Hothorn, Institut fuer Medizininformatik, Biometrie und Epidemiologie, Germany. Wolfgang Huber, DKFZ Heidelberg, Molecular Genome Analysis, Germany. Stefano Iacus, Italy Rafael Irizarry, Department of Biostatistics (JHU), USA. Friedrich Leisch, Technische Universitat Wien, Austria. Martin Maechler, Federal Inst. Technology, Switzerland. Anthony Rossini, Univer
Re: [R] r-help-bounces and r-devel-bounces e-mail?
> Any clues? I just noticed that my e-mail filter rule suddenly stopped > putting these messages in their respective folders this morning (my > time). I believe they're upgrading the Mailman software that runs the list. __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] function
On Wed, 19 Feb 2003 [EMAIL PROTECTED] wrote: > The following function: > match(myvec,myscaler)!="NA" > I need a return > FALSE FALSE TRUE TRUE TRUE TRUE TRUE FALSE FALSE ...FALSE > Is there any function to perform this? Try: myvec == myscaler > z <- c(24, 24, 10, 10, 10, 10, 44, 44, 44, 45, 45, 45, 54, 54, 54, 54, 42, 42)> a <- 10 > match(z,a) [1] NA NA 1 1 1 1 NA NA NA NA NA NA NA NA NA NA NA NA > which(z == a) [1] 3 4 5 6 > z == a [1] FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE [13] FALSE FALSE FALSE FALSE FALSE FALSE -J __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R CMD check .
> * checking for CRLF line endings in C sources/headers ... OK > * creating Davies-Ex.R ... OK > * checking examples ... ERROR > Running examples failed. > r:Davies% > How do I tell which .Rd file is the problem? (I suspect that the > examples aren't actually being executed because most of them take a > long time and the error is pretty much instantaneous). You should have a directory named .Rcheck, inside of that there should be a file -Ex.Rout that should give you a clue as to what is happening (it is the R output from the examples running). -Jeff __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] loading functions from files
On Thu, 23 Jan 2003, Saurav Pathak wrote:
> how may i load this file in R so that i may say at the prompt:
source("filename.R") should do the trick
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Re: [R] how to record the CPU time
On Wed, 15 Jan 2003, chenwj wrote:
> is there any function can record the CPU time when running a paragraph of
> code?
system.time() should do what you want, I believe.
> if it is, can anyone show me an little example of how-to?
There are examples of usage in help("system.time")
-J
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Re: [R] Warnings with no INDEX file in a package.
On Thu, 9 Jan 2003, David Kane I have read the suggested sections of the manual. It would seem to me that I > should be able to continue to follow my prior practice by turning off the > warning for missing INDEX. Certainly, the fact that R CMD build creates an > INDEX for you if one is not present would suggest that this is an acceptable > practice. > Or am I missing something? I just hate to ignore a warning each time I build a > package . . . R CMD build --force should build all of the appropriate index files for you. -J __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Packages w/ S4 classes in C?
Hello ... Does anyone know of a package (or other code) out there which has handled S4 classes in C? I realize that a lot of this stuff is fairly new in R-devel, so my assumption is no - but there seems to be some deviation from the green book that is really throwing me off, and I'm looking for some sort of front-to-back example. Thanks -Jeff __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Check whether a file exits ...
> I need to write a R program that checks whether a file exists in the > directory. Any easy ways > to do that? Thanks! file.exists() __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] pasting "\" into character strings
> write an R function that writes references to Windows files into a text > file, where a different Windows programs will later read these references > in the standard Windows syntax. >Can someone tell me how to create the character string > 'c:\work\part1.txt' from the parts, "c:", "work", an "part1.txt"? I don't have access to a Windows machine right now to test this, but might file.path() help here? -J __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R function similar to UNIX "uniq -c"?
On Thu, 19 Dec 2002, Hilmar M. Carders wrote:
> Is there an R function that gives the equivalent of the UNIX command
> "uniq -c" which could be applied to a vector with duplicate values?
There must be a better way to do this, but this would get you the
information you're looking for:
> z <- c("a","b","c","d","a","a","c")
> unique(z)
[1] "a" "b" "c" "d"
> lapply(unique(z),function(x){length(z[z==x])})
[[1]]
[1] 3
[[2]]
[1] 1
[[3]]
[1] 2
[[4]]
[1] 1
-J
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Re: [R] Memory leak in R v1.6.0?
> When I look at the task manager, I see that the > memory used by R keep going up and reach more than 1G > byte after 700 iteration or so. I have try including > gc after every loop. No help at all. I'll appreciate > any suggestion. Have you tried R1.6.1? I believe it fixes this problem. -J __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
