Re: [R] Problem with R coding

[Ivan Krylov via R-help]

В Tue, 12 Mar 2024 14:57:28 +
CALUM POLWART  пишет:

> That's almost certainly going to be either the utf-8 character in the
> path

The problem, as diagnosed by Maria in the first post of the thread, is
that the user home directory as known to R is stored in the ANSI
encoding instead of UTF-8, despite the session charset should be UTF-8
as Maria's Windows is sufficiently new [*]. As soon as any bit of R
tries to perform an encoding conversion using this path (for example,
file.exists() converting it from UTF-8 to UCS-2 in order to interact
with Windows filesystem APIs), the conversion fails. Since tcltk2 uses
file.exists('~/...') in its .onLoad, the package and any of its hard
dependencies are now broken.

Normally, this path is determined automatically to be something like
C:\Users\username\Documents. With OneDrive taking over, it turns out to
be something else and for some reason in the wrong encoding (ANSI but
marked as native == UTF-8).

The function that determines this path lives in src/gnuwin32/shext.c
(char *getRUser(void)). It starts by looking at the environment
variable R_USER, which is why in order to override OneDrive, the user
has to set it first (in the command line or system settings). If that
fails, R tries the environment variable HOME (which is usually set on
Windows, isn't it?), consults SHGetKnownFolderPath(FOLDERID_Documents)
(which returns the result as a wchar_t[] to be manually converted to
UTF-8 by R), consults a few more environment variables, and finally
tries to use the current directory. There is likely no easy way to use
`subst` to give a different home drive to R.

If I set %HOME% or even %R_USER% to a non-ASCII path without setting up
OneDrive, R works normally, so getenv() must be able to return
UTF-8-encoded variables. I don't see how ShellGetPersonalDirectory()
could fail in this manner. My remaining hypothesis is that OneDrive
somehow causes getenv("HOME") to return "C:\\Users\\marga\\OneDrive
- Fundación Universitaria San Pablo CEU\\Documentos" in ANSI instead of
UTF-8.

If anyone here has OneDrive set up in this manner and can debug R,
a trace of what getRUser() actually does would be very useful.

-- 
Best regards,
Ivan

[*]
https://blog.r-project.org/2020/05/02/utf-8-support-on-windows/index.html
https://blog.r-project.org/2022/11/07/issues-while-switching-r-to-utf-8-and-ucrt-on-windows/index.html

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Re: [R] Problem with R coding

[Iris Simmons]

Hi Maria,


I had something similar on my Windows work laptop at some point where the
home directory was something containing non ASCII characters. The easy
solution is to copy said directly from the file explorer into
utils::shortPathName, and then set that as the home directory. In my case,

> writeLines(utils::shortPathName(r"(C:\Users\iris\OneDrive - Organization
Name Non ASCII\Documents)"))
C:\Users\iris\ONEDRI~1\DOCUME~1

and then in the control panel, then user accounts (twice), then Change My
Environment Variables, enter the variable name HOME and the directory that
was produced by R. Now the HOME directory contains all ASCII characters so
everything works as expected.


I hope this helps!



On Tue, Mar 12, 2024, 04:49 Maria Del Mar García Zamora <
mar.garc...@alumnos.uchceu.es> wrote:

> Hello,
>
> This is the error that appears when I try to load library(Rcmdr). I am
> using R version 4.3.3. I have tried to upload the packages, uninstall them
> and intalling them again and nothing.
> Loading required package: splines
> Loading required package: RcmdrMisc
> Loading required package: car
> Loading required package: carData
> Loading required package: sandwich
> Loading required package: effects
> lattice theme set by effectsTheme()
> See ?effectsTheme for details.
> Error: package or namespace load failed for ‘Rcmdr’:
>  .onLoad failed in loadNamespace() for 'tcltk2', details:
>   call: file.exists("~/.Rtk2theme")
>   error: file name conversion problem -- name too long?
>
> Once this appears I use path.expand('~') and this is R's answer:
> [1] "C:\\Users\\marga\\OneDrive - Fundaci\xf3n Universitaria San Pablo
> CEU\\Documentos"
>
> The thing is that in spanish we use accents, so this word (Fundaci\xf3n)
> really is Fundación, but I can't change it.
>
> I have tried to start R from CDM using: C:\Users\marga>set
> R_USER=C:\Users\marga\R_USER
>
> C:\Users\marga>"C:\Users\marga\Desktop\R-4.3.3\bin\R.exe" CMD Rgui
>
> At the beginning this worked but right now a message saying that this app
> cannot be used and that I have to ask the software company (photo attached)
>
> What should I do?
>
> Thanks,
>
> Mar
>
>
> [https://www.uchceu.es/img/externos/correo/ceu_uch.gif]<
> https://www.uchceu.es/>
>
> Maria Del Mar García Zamora
> Alumno UCHCEU -
> Universidad CEU Cardenal Herrera
> -
> Tel.
> www.uchceu.es
>
> [https://www.uchceu.es/img/logos/wur.jpg]
> [https://www.uchceu.es/img/externos/correo/medio_ambiente.gif] Por favor,
> piensa en el medio ambiente antes de imprimir este contenido
>
>
>
> [http://www.uchceu.es/img/externos/correo/ceu_uch.gif]<
> http://www.uchceu.es/>
>
> Maria Del Mar García Zamora
>
> www.uchceu.es
>
> [http://www.uchceu.es/img/externos/correo/medio_ambiente.gif] Por favor,
> piensa en el medio ambiente antes de imprimir este contenido
>
>
>
>
> Este mensaje y sus archivos adjuntos, enviados desde FUNDACIÓN
> UNIVERSITARIA SAN PABLO-CEU, pueden contener información confidencial y
> está destinado a ser leído sólo por la persona a la que va dirigido, por lo
> que queda prohibida la difusión, copia o utilización de dicha información
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Re: [R] Problem with R coding

[CALUM POLWART]

That's almost certainly going to be either the utf-8 character in the path
OR the use of one drive which isn't really a subfolder as I understand it.

When I've had these issues in the past, I've been able to mount a drive
(say U:/ ) which sites further down /up the folder tree so that R just
called "U:/RCodeFolder/Rfile.R"

Is that possible with an C drive?

On Tue, 12 Mar 2024, 10:40 Ivan Krylov via R-help, 
wrote:

> Dear Maria,
>
> I'm sorry for somehow completely missing the second half of your
> message where you say that you've already tried the workaround.
>
> В Tue, 12 Mar 2024 07:43:08 +
> Maria Del Mar García Zamora  пишет:
>
> > I have tried to start R from CDM using: C:\Users\marga>set
> > R_USER=C:\Users\marga\R_USER
> >
> > C:\Users\marga>"C:\Users\marga\Desktop\R-4.3.3\bin\R.exe" CMD Rgui
> >
> > At the beginning this worked but right now a message saying that this
> > app cannot be used and that I have to ask the software company (photo
> > attached)
>
> Glad to know the workaround helped. It sounds like your Windows
> 10 is set up in a user-hostile way.
>
> It may help to visit the Windows Security settings and make an
> exception for C:\Users\marga\Desktop\R-4.3.3\bin\R.exe. An approximate
> instruction can be found at
> , but it
> might be the case that your university IT must take a look at it before
> allowing you to run R on your computer.
>
> Feel free to disregard this advice if someone with more Windows
> experience shows up.
>
> --
> Best regards,
> Ivan
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

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Re: [R] Problem with R coding

[Ivan Krylov via R-help]

Dear Maria,

I'm sorry for somehow completely missing the second half of your
message where you say that you've already tried the workaround.

В Tue, 12 Mar 2024 07:43:08 +
Maria Del Mar García Zamora  пишет:

> I have tried to start R from CDM using: C:\Users\marga>set
> R_USER=C:\Users\marga\R_USER
> 
> C:\Users\marga>"C:\Users\marga\Desktop\R-4.3.3\bin\R.exe" CMD Rgui  
> 
> At the beginning this worked but right now a message saying that this
> app cannot be used and that I have to ask the software company (photo
> attached)

Glad to know the workaround helped. It sounds like your Windows
10 is set up in a user-hostile way.

It may help to visit the Windows Security settings and make an
exception for C:\Users\marga\Desktop\R-4.3.3\bin\R.exe. An approximate
instruction can be found at
, but it
might be the case that your university IT must take a look at it before
allowing you to run R on your computer.

Feel free to disregard this advice if someone with more Windows
experience shows up.

-- 
Best regards,
Ivan

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Re: [R] Problem with R coding

[Ivan Krylov via R-help]

В Tue, 12 Mar 2024 07:43:08 +
Maria Del Mar García Zamora  пишет:

> Error: package or namespace load failed for ‘Rcmdr’:
>  .onLoad failed in loadNamespace() for 'tcltk2', details:
>   call: file.exists("~/.Rtk2theme")
>   error: file name conversion problem -- name too long?
> 
> Once this appears I use path.expand('~') and this is R's answer:
> [1] "C:\\Users\\marga\\OneDrive - Fundaci\xf3n Universitaria San
> Pablo CEU\\Documentos"

We've seen this problem before:
https://stat.ethz.ch/pipermail/r-help/2023-December/478732.html

The workaround that should help is to set the R_USER environment
variable to C:\Users\marga before launching R.

Please let me know if you're willing to debug R. (This will likely
involve compiling R from source with debugging symbols enabled and
stepping through the code.) There are no places in the Windows code
where R gets the conversion obviously wrong. I don't have OneDrive and I
wasn't able to convince R to return an invalid R_USER path without it.
I'm halfway convinced this is due to a bug in OneDrive itself.

-- 
Best regards,
Ivan

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Re: [R] Problem with R coding

[Rui Barradas]

Às 07:43 de 12/03/2024, Maria Del Mar García Zamora escreveu:

Hello,

This is the error that appears when I try to load library(Rcmdr). I am using R 
version 4.3.3. I have tried to upload the packages, uninstall them and 
intalling them again and nothing.
Loading required package: splines
Loading required package: RcmdrMisc
Loading required package: car
Loading required package: carData
Loading required package: sandwich
Loading required package: effects
lattice theme set by effectsTheme()
See ?effectsTheme for details.
Error: package or namespace load failed for ‘Rcmdr’:
  .onLoad failed in loadNamespace() for 'tcltk2', details:
   call: file.exists("~/.Rtk2theme")
   error: file name conversion problem -- name too long?

Once this appears I use path.expand('~') and this is R's answer:
[1] "C:\\Users\\marga\\OneDrive - Fundaci\xf3n Universitaria San Pablo 
CEU\\Documentos"

The thing is that in spanish we use accents, so this word (Fundaci\xf3n) really 
is Fundación, but I can't change it.

I have tried to start R from CDM using: C:\Users\marga>set 
R_USER=C:\Users\marga\R_USER

C:\Users\marga>"C:\Users\marga\Desktop\R-4.3.3\bin\R.exe" CMD Rgui

At the beginning this worked but right now a message saying that this app 
cannot be used and that I have to ask the software company (photo attached)

What should I do?

Thanks,

Mar


[https://www.uchceu.es/img/externos/correo/ceu_uch.gif]

Maria Del Mar García Zamora
Alumno UCHCEU -
Universidad CEU Cardenal Herrera
-
Tel.
www.uchceu.es

[https://www.uchceu.es/img/logos/wur.jpg]
[https://www.uchceu.es/img/externos/correo/medio_ambiente.gif] Por favor, 
piensa en el medio ambiente antes de imprimir este contenido



[http://www.uchceu.es/img/externos/correo/ceu_uch.gif]

Maria Del Mar García Zamora

www.uchceu.es

[http://www.uchceu.es/img/externos/correo/medio_ambiente.gif] Por favor, piensa 
en el medio ambiente antes de imprimir este contenido




Este mensaje y sus archivos adjuntos, enviados desde FUNDACIÓN UNIVERSITARIA 
SAN PABLO-CEU, pueden contener información confidencial y está destinado a ser 
leído sólo por la persona a la que va dirigido, por lo que queda prohibida la 
difusión, copia o utilización de dicha información por terceros. Si usted lo 
recibiera por error, por favor, notifíquelo al remitente y destruya el mensaje 
y cualquier documento adjunto que pudiera contener. Cualquier información, 
opinión, conclusión, recomendación, etc. contenida en el presente mensaje no 
relacionada con la actividad de FUNDACIÓN UNIVERSITARIA SAN PABLO-CEU, y/o 
emitida por persona no autorizada para ello, deberá considerarse como no 
proporcionada ni aprobada por FUNDACIÓN UNIVERSITARIA SAN PABLO-CEU, que pone 
los medios a su alcance para garantizar la seguridad y ausencia de errores en 
la correspondencia electrónica, pero no puede asegurar la inexistencia de virus 
o la no alteración de los documentos transmitidos electrónicamente, por lo que 
declina cualquier responsabilidad a este respecto.

This message and its attachments, sent from FUNDACIÓN UNIVERSITARIA SAN 
PABLO-CEU, may contain confidential information and is intended to be read only 
by the person it is directed. Therefore any disclosure, copying or use by third 
parties of this information is prohibited. If you receive this in error, please 
notify the sender and destroy the message and any attachments may contain. Any 
information, opinion, conclusion, recommendation,... contained in this message 
and which is unrelated to the business activity of FUNDACIÓN UNIVERSITARIA SAN 
PABLO-CEU and/or issued by unauthorized personnel, shall be considered 
unapproved by FUNDACIÓN UNIVERSITARIA SAN PABLO-CEU. FUNDACIÓN UNIVERSITARIA 
SAN PABLO-CEU implements control measures to ensure, as far as possible, the 
security and reliability of all its electronic correspondence. However, 
FUNDACIÓN UNIVERSITARIA SAN PABLO-CEU does not guarantee that emails are 
virus-free or that documents have not be altered, and does not take 
responsibility in this respect.


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Hello,

First of all, try running Rgui only, no R.exe CMD. Just Rgui.exe or
C:\Users\marga\Desktop\R-4.3.3\bin\Rgui.exe
Then, in Rgui, try loading Rcmdr

library(Rcmdr)


Also, do you have R in your Windows PATH variable? The directory to put 
in PATH should be


C:\Users\marga\Desktop\R-4.3.3\bin

so that Windows can find R.exe and Rgui.exe without the full path name.

Hope this helps,

Rui Barradas



--
Este e-mail foi analisado pelo software antivírus AVG para verificar a presença 
de vírus.
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__

Re: [R] Problem in R code

[Ivan Krylov]

В Wed, 8 Nov 2023 16:03:15 +0530
Crown Flame  пишет:

> for(i in 1:8)
> {
>   LST_city <- extract(LST, c(lon[i],lat[i]), fun = mean, buffer =
> 1, na.rm = TRUE)   #error
> }

Three things you might need to change:

1. You are trying to assign the output of extract() to the same
variable LST_city in all 8 iterations of the loop. You will probably
need to make it a list and assign to the list elements, e.g.
LST_city[[i]] <- ...

It will also help to learn about lapply() and other functions that
encapsulate loops, although that is more of a matter of taste.

2. You are giving a single vector c(lon[i], lat[i]) to extract() as the
y=... argument. According to help(extract), this is interpreted as
_numbers_ of cells inside x, not coordinates. You should probably
construct a spPolygons() object and use that as the `y` argument to
extract().

3. The description of the 'raster' package says that it's been
superseded by the 'terra' package. You don't have to rewrite all your
code now, but it may be beneficial to check whether 'terra' can
accomplish what you want.

> Error in optim(c(mu_x0, mu_y0, sigma_x0, sigma_y0, amp0), sse) :
>   non-finite value supplied by optim

This must be self-explanatory: your `sse` function returns something
that is not a real number. Try options(error = recover) to see which
arguments it is given when it fails in such a manner. See the free book
"The R Inferno" for more R debugging tips
. Consider
using the 'optimx' package which contains optimisation algorithms that
might work better for you.

-- 
Best regards,
Ivan

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[R] Problem in R code

[Crown Flame]

Good afternoon,
I have been working on my thesis project on the topic "Urban Heat Island
Pattern in India". To achieve the results I am applying a* two-dimensional
Gaussian fit* on an LST raster of 1 km spatial resolution but I am facing
two errors in the following code.

library(raster)
LST <- raster("D:/Celsius_Day/MOD_01.tif")
gaussian2d <- function(x, y, mu_x, mu_y, sigma_x, sigma_y, amp)
{
  exp(-((x - mu_x)^2/(2*sigma_x^2) + (y - mu_y)^2/(2*sigma_y^2)))*amp
}

#define a function for the sum of squared errors between the data and the
Gaussian
sse <- function(p)
{ mu_x <- p
mu_y <- p
sigma_x <- p
sigma_y <- p
amp <- p[5]
fitted <- gaussian2d(x, y, mu_x, mu_y, sigma_x, sigma_y, amp)
sum((z - fitted)^2)
}

#loop over 8 cities
cities <-
c("Delhi","Jaipur","Kolkata","Mumbai","Pune","Hyderabad","Bangalore","Chennai")
lon <-
c(77.219934,75.793261,88.365394,72.900361,73.875199,78.47476,77.602114,80.192181)
lat <-
c(28.589256,26.892024,22.619754,19.110629,18.50269,17.422973,12.974087,13.044415)
results <- data.frame() #A data frame to store the results
for(i in 1:8)
{
  LST_city <- extract(LST, c(lon[i],lat[i]), fun = mean, buffer = 1,
na.rm = TRUE)   #error
}

# Fit a 2D Gaussian surface to the LST data
x <- coordinates(LST)[,1]
y <- coordinates(LST)[,2]
z <- values(LST)
mu_x0 <- mean(x)
mu_y0 <- mean(y)
sigma_x0 <- sd(x)/2
sigma_y0 <- sd(y)/2
amp0 <- max(z)
opt <- optim(c(mu_x0, mu_y0, sigma_x0, sigma_y0, amp0), sse) #error 2

#Calculate the footprint of SUHI effect (FP) by the Gaussian surface
FP <- which(gaussian2d(x, y, opt$par, opt$par, opt$par, opt$par,
opt$par[5]) >= threshold)

#store the results for each city in the data frame
results <- rbind(results, data.frame(city=cities[i], FP=mean(FP)))

#print the results
results


The two errors are in the row which are defining the variables "LST_city"
and "opt".
The first error is:
Error in .cellValues(x, y, ...) : unused arguments (fun =
new("standardGeneric", .Data = function (x, ...) standardGeneric("mean"),
generic = "mean", package = "base", group = list(), valueClass =
character(0), signature = "x", default = new("derivedDefaultMethod", .Data
= function (x, ...) UseMethod("mean"), target = new("signature", .Data =
"ANY", names = "x", package = "methods"), defined = new("signature", .Data
= "ANY", names = "x", package = "methods"), generic = "mean"), skeleton =
(new("derivedDefaultMethod", .Data = function (x, ...) UseMethod("mean"),
target = new("signature", .Data = "ANY", names = "x", package = "methods"),
defined = new("signature", .Data = "ANY", names = "x", package =
"methods"), generic = "mean"))(x, ...)), buffer = 2, na.rm = TRUE)


The second error is:

Error in optim(c(mu_x0, mu_y0, sigma_x0, sigma_y0, amp0), sse) :
  non-finite value supplied by optim



What could be the possible reason behind these errors and most
importantly how can I get rid of these errors?



Thank you


Regards

DD

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Re: [R] Problem installing R 4.2 on Ubuntu 20-04

[Micha Silver]

Just a guess:


On 25/07/2022 17:43, Witold E Wolski wrote:

I am failing to get R 4 installed on Ubuntu. I am following the
instructions given here:
https://cran.r-project.org/bin/linux/ubuntu/

These are the errors I am getting:

parallels@ubuntu-linux-20-04-desktop:~/Downloads/fragpipe/bin$ sudo
apt install --no-install-recommends r-base


--no-install-recommends might be your problem

Try running without that.


(And also do sudo apt update first)



The following packages have unmet dependencies:
And this is why that --no-install-recommends is causing the install to 
fail:

  r-base : Depends: r-base-core (>= 4.2.1-1.2004.0) but it is not going
to be installed
   Depends: r-recommended (= 4.2.1-1.2004.0) but it is not
going to be installed
E: Unable to correct problems, you have held broken packages.



Best regards
Witek


--
Witold Eryk Wolski

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--
Micha Silver
Ben Gurion Univ.
Sde Boker, Remote Sensing Lab
cell: +972-523-665918

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Re: [R] Problem installing R 4.2 on Ubuntu 20-04

[Bert Gunter]

Better posted on R-sig-debian, I think.

Cheers,
Bert

On Mon, Jul 25, 2022 at 7:44 AM Witold E Wolski  wrote:

> I am failing to get R 4 installed on Ubuntu. I am following the
> instructions given here:
> https://cran.r-project.org/bin/linux/ubuntu/
>
> These are the errors I am getting:
> 
> parallels@ubuntu-linux-20-04-desktop:~/Downloads/fragpipe/bin$ sudo
> apt install --no-install-recommends r-base
> [sudo] password for parallels:
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> Some packages could not be installed. This may mean that you have
> requested an impossible situation or if you are using the unstable
> distribution that some required packages have not yet been created
> or been moved out of Incoming.
> The following information may help to resolve the situation:
>
> The following packages have unmet dependencies:
>  r-base : Depends: r-base-core (>= 4.2.1-1.2004.0) but it is not going
> to be installed
>   Depends: r-recommended (= 4.2.1-1.2004.0) but it is not
> going to be installed
> E: Unable to correct problems, you have held broken packages.
> 
>
>
> This is the tail of the source.lists file:
>
> 
> deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/
> # deb-src https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/
> 
>
> This is the head of executing: apt-cache policy r-base
> 
> arallels@ubuntu-linux-20-04-desktop:~/Downloads/fragpipe/bin$
> apt-cache policy r-base
> r-base:
>   Installed: (none)
>   Candidate: 4.2.1-1.2004.0
>   Version table:
>  4.2.1-1.2004.0 500
> 500 https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/
> Packages
>  4.2.0-1.2004.0 500
> 500 https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/
> Packages
>  4.1.3-1.2004.0 500
> 500 https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/
> Packages
>  4.1.2-1.2004.0 500
>
> 
>
> End this is for executing apt-cache policy r-base-core
>
> 
> parallels@ubuntu-linux-20-04-desktop:~/Downloads/fragpipe/bin$
> apt-cache policy r-base-core
> r-base-core:
>   Installed: (none)
>   Candidate: 3.6.3-2
>   Version table:
>  3.6.3-2 500
> 500 http://ports.ubuntu.com/ubuntu-ports focal/universe arm64
> Packages
> 100 /var/lib/dpkg/status
>
> 
>
> Someone else described the same/similar problem here:
>
>
> https://askubuntu.com/questions/1373827/problems-installing-latest-version-of-r-in-ubuntu-20-04-lts
>
> What step did I miss executing?
>
> Best regards
> Witek
>
>
> --
> Witold Eryk Wolski
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

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Re: [R] problem downloading R

[Abby Spurdle]

This was quite some time ago.
Namely, 2019.

At the time, I was using a mix of old Windows 8 and 9 computers.
The problem happened on Windows 8, but not Windows 9.

Note that I was trying to help the OP.
Beyond that, I'm not concerned about it.


On Fri, Mar 5, 2021 at 9:30 PM Uwe Ligges
 wrote:
>
> Sounds like you always got corrupted vesions. Either an issue with your
> connection or the mirror. What happens if you try another mirror and
> clear your browser caches?
>
> Best,
> Uwe Ligges
>
> On 05.03.2021 08:58, Abby Spurdle wrote:
> > Does the following sound familiar?
> >
> > The Windows installer starts installing (or decompressing) R, flashing
> > one file name at a time.
> > And then, part way through, says  file is corrupt, and gives you
> > the choice to ignore.
> > And if you click ignore, then the next file does the same thing.
> > And one quickly realizes, that every subsequent file will have the same 
> > message.
> >
> > Then if you re-download the installation file, the same thing happens.
> > Except that the first file flagged as corrupted, is not necessarily
> > the same file.
> >
> >
> > On Fri, Mar 5, 2021 at 5:55 AM Dick Mathews  
> > wrote:
> >>
> >> I am trying to download the Windows version of R. This computer is Win7,
> >> I do have Win10 computers also.
> >>
> >> Tried R4.0.4, got message these files are corrupted.
> >>
> >> Then tried R4.0.3, got same message as above.
> >>
> >> Tried the next, R4.0.2, got same message.
> >>
> >> I checked to see if I was downloading the proper version, seems okay.
> >>
> >> What is the problem? Can anybody help me with this?
> >>
> >> Dick Mathews
> >>
> >> __
> >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide 
> >> http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem downloading R

[Uwe Ligges]

Sounds like you always got corrupted vesions. Either an issue with your 
connection or the mirror. What happens if you try another mirror and 
clear your browser caches?


Best,
Uwe Ligges

On 05.03.2021 08:58, Abby Spurdle wrote:

Does the following sound familiar?

The Windows installer starts installing (or decompressing) R, flashing
one file name at a time.
And then, part way through, says  file is corrupt, and gives you
the choice to ignore.
And if you click ignore, then the next file does the same thing.
And one quickly realizes, that every subsequent file will have the same message.

Then if you re-download the installation file, the same thing happens.
Except that the first file flagged as corrupted, is not necessarily
the same file.


On Fri, Mar 5, 2021 at 5:55 AM Dick Mathews  wrote:


I am trying to download the Windows version of R. This computer is Win7,
I do have Win10 computers also.

Tried R4.0.4, got message these files are corrupted.

Then tried R4.0.3, got same message as above.

Tried the next, R4.0.2, got same message.

I checked to see if I was downloading the proper version, seems okay.

What is the problem? Can anybody help me with this?

Dick Mathews

__
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and provide commented, minimal, self-contained, reproducible code.


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and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem downloading R

[Abby Spurdle]

Does the following sound familiar?

The Windows installer starts installing (or decompressing) R, flashing
one file name at a time.
And then, part way through, says  file is corrupt, and gives you
the choice to ignore.
And if you click ignore, then the next file does the same thing.
And one quickly realizes, that every subsequent file will have the same message.

Then if you re-download the installation file, the same thing happens.
Except that the first file flagged as corrupted, is not necessarily
the same file.


On Fri, Mar 5, 2021 at 5:55 AM Dick Mathews  wrote:
>
> I am trying to download the Windows version of R. This computer is Win7,
> I do have Win10 computers also.
>
> Tried R4.0.4, got message these files are corrupted.
>
> Then tried R4.0.3, got same message as above.
>
> Tried the next, R4.0.2, got same message.
>
> I checked to see if I was downloading the proper version, seems okay.
>
> What is the problem? Can anybody help me with this?
>
> Dick Mathews
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem downloading R

[Duncan Murdoch]

On 04/03/2021 11:02 a.m., Dick Mathews wrote:

I am trying to download the Windows version of R. This computer is Win7,
I do have Win10 computers also.

Tried R4.0.4, got message these files are corrupted.

Then tried R4.0.3, got same message as above.

Tried the next, R4.0.2, got same message.

I checked to see if I was downloading the proper version, seems okay.

What is the problem? Can anybody help me with this?


Which mirror are you using?  I'd recommend using cloud.r-project.org . 
If you get the same problem on that mirror, then you've likely got 
something interfering with your download.  You could try using a 
different machine to download, and install from a USB stick or some 
other non-network method.


Duncan Murdoch

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Re: [R] problem downloading R

[Jeff Newmiller]

Not much. Try a different mirror site. Try disabling anti-virus download 
filters. If you are using a cloud-backed directory like OneDrive, try 
downloading and installing on a standard local disk.

On March 4, 2021 8:02:43 AM PST, Dick Mathews  wrote:
>I am trying to download the Windows version of R. This computer is
>Win7, 
>I do have Win10 computers also.
>
>Tried R4.0.4, got message these files are corrupted.
>
>Then tried R4.0.3, got same message as above.
>
>Tried the next, R4.0.2, got same message.
>
>I checked to see if I was downloading the proper version, seems okay.
>
>What is the problem? Can anybody help me with this?
>
>Dick Mathews
>
>__
>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

-- 
Sent from my phone. Please excuse my brevity.

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] problem downloading R

[Dick Mathews]

I am trying to download the Windows version of R. This computer is Win7, 
I do have Win10 computers also.


Tried R4.0.4, got message these files are corrupted.

Then tried R4.0.3, got same message as above.

Tried the next, R4.0.2, got same message.

I checked to see if I was downloading the proper version, seems okay.

What is the problem? Can anybody help me with this?

Dick Mathews

__
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem installing R and RStudio

[Carlos Gonzalez]

Thank you @LucyNjoki!!! Everything runs ok now.

El mar, 26 de ene. de 2021 a la(s) 16:51, John Kane (jrkrid...@gmail.com)
escribió:

> A couple of Window solutions
>
> https://community.rstudio.com/t/problems-with-r-4-0-0-windows-error-package-or-namespace-load-failed-for-stats-in-indl-x-as-logical-local-as-logical-now/62958
>
> https://github.com/rdotnet/rdotnet/issues/62
>
> No idea if they are of any use.
>
> On Mon, 25 Jan 2021 at 19:43, Jeff Newmiller 
> wrote:
>
>> Your installation of R seems broken. Since RStudio sometimes tries to
>> simplify things and sometimes misses and we aren't typically up to speed
>> with their latest procedures, please describe what you did to install R in
>> terms related to the instructions on CRAN [1] and its install program. When
>> you can run R from RGui or the CMD prompt then you may get lucky and
>> RStudio will just work. If you aren't lucky connecting your working R to
>> RStudio  then you will probably need to ask them [2] for assistance.
>>
>> Also, the Posting Guide points out that this is a plain text mailing
>> list... sending HTML email through this list is erratic... if you want to
>> insure we get your message as you sent it, set your email client to send
>> plain text format.
>>
>> [1] https://cran.r-project.org/bin/windows/base/
>> [2] https://community.rstudio.com/
>>
>> On January 25, 2021 2:40:45 PM PST, Carlos Gonzalez 
>> wrote:
>> >Dear,
>> >
>> >I've just installed R and RStudio. Opening RStudio the following
>> >appears in
>> >the console.
>> >
>> >
>> >R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
>> >Copyright (C) 2020 The R Foundation for Statistical Computing
>> >Platform: x86_64-w64-mingw32/x64 (64-bit)
>> >
>> >R is free software and comes with ABSOLUTELY NO WARRANTY.
>> >You are welcome to redistribute it under certain conditions.
>> >Type 'license()' or 'licence()' for distribution details.
>> >
>> >  Natural language support but running in an English locale
>> >
>> >R is a collaborative project with many contributors.
>> >Type 'contributors()' for more information and
>> >'citation()' on how to cite R or R packages in publications.
>> >
>> >Type 'demo()' for some demos, 'help()' for on-line help, or
>> >'help.start()' for an HTML browser interface to help.
>> >Type 'q()' to quit R.
>> >
>> >Error: package or namespace load failed for ‘stats’ in inDL(x,
>> >as.logical(local), as.logical(now), ...):
>> > unable to load shared object 'C:/Program
>> >Files/R/R-4.0.3/library/stats/libs/x64/stats.dll':
>> >  LoadLibrary failure:  The specified module could not be found.
>> >
>> >During startup - Warning message:
>> >package ‘stats’ in options("defaultPackages") was not found
>> >Error in inDL(x, as.logical(local), as.logical(now), ...) :
>> >  unable to load shared object 'C:/Program
>> >Files/R/R-4.0.3/library/stats/libs/x64/stats.dll':
>> >  LoadLibrary failure:  The specified module could not be found.
>> >>
>> >I would very much appreciate it if you could help solving this problem.
>> >
>> >Saludos / Regards
>> >
>> >Carlos A. Gonzalez
>> >Mobile +598 94 234 653
>> >cag...@gmail.com
>> >
>> >   [[alternative HTML version deleted]]
>> >
>> >__
>> >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> >https://stat.ethz.ch/mailman/listinfo/r-help
>> >PLEASE do read the posting guide
>> >http://www.R-project.org/posting-guide.html
>> >and provide commented, minimal, self-contained, reproducible code.
>>
>> --
>> Sent from my phone. Please excuse my brevity.
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
> --
> John Kane
> Kingston ON Canada
>


-- 
Saludos / Regards

Carlos A. Gonzalez
Mobile +598 94 234 653
cag...@gmail.com

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem installing R and RStudio

[John Kane]

A couple of Window solutions
https://community.rstudio.com/t/problems-with-r-4-0-0-windows-error-package-or-namespace-load-failed-for-stats-in-indl-x-as-logical-local-as-logical-now/62958

https://github.com/rdotnet/rdotnet/issues/62

No idea if they are of any use.

On Mon, 25 Jan 2021 at 19:43, Jeff Newmiller 
wrote:

> Your installation of R seems broken. Since RStudio sometimes tries to
> simplify things and sometimes misses and we aren't typically up to speed
> with their latest procedures, please describe what you did to install R in
> terms related to the instructions on CRAN [1] and its install program. When
> you can run R from RGui or the CMD prompt then you may get lucky and
> RStudio will just work. If you aren't lucky connecting your working R to
> RStudio  then you will probably need to ask them [2] for assistance.
>
> Also, the Posting Guide points out that this is a plain text mailing
> list... sending HTML email through this list is erratic... if you want to
> insure we get your message as you sent it, set your email client to send
> plain text format.
>
> [1] https://cran.r-project.org/bin/windows/base/
> [2] https://community.rstudio.com/
>
> On January 25, 2021 2:40:45 PM PST, Carlos Gonzalez 
> wrote:
> >Dear,
> >
> >I've just installed R and RStudio. Opening RStudio the following
> >appears in
> >the console.
> >
> >
> >R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
> >Copyright (C) 2020 The R Foundation for Statistical Computing
> >Platform: x86_64-w64-mingw32/x64 (64-bit)
> >
> >R is free software and comes with ABSOLUTELY NO WARRANTY.
> >You are welcome to redistribute it under certain conditions.
> >Type 'license()' or 'licence()' for distribution details.
> >
> >  Natural language support but running in an English locale
> >
> >R is a collaborative project with many contributors.
> >Type 'contributors()' for more information and
> >'citation()' on how to cite R or R packages in publications.
> >
> >Type 'demo()' for some demos, 'help()' for on-line help, or
> >'help.start()' for an HTML browser interface to help.
> >Type 'q()' to quit R.
> >
> >Error: package or namespace load failed for ‘stats’ in inDL(x,
> >as.logical(local), as.logical(now), ...):
> > unable to load shared object 'C:/Program
> >Files/R/R-4.0.3/library/stats/libs/x64/stats.dll':
> >  LoadLibrary failure:  The specified module could not be found.
> >
> >During startup - Warning message:
> >package ‘stats’ in options("defaultPackages") was not found
> >Error in inDL(x, as.logical(local), as.logical(now), ...) :
> >  unable to load shared object 'C:/Program
> >Files/R/R-4.0.3/library/stats/libs/x64/stats.dll':
> >  LoadLibrary failure:  The specified module could not be found.
> >>
> >I would very much appreciate it if you could help solving this problem.
> >
> >Saludos / Regards
> >
> >Carlos A. Gonzalez
> >Mobile +598 94 234 653
> >cag...@gmail.com
> >
> >   [[alternative HTML version deleted]]
> >
> >__
> >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >https://stat.ethz.ch/mailman/listinfo/r-help
> >PLEASE do read the posting guide
> >http://www.R-project.org/posting-guide.html
> >and provide commented, minimal, self-contained, reproducible code.
>
> --
> Sent from my phone. Please excuse my brevity.
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
John Kane
Kingston ON Canada

[[alternative HTML version deleted]]

__
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem installing R and RStudio

[Jeff Newmiller]

Your installation of R seems broken. Since RStudio sometimes tries to simplify 
things and sometimes misses and we aren't typically up to speed with their 
latest procedures, please describe what you did to install R in terms related 
to the instructions on CRAN [1] and its install program. When you can run R 
from RGui or the CMD prompt then you may get lucky and RStudio will just work. 
If you aren't lucky connecting your working R to RStudio  then you will 
probably need to ask them [2] for assistance.

Also, the Posting Guide points out that this is a plain text mailing list... 
sending HTML email through this list is erratic... if you want to insure we get 
your message as you sent it, set your email client to send plain text format.

[1] https://cran.r-project.org/bin/windows/base/
[2] https://community.rstudio.com/

On January 25, 2021 2:40:45 PM PST, Carlos Gonzalez  wrote:
>Dear,
>
>I've just installed R and RStudio. Opening RStudio the following
>appears in
>the console.
>
>
>R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
>Copyright (C) 2020 The R Foundation for Statistical Computing
>Platform: x86_64-w64-mingw32/x64 (64-bit)
>
>R is free software and comes with ABSOLUTELY NO WARRANTY.
>You are welcome to redistribute it under certain conditions.
>Type 'license()' or 'licence()' for distribution details.
>
>  Natural language support but running in an English locale
>
>R is a collaborative project with many contributors.
>Type 'contributors()' for more information and
>'citation()' on how to cite R or R packages in publications.
>
>Type 'demo()' for some demos, 'help()' for on-line help, or
>'help.start()' for an HTML browser interface to help.
>Type 'q()' to quit R.
>
>Error: package or namespace load failed for ‘stats’ in inDL(x,
>as.logical(local), as.logical(now), ...):
> unable to load shared object 'C:/Program
>Files/R/R-4.0.3/library/stats/libs/x64/stats.dll':
>  LoadLibrary failure:  The specified module could not be found.
>
>During startup - Warning message:
>package ‘stats’ in options("defaultPackages") was not found
>Error in inDL(x, as.logical(local), as.logical(now), ...) :
>  unable to load shared object 'C:/Program
>Files/R/R-4.0.3/library/stats/libs/x64/stats.dll':
>  LoadLibrary failure:  The specified module could not be found.
>>
>I would very much appreciate it if you could help solving this problem.
>
>Saludos / Regards
>
>Carlos A. Gonzalez
>Mobile +598 94 234 653
>cag...@gmail.com
>
>   [[alternative HTML version deleted]]
>
>__
>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

-- 
Sent from my phone. Please excuse my brevity.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] problem installing R and RStudio

[Carlos Gonzalez]

Dear,

I've just installed R and RStudio. Opening RStudio the following appears in
the console.


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Error: package or namespace load failed for ‘stats’ in inDL(x,
as.logical(local), as.logical(now), ...):
 unable to load shared object 'C:/Program
Files/R/R-4.0.3/library/stats/libs/x64/stats.dll':
  LoadLibrary failure:  The specified module could not be found.

During startup - Warning message:
package ‘stats’ in options("defaultPackages") was not found
Error in inDL(x, as.logical(local), as.logical(now), ...) :
  unable to load shared object 'C:/Program
Files/R/R-4.0.3/library/stats/libs/x64/stats.dll':
  LoadLibrary failure:  The specified module could not be found.
>
I would very much appreciate it if you could help solving this problem.

Saludos / Regards

Carlos A. Gonzalez
Mobile +598 94 234 653
cag...@gmail.com

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem reading R files

[David Winsemius]

> On Apr 19, 2018, at 11:21 PM, Jack Frazer  wrote:
> 
> Dear R Developers,
> 
> I hope this email finds you well.
> 
> As a newcomer to the world of R, I'm trying different exercises. In my way,
> I faced with some, seemingly, trivial problems but there is not any
> response for that around the web. So, I thought can get help from you.
> Specifically, in tutorial presented at http://www.rdatamining.com/doc
> s/twitter-analysis-with-r,  I faced with a problem on using OAuth. When I
> use the first approach, the following error will be occurred:
> 
> [1] "Using browser based authentication"
> Error in curl::curl_fetch_memory(url, handle = handle) :
>  Failed to connect to api.twitter.com port 443: Connection refused

Looks like you have not obtained a proper Twitter account and obtained a valid 
registration code to use the API. That should have been covered in your course 
materials. 

> And when it comes to the second approach,

... the second approach? We are expected to work through that tutorial for you?

> the following error rises:
> 
> [1] "Using direct authentication"
> Error in check_twitter_oauth() : OAuth authentication error:
> This most likely means that you have incorrectly called
> setup_twitter_oauth()'
> 

Same issue most likely?

> Unfortunately, the online resources could not help. For example, all the
> solutions introduced in StackOverflow could not work for me.
> 
> https://stackoverflow.com/questions/31128492/twitter-setup-t
> witter-oauth-failing
> 
> *Moreover, in reading data from the current directory, the readRDS method
> sucks*.

Generally use of such a description will be viewed as at best useless and at 
worst offensive.

> I got same error using import() in rio package.


> 
> https://stackoverflow.com/questions/49908803/error-in-reading-files-in-r

That posting describes entirely different issue. The first issue was that the 
file wasn't where you thought it was and the second error message that you 
posted in comments said it was the wrong format for the readRDS function.

There are two files with that name listed on the website and only one of them 
loads properly with readRDS.

 
> 
> So, please  let me know if you have some solution for the issues.
> 
> Thanks for your consideration.
> 
> Regards,
> 
> Jack
> 
>   [[alternative HTML version deleted]]

Jack, you really should read the Posting Guide.

> 
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Problem reading R files

[Jack Frazer]

 Dear R Developers,

I hope this email finds you well.

As a newcomer to the world of R, I'm trying different exercises. In my way,
I faced with some, seemingly, trivial problems but there is not any
response for that around the web. So, I thought can get help from you.
Specifically, in tutorial presented at http://www.rdatamining.com/doc
s/twitter-analysis-with-r,  I faced with a problem on using OAuth. When I
use the first approach, the following error will be occurred:

[1] "Using browser based authentication"
Error in curl::curl_fetch_memory(url, handle = handle) :
  Failed to connect to api.twitter.com port 443: Connection refused


And when it comes to the second approach, the following error rises:

[1] "Using direct authentication"
Error in check_twitter_oauth() : OAuth authentication error:
This most likely means that you have incorrectly called
setup_twitter_oauth()'

Unfortunately, the online resources could not help. For example, all the
solutions introduced in StackOverflow could not work for me.

https://stackoverflow.com/questions/31128492/twitter-setup-t
witter-oauth-failing

*Moreover, in reading data from the current directory, the readRDS method
sucks*. I got same error using import() in rio package.

https://stackoverflow.com/questions/49908803/error-in-reading-files-in-r

So, please  let me know if you have some solution for the issues.

Thanks for your consideration.

Regards,

Jack

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem with r project in ubuntu xenial

[Ista Zahn]

On Tue, Nov 7, 2017 at 6:46 PM, George Balas <gbala...@gmail.com> wrote:
> For anyone who sees this conversation.
>
> There is a bug in installation of igraph in R language in Ubuntu. There is
> a solution in stackoverflow.

A link would be nice.

 We have to use the devtools. Write this code:
> install.packages("devtools")
> library(devtools)
> install_github("igraph/rigraph")

This is a temporary work-around that is only needed until igraph is
updated in CRAN. The bug report is at
https://github.com/igraph/rigraph/issues/234

>
> If there are errors installing devtools just install any package that
> comments.

I don't follow this part.

Best,
Ista

>
> On Nov 5, 2017 00:07, "George Balas" <gbala...@gmail.com> wrote:
>
>> -Well it seems that it is getting "el_GR.UTF-8" but still I am not able
>> to read files written in greek, there are only "" instead of letters.
>> -Also, I forgot to mention that I do load igraph library when I try 
>> "graph_from_adjacency_matrix".
>> When I check igraph in packages dialog I can not see functions with
>> underscores between words, only dots.
>>
>> 2017-11-04 2:22 GMT+02:00 David Winsemius <dwinsem...@comcast.net>:
>>
>>>
>>> > On Nov 3, 2017, at 5:09 PM, peter dalgaard <pda...@gmail.com> wrote:
>>> >
>>> >
>>> >> On 3 Nov 2017, at 23:39 , George Balas <gbala...@gmail.com> wrote:
>>> >>
>>> >> I have a problem with R in Ubuntu 16.04. I do not know if it is mine
>>> pc or
>>> >> general problem but I was not able to find solution on Internet.
>>> >> First of all I can not change locale to greek by getting this message:
>>> >> "In Sys.setlocale("LC_CTYPE", "Greek") :
>>> >> OS reports request to set locale to "Greek" cannot be honored"
>>> >
>>> > The Greek locale is likely not called "Greek" outside of Windows. More
>>> likely "el_GR.UTF-8" or thereabouts (check your locale database, I'm on a
>>> Mac). These things are not standardized across platforms.
>>> >
>>>
>>> Also
>>>
>>> From help(locales): Attempts to change the character set by
>>> Sys.setlocale("LC_CTYPE") that implies a different character set during a
>>> session may not work and are likely to lead to some confusion because it
>>> may not affect the native encoding.
>>>
>>>
>>> >> Second and more serious is that I can not use some functions like
>>> >> graph_from_adjacency_matrix or print_all I get these messeges:
>>> >> "could not find function "graph_from_adjacency_matrix""
>>> >> "could not find function "print_all"".
>>> >
>>> > Missing library(igraph)?
>>> >
>>> > -pd
>>> >
>>> >> I am using R version 3.4.2 (2017-09-28) -- "Short Summer" either on
>>> rstudio
>>> >> or ubuntu terminal.
>>> >> On my pc I also run win 10 with the same installs and I do not have the
>>> >> above problems, but I work on ubuntu and can not change Os all the
>>> time.
>>> >> Please help me.
>>> >>
>>> >> Thank you for your time,
>>> >> George
>>> >> gbala...@gmail.com
>>> >>
>>> >>  [[alternative HTML version deleted]]
>>> >>
>>> >> __
>>> >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> >> https://stat.ethz.ch/mailman/listinfo/r-help
>>> >> PLEASE do read the posting guide http://www.R-project.org/posti
>>> ng-guide.html
>>> >> and provide commented, minimal, self-contained, reproducible code.
>>> >
>>> > --
>>> > Peter Dalgaard, Professor,
>>> > Center for Statistics, Copenhagen Business School
>>> > Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>>> > Phone: (+45)38153501
>>> > Office: A 4.23
>>> > Email: pd@cbs.dk  Priv: pda...@gmail.com
>>> >
>>> > __
>>> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> > https://stat.ethz.ch/mailman/listinfo/r-help
>>> > PLEASE do read the posting guide http://www.R-project.org/posti
>>> ng-guide.html
>>> > and provide commented, minimal, self-contained, reproducible code.
>>>
>>> David Winsemius
>>> Alameda, CA, USA
>>>
>>> 'Any technology distinguishable from magic is insufficiently advanced.'
>>>  -Gehm's Corollary to Clarke's Third Law
>>>
>>>
>>>
>>>
>>>
>>>
>>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem with r project in ubuntu xenial

[David Winsemius]

> On Nov 7, 2017, at 3:46 PM, George Balas <gbala...@gmail.com> wrote:
> 
> For anyone who sees this conversation.
> 
> There is a bug in installation of igraph in R language in Ubuntu. There is
> a solution in stackoverflow. We have to use the devtools. Write this code:
> install.packages("devtools")
> library(devtools)
> install_github("igraph/rigraph")

If there is a bug in the development version of igraph (which is not really 
part of R but rather a contributed package) then the correct place to send a 
message would have been, not to rhelp, but rather to the maintainer. It would 
of course be necessary to say what the bug appears to be. I don't see any error 
message or description of a bug in this message. The package DESCRIPTION files 
says:

BugReports: https://github.com/igraph/igraph/issues

The github page says the proper installation sequence for the development 
version is:

devtools::install_github("gaborcsardi/pkgconfig")
devtools::install_github("igraph/rigraph")

Rhelp is not the correct place for pre-release bug discussion of contributed 
packages.

Again, the github pages suggests that you send issues to the correct mailing 
list: igraph-help mailing list

https://lists.nongnu.org/mailman/listinfo/igraph-help


-- 
David.
> 
> If there are errors installing devtools just install any package that
> comments.
> 
> On Nov 5, 2017 00:07, "George Balas" <gbala...@gmail.com> wrote:
> 
>> -Well it seems that it is getting "el_GR.UTF-8" but still I am not able
>> to read files written in greek, there are only "" instead of letters.
>> -Also, I forgot to mention that I do load igraph library when I try 
>> "graph_from_adjacency_matrix".
>> When I check igraph in packages dialog I can not see functions with
>> underscores between words, only dots.
>> 
>> 2017-11-04 2:22 GMT+02:00 David Winsemius <dwinsem...@comcast.net>:
>> 
>>> 
>>>> On Nov 3, 2017, at 5:09 PM, peter dalgaard <pda...@gmail.com> wrote:
>>>> 
>>>> 
>>>>> On 3 Nov 2017, at 23:39 , George Balas <gbala...@gmail.com> wrote:
>>>>> 
>>>>> I have a problem with R in Ubuntu 16.04. I do not know if it is mine
>>> pc or
>>>>> general problem but I was not able to find solution on Internet.
>>>>> First of all I can not change locale to greek by getting this message:
>>>>> "In Sys.setlocale("LC_CTYPE", "Greek") :
>>>>> OS reports request to set locale to "Greek" cannot be honored"
>>>> 
>>>> The Greek locale is likely not called "Greek" outside of Windows. More
>>> likely "el_GR.UTF-8" or thereabouts (check your locale database, I'm on a
>>> Mac). These things are not standardized across platforms.
>>>> 
>>> 
>>> Also
>>> 
>>> From help(locales): Attempts to change the character set by
>>> Sys.setlocale("LC_CTYPE") that implies a different character set during a
>>> session may not work and are likely to lead to some confusion because it
>>> may not affect the native encoding.
>>> 
>>> 
>>>>> Second and more serious is that I can not use some functions like
>>>>> graph_from_adjacency_matrix or print_all I get these messeges:
>>>>> "could not find function "graph_from_adjacency_matrix""
>>>>> "could not find function "print_all"".
>>>> 
>>>> Missing library(igraph)?
>>>> 
>>>> -pd
>>>> 
>>>>> I am using R version 3.4.2 (2017-09-28) -- "Short Summer" either on
>>> rstudio
>>>>> or ubuntu terminal.
>>>>> On my pc I also run win 10 with the same installs and I do not have the
>>>>> above problems, but I work on ubuntu and can not change Os all the
>>> time.
>>>>> Please help me.
>>>>> 
>>>>> Thank you for your time,
>>>>> George
>>>>> gbala...@gmail.com
>>>>> 
>>>>> [[alternative HTML version deleted]]
>>>>> 
>>>>> __
>>>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>> PLEASE do read the posting guide http://www.R-project.org/posti
>>> ng-guide.html
>>>>> and provide commented, minimal, self-contained, reproduc

Re: [R] Problem with r project in ubuntu xenial

[George Balas]

For anyone who sees this conversation.

There is a bug in installation of igraph in R language in Ubuntu. There is
a solution in stackoverflow. We have to use the devtools. Write this code:
install.packages("devtools")
library(devtools)
install_github("igraph/rigraph")

If there are errors installing devtools just install any package that
comments.

On Nov 5, 2017 00:07, "George Balas" <gbala...@gmail.com> wrote:

> -Well it seems that it is getting "el_GR.UTF-8" but still I am not able
> to read files written in greek, there are only "" instead of letters.
> -Also, I forgot to mention that I do load igraph library when I try 
> "graph_from_adjacency_matrix".
> When I check igraph in packages dialog I can not see functions with
> underscores between words, only dots.
>
> 2017-11-04 2:22 GMT+02:00 David Winsemius <dwinsem...@comcast.net>:
>
>>
>> > On Nov 3, 2017, at 5:09 PM, peter dalgaard <pda...@gmail.com> wrote:
>> >
>> >
>> >> On 3 Nov 2017, at 23:39 , George Balas <gbala...@gmail.com> wrote:
>> >>
>> >> I have a problem with R in Ubuntu 16.04. I do not know if it is mine
>> pc or
>> >> general problem but I was not able to find solution on Internet.
>> >> First of all I can not change locale to greek by getting this message:
>> >> "In Sys.setlocale("LC_CTYPE", "Greek") :
>> >> OS reports request to set locale to "Greek" cannot be honored"
>> >
>> > The Greek locale is likely not called "Greek" outside of Windows. More
>> likely "el_GR.UTF-8" or thereabouts (check your locale database, I'm on a
>> Mac). These things are not standardized across platforms.
>> >
>>
>> Also
>>
>> From help(locales): Attempts to change the character set by
>> Sys.setlocale("LC_CTYPE") that implies a different character set during a
>> session may not work and are likely to lead to some confusion because it
>> may not affect the native encoding.
>>
>>
>> >> Second and more serious is that I can not use some functions like
>> >> graph_from_adjacency_matrix or print_all I get these messeges:
>> >> "could not find function "graph_from_adjacency_matrix""
>> >> "could not find function "print_all"".
>> >
>> > Missing library(igraph)?
>> >
>> > -pd
>> >
>> >> I am using R version 3.4.2 (2017-09-28) -- "Short Summer" either on
>> rstudio
>> >> or ubuntu terminal.
>> >> On my pc I also run win 10 with the same installs and I do not have the
>> >> above problems, but I work on ubuntu and can not change Os all the
>> time.
>> >> Please help me.
>> >>
>> >> Thank you for your time,
>> >> George
>> >> gbala...@gmail.com
>> >>
>> >>  [[alternative HTML version deleted]]
>> >>
>> >> __
>> >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> >> https://stat.ethz.ch/mailman/listinfo/r-help
>> >> PLEASE do read the posting guide http://www.R-project.org/posti
>> ng-guide.html
>> >> and provide commented, minimal, self-contained, reproducible code.
>> >
>> > --
>> > Peter Dalgaard, Professor,
>> > Center for Statistics, Copenhagen Business School
>> > Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> > Phone: (+45)38153501
>> > Office: A 4.23
>> > Email: pd@cbs.dk  Priv: pda...@gmail.com
>> >
>> > __
>> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide http://www.R-project.org/posti
>> ng-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>>
>> David Winsemius
>> Alameda, CA, USA
>>
>> 'Any technology distinguishable from magic is insufficiently advanced.'
>>  -Gehm's Corollary to Clarke's Third Law
>>
>>
>>
>>
>>
>>
>

[[alternative HTML version deleted]]

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem with r project in ubuntu xenial

[George Balas]

-Well it seems that it is getting "el_GR.UTF-8" but still I am not able to
read files written in greek, there are only "" instead of letters.
-Also, I forgot to mention that I do load igraph library when I try
"graph_from_adjacency_matrix".
When I check igraph in packages dialog I can not see functions with
underscores between words, only dots.

2017-11-04 2:22 GMT+02:00 David Winsemius <dwinsem...@comcast.net>:

>
> > On Nov 3, 2017, at 5:09 PM, peter dalgaard <pda...@gmail.com> wrote:
> >
> >
> >> On 3 Nov 2017, at 23:39 , George Balas <gbala...@gmail.com> wrote:
> >>
> >> I have a problem with R in Ubuntu 16.04. I do not know if it is mine pc
> or
> >> general problem but I was not able to find solution on Internet.
> >> First of all I can not change locale to greek by getting this message:
> >> "In Sys.setlocale("LC_CTYPE", "Greek") :
> >> OS reports request to set locale to "Greek" cannot be honored"
> >
> > The Greek locale is likely not called "Greek" outside of Windows. More
> likely "el_GR.UTF-8" or thereabouts (check your locale database, I'm on a
> Mac). These things are not standardized across platforms.
> >
>
> Also
>
> From help(locales): Attempts to change the character set by
> Sys.setlocale("LC_CTYPE") that implies a different character set during a
> session may not work and are likely to lead to some confusion because it
> may not affect the native encoding.
>
>
> >> Second and more serious is that I can not use some functions like
> >> graph_from_adjacency_matrix or print_all I get these messeges:
> >> "could not find function "graph_from_adjacency_matrix""
> >> "could not find function "print_all"".
> >
> > Missing library(igraph)?
> >
> > -pd
> >
> >> I am using R version 3.4.2 (2017-09-28) -- "Short Summer" either on
> rstudio
> >> or ubuntu terminal.
> >> On my pc I also run win 10 with the same installs and I do not have the
> >> above problems, but I work on ubuntu and can not change Os all the time.
> >> Please help me.
> >>
> >> Thank you for your time,
> >> George
> >> gbala...@gmail.com
> >>
> >>  [[alternative HTML version deleted]]
> >>
> >> __
> >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >
> > --
> > Peter Dalgaard, Professor,
> > Center for Statistics, Copenhagen Business School
> > Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> > Phone: (+45)38153501
> > Office: A 4.23
> > Email: pd@cbs.dk  Priv: pda...@gmail.com
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius
> Alameda, CA, USA
>
> 'Any technology distinguishable from magic is insufficiently advanced.'
>  -Gehm's Corollary to Clarke's Third Law
>
>
>
>
>
>

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem with r project in ubuntu xenial

[David Winsemius]

> On Nov 3, 2017, at 5:09 PM, peter dalgaard <pda...@gmail.com> wrote:
> 
> 
>> On 3 Nov 2017, at 23:39 , George Balas <gbala...@gmail.com> wrote:
>> 
>> I have a problem with R in Ubuntu 16.04. I do not know if it is mine pc or
>> general problem but I was not able to find solution on Internet.
>> First of all I can not change locale to greek by getting this message:
>> "In Sys.setlocale("LC_CTYPE", "Greek") :
>> OS reports request to set locale to "Greek" cannot be honored"
> 
> The Greek locale is likely not called "Greek" outside of Windows. More likely 
> "el_GR.UTF-8" or thereabouts (check your locale database, I'm on a Mac). 
> These things are not standardized across platforms.
> 

Also

>From help(locales): Attempts to change the character set by 
>Sys.setlocale("LC_CTYPE") that implies a different character set during a 
>session may not work and are likely to lead to some confusion because it may 
>not affect the native encoding.


>> Second and more serious is that I can not use some functions like
>> graph_from_adjacency_matrix or print_all I get these messeges:
>> "could not find function "graph_from_adjacency_matrix""
>> "could not find function "print_all"".
> 
> Missing library(igraph)?
> 
> -pd
> 
>> I am using R version 3.4.2 (2017-09-28) -- "Short Summer" either on rstudio
>> or ubuntu terminal.
>> On my pc I also run win 10 with the same installs and I do not have the
>> above problems, but I work on ubuntu and can not change Os all the time.
>> Please help me.
>> 
>> Thank you for your time,
>> George
>> gbala...@gmail.com
>> 
>>  [[alternative HTML version deleted]]
>> 
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> 
> -- 
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd@cbs.dk  Priv: pda...@gmail.com
> 
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.'   
-Gehm's Corollary to Clarke's Third Law

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem with r project in ubuntu xenial

[peter dalgaard]

> On 3 Nov 2017, at 23:39 , George Balas <gbala...@gmail.com> wrote:
> 
> I have a problem with R in Ubuntu 16.04. I do not know if it is mine pc or
> general problem but I was not able to find solution on Internet.
> First of all I can not change locale to greek by getting this message:
> "In Sys.setlocale("LC_CTYPE", "Greek") :
>  OS reports request to set locale to "Greek" cannot be honored"

The Greek locale is likely not called "Greek" outside of Windows. More likely 
"el_GR.UTF-8" or thereabouts (check your locale database, I'm on a Mac). These 
things are not standardized across platforms.

> Second and more serious is that I can not use some functions like
> graph_from_adjacency_matrix or print_all I get these messeges:
> "could not find function "graph_from_adjacency_matrix""
> "could not find function "print_all"".

Missing library(igraph)?

-pd

> I am using R version 3.4.2 (2017-09-28) -- "Short Summer" either on rstudio
> or ubuntu terminal.
> On my pc I also run win 10 with the same installs and I do not have the
> above problems, but I work on ubuntu and can not change Os all the time.
> Please help me.
> 
> Thank you for your time,
> George
> gbala...@gmail.com
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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[R] Problem with r project in ubuntu xenial

[George Balas]

I have a problem with R in Ubuntu 16.04. I do not know if it is mine pc or
general problem but I was not able to find solution on Internet.
First of all I can not change locale to greek by getting this message:
"In Sys.setlocale("LC_CTYPE", "Greek") :
  OS reports request to set locale to "Greek" cannot be honored"
Second and more serious is that I can not use some functions like
graph_from_adjacency_matrix or print_all I get these messeges:
"could not find function "graph_from_adjacency_matrix""
"could not find function "print_all"".
I am using R version 3.4.2 (2017-09-28) -- "Short Summer" either on rstudio
or ubuntu terminal.
On my pc I also run win 10 with the same installs and I do not have the
above problems, but I work on ubuntu and can not change Os all the time.
Please help me.

Thank you for your time,
George
gbala...@gmail.com

[[alternative HTML version deleted]]

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Re: [R] problem with R. program

[S Ellison]

> After a run multdrc comment in R program, show warning sign in this
> program. I attached the saving page of the script. I hope you could help me,
> please.

Your model is probably generating negative or zero estimates, resulting in NaN 
when logs are taken.

But multdrc is no longer in drc. Suggest you update the package (current 
version is 3 or so) and use drm instead of multdrc. That is now tolerant off 
very small responses and simply running your model with drm gives (visually) a 
reasonably sensible-looking pair of curves.

Note that you probably no longer need to specify Upper limit and Lower limit, 
though I've not tried omitting them.

S Ellison



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[R] problem with R. program

[AHMAD rahbary]

After a run multdrc comment in R program, show warning sign in this
program. I attached the saving page of the script. I hope you could help
me, please.
Thanks a lot
A. Rahbari

R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.0  (2005-04-18), ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for a HTML browser interface to help.
Type 'q()' to quit R.

> library(drc)
Loading required package: MASS
> library(drc)
> choose.files()
[1] "D:\\R\\EPTC.csv"
> mydata<- read.csv ("D:\\R\\EPTC.csv", sep=",", dec=".", header=TRUE)
> mydata
   Dose Herbicide  Survival
1  0.00EC 100.0
2  1.23EC  89.76064
3  2.46EC  59.84043
4  3.69EC  29.92021
5  4.92EC  33.24468
6  0.00EC 100.0
7  1.23EC  96.55172
8  2.46EC  37.93103
9  3.69EC  30.34483
10 4.92EC  27.58621
11 0.00EC 100.0
12 1.23EC  88.23529
13 2.46EC  50.0
14 3.69EC  37.64706
15 4.92EC  32.35294
16 0.00MC 100.0
17 1.23MC  43.47826
18 2.46MC  52.17391
19 3.69MC  43.47826
20 4.92MC  39.13043
21 0.00MC 100.0
22 1.23MC  61.1
23 2.46MC  16.7
24 3.69MC  33.3
25 4.92MC  38.9
26 0.00MC 100.0
27 1.23MC  81.81818
28 2.46MC  54.54545
29 3.69MC  45.45455
30 4.92MC  31.81818
> mydata1 <- multdrc (Survival ~ Dose, Herbicide, fct = l4(names = c("Slope", 
> "Upper Limit", "Lower Limit", "ED50")), data=mydata)
There were 36 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: NaNs produced in: log(x) 
2: NaNs produced in: log(x) 
3: NaNs produced in: log(x) 
4: NaNs produced in: log(x) 
5: NaNs produced in: log(x) 
6: NaNs produced in: log(x) 
7: NaNs produced in: log(x) 
8: NaNs produced in: log(x) 
9: NaNs produced in: log(x) 
10: NaNs produced in: log(x) 
11: NaNs produced in: log(x) 
12: NaNs produced in: log(x) 
13: NaNs produced in: log(x) 
14: NaNs produced in: log(x) 
15: NaNs produced in: log(x) 
16: NaNs produced in: log(x) 
17: NaNs produced in: log(x) 
18: NaNs produced in: log(x) 
19: NaNs produced in: log(x) 
20: NaNs produced in: log(x) 
21: NaNs produced in: log(x) 
22: NaNs produced in: log(x) 
23: NaNs produced in: log(x) 
24: NaNs produced in: log(x) 
25: NaNs produced in: log(x) 
26: NaNs produced in: log(x) 
27: NaNs produced in: log(x) 
28: NaNs produced in: log(x) 
29: NaNs produced in: log(x) 
30: NaNs produced in: log(x) 
31: NaNs produced in: log(x) 
32: NaNs produced in: log(x) 
33: NaNs produced in: log(x) 
34: NaNs produced in: log(x) 
35: NaNs produced in: log(x) 
36: NaNs produced in: log(x) 
> save.image("C:/Documents and Settings/Spring/Desktop/1.RData")
> 


GraphAppPrintJob.pdf
Description: Adobe PDF document
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Re: [R] Problem installing R 2.12.1 on Mac OS X Yosemite 10.10.5

[Martin Maechler]

> David Winsemius 
> on Wed, 11 Jan 2017 22:45:38 -0800 writes:

>> On Jan 11, 2017, at 10:20 PM, David Winsemius  
wrote:
>> 
>> 
>>> On Jan 11, 2017, at 4:15 PM, Florence Lui  wrote:
>>> 
>>> I'm trying to download version 2.12.1 of R in order for it to be 
compatible
>>> with the version of SPSS I have on my computer (SPSS V. 20), so that I 
can
>>> install the Essentials for R plugin for SPSS.
>>> 
>>> However, when I try to install this version of R, I get a popup saying 
it
>>> can't be installed because it requires Mac OS X 10.5 or higher (see
>>> attached).
>> 
>> I suspect that there is code that does a comparison of the character 
version of your numeric version of OSX and finds that it is less than "10.5" 
since if you do that comparison at your console you will see 
>> 
>>> "10.10" < "10.5"
>> [1] TRUE
>> 
>> 
>>> But I do have a higher operating system--Mac OS X Yosemite
>>> 10.10.5.
>>> 
>>> Any idea what might be wrong?
>> 
>> I suspect this has been discussed with in the past. Search the Archives 
of the R-SIG-Mac mailing list (which would have been the correct place to post 
this question in the first place.) I have vague memory that such a request 
appeared in the not so distant past.

> I think this is the message I remember, but probably encountered it 
during a different search since it cannot be called recent. Peter Dalgaard 
suggests temporarily setting your version to 10.9.

> 
http://markmail.org/message/rl3ym7cjo45gpo5n?q=list:org%2Er-project+spss+version

> 
http://markmail.org/search/?q=list%3Aorg.r-project+spss+version#query:list%3Aorg.r-project%20spss%20version+page:1+mid:rl3ym7cjo45gpo5n+state:results


> Despite being a Mac user of long standing, I had no idea how one would do 
that, but thought a google-search would help:

> 
http://justindaigle.com/blog/2010/02/tutorial-change-mac-os-x-system-version/

> Perhaps the SPSS administration should distribute free copies of their 
software to all of the R-Core, since they seem to expect that R-help should be 
the unpaid support staff for a commercial product.

Well, but don't we all want to reduce unnecessary waste - thinking
of CO2 when burning all those CDs ?
Do you think R core would have any other use for such free copies
but to heat a bit during this cold (northern hemisphere) winter ?

;-)

Martin

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Re: [R] Problem installing R 2.12.1 on Mac OS X Yosemite 10.10.5

[David Winsemius]

> On Jan 11, 2017, at 10:20 PM, David Winsemius  wrote:
> 
> 
>> On Jan 11, 2017, at 4:15 PM, Florence Lui  wrote:
>> 
>> I'm trying to download version 2.12.1 of R in order for it to be compatible
>> with the version of SPSS I have on my computer (SPSS V. 20), so that I can
>> install the Essentials for R plugin for SPSS.
>> 
>> However, when I try to install this version of R, I get a popup saying it
>> can't be installed because it requires Mac OS X 10.5 or higher (see
>> attached).
> 
> I suspect that there is code that does a comparison of the character version 
> of your numeric version of OSX and finds that it is less than "10.5" since if 
> you do that comparison at your console you will see 
> 
>> "10.10" < "10.5"
> [1] TRUE
> 
> 
>> But I do have a higher operating system--Mac OS X Yosemite
>> 10.10.5.
>> 
>> Any idea what might be wrong?
> 
> I suspect this has been discussed with in the past. Search the Archives of 
> the R-SIG-Mac mailing list (which would have been the correct place to post 
> this question in the first place.) I have vague memory that such a request 
> appeared in the not so distant past.

I think this is the message I remember, but probably encountered it during a 
different search since it cannot be called recent. Peter Dalgaard suggests 
temporarily setting your version to 10.9.

http://markmail.org/message/rl3ym7cjo45gpo5n?q=list:org%2Er-project+spss+version

http://markmail.org/search/?q=list%3Aorg.r-project+spss+version#query:list%3Aorg.r-project%20spss%20version+page:1+mid:rl3ym7cjo45gpo5n+state:results


Despite being a Mac user of long standing, I had no idea how one would do that, 
but thought a google-search would help:

http://justindaigle.com/blog/2010/02/tutorial-change-mac-os-x-system-version/

Perhaps the SPSS administration should distribute free copies of their software 
to all of the R-Core, since they seem to expect that R-help should be the 
unpaid support staff for a commercial product.



>> 
>>  [[alternative HTML version deleted]]

And please do read the Posting Guide.
Best;
-- 

David Winsemius
Alameda, CA, USA

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Re: [R] Problem installing R 2.12.1 on Mac OS X Yosemite 10.10.5

[David Winsemius]

> On Jan 11, 2017, at 4:15 PM, Florence Lui  wrote:
> 
> I'm trying to download version 2.12.1 of R in order for it to be compatible
> with the version of SPSS I have on my computer (SPSS V. 20), so that I can
> install the Essentials for R plugin for SPSS.
> 
> However, when I try to install this version of R, I get a popup saying it
> can't be installed because it requires Mac OS X 10.5 or higher (see
> attached).

I suspect that there is code that does a comparison of the character version of 
your numeric version of OSX and finds that it is less than "10.5" since if you 
do that comparison at your console you will see 

> "10.10" < "10.5"
[1] TRUE


> But I do have a higher operating system--Mac OS X Yosemite
> 10.10.5.
> 
> Any idea what might be wrong?

I suspect this has been discussed with in the past. Search the Archives of the 
R-SIG-Mac mailing list (which would have been the correct place to post this 
question in the first place.) I have vague memory that such a request appeared 
in the not so distant past.

-- 
David.




> Thanks for your help!
> -- 
> Florence Lui
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

David Winsemius
Alameda, CA, USA

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[R] Problem installing R 2.12.1 on Mac OS X Yosemite 10.10.5

[Florence Lui]

I'm trying to download version 2.12.1 of R in order for it to be compatible
with the version of SPSS I have on my computer (SPSS V. 20), so that I can
install the Essentials for R plugin for SPSS.

However, when I try to install this version of R, I get a popup saying it
can't be installed because it requires Mac OS X 10.5 or higher (see
attached). But I do have a higher operating system--Mac OS X Yosemite
10.10.5.

Any idea what might be wrong? Thanks for your help!
-- 
Florence Lui

[[alternative HTML version deleted]]

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Re: [R] problem installing R 2.5

[peter dalgaard]

Notice that it is pretty much mandatory to study the Admin manual, e.g.,

https://cran.r-project.org/doc/manuals/r-release/R-admin.html

and its appendices in particular. It is also included in the sources (in .texi 
format). As you are building an old R on a recent OS, some interpolation may be 
required.

-pd

On 08 Nov 2016, at 15:07 , Lentes, Bernd via R-help  
wrote:

> 
> 
>> Hi,
> 
>> I would like to suggest that this discussion be moved to R-SIG-Debian, since
>> this is Linux distribution specific:
> 
>> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
> 
>> You will avail yourself of a more focused audience there as well.
> 
>> Regards,
> 
>> Marc Schwartz
> 
> Ok. I subscribed to that ML and asked there. But if someone here has a 
> further idea
> i would appreciate it.
> 
> Thanks.
> 
> Bernd
> 
> 
> Helmholtz Zentrum Muenchen
> Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)
> Ingolstaedter Landstr. 1
> 85764 Neuherberg
> www.helmholtz-muenchen.de
> Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe
> Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen
> Registergericht: Amtsgericht Muenchen HRB 6466
> USt-IdNr: DE 129521671
> 
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [R] problem installing R 2.5

[Marc Schwartz]

> On Nov 8, 2016, at 7:08 AM, Lentes, Bernd via R-help  
> wrote:
> 
> 
> 
> - Am 8. Nov 2016 um 7:53 schrieb Göran Broström goran.brost...@umu.se:
> 
>> libX11-dev?
>> 
>> Göran
> 
> Hi,
> 
> is already installed:
> 
> i A libx11-dev  - Client-seitige Bibliothek für X11 
> (Entwick
> 
> (ubuntu system)
> 
> 
> Bernd


Hi,

I would like to suggest that this discussion be moved to R-SIG-Debian, since 
this is Linux distribution specific:

  https://stat.ethz.ch/mailman/listinfo/r-sig-debian 


You will avail yourself of a more focused audience there as well.

Regards,

Marc Schwartz


[[alternative HTML version deleted]]

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Re: [R] problem installing R 2.5

[Lentes, Bernd via R-help]

> Hi,

> I would like to suggest that this discussion be moved to R-SIG-Debian, since
> this is Linux distribution specific:

> https://stat.ethz.ch/mailman/listinfo/r-sig-debian

> You will avail yourself of a more focused audience there as well.

> Regards,

> Marc Schwartz

Ok. I subscribed to that ML and asked there. But if someone here has a further 
idea
i would appreciate it.

Thanks.

Bernd
 

Helmholtz Zentrum Muenchen
Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)
Ingolstaedter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe
Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen
Registergericht: Amtsgericht Muenchen HRB 6466
USt-IdNr: DE 129521671

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Re: [R] problem installing R 2.5

[Lentes, Bernd via R-help]

- Am 8. Nov 2016 um 7:53 schrieb Göran Broström goran.brost...@umu.se:

> libX11-dev?
> 
> Göran

Hi,

is already installed:

i A libx11-dev  - Client-seitige Bibliothek für X11 (Entwick

(ubuntu system)


Bernd
 

Helmholtz Zentrum Muenchen
Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)
Ingolstaedter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe
Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen
Registergericht: Amtsgericht Muenchen HRB 6466
USt-IdNr: DE 129521671

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Re: [R] problem installing R 2.5

[Göran Broström]

libX11-dev?

Göran

On 2016-11-07 19:27, Lentes, Bernd via R-help wrote:

Hi,

i'd like to install R 2.5 on an Ubuntu 14.04. I have a special
software requiring this old version.

While ./configure, i get the following error:

checking for mbstate_t... yes checking for X... no configure: error:
--with-x=yes (default) and X11 headers/libs are not available

The problem is that i don't know which headers or libraries are
missing, and when i search with aptitude in the Ubuntu repositories i
find a ton of them and don't know which one to install.

Can anyone help me ?

Thanks.


Bernd



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[R] problem installing R 2.5

[Lentes, Bernd via R-help]

Hi,

i'd like to install R 2.5 on an Ubuntu 14.04.
I have a special software requiring this old version.

While ./configure, i get the following error:

checking for mbstate_t... yes
checking for X... no
configure: error: --with-x=yes (default) and X11 headers/libs are not available

The problem is that i don't know which headers or libraries are missing, and 
when i search with aptitude in the Ubuntu repositories i find a ton of them and 
don't know which one to install.

Can anyone help me ?

Thanks.


Bernd

-- 
Bernd Lentes 

Systemadministration 
institute of developmental genetics 
Gebäude 35.34 - Raum 208 
HelmholtzZentrum München 
bernd.len...@helmholtz-muenchen.de 
phone: +49 (0)89 3187 1241 
fax: +49 (0)89 3187 2294 

Erst wenn man sich auf etwas festlegt kann man Unrecht haben 
Scott Adams
 

Helmholtz Zentrum Muenchen
Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)
Ingolstaedter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe
Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen
Registergericht: Amtsgericht Muenchen HRB 6466
USt-IdNr: DE 129521671

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Re: [R] problem in R

[Marco]

Excerpts from Rolf Turner's message of 2015-11-06 00:34:06 -0200:
> 
> On 06/11/15 14:31, Jim Lemon wrote:
> 
> 
> 
> > The fundamental problem that has emerged in this discussion is that
> > you seem to be applying the method of post-modernist deconstruction
> > to programming in R. I see no future in this enterprise.
> 
> 
> 
> *Gotta* be a fortune!!!
> 
> cheers,
> 
> Rolf
> 

Jim++
Rolf++

must be.

-- 
Marco Arthur @ (M)arco Creatives

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Re: [R] problem in R

[Jim Lemon]

Hi thanoon,
When I run your code, I get two error messages. Those error messages tell
you all you need to know to solve the first part of your problem (i.e. that
none of the values in W1 and W2 are changed from NA). The second part of
your problem is that even if you attend to those error messages, you will
only change the first values in W1 and W2. The fundamental problem that has
emerged in this discussion is that you seem to be applying the method of
post-modernist deconstruction to programming in R. I see no future in this
enterprise.

Jim


On Fri, Nov 6, 2015 at 1:10 AM, thanoon younis 
wrote:

> Dear Dr. Lemon
>
> I have a problem in the code below same the previous problem but the data
> now is dichotomous with two categories 0,1. I want to transfer the vector
> BZ with missing data to vector W with dichotomous data but the result is NA
> for W how can i solve this problem please?
>
> Mnay thanks in advance
>
>
>
>
> N1<-200;N2<-200;P<-9
> BZ1=matrix(NA, nrow=N1, ncol=1)
> BZ2=matrix(NA, nrow=N2, ncol=1)
> W1=matrix(NA, nrow=N1, ncol=1)
> W2=matrix(NA, nrow=N2, ncol=1)
>
> BZ1=rbinom(200,1,0.7)
>
>
> for (j in 1:1) { if (BZ1[i]>=0) W1[i]<-1 else W1[i]<-0 }
>
>  BZ2=rbinom(200,1,0.7)
>
>
>
>  for (j in 1:1) { if (BZ2[i]>=0) W2[i]<-1 else W2[i]<-0 }
>
>
>   #Input data set for OpenBUGS
>   data<-list(N1=200,N2=200,P=9,R=Ro,W1,W2)
>
>
> #end
>
> W1
> W2
>
> --
> Thanoon Y. Thanoon
> PhD Candidate
> Department of Mathematical Sciences
> Faculty of Science
> University Technology Malaysia, UTM
> E.Mail: thanoon.youni...@gmail.com
> E.Mail: dawn_praye...@yahoo.com
> Facebook:Thanoon Younis AL-Shakerchy
> Twitter: Thanoon Alshakerchy
> H.P:00601127550205
>

[[alternative HTML version deleted]]

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Re: [R] problem in R

[Rolf Turner]

On 06/11/15 14:31, Jim Lemon wrote:




The fundamental problem that has emerged in this discussion is that
you seem to be applying the method of post-modernist deconstruction
to programming in R. I see no future in this enterprise.




*Gotta* be a fortune!!!

cheers,

Rolf

--
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276

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Re: [R] problem in R-code

[thanoon younis]

Dear R-Users

After correct some errors in the code below i have only this error

"Error in if (BZ[i] < 0.25) { : missing value where TRUE/FALSE needed"

how can i solve this problem please?



N<-200;P<-9   #Sample size
BZ=matrix(NA, nrow=N, ncol=1)


W=matrix(NA, nrow=N, ncol=1)


for (t in 1:100) {
  #Generate the data for the simulation study
  for (i in 1:N) {

#transform theta to ordered categorical variables


for(j in 1:1){
  if(BZ[i] < 0.25){
W[i] = 1
  }else if(BZ[i] >=0.25 & BZ[i] < 0.5){
W[i] = 2
  }else if(BZ[i] >=0.5 & BZ[i] < 0.75){
W[i] = 3
  }else{
W[i] = 4
  

[[alternative HTML version deleted]]

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Re: [R] problem in R-code

[Jim Lemon]

Hi thanoon,
Well, you have generated a one column matrix of missing values (NA) and
then tried to use those values in a logical test...

Jim

On Wed, Nov 4, 2015 at 8:02 PM, thanoon younis 
wrote:

> Dear R-Users
>
> After correct some errors in the code below i have only this error
>
> "Error in if (BZ[i] < 0.25) { : missing value where TRUE/FALSE needed"
>
> how can i solve this problem please?
>
>
>
> N<-200;P<-9   #Sample size
> BZ=matrix(NA, nrow=N, ncol=1)
>
>
> W=matrix(NA, nrow=N, ncol=1)
>
>
> for (t in 1:100) {
>   #Generate the data for the simulation study
>   for (i in 1:N) {
>
> #transform theta to ordered categorical variables
>
>
> for(j in 1:1){
>   if(BZ[i] < 0.25){
> W[i] = 1
>   }else if(BZ[i] >=0.25 & BZ[i] < 0.5){
> W[i] = 2
>   }else if(BZ[i] >=0.5 & BZ[i] < 0.75){
> W[i] = 3
>   }else{
> W[i] = 4
>   
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem in R-code

[Boris Steipe]

Why don't you just multiply by four, round, and add one?



B.
On Nov 3, 2015, at 10:02 PM, thanoon younis  wrote:

> Dear R-users
> 
> I have a problem in the code below, the problem is because i want to change
> the variable BZ which is a vector with 200x1 dimension to the var. W which
> is categorical variable with same dimension of BZ but with categorical
> values with 4 categories but i got on only zero values in w why?  any help
> would be appreciated.
> 
> N<-200;P<-9   #Sample size
> BZ=numeric(N)
> 
> W<-numeric(N)
> 
> for (t in 1:1) {
>  #Generate the data for the simulation study
>  for (i in 1:N) {
> 
>#transform theta to ordered categorical variables
> 
> 
>for(j in 1:1){
>  if(BZ[j] < 0.25){
>W[j] = 1
>  }else if(BZ[j] >=0.25 & BZ[j] < 0.5){
>W[j] = 2
>  }else if(BZ[j] >=0.5 & BZ[j] < 0.75){
>W[j] = 3
>  }else{
>W[j] = 4
>  }}
> 
> 
>#Input data set
>data<-list(N=200,P=9,Q=W)
> 
>  }} #end
> 
> W
> 
> 
> 
> 
> Regards
> 
> 
> -- 
> Thanoon Y. Thanoon
> PhD Candidate
> Department of Mathematical Sciences
> Faculty of Science
> University Technology Malaysia, UTM
> E.Mail: thanoon.youni...@gmail.com
> E.Mail: dawn_praye...@yahoo.com
> Facebook:Thanoon Younis AL-Shakerchy
> Twitter: Thanoon Alshakerchy
> H.P:00601127550205
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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[R] problem in R-code

[thanoon younis]

Dear R-users

I have a problem in the code below, the problem is because i want to change
the variable BZ which is a vector with 200x1 dimension to the var. W which
is categorical variable with same dimension of BZ but with categorical
values with 4 categories but i got on only zero values in w why?  any help
would be appreciated.

N<-200;P<-9   #Sample size
BZ=numeric(N)

W<-numeric(N)

for (t in 1:1) {
  #Generate the data for the simulation study
  for (i in 1:N) {

#transform theta to ordered categorical variables


for(j in 1:1){
  if(BZ[j] < 0.25){
W[j] = 1
  }else if(BZ[j] >=0.25 & BZ[j] < 0.5){
W[j] = 2
  }else if(BZ[j] >=0.5 & BZ[j] < 0.75){
W[j] = 3
  }else{
W[j] = 4
  }}


#Input data set
data<-list(N=200,P=9,Q=W)

  }} #end

W




Regards


-- 
Thanoon Y. Thanoon
PhD Candidate
Department of Mathematical Sciences
Faculty of Science
University Technology Malaysia, UTM
E.Mail: thanoon.youni...@gmail.com
E.Mail: dawn_praye...@yahoo.com
Facebook:Thanoon Younis AL-Shakerchy
Twitter: Thanoon Alshakerchy
H.P:00601127550205

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem in R-code

[Boris Steipe]

Are you telling me it contains only zeros? Or is it a vector of length zero?

B.


On Nov 3, 2015, at 11:07 PM, thanoon younis  wrote:

> BZ is hidden variable with zero values.
> 
> On 4 November 2015 at 07:02, Boris Steipe  wrote:
> Your approach does not make sense.
> 
> If you initialize a vector as say ...
> 
>BZ <- numeric(5)
> ... what do you _expect BZ contains?
> 
> Also: if you run a loop like you do
> for (j in 1:1) {
>print(j)
> }
> ... what do you _expect_ will happen?
> 
> 
> B.
> 
> On Nov 3, 2015, at 10:43 PM, thanoon younis  
> wrote:
> 
> > Thank you for your response
> >
> > I have a vector of unknown values BZ which is defined already BZ=numeric(N) 
> >  and i want to transfer BZ to ordered categorical variable with 4 
> > categories W but when i write this code
> >
> >   for(j in 1:1){
> >   if(BZ[j] < 0.25){
> > W[j] = 1
> >   }else if(BZ[j] >=0.25 & BZ[j] < 0.5){
> > W[j] = 2
> >   }else if(BZ[j] >=0.5 & BZ[j] < 0.75){
> > W[j] = 3
> >   }else{
> > W[j] = 4
> >   }}
> >
> > i found the values of W are only 0, but if i change  for(j in 1:N) the 
> > values of W will be only 1. how can i solve this problem?
> > Regards
> >
> > On 4 November 2015 at 06:35, Boris Steipe  wrote:
> > Why don't you just multiply by four, round, and add one?
> >
> >
> >
> > B.
> > On Nov 3, 2015, at 10:02 PM, thanoon younis  
> > wrote:
> >
> > > Dear R-users
> > >
> > > I have a problem in the code below, the problem is because i want to 
> > > change
> > > the variable BZ which is a vector with 200x1 dimension to the var. W which
> > > is categorical variable with same dimension of BZ but with categorical
> > > values with 4 categories but i got on only zero values in w why?  any help
> > > would be appreciated.
> > >
> > > N<-200;P<-9   #Sample size
> > > BZ=numeric(N)
> > >
> > > W<-numeric(N)
> > >
> > > for (t in 1:1) {
> > >  #Generate the data for the simulation study
> > >  for (i in 1:N) {
> > >
> > >#transform theta to ordered categorical variables
> > >
> > >
> > >for(j in 1:1){
> > >  if(BZ[j] < 0.25){
> > >W[j] = 1
> > >  }else if(BZ[j] >=0.25 & BZ[j] < 0.5){
> > >W[j] = 2
> > >  }else if(BZ[j] >=0.5 & BZ[j] < 0.75){
> > >W[j] = 3
> > >  }else{
> > >W[j] = 4
> > >  }}
> > >
> > >
> > >#Input data set
> > >data<-list(N=200,P=9,Q=W)
> > >
> > >  }} #end
> > >
> > > W
> > >
> > >
> > >
> > >
> > > Regards
> > >
> > >
> > > --
> > > Thanoon Y. Thanoon
> > > PhD Candidate
> > > Department of Mathematical Sciences
> > > Faculty of Science
> > > University Technology Malaysia, UTM
> > > E.Mail: thanoon.youni...@gmail.com
> > > E.Mail: dawn_praye...@yahoo.com
> > > Facebook:Thanoon Younis AL-Shakerchy
> > > Twitter: Thanoon Alshakerchy
> > > H.P:00601127550205
> > >
> > >   [[alternative HTML version deleted]]
> > >
> > > __
> > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide 
> > > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> >
> >
> >
> >
> > --
> > Thanoon Y. Thanoon
> > PhD Candidate
> > Department of Mathematical Sciences
> > Faculty of Science
> > University Technology Malaysia, UTM
> > E.Mail: thanoon.youni...@gmail.com
> > E.Mail: dawn_praye...@yahoo.com
> > Facebook:Thanoon Younis AL-Shakerchy
> > Twitter: Thanoon Alshakerchy
> > H.P:00601127550205
> 
> 
> 
> 
> -- 
> Thanoon Y. Thanoon
> PhD Candidate 
> Department of Mathematical Sciences 
> Faculty of Science
> University Technology Malaysia, UTM
> E.Mail: thanoon.youni...@gmail.com
> E.Mail: dawn_praye...@yahoo.com
> Facebook:Thanoon Younis AL-Shakerchy
> Twitter: Thanoon Alshakerchy
> H.P:00601127550205

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem in R-code

[Jim Lemon]

Hi thanoon,
The problem may lie in your definition of BZ (which I see Boris has also
noticed). Given your code, it will be a vector containing 200 zeros. Your
code will generate 200 ones as zero is less than 0.25. Try defining BZ as
follows:

BZ<-runif(200)

You should get something more interesting from your code or that suggested
by Boris, or even this:

W<-as.numeric(cut(BZ,breaks=c(0,0.25,0.5,0.75,1)))

Jim

On Wed, Nov 4, 2015 at 2:43 PM, thanoon younis 
wrote:

> Thank you for your response
>
> I have a vector of unknown values BZ which is defined already BZ=numeric(N)
>  and i want to transfer BZ to ordered categorical variable with 4
> categories W but when i write this code
>
>   for(j in 1:1){
>   if(BZ[j] < 0.25){
> W[j] = 1
>   }else if(BZ[j] >=0.25 & BZ[j] < 0.5){
> W[j] = 2
>   }else if(BZ[j] >=0.5 & BZ[j] < 0.75){
> W[j] = 3
>   }else{
> W[j] = 4
>   }}
>
> i found the values of W are only 0, but if i change  for(j in 1:N) the
> values of W will be only 1. how can i solve this problem?
> Regards
>
> On 4 November 2015 at 06:35, Boris Steipe 
> wrote:
>
> > Why don't you just multiply by four, round, and add one?
> >
> >
> >
> > B.
> > On Nov 3, 2015, at 10:02 PM, thanoon younis 
> > wrote:
> >
> > > Dear R-users
> > >
> > > I have a problem in the code below, the problem is because i want to
> > change
> > > the variable BZ which is a vector with 200x1 dimension to the var. W
> > which
> > > is categorical variable with same dimension of BZ but with categorical
> > > values with 4 categories but i got on only zero values in w why?  any
> > help
> > > would be appreciated.
> > >
> > > N<-200;P<-9   #Sample size
> > > BZ=numeric(N)
> > >
> > > W<-numeric(N)
> > >
> > > for (t in 1:1) {
> > >  #Generate the data for the simulation study
> > >  for (i in 1:N) {
> > >
> > >#transform theta to ordered categorical variables
> > >
> > >
> > >for(j in 1:1){
> > >  if(BZ[j] < 0.25){
> > >W[j] = 1
> > >  }else if(BZ[j] >=0.25 & BZ[j] < 0.5){
> > >W[j] = 2
> > >  }else if(BZ[j] >=0.5 & BZ[j] < 0.75){
> > >W[j] = 3
> > >  }else{
> > >W[j] = 4
> > >  }}
> > >
> > >
> > >#Input data set
> > >data<-list(N=200,P=9,Q=W)
> > >
> > >  }} #end
> > >
> > > W
> > >
> > >
> > >
> > >
> > > Regards
> > >
> > >
> > > --
> > > Thanoon Y. Thanoon
> > > PhD Candidate
> > > Department of Mathematical Sciences
> > > Faculty of Science
> > > University Technology Malaysia, UTM
> > > E.Mail: thanoon.youni...@gmail.com
> > > E.Mail: dawn_praye...@yahoo.com
> > > Facebook:Thanoon Younis AL-Shakerchy
> > > Twitter: Thanoon Alshakerchy
> > > H.P:00601127550205
> > >
> > >   [[alternative HTML version deleted]]
> > >
> > > __
> > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible code.
> >
> >
>
>
> --
> Thanoon Y. Thanoon
> PhD Candidate
> Department of Mathematical Sciences
> Faculty of Science
> University Technology Malaysia, UTM
> E.Mail: thanoon.youni...@gmail.com
> E.Mail: dawn_praye...@yahoo.com
> Facebook:Thanoon Younis AL-Shakerchy
> Twitter: Thanoon Alshakerchy
> H.P:00601127550205
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

[[alternative HTML version deleted]]

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Re: [R] problem in R-code

[thanoon younis]

Thank you for your response

I have a vector of unknown values BZ which is defined already BZ=numeric(N)
 and i want to transfer BZ to ordered categorical variable with 4
categories W but when i write this code

  for(j in 1:1){
  if(BZ[j] < 0.25){
W[j] = 1
  }else if(BZ[j] >=0.25 & BZ[j] < 0.5){
W[j] = 2
  }else if(BZ[j] >=0.5 & BZ[j] < 0.75){
W[j] = 3
  }else{
W[j] = 4
  }}

i found the values of W are only 0, but if i change  for(j in 1:N) the
values of W will be only 1. how can i solve this problem?
Regards

On 4 November 2015 at 06:35, Boris Steipe  wrote:

> Why don't you just multiply by four, round, and add one?
>
>
>
> B.
> On Nov 3, 2015, at 10:02 PM, thanoon younis 
> wrote:
>
> > Dear R-users
> >
> > I have a problem in the code below, the problem is because i want to
> change
> > the variable BZ which is a vector with 200x1 dimension to the var. W
> which
> > is categorical variable with same dimension of BZ but with categorical
> > values with 4 categories but i got on only zero values in w why?  any
> help
> > would be appreciated.
> >
> > N<-200;P<-9   #Sample size
> > BZ=numeric(N)
> >
> > W<-numeric(N)
> >
> > for (t in 1:1) {
> >  #Generate the data for the simulation study
> >  for (i in 1:N) {
> >
> >#transform theta to ordered categorical variables
> >
> >
> >for(j in 1:1){
> >  if(BZ[j] < 0.25){
> >W[j] = 1
> >  }else if(BZ[j] >=0.25 & BZ[j] < 0.5){
> >W[j] = 2
> >  }else if(BZ[j] >=0.5 & BZ[j] < 0.75){
> >W[j] = 3
> >  }else{
> >W[j] = 4
> >  }}
> >
> >
> >#Input data set
> >data<-list(N=200,P=9,Q=W)
> >
> >  }} #end
> >
> > W
> >
> >
> >
> >
> > Regards
> >
> >
> > --
> > Thanoon Y. Thanoon
> > PhD Candidate
> > Department of Mathematical Sciences
> > Faculty of Science
> > University Technology Malaysia, UTM
> > E.Mail: thanoon.youni...@gmail.com
> > E.Mail: dawn_praye...@yahoo.com
> > Facebook:Thanoon Younis AL-Shakerchy
> > Twitter: Thanoon Alshakerchy
> > H.P:00601127550205
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
>


-- 
Thanoon Y. Thanoon
PhD Candidate
Department of Mathematical Sciences
Faculty of Science
University Technology Malaysia, UTM
E.Mail: thanoon.youni...@gmail.com
E.Mail: dawn_praye...@yahoo.com
Facebook:Thanoon Younis AL-Shakerchy
Twitter: Thanoon Alshakerchy
H.P:00601127550205

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem in R-code

[Boris Steipe]

Your approach does not make sense.

If you initialize a vector as say ...

   BZ <- numeric(5)
... what do you _expect BZ contains?

Also: if you run a loop like you do
for (j in 1:1) {
   print(j)
}
... what do you _expect_ will happen?


B.

On Nov 3, 2015, at 10:43 PM, thanoon younis  wrote:

> Thank you for your response
> 
> I have a vector of unknown values BZ which is defined already BZ=numeric(N)  
> and i want to transfer BZ to ordered categorical variable with 4 categories W 
> but when i write this code
> 
>   for(j in 1:1){
>   if(BZ[j] < 0.25){
> W[j] = 1
>   }else if(BZ[j] >=0.25 & BZ[j] < 0.5){
> W[j] = 2
>   }else if(BZ[j] >=0.5 & BZ[j] < 0.75){
> W[j] = 3
>   }else{
> W[j] = 4
>   }}
> 
> i found the values of W are only 0, but if i change  for(j in 1:N) the values 
> of W will be only 1. how can i solve this problem?
> Regards
> 
> On 4 November 2015 at 06:35, Boris Steipe  wrote:
> Why don't you just multiply by four, round, and add one?
> 
> 
> 
> B.
> On Nov 3, 2015, at 10:02 PM, thanoon younis  
> wrote:
> 
> > Dear R-users
> >
> > I have a problem in the code below, the problem is because i want to change
> > the variable BZ which is a vector with 200x1 dimension to the var. W which
> > is categorical variable with same dimension of BZ but with categorical
> > values with 4 categories but i got on only zero values in w why?  any help
> > would be appreciated.
> >
> > N<-200;P<-9   #Sample size
> > BZ=numeric(N)
> >
> > W<-numeric(N)
> >
> > for (t in 1:1) {
> >  #Generate the data for the simulation study
> >  for (i in 1:N) {
> >
> >#transform theta to ordered categorical variables
> >
> >
> >for(j in 1:1){
> >  if(BZ[j] < 0.25){
> >W[j] = 1
> >  }else if(BZ[j] >=0.25 & BZ[j] < 0.5){
> >W[j] = 2
> >  }else if(BZ[j] >=0.5 & BZ[j] < 0.75){
> >W[j] = 3
> >  }else{
> >W[j] = 4
> >  }}
> >
> >
> >#Input data set
> >data<-list(N=200,P=9,Q=W)
> >
> >  }} #end
> >
> > W
> >
> >
> >
> >
> > Regards
> >
> >
> > --
> > Thanoon Y. Thanoon
> > PhD Candidate
> > Department of Mathematical Sciences
> > Faculty of Science
> > University Technology Malaysia, UTM
> > E.Mail: thanoon.youni...@gmail.com
> > E.Mail: dawn_praye...@yahoo.com
> > Facebook:Thanoon Younis AL-Shakerchy
> > Twitter: Thanoon Alshakerchy
> > H.P:00601127550205
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> 
> 
> 
> 
> -- 
> Thanoon Y. Thanoon
> PhD Candidate 
> Department of Mathematical Sciences 
> Faculty of Science
> University Technology Malaysia, UTM
> E.Mail: thanoon.youni...@gmail.com
> E.Mail: dawn_praye...@yahoo.com
> Facebook:Thanoon Younis AL-Shakerchy
> Twitter: Thanoon Alshakerchy
> H.P:00601127550205

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem in R-code

[Boris Steipe]

Sorry, not round. floor()


B.

On Nov 3, 2015, at 10:35 PM, Boris Steipe  wrote:

> Why don't you just multiply by four, round, and add one?
> 
> 
> 
> B.
> On Nov 3, 2015, at 10:02 PM, thanoon younis  
> wrote:
> 
>> Dear R-users
>> 
>> I have a problem in the code below, the problem is because i want to change
>> the variable BZ which is a vector with 200x1 dimension to the var. W which
>> is categorical variable with same dimension of BZ but with categorical
>> values with 4 categories but i got on only zero values in w why?  any help
>> would be appreciated.
>> 
>> N<-200;P<-9   #Sample size
>> BZ=numeric(N)
>> 
>> W<-numeric(N)
>> 
>> for (t in 1:1) {
>> #Generate the data for the simulation study
>> for (i in 1:N) {
>> 
>>   #transform theta to ordered categorical variables
>> 
>> 
>>   for(j in 1:1){
>> if(BZ[j] < 0.25){
>>   W[j] = 1
>> }else if(BZ[j] >=0.25 & BZ[j] < 0.5){
>>   W[j] = 2
>> }else if(BZ[j] >=0.5 & BZ[j] < 0.75){
>>   W[j] = 3
>> }else{
>>   W[j] = 4
>> }}
>> 
>> 
>>   #Input data set
>>   data<-list(N=200,P=9,Q=W)
>> 
>> }} #end
>> 
>> W
>> 
>> 
>> 
>> 
>> Regards
>> 
>> 
>> -- 
>> Thanoon Y. Thanoon
>> PhD Candidate
>> Department of Mathematical Sciences
>> Faculty of Science
>> University Technology Malaysia, UTM
>> E.Mail: thanoon.youni...@gmail.com
>> E.Mail: dawn_praye...@yahoo.com
>> Facebook:Thanoon Younis AL-Shakerchy
>> Twitter: Thanoon Alshakerchy
>> H.P:00601127550205
>> 
>>  [[alternative HTML version deleted]]
>> 
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> 

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem in R-code

[Boris Steipe]

Whatever -
just type:

W <- floor(BZ * 4) + 1



B.

On Nov 3, 2015, at 11:09 PM, Boris Steipe  wrote:

> Are you telling me it contains only zeros? Or is it a vector of length zero?
> 
> B.
> 
> 
> On Nov 3, 2015, at 11:07 PM, thanoon younis  
> wrote:
> 
>> BZ is hidden variable with zero values.
>> 
>> On 4 November 2015 at 07:02, Boris Steipe  wrote:
>> Your approach does not make sense.
>> 
>> If you initialize a vector as say ...
>> 
>>   BZ <- numeric(5)
>> ... what do you _expect BZ contains?
>> 
>> Also: if you run a loop like you do
>> for (j in 1:1) {
>>   print(j)
>> }
>> ... what do you _expect_ will happen?
>> 
>> 
>> B.
>> 
>> On Nov 3, 2015, at 10:43 PM, thanoon younis  
>> wrote:
>> 
>>> Thank you for your response
>>> 
>>> I have a vector of unknown values BZ which is defined already BZ=numeric(N) 
>>>  and i want to transfer BZ to ordered categorical variable with 4 
>>> categories W but when i write this code
>>> 
>>>  for(j in 1:1){
>>>  if(BZ[j] < 0.25){
>>>W[j] = 1
>>>  }else if(BZ[j] >=0.25 & BZ[j] < 0.5){
>>>W[j] = 2
>>>  }else if(BZ[j] >=0.5 & BZ[j] < 0.75){
>>>W[j] = 3
>>>  }else{
>>>W[j] = 4
>>>  }}
>>> 
>>> i found the values of W are only 0, but if i change  for(j in 1:N) the 
>>> values of W will be only 1. how can i solve this problem?
>>> Regards
>>> 
>>> On 4 November 2015 at 06:35, Boris Steipe  wrote:
>>> Why don't you just multiply by four, round, and add one?
>>> 
>>> 
>>> 
>>> B.
>>> On Nov 3, 2015, at 10:02 PM, thanoon younis  
>>> wrote:
>>> 
 Dear R-users
 
 I have a problem in the code below, the problem is because i want to change
 the variable BZ which is a vector with 200x1 dimension to the var. W which
 is categorical variable with same dimension of BZ but with categorical
 values with 4 categories but i got on only zero values in w why?  any help
 would be appreciated.
 
 N<-200;P<-9   #Sample size
 BZ=numeric(N)
 
 W<-numeric(N)
 
 for (t in 1:1) {
 #Generate the data for the simulation study
 for (i in 1:N) {
 
   #transform theta to ordered categorical variables
 
 
   for(j in 1:1){
 if(BZ[j] < 0.25){
   W[j] = 1
 }else if(BZ[j] >=0.25 & BZ[j] < 0.5){
   W[j] = 2
 }else if(BZ[j] >=0.5 & BZ[j] < 0.75){
   W[j] = 3
 }else{
   W[j] = 4
 }}
 
 
   #Input data set
   data<-list(N=200,P=9,Q=W)
 
 }} #end
 
 W
 
 
 
 
 Regards
 
 
 --
 Thanoon Y. Thanoon
 PhD Candidate
 Department of Mathematical Sciences
 Faculty of Science
 University Technology Malaysia, UTM
 E.Mail: thanoon.youni...@gmail.com
 E.Mail: dawn_praye...@yahoo.com
 Facebook:Thanoon Younis AL-Shakerchy
 Twitter: Thanoon Alshakerchy
 H.P:00601127550205
 
  [[alternative HTML version deleted]]
 
 __
 R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide 
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.
>>> 
>>> 
>>> 
>>> 
>>> --
>>> Thanoon Y. Thanoon
>>> PhD Candidate
>>> Department of Mathematical Sciences
>>> Faculty of Science
>>> University Technology Malaysia, UTM
>>> E.Mail: thanoon.youni...@gmail.com
>>> E.Mail: dawn_praye...@yahoo.com
>>> Facebook:Thanoon Younis AL-Shakerchy
>>> Twitter: Thanoon Alshakerchy
>>> H.P:00601127550205
>> 
>> 
>> 
>> 
>> -- 
>> Thanoon Y. Thanoon
>> PhD Candidate 
>> Department of Mathematical Sciences 
>> Faculty of Science
>> University Technology Malaysia, UTM
>> E.Mail: thanoon.youni...@gmail.com
>> E.Mail: dawn_praye...@yahoo.com
>> Facebook:Thanoon Younis AL-Shakerchy
>> Twitter: Thanoon Alshakerchy
>> H.P:00601127550205
> 
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem Regarding R Packages installation

[MacQueen, Don]

the first error message is
  configuration failed for package RCurl
immediately before that it said
  Cannot find curl-config.

It would appear that you don't have curl installed on your computer.
Unfortunately, I cannot help you with that. But you might look at the
documentation for RCurl (available from CRAN) to start trying to find
where to get curl.

-- 
Don MacQueen

Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062





On 7/15/15, 8:23 PM, R-help on behalf of Muhammad Sohail Raza
r-help-boun...@r-project.org on behalf of muhammadsohailr...@live.com
wrote:

Hi Everyone!
I am trying to install R Package VariantAnnotation. I entered commands:

source(http://bioconductor.org/biocLite.R;)
 biocLite(VariantAnnotation)


But i am getting the following errors,

ERROR: configuration failed for package �XML�
* removing �/usr/lib64/R/library/XML�
* installing *source* package �RCurl� ...
** package �RCurl� successfully unpacked and MD5 sums checked
configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package �RCurl�
* removing �/usr/lib64/R/library/RCurl�
* installing *source* package �Rsamtools� ...
** libs
gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG  -I/usr/local/include
-I/usr/lib64/R/library/S4Vectors/include
-I/usr/lib64/R/library/IRanges/include
-I/usr/lib64/R/library/XVector/include
-I/usr/lib64/R/library/Biostrings/include  -fopenmp -D_USE_KNETFILE
-D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE
-Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort
-I./samtools -I./samtools/bcftools -I./tabix -fpic  -fmessage-length=0
-grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector
-funwind-tables -fasynchronous-unwind-tables  -c Biostrings_stubs.c -o
Biostrings_stubs.o
gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG  -I/usr/local/include
-I/usr/lib64/R/library/S4Vectors/include
-I/usr/lib64/R/library/IRanges/include
-I/usr/lib64/R/library/XVector/include
-I/usr/lib64/R/library/Biostrings/include  -fopenmp -D_USE_KNETFILE
-D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE
-Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort
-I./samtools -I./samtools/bcftools -I./tabix -fpic  -fmessage-length=0
-grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector
-funwind-tables -fasynchronous-unwind-tables  -c IRanges_stubs.c -o
IRanges_stubs.o
g++ -I/usr/lib64/R/include -DNDEBUG  -I/usr/local/include
-I/usr/lib64/R/library/S4Vectors/include
-I/usr/lib64/R/library/IRanges/include
-I/usr/lib64/R/library/XVector/include
-I/usr/lib64/R/library/Biostrings/include   -fpic  -fmessage-length=0
-grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector
-funwind-tables -fasynchronous-unwind-tables  -c PileupBuffer.cpp -o
PileupBuffer.o
/bin/sh: g++: command not found
/usr/lib64/R/etc/Makeconf:143: recipe for target 'PileupBuffer.o' failed
make: *** [PileupBuffer.o] Error 127
ERROR: compilation failed for package �Rsamtools�
* removing �/usr/lib64/R/library/Rsamtools�
* installing *source* package �futile.logger� ...
** package �futile.logger� successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (futile.logger)
ERROR: dependencies �XML�, �RCurl� are not available for package �biomaRt�
* removing �/usr/lib64/R/library/biomaRt�
* installing *source* package �BiocParallel� ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiocParallel)
ERROR: dependency �Rsamtools� is not available for package
�GenomicAlignments�
* removing �/usr/lib64/R/library/GenomicAlignments�
ERROR: dependencies �XML�, �RCurl�, �Rsamtools�, �GenomicAlignments� are
not available for package �rtracklayer�
* removing �/usr/lib64/R/library/rtracklayer�
ERROR: dependencies �rtracklayer�, �Rsamtools� are not available for
package �BSgenome�
* removing �/usr/lib64/R/library/BSgenome�
ERROR: dependencies �rtracklayer�, �biomaRt�, �RCurl� are not available
for package �GenomicFeatures�
* removing �/usr/lib64/R/library/GenomicFeatures�
ERROR: dependencies �Rsamtools�, �BSgenome�, �rtracklayer�,
�GenomicFeatures� are not available for package �VariantAnnotation�
* removing �/usr/lib64/R/library/VariantAnnotation�

The downloaded source packages are in
�/tmp/RtmpvpoYjO/downloaded_packages�
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package �XML� had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package �RCurl� had non-zero exit status
3: In install.packages(pkgs = doing, 

[R] Problem Regarding R Packages installation

[Muhammad Sohail Raza]

Hi Everyone!
I am trying to install R Package VariantAnnotation. I entered commands:

source(http://bioconductor.org/biocLite.R;)
 biocLite(VariantAnnotation)


But i am getting the following errors, 

ERROR: configuration failed for package �XML�
* removing �/usr/lib64/R/library/XML�
* installing *source* package �RCurl� ...
** package �RCurl� successfully unpacked and MD5 sums checked
configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package �RCurl�
* removing �/usr/lib64/R/library/RCurl�
* installing *source* package �Rsamtools� ...
** libs
gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG  -I/usr/local/include 
-I/usr/lib64/R/library/S4Vectors/include 
-I/usr/lib64/R/library/IRanges/include 
-I/usr/lib64/R/library/XVector/include 
-I/usr/lib64/R/library/Biostrings/include  -fopenmp -D_USE_KNETFILE 
-D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE 
-Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort 
-I./samtools -I./samtools/bcftools -I./tabix -fpic  -fmessage-length=0 
-grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector 
-funwind-tables -fasynchronous-unwind-tables  -c Biostrings_stubs.c -o 
Biostrings_stubs.o
gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG  -I/usr/local/include 
-I/usr/lib64/R/library/S4Vectors/include 
-I/usr/lib64/R/library/IRanges/include 
-I/usr/lib64/R/library/XVector/include 
-I/usr/lib64/R/library/Biostrings/include  -fopenmp -D_USE_KNETFILE 
-D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE 
-Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort 
-I./samtools -I./samtools/bcftools -I./tabix -fpic  -fmessage-length=0 
-grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector 
-funwind-tables -fasynchronous-unwind-tables  -c IRanges_stubs.c -o 
IRanges_stubs.o
g++ -I/usr/lib64/R/include -DNDEBUG  -I/usr/local/include 
-I/usr/lib64/R/library/S4Vectors/include 
-I/usr/lib64/R/library/IRanges/include 
-I/usr/lib64/R/library/XVector/include 
-I/usr/lib64/R/library/Biostrings/include   -fpic  -fmessage-length=0 
-grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector 
-funwind-tables -fasynchronous-unwind-tables  -c PileupBuffer.cpp -o 
PileupBuffer.o
/bin/sh: g++: command not found
/usr/lib64/R/etc/Makeconf:143: recipe for target 'PileupBuffer.o' failed
make: *** [PileupBuffer.o] Error 127
ERROR: compilation failed for package �Rsamtools�
* removing �/usr/lib64/R/library/Rsamtools�
* installing *source* package �futile.logger� ...
** package �futile.logger� successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (futile.logger)
ERROR: dependencies �XML�, �RCurl� are not available for package �biomaRt�
* removing �/usr/lib64/R/library/biomaRt�
* installing *source* package �BiocParallel� ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiocParallel)
ERROR: dependency �Rsamtools� is not available for package �GenomicAlignments�
* removing �/usr/lib64/R/library/GenomicAlignments�
ERROR: dependencies �XML�, �RCurl�, �Rsamtools�, �GenomicAlignments� are not 
available for package �rtracklayer�
* removing �/usr/lib64/R/library/rtracklayer�
ERROR: dependencies �rtracklayer�, �Rsamtools� are not available for package 
�BSgenome�
* removing �/usr/lib64/R/library/BSgenome�
ERROR: dependencies �rtracklayer�, �biomaRt�, �RCurl� are not available for 
package �GenomicFeatures�
* removing �/usr/lib64/R/library/GenomicFeatures�
ERROR: dependencies �Rsamtools�, �BSgenome�, �rtracklayer�, �GenomicFeatures� 
are not available for package �VariantAnnotation�
* removing �/usr/lib64/R/library/VariantAnnotation�

The downloaded source packages are in
�/tmp/RtmpvpoYjO/downloaded_packages�
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package �XML� had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package �RCurl� had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package �Rsamtools� had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package �biomaRt� had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package �GenomicAlignments� had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package �rtracklayer� had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package �BSgenome� had non-zero exit status
8: In 

Re: [R] Problem in r help me

[PIKAL Petr]

From: Ghada Almousa [mailto:ghada.f...@gmail.com]
Sent: Monday, May 04, 2015 9:20 PM
To: PIKAL Petr
Subject: Re: Problem in r help me

I used internet search to get info about methods but I can't find any info 
about the comparison between those methods
The comparison in the number of iterations , the time required to build each 
Cluster  and sum square error SSE for each cluster in the R programming

Pardon me, but does not number of iterations, time and SSE depends also on data 
used for the analysis?

Cheers
Petr

On Monday, May 4, 2015, PIKAL Petr 
petr.pi...@precheza.czmailto:petr.pi...@precheza.cz wrote:
Hi

Your question is rather cryptic. Data? Code?

You can use internet search to get info about methods

e.g

R hierarchical clustering

gives me many answer regarding clustering in R.

Be more specific to get more specific answer

Cheers
Petr


 -Original Message-
 From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Ghada
 Almousa
 Sent: Saturday, May 02, 2015 11:03 AM
 To: r-help@r-project.org
 Subject: Re: [R] Problem in r help me

  hello dears
 
  I have Search to compare the results between the three types of
  cluster k-maen ,Em and  Hierarchal clusters How i figured the number
  of iterations , the time required to build each Cluster ,
 and
  sum square error SSE for each cluster in the R programming
 

   [[alternative HTML version deleted]]

 __
 R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-
 guide.html
 and provide commented, minimal, self-contained, reproducible code.


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Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email 
jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat.
Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či 
zpožděním přenosu e-mailu.

V případě, že je tento e-mail součástí obchodního jednání:
- vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a 
to z jakéhokoliv důvodu i bez uvedení důvodu.
- a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; 
Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce 
s dodatkem či odchylkou.
- trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným 
dosažením shody na všech jejích náležitostech.
- odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost 
žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně 
pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně 
osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi 
či osobě jím zastoupené známá.

This e-mail and any documents attached to it may be confidential and are 
intended only for its intended recipients.
If you received this e-mail by mistake, please immediately inform its sender. 
Delete the contents of this e-mail with all attachments and its copies from 
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use, disseminate, copy or disclose this e-mail in any manner.
The sender of this e-mail shall not be liable for any possible damage caused by 
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Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny 
pouze jeho adresátům.
Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně 
jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze 
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Nejste-li zamýšleným

Re: [R] Problem in r help me

[PIKAL Petr]

Hi

Your question is rather cryptic. Data? Code?

You can use internet search to get info about methods

e.g

R hierarchical clustering

gives me many answer regarding clustering in R.

Be more specific to get more specific answer

Cheers
Petr


 -Original Message-
 From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Ghada
 Almousa
 Sent: Saturday, May 02, 2015 11:03 AM
 To: r-help@r-project.org
 Subject: Re: [R] Problem in r help me

  hello dears
 
  I have Search to compare the results between the three types of
  cluster k-maen ,Em and  Hierarchal clusters How i figured the number
  of iterations , the time required to build each Cluster ,accuracy
 and
  sum square error SSE for each cluster in the R programming
 

   [[alternative HTML version deleted]]

 __
 R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-
 guide.html
 and provide commented, minimal, self-contained, reproducible code.


Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny 
pouze jeho adresátům.
Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně 
jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze 
svého systému.
Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email 
jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat.
Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či 
zpožděním přenosu e-mailu.

V případě, že je tento e-mail součástí obchodního jednání:
- vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a 
to z jakéhokoliv důvodu i bez uvedení důvodu.
- a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; 
Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce 
s dodatkem či odchylkou.
- trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným 
dosažením shody na všech jejích náležitostech.
- odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost 
žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně 
pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně 
osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi 
či osobě jím zastoupené známá.

This e-mail and any documents attached to it may be confidential and are 
intended only for its intended recipients.
If you received this e-mail by mistake, please immediately inform its sender. 
Delete the contents of this e-mail with all attachments and its copies from 
your system.
If you are not the intended recipient of this e-mail, you are not authorized to 
use, disseminate, copy or disclose this e-mail in any manner.
The sender of this e-mail shall not be liable for any possible damage caused by 
modifications of the e-mail or by delay with transfer of the email.

In case that this e-mail forms part of business dealings:
- the sender reserves the right to end negotiations about entering into a 
contract in any time, for any reason, and without stating any reasoning.
- if the e-mail contains an offer, the recipient is entitled to immediately 
accept such offer; The sender of this e-mail (offer) excludes any acceptance of 
the offer on the part of the recipient containing any amendment or variation.
- the sender insists on that the respective contract is concluded only upon an 
express mutual agreement on all its aspects.
- the sender of this e-mail informs that he/she is not authorized to enter into 
any contracts on behalf of the company except for cases in which he/she is 
expressly authorized to do so in writing, and such authorization or power of 
attorney is submitted to the recipient or the person represented by the 
recipient, or the existence of such authorization is known to the recipient of 
the person represented by the recipient.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem in r help me

[Ghada Almousa]

 hello dears

 I have Search to compare the results between the three types of cluster
 k-maen ,Em and  Hierarchal clusters
 How i figured the number of iterations , the time required to build each
 Cluster ,accuracy  and sum square error SSE for each cluster in the R
 programming


[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Problem in r help me

[Ghada Almousa]

hello dears

I have Search to compare the results between the three types of cluster
k-maen ,Em and  Hierarchal clusters
How i figured the number of iterations , the time required to build each
Cluster ,accuracy  and sum square error SSE for each cluster in the R
programming

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] problem in R

[thanoon younis]

Dear all members

I have the following matrix in R

 thd - matrix(testJAGSdata$thd, ncol=6, byrow=TRUE)
 head(thd)
 [,1]   [,2]   [,3]   [,4]  [,5] [,6]
[1,] -200 -2.517 -1.245 -0.444 0.848  200
[2,] -200 -1.447 -0.420  0.119  1.245 200
[3,] -200 -1.671 -0.869 -0.194  0.679 200
[4,] -200 -1.642 -0.869 -0.293  0.332 200
[5,] -200 -1.671 -0.827  0.052  0.756 200
[6,] -200 -1.769 -1.098 -0.469  0.255 200
[7,] -200 -1.490 -0.670 -0.082  0.880 200
[8,] -200 -1.933 -0.880 -0.317  1.008 200
[9,] -200  -1.587 -0.624  0.000  1.008 200
[10,] -200 -1.983 -1.348 -0.348  1.045 200
[11,] -200 -1.983 -1.229 -0.247  0.869 200
[12,] -200 -2.262 -1.426  0.037  1.330 200
[13,] -200 -2.371 -1.295 -0.224  0.651 200
[14,] -200 -2.039 -1.112 -0.149  1.169 200
[15,] -200 -2.262 -1.198 -0.309  1.198 200
[16,] -200 -2.176 -1.537 -0.717  0.597 200
[17,] -200 -1.447 -0.786  0.119  1.008 200
[18,] -200 -2.039 -1.769 -0.661  0.642 200

and when i implemented this matrix i found this error


+  head(thd)
+  [,1]   [,2]   [,3]   [,4]  [,5] [,6]
+ [1,] -200 -2.517 -1.245 -0.444 0.848  200
Error: unexpected numeric constant in:
 [,1]   [,2]   [,3]   [,4]  [,5] [,6]
[1,] -200 -2.517 -1.245 -0.444 0.848
 [2,] -200 -1.447 -0.420  0.119  1.245 200
Error: unexpected '[' in [
 [3,] -200 -1.671 -0.869 -0.194  0.679 200
Error: unexpected '[' in [
 [4,] -200 -1.642 -0.869 -0.293  0.332 200
Error: unexpected '[' in [
 [5,] -200 -1.671 -0.827  0.052  0.756 200
Error: unexpected '[' in [
 [6,] -200 -1.769 -1.098 -0.469  0.255 200
Error: unexpected '[' in [
 [7,] -200 -1.490 -0.670 -0.082  0.880 200
Error: unexpected '[' in [
 [8,] -200 -1.933 -0.880 -0.317  1.008 200
Error: unexpected '[' in [
 [9,] -200  -1.587 -0.624  0.000  1.008 200
Error: unexpected '[' in [
 [10,] -200 -1.983 -1.348 -0.348  1.045 200
Error: unexpected '[' in [
 [11,] -200 -1.983 -1.229 -0.247  0.869 200
Error: unexpected '[' in [
 [12,] -200 -2.262 -1.426  0.037  1.330 200
Error: unexpected '[' in [
 [13,] -200 -2.371 -1.295 -0.224  0.651 200
Error: unexpected '[' in [
 [14,] -200 -2.039 -1.112 -0.149  1.169 200
Error: unexpected '[' in [
 [15,] -200 -2.262 -1.198 -0.309  1.198 200
Error: unexpected '[' in [
 [16,] -200 -2.176 -1.537 -0.717  0.597 200
Error: unexpected '[' in [
 [17,] -200 -1.447 -0.786  0.119  1.008 200
Error: unexpected '[' in [
 [18,] -200 -2.039 -1.769 -0.661  0.642 200
Error: unexpected '[' in [


Any help would be very appreciated

thanks in advance
-- 
Thanoon Y. Thanoon
PhD Candidate
Department of Mathematical Sciences
Faculty of Science
University Technology Malaysia, UTM
E.Mail: thanoon.youni...@gmail.com
E.Mail: dawn_praye...@yahoo.com
Facebook:Thanoon Younis AL-Shakerchy
Twitter: Thanoon Alshakerchy
H.P:00601127550205

[[alternative HTML version deleted]]

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem in R

[Sarah Goslee]

Hi,

On Fri, Feb 20, 2015 at 9:48 AM, thanoon younis
thanoon.youni...@gmail.com wrote:
 Dear all members

 I have the following matrix in R

 thd - matrix(testJAGSdata$thd, ncol=6, byrow=TRUE)
 head(thd)
  [,1]   [,2]   [,3]   [,4]  [,5] [,6]
 [1,] -200 -2.517 -1.245 -0.444 0.848  200
 [2,] -200 -1.447 -0.420  0.119  1.245 200
 [3,] -200 -1.671 -0.869 -0.194  0.679 200
 [4,] -200 -1.642 -0.869 -0.293  0.332 200
 [5,] -200 -1.671 -0.827  0.052  0.756 200
 [6,] -200 -1.769 -1.098 -0.469  0.255 200
 [7,] -200 -1.490 -0.670 -0.082  0.880 200
 [8,] -200 -1.933 -0.880 -0.317  1.008 200
 [9,] -200  -1.587 -0.624  0.000  1.008 200
 [10,] -200 -1.983 -1.348 -0.348  1.045 200
 [11,] -200 -1.983 -1.229 -0.247  0.869 200
 [12,] -200 -2.262 -1.426  0.037  1.330 200
 [13,] -200 -2.371 -1.295 -0.224  0.651 200
 [14,] -200 -2.039 -1.112 -0.149  1.169 200
 [15,] -200 -2.262 -1.198 -0.309  1.198 200
 [16,] -200 -2.176 -1.537 -0.717  0.597 200
 [17,] -200 -1.447 -0.786  0.119  1.008 200
 [18,] -200 -2.039 -1.769 -0.661  0.642 200

This is not reproducible, so the below are guesses.

 and when i implemented this matrix i found this error

I have no idea what implemented this matrix might mean.


 +  head(the)

First problem: the + means R expects continuation of a previous line,
because the command is incomplete. So whatever you did BEFORE this
line is wrong.

 +  [,1]   [,2]   [,3]   [,4]  [,5] [,6]
 + [1,] -200 -2.517 -1.245 -0.444 0.848  200
 Error: unexpected numeric constant in:
  [,1]   [,2]   [,3]   [,4]  [,5] [,6]
 [1,] -200 -2.517 -1.245 -0.444 0.848

These and subsequent errors are what you'd get if you pasted the above
R output back into the R console. Why would you do that?

So: check your previous commands.
If you can't find your mistake, respond to the list with a clear
reproducible example.

 [2,] -200 -1.447 -0.420  0.119  1.245 200
 Error: unexpected '[' in [
 [3,] -200 -1.671 -0.869 -0.194  0.679 200
 Error: unexpected '[' in [
 [4,] -200 -1.642 -0.869 -0.293  0.332 200
 Error: unexpected '[' in [
 [5,] -200 -1.671 -0.827  0.052  0.756 200
 Error: unexpected '[' in [
 [6,] -200 -1.769 -1.098 -0.469  0.255 200
 Error: unexpected '[' in [
 [7,] -200 -1.490 -0.670 -0.082  0.880 200
 Error: unexpected '[' in [
 [8,] -200 -1.933 -0.880 -0.317  1.008 200
 Error: unexpected '[' in [
 [9,] -200  -1.587 -0.624  0.000  1.008 200
 Error: unexpected '[' in [
 [10,] -200 -1.983 -1.348 -0.348  1.045 200
 Error: unexpected '[' in [
 [11,] -200 -1.983 -1.229 -0.247  0.869 200
 Error: unexpected '[' in [
 [12,] -200 -2.262 -1.426  0.037  1.330 200
 Error: unexpected '[' in [
 [13,] -200 -2.371 -1.295 -0.224  0.651 200
 Error: unexpected '[' in [
 [14,] -200 -2.039 -1.112 -0.149  1.169 200
 Error: unexpected '[' in [
 [15,] -200 -2.262 -1.198 -0.309  1.198 200
 Error: unexpected '[' in [
 [16,] -200 -2.176 -1.537 -0.717  0.597 200
 Error: unexpected '[' in [
 [17,] -200 -1.447 -0.786  0.119  1.008 200
 Error: unexpected '[' in [
 [18,] -200 -2.039 -1.769 -0.661  0.642 200
 Error: unexpected '[' in [


 Any help would be very appreciated

 thanks in advance
 --
 Thanoon Y. Thanoon
 PhD Candidate
 Department of Mathematical Sciences
 Faculty of Science
 University Technology Malaysia, UTM
 E.Mail: thanoon.youni...@gmail.com
 E.Mail: dawn_praye...@yahoo.com
 Facebook:Thanoon Younis AL-Shakerchy
 Twitter: Thanoon Alshakerchy
 H.P:00601127550205


-- 
Sarah Goslee
http://www.functionaldiversity.org

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R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem in R

[Sarah Goslee]

First, please reply to the list, not just me.

On Fri, Feb 20, 2015 at 10:22 AM, thanoon younis
thanoon.youni...@gmail.com wrote:
 thank you very much for your help

 actually, my data set like this

 #Data Set
 testJAGSdata =  list(N1=200, N2=200, P=18,

R=structure(
   .Data=c(8.0, 1.0,1.0, 8.0),
   .Dim=c(2,2)),

 thd - matrix(testJAGSdata$thd, ncol=6, byrow=TRUE)
 head(thd)
  [,1]   [,2]   [,3]   [,4]  [,5] [,6]
 [1,] -200 -2.517 -1.245 -0.444 0.848  200
 [2,] -200 -1.447 -0.420  0.119  1.245 200
 [3,] -200 -1.671 -0.869 -0.194  0.679 200
 [4,] -200 -1.642 -0.869 -0.293  0.332 200
 [5,] -200 -1.671 -0.827  0.052  0.756 200
 [6,] -200 -1.769 -1.098 -0.469  0.255 200
 [7,] -200 -1.490 -0.670 -0.082  0.880 200
 [8,] -200 -1.933 -0.880 -0.317  1.008 200
 [9,] -200  -1.587 -0.624  0.000  1.008 200
 [10,] -200 -1.983 -1.348 -0.348  1.045 200
 [11,] -200 -1.983 -1.229 -0.247  0.869 200
 [12,] -200 -2.262 -1.426  0.037  1.330 200
 [13,] -200 -2.371 -1.295 -0.224  0.651 200
 [14,] -200 -2.039 -1.112 -0.149  1.169 200
 [15,] -200 -2.262 -1.198 -0.309  1.198 200
 [16,] -200 -2.176 -1.537 -0.717  0.597 200
 [17,] -200 -1.447 -0.786  0.119  1.008 200
 [18,] -200 -2.039 -1.769 -0.661  0.642 200


 #Data Set
 testJAGSdata =  list(N1=200, N2=200, P=18,
 +
 +R=structure(
 +   .Data=c(8.0, 1.0,1.0, 8.0),
 +   .Dim=c(2,2)),
 +
 + thd - matrix(testJAGSdata$thd, ncol=6, byrow=TRUE)
 +  head(the)

Did you do what I suggested and look at your commands?

R is expecting the rest of whatever your first command is supposed to
do, and it isn't complete. That's what the + prompt is trying to tell
you.

The first command ends with a , and doesn't have enough parentheses -
something is missing there.
After that, you continue trying to paste in R output to the console.

It looks to  me like you are working by copying and pasting from notes
that you don't understand. Maybe going back and rereading an
introduction to R would help you.


 +  [,1]   [,2]   [,3]   [,4]  [,5] [,6]
 + [1,] -200 -2.517 -1.245 -0.444 0.848  200
 Error: unexpected numeric constant in:
  [,1]   [,2]   [,3]   [,4]  [,5] [,6]
 [1,] -200 -2.517 -1.245 -0.444 0.848
 [2,] -200 -1.447 -0.420  0.119  1.245 200
 Error: unexpected '[' in [
 [3,] -200 -1.671 -0.869 -0.194  0.679 200
 Error: unexpected '[' in [
 [4,] -200 -1.642 -0.869 -0.293  0.332 200
 Error: unexpected '[' in [
 [5,] -200 -1.671 -0.827  0.052  0.756 200
 Error: unexpected '[' in [
 [6,] -200 -1.769 -1.098 -0.469  0.255 200
 Error: unexpected '[' in [
 [7,] -200 -1.490 -0.670 -0.082  0.880 200
 Error: unexpected '[' in [
 [8,] -200 -1.933 -0.880 -0.317  1.008 200
 Error: unexpected '[' in [
 [9,] -200  -1.587 -0.624  0.000  1.008 200
 Error: unexpected '[' in [
 [10,] -200 -1.983 -1.348 -0.348  1.045 200
 Error: unexpected '[' in [
 [11,] -200 -1.983 -1.229 -0.247  0.869 200
 Error: unexpected '[' in [
 [12,] -200 -2.262 -1.426  0.037  1.330 200
 Error: unexpected '[' in [
 [13,] -200 -2.371 -1.295 -0.224  0.651 200
 Error: unexpected '[' in [
 [14,] -200 -2.039 -1.112 -0.149  1.169 200
 Error: unexpected '[' in [
 [15,] -200 -2.262 -1.198 -0.309  1.198 200
 Error: unexpected '[' in [
 [16,] -200 -2.176 -1.537 -0.717  0.597 200
 Error: unexpected '[' in [
 [17,] -200 -1.447 -0.786  0.119  1.008 200
 Error: unexpected '[' in [
 [18,] -200 -2.039 -1.769 -0.661  0.642 200
 Error: unexpected '[' in [


 Many thanks in advance

 On 20 February 2015 at 18:04, Sarah Goslee sarah.gos...@gmail.com wrote:

 Hi,

 On Fri, Feb 20, 2015 at 9:48 AM, thanoon younis
 thanoon.youni...@gmail.com wrote:
  Dear all members
 
  I have the following matrix in R
 
  thd - matrix(testJAGSdata$thd, ncol=6, byrow=TRUE)
  head(thd)
   [,1]   [,2]   [,3]   [,4]  [,5] [,6]
  [1,] -200 -2.517 -1.245 -0.444 0.848  200
  [2,] -200 -1.447 -0.420  0.119  1.245 200
  [3,] -200 -1.671 -0.869 -0.194  0.679 200
  [4,] -200 -1.642 -0.869 -0.293  0.332 200
  [5,] -200 -1.671 -0.827  0.052  0.756 200
  [6,] -200 -1.769 -1.098 -0.469  0.255 200
  [7,] -200 -1.490 -0.670 -0.082  0.880 200
  [8,] -200 -1.933 -0.880 -0.317  1.008 200
  [9,] -200  -1.587 -0.624  0.000  1.008 200
  [10,] -200 -1.983 -1.348 -0.348  1.045 200
  [11,] -200 -1.983 -1.229 -0.247  0.869 200
  [12,] -200 -2.262 -1.426  0.037  1.330 200
  [13,] -200 -2.371 -1.295 -0.224  0.651 200
  [14,] -200 -2.039 -1.112 -0.149  1.169 200
  [15,] -200 -2.262 -1.198 -0.309  1.198 200
  [16,] -200 -2.176 -1.537 -0.717  0.597 200
  [17,] -200 -1.447 -0.786  0.119  1.008 200
  [18,] -200 -2.039 -1.769 -0.661  0.642 200

 This is not reproducible, so the below are guesses.

  and when i implemented this matrix i found this error

 I have no idea what implemented this matrix might mean.

 
  +  head(the)

 First problem: the + means R expects continuation of a previous line,
 because the command is incomplete. So whatever you did BEFORE this
 line is wrong.

  +  [,1]   [,2]   [,3]   [,4]  [,5] [,6]
  + [1,] -200

Re: [R] problem in R

[Uwe Ligges]

On 05.01.2015 18:03, thanoon younis wrote:

Dear all R members
I have a problem in the R when i wanted to call winbugs as following

#Input data set for WinBUGS
 thd18 -read.table(C:/Users/hp/Desktop/thd18.txt)

 #Input data set for WinBUGS
 data-list(N1=2000,N2=2000,P=9,R=Ro,z1=yo1,z2=yo2,thd18)



thd18 is a data.frame but WinBUGS does not know about a data.frame. You 
probably want to convert to a matrix first.


Best,
Uwe Ligges




#Call WinBUGS
 model-bugs (data,inits,parameters,model.file=D:/Run/model.txt,
 n.chains=2,n.iter=5000,n.burnin=1000,n.thin=1,DIC=TRUE,
 bugs.directory=c:/Program Files/WinBUGS14/,
 working.directory=D:/Run/)

and the problem is
Error in is.finite(x) : default method not implemented for type 'list'

Any guidance would be highly appreciated



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[R] problem in R

[thanoon younis]

Dear all R members
I have a problem in the R when i wanted to call winbugs as following

#Input data set for WinBUGS
thd18 -read.table(C:/Users/hp/Desktop/thd18.txt)

#Input data set for WinBUGS
data-list(N1=2000,N2=2000,P=9,R=Ro,z1=yo1,z2=yo2,thd18)

#Call WinBUGS
model-bugs (data,inits,parameters,model.file=D:/Run/model.txt,
n.chains=2,n.iter=5000,n.burnin=1000,n.thin=1,DIC=TRUE,
bugs.directory=c:/Program Files/WinBUGS14/,
working.directory=D:/Run/)

and the problem is
Error in is.finite(x) : default method not implemented for type 'list'

Any guidance would be highly appreciated

-- 
Thanoon Y. Thanoon
PhD Candidate
Department of Mathematical Sciences
Faculty of Science
University Technology Malaysia, UTM
E.Mail: thanoon.youni...@gmail.com
E.Mail: dawn_praye...@yahoo.com
Facebook:Thanoon Younis AL-Shakerchy
Twitter: Thanoon Alshakerchy
H.P:00601127550205

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Re: [R] Problem with R CMD check and the inconsolata font business.

[BenTaylor]

Not sure if this is because things have changed with MikTeX, but I had to do 

updmap

rather than 

initexmf --mkmaps



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[R] Problem with R density function

[DHIMAN BHADRA]

Hello,
My friend has the following issue with R. I will be glad to receive any
response.
Thanks,
Dhiman Bhadra

Hello everyone,

I am trying to use the 'density' function available with the base package
of R to estimate the density of a data set for subsequent use. I just
noticed that with even 1000 data points, the numerical integral of the
estimated density using the Epanechnikov kernel is far from 1. I wonder if
I am doing something wrong, or whether there is a bug:

x=rnorm(1)
 dd=density(x,kernel=epanechnikov,n=101,bw=0.001)
 sum(dd$y)*(dd$x[2]-dd$x[1])
[1] 5.7245

 dd=density(x,kernel=epanechnikov,n=1001,bw=0.001)
 sum(dd$y)*(dd$x[2]-dd$x[1])
[1] 2.870922

 dd=density(x,kernel=epanechnikov,n=10001,bw=0.001)
 sum(dd$y)*(dd$x[2]-dd$x[1])
[1] 0.9989762

So unless I use around 1 or more data points, the integral is wrong:
there seems to be a scaling factor creeping in. Am I missing something?


Best regards,
*Apratim Guha*

__
*Dr. Apratim Guha*
*Associate Professor, Production  Quantitative Methods Area, IIM
Ahmedabad, *

*Vastrapur, Ahmedabad 380015, INDIA. Phone: (91) 79 6632 4803*
*Secretary: Ms. Sujatha Jayprakash: (91) 79 6632 4911*

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Re: [R] Problem with R density function

[Martyn Byng]

Hi,

Have you tried using a different bandwidth rather than the number of points,  
the default bandwidth gives ...

x - rnorm(1)
dd - density(x,kernel=epanechnikov,n=101)
sum(dd$y)*(dd$x[2]-dd$x[1])
[1] 1.001014

Martyn
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
Behalf Of DHIMAN BHADRA
Sent: 14 May 2014 10:36
To: r-help@r-project.org
Subject: [R] Problem with R density function

Hello,
My friend has the following issue with R. I will be glad to receive any 
response.
Thanks,
Dhiman Bhadra

Hello everyone,

I am trying to use the 'density' function available with the base package of R 
to estimate the density of a data set for subsequent use. I just noticed that 
with even 1000 data points, the numerical integral of the estimated density 
using the Epanechnikov kernel is far from 1. I wonder if I am doing something 
wrong, or whether there is a bug:

x=rnorm(1)
 dd=density(x,kernel=epanechnikov,n=101,bw=0.001)
 sum(dd$y)*(dd$x[2]-dd$x[1])
[1] 5.7245

 dd=density(x,kernel=epanechnikov,n=1001,bw=0.001)
 sum(dd$y)*(dd$x[2]-dd$x[1])
[1] 2.870922

 dd=density(x,kernel=epanechnikov,n=10001,bw=0.001)
 sum(dd$y)*(dd$x[2]-dd$x[1])
[1] 0.9989762

So unless I use around 1 or more data points, the integral is wrong:
there seems to be a scaling factor creeping in. Am I missing something?


Best regards,
*Apratim Guha*

__
*Dr. Apratim Guha*
*Associate Professor, Production  Quantitative Methods Area, IIM Ahmedabad, *

*Vastrapur, Ahmedabad 380015, INDIA. Phone: (91) 79 6632 4803*
*Secretary: Ms. Sujatha Jayprakash: (91) 79 6632 4911*

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.


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Re: [R] Problem with R density function

[Andrews, Chris]

Try adding plots, e.g. 

set.seed(20140514)
x - rnorm(100)
hist(x, prob=TRUE, ylim=c(0,10))
dd - density(x, n=10001, bw=0.001)
lines(dd, col=2, type=s)
dd - density(x, n=101, bw=0.001)
lines(dd, col=3, type=s)

The density function you produce with bw=0.001 is very irregular (many sharp, 
narrow peaks).  You should expect to need many intervals (i.e., large n) in 
your Reimann integral to get an accurate estimate of the area under it.

Chris


-Original Message-
From: Martyn Byng [mailto:martyn.b...@nag.co.uk] 
Sent: Wednesday, May 14, 2014 5:58 AM
To: DHIMAN BHADRA; r-help@r-project.org
Subject: Re: [R] Problem with R density function

Hi,

Have you tried using a different bandwidth rather than the number of points,  
the default bandwidth gives ...

x - rnorm(1)
dd - density(x,kernel=epanechnikov,n=101)
sum(dd$y)*(dd$x[2]-dd$x[1])
[1] 1.001014

Martyn
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
Behalf Of DHIMAN BHADRA
Sent: 14 May 2014 10:36
To: r-help@r-project.org
Subject: [R] Problem with R density function

Hello,
My friend has the following issue with R. I will be glad to receive any 
response.
Thanks,
Dhiman Bhadra

Hello everyone,

I am trying to use the 'density' function available with the base package of R 
to estimate the density of a data set for subsequent use. I just noticed that 
with even 1000 data points, the numerical integral of the estimated density 
using the Epanechnikov kernel is far from 1. I wonder if I am doing something 
wrong, or whether there is a bug:

x=rnorm(1)
 dd=density(x,kernel=epanechnikov,n=101,bw=0.001)
 sum(dd$y)*(dd$x[2]-dd$x[1])
[1] 5.7245

 dd=density(x,kernel=epanechnikov,n=1001,bw=0.001)
 sum(dd$y)*(dd$x[2]-dd$x[1])
[1] 2.870922

 dd=density(x,kernel=epanechnikov,n=10001,bw=0.001)
 sum(dd$y)*(dd$x[2]-dd$x[1])
[1] 0.9989762

So unless I use around 1 or more data points, the integral is wrong:
there seems to be a scaling factor creeping in. Am I missing something?


Best regards,
*Apratim Guha*

__
*Dr. Apratim Guha*
*Associate Professor, Production  Quantitative Methods Area, IIM Ahmedabad, *

*Vastrapur, Ahmedabad 380015, INDIA. Phone: (91) 79 6632 4803*
*Secretary: Ms. Sujatha Jayprakash: (91) 79 6632 4911*

[[alternative HTML version deleted]]

__
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https://stat.ethz.ch/mailman/listinfo/r-help
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and provide commented, minimal, self-contained, reproducible code.


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and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem in r-code

[Suzen, Mehmet]

Wrong list. This is an R list not Bugs.
You may want to consult Bugs materials:
http://www2.mrc-bsu.cam.ac.uk/bugs/weblinks/webresource.shtml

On 8 May 2014 11:36, thanoon younis thanoon.youni...@gmail.com wrote:
 dear all members

 is there anyone explain to me the code below and how can i transfer this
 code to winbugs program.

 q[i,1]=qnorm(runif(1,min=.5,max=1),0,1)

 thanks in advance

 thanoon

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 __
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 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

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and provide commented, minimal, self-contained, reproducible code.

[R] problem in r-code

[thanoon younis]

dear all members

is there anyone explain to me the code below and how can i transfer this
code to winbugs program.

q[i,1]=qnorm(runif(1,min=.5,max=1),0,1)

thanks in advance

thanoon

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and provide commented, minimal, self-contained, reproducible code.

[R] Problem with R

[Campaner, Fabio]

Hello,

I am a student at the University College of London in the Civil Engineering 
Department and I need to use the R program for my final year project even if I 
do not have any programming background.

I have downloaded the program and I was following the instructions given to me 
by my supervisor that included adding some packages to the program, like 
“lmtest and “betareg.

However, each time I try to download the packages the program would not like it 
and it would tell me that other packages like “zoo or “formula are needed. I 
tried to download each package the program would tell me it is missing but it 
seems that the packages needed are infinite since it does not stop asking for 
more packages.

Please help me if you can, the submission for my project is next week and I 
still have not figured out how to use this program.

Thank you,

Regards,

Fabio Campaner
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem with R

[Rui Barradas]

Hello,

Try, at an R prompt,

install.packages(lmtest, dependencies = TRUE)
install.packages(betareg, dependencies = TRUE)


Hope this helps,

Rui Barradas

Em 26-03-2014 17:44, Campaner, Fabio escreveu:

Hello,

I am a student at the University College of London in the Civil Engineering 
Department and I need to use the R program for my final year project even if I 
do not have any programming background.

I have downloaded the program and I was following the instructions given to me by my 
supervisor that included adding some packages to the program, like “lmtest and 
“betareg.

However, each time I try to download the packages the program would not like it and it 
would tell me that other packages like “zoo or “formula are needed. I tried 
to download each package the program would tell me it is missing but it seems that the 
packages needed are infinite since it does not stop asking for more packages.

Please help me if you can, the submission for my project is next week and I 
still have not figured out how to use this program.

Thank you,

Regards,

Fabio Campaner
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



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and provide commented, minimal, self-contained, reproducible code.

[R] Problem with R colors

[Katharine Miller]

Hello,

I am having difficulty obtaining the correct colors in my R charts.

 colors()[c(552, 254, 26)]
[1] red   green blue

But, if I specify col=552 in my barplot, I get gray bars.  Likewise,
col=254 gives bright pink, and col=26 is a red-orange.   I get accurate
results when I spell out the names, but I am making a pallet with 20- 30
colors and it is a real pain to have to do that.  Can anyone help me figure
out what I am doing wrong?

Thanks

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem with R colors

[Sarah Goslee]

Hi,

col=552 isn't the same as colors()[552] - I think the former is drawn
from your current palette, with recycling of indices. The default
color palette has only eight colors.

You need instead

col=colors()[552]

It's very difficult to get 20-30 readily distinguishable colors. You
might try the RColorBrewer package for smaller tasks, though.


Sarah


On Mon, Dec 9, 2013 at 5:12 PM, Katharine Miller kmill...@alaska.edu wrote:
 Hello,

 I am having difficulty obtaining the correct colors in my R charts.

 colors()[c(552, 254, 26)]
 [1] red   green blue

 But, if I specify col=552 in my barplot, I get gray bars.  Likewise,
 col=254 gives bright pink, and col=26 is a red-orange.   I get accurate
 results when I spell out the names, but I am making a pallet with 20- 30
 colors and it is a real pain to have to do that.  Can anyone help me figure
 out what I am doing wrong?

 Thanks

-- 
Sarah Goslee
http://www.functionaldiversity.org

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem with R colors

[David Carlson]

The full details on the col= argument can be found in the
section titled Color Specification on the help page for par -
?par.

Basically, col= accepts color names, hexadecimal RGB, or an
integer designating a position on the current palette. You can
get the current palette using

 palette()
[1] black   red green3  bluecyanmagenta
yellow 
[8] gray 

Any of these will give you red

col=red
col=#FF
col=2

You can change the palette colors with the palette() function,
but some graphics functions draw axes, text, etc assuming the
first color in the palette is black so it may be better to
create a vector of the colors you want, eg. 

mc - colors()[c(552, 254, 26)]

and then use 

col=mc[1]

-
David L Carlson
Department of Anthropology
Texas AM University
College Station, TX 77840-4352

-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Katharine
Miller
Sent: Monday, December 9, 2013 4:12 PM
To: r-help@r-project.org
Subject: [R] Problem with R colors

Hello,

I am having difficulty obtaining the correct colors in my R
charts.

 colors()[c(552, 254, 26)]
[1] red   green blue

But, if I specify col=552 in my barplot, I get gray bars.
Likewise,
col=254 gives bright pink, and col=26 is a red-orange.   I get
accurate
results when I spell out the names, but I am making a pallet
with 20- 30
colors and it is a real pain to have to do that.  Can anyone
help me figure
out what I am doing wrong?

Thanks

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible
code.

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem with R colors

[Katharine Miller]

Thanks everyone!  You've been a big help.  I've only ever worked with a few
colors before, so this is something new!


On Mon, Dec 9, 2013 at 1:46 PM, David Carlson dcarl...@tamu.edu wrote:

 The full details on the col= argument can be found in the
 section titled Color Specification on the help page for par -
 ?par.

 Basically, col= accepts color names, hexadecimal RGB, or an
 integer designating a position on the current palette. You can
 get the current palette using

  palette()
 [1] black   red green3  bluecyanmagenta
 yellow
 [8] gray

 Any of these will give you red

 col=red
 col=#FF
 col=2

 You can change the palette colors with the palette() function,
 but some graphics functions draw axes, text, etc assuming the
 first color in the palette is black so it may be better to
 create a vector of the colors you want, eg.

 mc - colors()[c(552, 254, 26)]

 and then use

 col=mc[1]

 -
 David L Carlson
 Department of Anthropology
 Texas AM University
 College Station, TX 77840-4352

 -Original Message-
 From: r-help-boun...@r-project.org
 [mailto:r-help-boun...@r-project.org] On Behalf Of Katharine
 Miller
 Sent: Monday, December 9, 2013 4:12 PM
 To: r-help@r-project.org
 Subject: [R] Problem with R colors

 Hello,

 I am having difficulty obtaining the correct colors in my R
 charts.

  colors()[c(552, 254, 26)]
 [1] red   green blue

 But, if I specify col=552 in my barplot, I get gray bars.
 Likewise,
 col=254 gives bright pink, and col=26 is a red-orange.   I get
 accurate
 results when I spell out the names, but I am making a pallet
 with 20- 30
 colors and it is a real pain to have to do that.  Can anyone
 help me figure
 out what I am doing wrong?

 Thanks

 [[alternative HTML version deleted]]

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible
 code.



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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem loading .r file

[balevick1]

Bogaso wrote
 Hello all,
 
 I was trying to load a .r file using source() ...  functions ... however
 getting
 following error:
 
 source(D:/Book Code.r)
 Error in sys.call(sys.parent()) : node stack overflow


I realise the above message is quite old, just a quick reply if anyone is
encountering the same error and was trying to find a solution (and ending up
here). 

The error is occurring because the line:
 source( filename.r )
is in the file (filename.r) that you're trying to open.

Hash this out in the document
#source(filename.r)
and then it's there for you to copy-paste in and run the code, but shouldn't
cause the error above. 

I would advise copy-pasting the code you're trying to run in the document
first, to make sure that there are no errors in there either!

Hope that helps anyone encountering the error.



--
View this message in context: 
http://r.789695.n4.nabble.com/Problem-loading-r-file-tp4653624p4673413.html
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and provide commented, minimal, self-contained, reproducible code.

[R] Problem building R-2.15.3 from source

[Mark Dalphin]

Hi,

I have for many years build R from source for Linux. I have just run 
into my first problem with this in ... I don't know how long.


uname -a
Linux douglas 3.2.0-4-686-pae #1 SMP Debian 3.2.46-1 i686 GNU/Linux

cat /etc/issue
Debian GNU/Linux 7 \n \l


The version of R is 2.15.3. I know it is old, but we are in a regulated 
environment and changes to R versions are painful. I have built R 2.15.3 
elsewhere and have it running on multiple Linux boxes around here, both 
32-bit and 64-bit; Ubuntu distributions, however, not Debian.


This build is on a virtual machine under OpenBox. The host is a 64-bit 
Debian; the guest is a 32-bit Debian installation.


The symptoms are strange (to me). I get segfaults during the 
byte-compiling phase of libraries. If I re-run 'make', the make proceeds 
as if it finished the previous seg-faulted step, and then segfaults on 
the next byte-compile. The permissions makes me wonder about file 
permissions, but the whole 'make' is under my HOME. Furthermore, I have 
scanned the unpacked tar-gz package for something I don't own and it 
isn't there. I also think segfaults are usually in memory, though I 
don't know what permission I have there (don't I own the RAM I request?).


I have attached a section of the 'make' output  below, followed by a the 
next make output:

--
make[4]: Leaving directory `/home/mdalphin/src/R-2.15.3/src/library/splines'
make[4]: Entering directory 
`/home/mdalphin/src/R-2.15.3/src/library/splines'

byte-compiling package 'splines'

*** caught segfault ***
address 0x403ac3dc, cause 'invalid permissions'

Traceback:
1: fun(libname, pkgname)
2: doTryCatch(return(expr), name, parentenv, handler)
3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
4: tryCatchList(expr, classes, parentenv, handlers)
5: tryCatch(fun(libname, pkgname), error = identity)
6: runHook(.onLoad, env, package.lib, package)
7: loadNamespace(name)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(name), error = function(e) stop(e))
12: getNamespace(ns)
13: asNamespace(pkg)
14: get(name, envir = asNamespace(pkg), inherits = FALSE)
15: compiler:::tryCmpfun
16: .Call(R_lazyLoadDBinsertValue, x[[1L]], file, ascii, compress, 
hook, PACKAGE = base)
17: lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, 
compress, envhook)

18: makeLazyLoadDB(ns, dbbase, compress = compress)
19: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = 
keep.source, compress = compress)

20: tools:::makeLazyLoading(splines)
aborting ...
/bin/bash: line 8: 18709 Doneecho 
tools:::makeLazyLoading(\splines\)
18710 Segmentation fault  | R_COMPILE_PKGS=1 
R_COMPILER_SUPPRESS_ALL=1 R_DEFAULT_PACKAGES=NULL LC_ALL=C 
../../../bin/R --vanilla --slave  /dev/null

make[4]: *** [../../../library/splines/R/splines.rdb] Error 139
make[4]: Leaving directory `/home/mdalphin/src/R-2.15.3/src/library/splines'
make[3]: *** [all] Error 2
make[3]: Leaving directory `/home/mdalphin/src/R-2.15.3/src/library/splines'
make[2]: *** [R] Error 1
make[2]: Leaving directory `/home/mdalphin/src/R-2.15.3/src/library'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/home/mdalphin/src/R-2.15.3/src'
make: *** [R] Error 1
---
make[4]: Entering directory 
`/home/mdalphin/src/R-2.15.3/src/library/splines'

make[4]: Nothing to be done for `mklazycomp'.
make[4]: Leaving directory `/home/mdalphin/src/R-2.15.3/src/library/splines'
make[3]: Leaving directory `/home/mdalphin/src/R-2.15.3/src/library/splines'
make[3]: Entering directory `/home/mdalphin/src/R-2.15.3/src/library/stats4'
building package 'stats4'
mkdir -p -- ../../../library/stats4
make[4]: Entering directory `/home/mdalphin/src/R-2.15.3/src/library/stats4'
mkdir -p -- ../../../library/stats4/R
mkdir -p -- ../../../library/stats4/po
make[4]: Leaving directory `/home/mdalphin/src/R-2.15.3/src/library/stats4'
make[4]: Entering directory `/home/mdalphin/src/R-2.15.3/src/library/stats4'
byte-compiling package 'stats4'

*** caught segfault ***
address 0x403ac3dc, cause 'invalid permissions'

Traceback:
1: fun(libname, pkgname)
2: doTryCatch(return(expr), name, parentenv, handler)
3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
4: tryCatchList(expr, classes, parentenv, handlers)
5: tryCatch(fun(libname, pkgname), error = identity)
6: runHook(.onLoad, env, package.lib, package)
7: loadNamespace(name)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(loadNamespace(name), error = function(e) stop(e))
12: getNamespace(ns)
13: asNamespace(pkg)
14: get(name, envir = asNamespace(pkg), 

[R] Problem with R websocket package

[malej.gregy]

Hello to everybody,

 
 
I seem to be in struggle with the websockets in R. I wanted to download the 
streaming data from the BitCoin exchange MtGox directly to R, but R cannot 
establish the connection.

The websocket specs are defined as:

   * Host: websocket.mtgox.com or socketio.mtgox.com
   * Port: 80 or 443 ( ssl )
   * Namespace: /mtgox (Including beginning slash)
   

url for more details: https://en.bitcoin.it/wiki/MtGox/API/Streaming
(https://en.bitcoin.it/wiki/MtGox/API/Streaming)

and my code is:

codespan class='kwd'require/spanspan class='pun'(/spanspan 
class='pln'websockets/spanspan class='pun')/spanspan class='pln'
con /spanspan class='pun'=/spanspan class='pln' websocket/spanspan 
class='pun'(/spanspan 
class='str'https://socketio.mtgox.com/mtgox;/spanspan 
class='pun',/spanspan class='pln'port/spanspan 
class='pun'=/spanspan class='lit'443/spanspan 
class='pun')/span/code

and I always end up with an error:

codespan class='pun'/spanspan class='pln' con /spanspan 
class='pun'=/spanspan class='pln' websocket/spanspan 
class='pun'(/spanspan 
class='str'https://socketio.mtgox.com/mtgox;/spanspan 
class='pun',/spanspan class='pln'port/spanspan 
class='pun'=/spanspan class='lit'443/spanspan class='pun')/spanspan 
class='pln'
/spanspan class='typ'Error/spanspan class='pln' /spanspan 
class='kwd'in/spanspan class='pln' websocket/spanspan 
class='pun'(/spanspan 
class='str'https://socketio.mtgox.com/mtgox;/spanspan 
class='pun',/spanspan class='pln' port /spanspan 
class='pun'=/spanspan class='pln' /spanspan class='lit'443/spanspan 
class='pun')/spanspan class='pln' /spanspan class='pun':/spanspan 
class='pln'
/spanspan class='typ'Connection/spanspan class='pln' error/span/code

Does anyone have an idea what is wrong? I was informed that MtGox does not 
use the proper websocket protocol but something called Socket-io.

Is it the reason why it doesn't work? If so, is there any other way to 
handle socket-io in R? I searched all websockets packages but did not find 
any.

 
 
Many thanks for help.

Stepan
=
[[alternative HTML version deleted]]

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[R] Problem with R websocket package

[malej.gregy]

Hello to everybody,

I'm repeating my post as the previous one was posted in HTML - sorry guys! 

I seem to be in struggle with the websockets in R. I wanted to download the 
streaming data from the BitCoin exchange MtGox directly to R, but R cannot 
establish the connection.

The websocket specs are defined as:


Host: websocket.mtgox.com or socketio.mtgox.com
Port: 80 or 443 ( ssl )
Namespace:/mtgox (Including beginning slash)

url for more details: https://en.bitcoin.it/wiki/MtGox/API/Streaming

and my code is: 

 require(websockets)
 con = websocket(https://socketio.mtgox.com/mtgox,port=443)

and I always end up with an error:
  con = websocket(https://socketio.mtgox.com/mtgox,port=443)
 Error in websocket(https://socketio.mtgox.com/mtgox;, port = 443) : 
 Connection error

Does anyone have an idea what is wrong? I was informed that MtGox does not use
 the proper websocket protocol but something called Socket-io.
Is it the reason why it doesn't work? If so, is there any other way to handle 
socket-io in R? I searched all websockets packages but did not find any.

 

Many thanks for help.

Stepan

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Re: [R] Problem with R CMD check and the inconsolata font business

[Matthew Dowle]

On 11/3/2011 3:30 PM, Brian Diggs wrote:


Well, I figured it out.  Or at least got it working.  I had to run

initexmf --mkmaps

because apparently there was something wrong with my font mappings.  
I
don't know why; I don't know how.  But it works now.  I think 
installing

the font into the Windows Font directory was not necessary.  I'm
including the solution in case anyone else has this problem.


Many thanks Brian Diggs! I just had the same problem and that fixed it.

Matthew

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Re: [R] Problem loading .r file

[Jeff Newmiller]

I think your immediate problem is that you are asking this particular question 
in the wrong forum. It appears that you are following instructions (in a book? 
a class?) and you need to direct your questions to the author of those 
instructions.

You may find it helpful to know:

a) The load function does not work on R source code files (.R) but on R data 
files (.rda or .RData).
b) You can (and most likely should) open .R files in the text editor of your 
choice and start reading.
c) There is a Posting Guide for this mailing list mentioned at the bottom of 
this and every other email from this list.
d) There is a well-written Introduction to R pdf document supplied with the R 
software.
---
Jeff NewmillerThe .   .  Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live Go...
  Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
--- 
Sent from my phone. Please excuse my brevity.

Christofer Bogaso bogaso.christo...@gmail.com wrote:

Hello all,

I was trying to load a .r file using source() and load() functions.
Although I could be able to load the codes (mainly few user defined
functions) written in that .r. file correctly, however getting
following error:

 source(D:/Book Code.r)
Error in sys.call(sys.parent()) : node stack overflow


 load(D:/Book Code.r)
Error: bad restore file magic number (file may be corrupted) -- no data
loaded
In addition: Warning message:
file ‘NG Book Code.r’ has magic number 'Pos_T'
   Use of save versions prior to 2 is deprecated

What is the possible problem?

Thanks and regards,

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Re: [R] Problem loading .r file

[Ben Bolker]

Christofer Bogaso bogaso.christofer at gmail.com writes:

 


[snip]

 I was trying to load a .r file using source() and load() functions.
 Although I could be able to load the codes (mainly few user defined
 functions) written in that .r. file correctly, however getting
 following error:
 
  source(D:/Book Code.r)
 Error in sys.call(sys.parent()) : node stack overflow
 
  load(D:/Book Code.r)
 Error: bad restore file magic number (file may be corrupted) -- no data loaded
 In addition: Warning message:
 file ‘NG Book Code.r’ has magic number 'Pos_T'
Use of save versions prior to 2 is deprecated
 
 What is the possible problem?
 

 Really hard to say.

  source() seems to be the right choice (since the file seems to
contain R code -- load() is for stored *data*).  However, it's almost
impossible to diagnose the problem without more information about 
what's *in* the file.

  Googling r 'node stack overflow' shows unanswered questions at

http://stackoverflow.com/questions/13788306/error-in-as-dendrogram
http://r.789695.n4.nabble.com/
  Error-in-data-frame-srcfile-NA-character-using-R-CMD-check-td4369037.html

...

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[R] problem about R

[Leung Chen]

How to run pie chart for each categorical variable in a dataset?

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Re: [R] problem about R

[Rui Barradas]

Hello,

What is a dataset? In R there are lots of types, including 'data.frame' 
and 'list'. And R's type 'factor' corresponds to categorical variables. 
You must be more specific, show us an example dataset using dput().


dput( head(x, 30) )  # paste the output of this in a post


Hope this helps,

Rui Barradas

Em 02-10-2012 05:50, Leung Chen escreveu:

How to run pie chart for each categorical variable in a dataset?

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Re: [R] problem about R

[Jim Lemon]

On 10/02/2012 02:50 PM, Leung Chen wrote:

How to run pie chart for each categorical variable in a dataset?


Hi Leung,
I depends upon your definition of categorical. If a character variable 
has 100 possible values, you won't get a very informative pie chart out 
of it. Therefore I suggest the following function as a start:


pie_shopping-function(x,maxval=5) {
 xname-deparse(substitute(x))
 for(var in 1:length(x)) {
  if(length(unique(x[,var])) = maxval) {
   png(paste(xname,var,.png,sep=))
pie(table(x[,var]))
   dev.off()
  }
 }
}

Jim

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Re: [R] Problem with R script

[Jim Lemon]

On 09/24/2012 11:15 PM, Woo Back Lee wrote:

To whom I concern,

I am a recent user of program R

I do not know how to explain this but after I installed the program the
words on the scrpit does R console does not appear clear
but something square(?)/Cube(?) which seems like the words are broken

More suprisingly, the squared words are written in Korean (My mother
language... and could discover it by 'copy  paste' on word file...)


Besides after I inserted all the commendes to create a graph, the graph
does not actually appear but someting gray(?)

Can you help me about it?


Hi Woo,
Your script did not make it to the mailing list. Perhaps if you paste 
it into the email message it will come through. At the moment, we can't 
even guess what is happening.


Jim

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and provide commented, minimal, self-contained, reproducible code.

[R] Problem with R script

[Woo Back Lee]

To whom I concern,

I am a recent user of program R

I do not know how to explain this but after I installed the program the
words on the scrpit does R console does not appear clear
but something square(?)/Cube(?) which seems like the words are broken

More suprisingly, the squared words are written in Korean (My mother
language... and could discover it by 'copy  paste' on word file...)


Besides after I inserted all the commendes to create a graph, the graph
does not actually appear but someting gray(?)

Can you help me about it?

Sincerely yours,

p.s. I am attatching the file in this email..so please help me
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[R] problem in R related to import n export

[mukul purva]

hello,
i hav a prob in R lang. i want to do correlation of data frame
22810(gene) rows and 1436 colums(experiment) when i covert this file
in csv or xls format it reads only 1024 cloumns. n when i do
correlation of data mean 22810 *22810 matrix made in terminal then i
export in csv or xls by write.table it will give me only 1024 columns
rather than 22810 columns.wat i do
plzzz help me...


regards


mukul

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem in R related to import n export

[jim holtman]

My quick guess is that it not an R problem, but with your version of
EXCEL.  What version are you using, since this used to be a limitation
of Excel.  Just tried to output an object with 1436 columns and read
it fine into 2007 version of EXCEL.

On Sun, Jan 15, 2012 at 10:09 AM, mukul purva mukul.pu...@gmail.com wrote:
 hello,
        i hav a prob in R lang. i want to do correlation of data frame
 22810(gene) rows and 1436 colums(experiment) when i covert this file
 in csv or xls format it reads only 1024 cloumns. n when i do
 correlation of data mean 22810 *22810 matrix made in terminal then i
 export in csv or xls by write.table it will give me only 1024 columns
 rather than 22810 columns.wat i do
 plzzz help me...


 regards


 mukul

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 R-help@r-project.org mailing list
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 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.



-- 
Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.

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and provide commented, minimal, self-contained, reproducible code.

[R] Problem Installing R to SuSE 10 via RPM

[Matthew Pettis]

Hi,

I'm trying to install R from an rpm locally to my account (the reason I'm
not doing it through yast/yast2/zypper is that the sys admin isn't yet
willing to install it, and doesn't want to support it, but will help me
support it if I install it locally -- in short, policy problems rather than
technical).  Below is the SuSE version, Kernel version, and rpm install
error I'm getting, as well as the error...

Can anyone help me with the error?  I'm trying to install R-base 2.14.1,
but it is telling me that I need R-base version 2.14.1 as a dependency.  Am
I using the wrong rpm for an installation starting from scratch?

I got the rpm from:
http://download.opensuse.org/repositories/devel:/languages:/R:/base/SLE_10/x86_64/

Thanks,
Matt




pettis@swat:~/bin cat /etc/*-release
SUSE Linux Enterprise Server 10 (x86_64)
VERSION = 10
PATCHLEVEL = 2

pettis@swat:~/bin uname -a
Linux swat 2.6.16.60-0.34-smp #1 SMP Fri Jan 16 14:59:01 UTC 2009 x86_64
x86_64 x86_64 GNU/Linux

pettis@swat:~/bin rpm -ivh R-base-devel-2.14.1-30.1.x86_64.rpm
warning: R-base-devel-2.14.1-30.1.x86_64.rpm: Header V3 DSA signature:
NOKEY, key ID 793371fe
error: Failed dependencies:
R-base = 2.14.1 is needed by R-base-devel-2.14.1-30.1.x86_64

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem Installing R to SuSE 10 via RPM

[Gavin Blackburn]

I think it's saying you need to install R-base before R-base-devel.

You'll need to add a cran repository as SUSE might not have the most up-to-date 
version of R.

This is the code for Ubuntu I assume it's the same, just change the distro and 
keyserver:

sudo apt-get update
sudo add-apt-repository 'deb http://cran.ma.imperial.ac.uk/bin/linux/ubuntu 
oneiric/'
gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg -a --export E084DAB9 | sudo apt-key add -



You may also want to get Sun java, again, change distro and keyserver:

sudo add-apt-repository ppa:ferramroberto/java
sudo apt-key adv --recv-key --keyserver keyserver.ubuntu.com B725097B3ACC3965
sudo apt-get update
sudo apt-get install sun-java6-jdk sun-java6-plugin

Then run:


sudo apt-get install r-base r-base-dev
sudo R CMD javareconf

Cheers,

Gavin.

-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
Behalf Of Matthew Pettis
Sent: 13 January 2012 16:43
To: r-help@r-project.org
Subject: [R] Problem Installing R to SuSE 10 via RPM

Hi,

I'm trying to install R from an rpm locally to my account (the reason I'm
not doing it through yast/yast2/zypper is that the sys admin isn't yet
willing to install it, and doesn't want to support it, but will help me
support it if I install it locally -- in short, policy problems rather than
technical).  Below is the SuSE version, Kernel version, and rpm install
error I'm getting, as well as the error...

Can anyone help me with the error?  I'm trying to install R-base 2.14.1,
but it is telling me that I need R-base version 2.14.1 as a dependency.  Am
I using the wrong rpm for an installation starting from scratch?

I got the rpm from:
http://download.opensuse.org/repositories/devel:/languages:/R:/base/SLE_10/x86_64/

Thanks,
Matt




pettis@swat:~/bin cat /etc/*-release
SUSE Linux Enterprise Server 10 (x86_64)
VERSION = 10
PATCHLEVEL = 2

pettis@swat:~/bin uname -a
Linux swat 2.6.16.60-0.34-smp #1 SMP Fri Jan 16 14:59:01 UTC 2009 x86_64
x86_64 x86_64 GNU/Linux

pettis@swat:~/bin rpm -ivh R-base-devel-2.14.1-30.1.x86_64.rpm
warning: R-base-devel-2.14.1-30.1.x86_64.rpm: Header V3 DSA signature:
NOKEY, key ID 793371fe
error: Failed dependencies:
R-base = 2.14.1 is needed by R-base-devel-2.14.1-30.1.x86_64

[[alternative HTML version deleted]]

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem Installing R to SuSE 10 via RPM

[Matthew Pettis]

Thanks, will do!  I thought devel included base, but evidently, that's not
the case...

On Fri, Jan 13, 2012 at 10:58 AM, Gavin Blackburn 
gavin.blackb...@strath.ac.uk wrote:

 I think it's saying you need to install R-base before R-base-devel.

 You'll need to add a cran repository as SUSE might not have the most
 up-to-date version of R.

 This is the code for Ubuntu I assume it's the same, just change the distro
 and keyserver:

 sudo apt-get update
 sudo add-apt-repository 'deb
 http://cran.ma.imperial.ac.uk/bin/linux/ubuntu oneiric/'
 gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
 gpg -a --export E084DAB9 | sudo apt-key add -



 You may also want to get Sun java, again, change distro and keyserver:

 sudo add-apt-repository ppa:ferramroberto/java
 sudo apt-key adv --recv-key --keyserver keyserver.ubuntu.comB725097B3ACC3965
 sudo apt-get update
 sudo apt-get install sun-java6-jdk sun-java6-plugin

 Then run:


 sudo apt-get install r-base r-base-dev
 sudo R CMD javareconf

 Cheers,

 Gavin.

 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
 On Behalf Of Matthew Pettis
 Sent: 13 January 2012 16:43
 To: r-help@r-project.org
 Subject: [R] Problem Installing R to SuSE 10 via RPM

 Hi,

 I'm trying to install R from an rpm locally to my account (the reason I'm
 not doing it through yast/yast2/zypper is that the sys admin isn't yet
 willing to install it, and doesn't want to support it, but will help me
 support it if I install it locally -- in short, policy problems rather than
 technical).  Below is the SuSE version, Kernel version, and rpm install
 error I'm getting, as well as the error...

 Can anyone help me with the error?  I'm trying to install R-base 2.14.1,
 but it is telling me that I need R-base version 2.14.1 as a dependency.  Am
 I using the wrong rpm for an installation starting from scratch?

 I got the rpm from:

 http://download.opensuse.org/repositories/devel:/languages:/R:/base/SLE_10/x86_64/

 Thanks,
 Matt




 pettis@swat:~/bin cat /etc/*-release
 SUSE Linux Enterprise Server 10 (x86_64)
 VERSION = 10
 PATCHLEVEL = 2

 pettis@swat:~/bin uname -a
 Linux swat 2.6.16.60-0.34-smp #1 SMP Fri Jan 16 14:59:01 UTC 2009 x86_64
 x86_64 x86_64 GNU/Linux

 pettis@swat:~/bin rpm -ivh R-base-devel-2.14.1-30.1.x86_64.rpm
 warning: R-base-devel-2.14.1-30.1.x86_64.rpm: Header V3 DSA signature:
 NOKEY, key ID 793371fe
 error: Failed dependencies:
R-base = 2.14.1 is needed by R-base-devel-2.14.1-30.1.x86_64

 [[alternative HTML version deleted]]

 __
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 http://www.R-project.org/posting-guide.html
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-- 
Do not seek to follow in the footsteps of the wise men of old. Seek what
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[[alternative HTML version deleted]]

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R-help@r-project.org mailing list
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem Installing R to SuSE 10 via RPM

[Marc Schwartz]

Two things:

1. Looking at the sizes of the RPMs at the URL provided, the 'R-base-devel' RPM 
is only 84k. So as with other Linux distros, that is likely to contain R header 
files and other such things to enable compilation of CRAN packages during their 
installation using the source tarballs. The 'R-base' RPM is 33Mb, so that is 
your primary install for R. You will want both.

2. I don't know about the configuration of the RPMs on SUSE, but presume that 
as with RH/Fedora, the RPMs can be created in such a fashion that they are not 
relocatable. That means that they are configured to be only installed 
'system-wide', not to a specific user's directory tree. You may have issues 
trying to install them without root access on your computer, thus may get other 
permission related errors when you get the correct RPM. Whether they are or are 
not relocatable would be a question for the SUSE maintainer for the R package. 
If they are, there are 'rpm' command line arguments that are relevant. So use 
'man rpm' for more details. If the RPMs are not relocatable, you will be left 
with the option of building R from source in order to install R locally and 
will want to read the R Installation and Administration manual for details.

HTH,

Marc Schwartz

On Jan 13, 2012, at 11:00 AM, Matthew Pettis wrote:

 Thanks, will do!  I thought devel included base, but evidently, that's not
 the case...
 
 On Fri, Jan 13, 2012 at 10:58 AM, Gavin Blackburn 
 gavin.blackb...@strath.ac.uk wrote:
 
 I think it's saying you need to install R-base before R-base-devel.
 
 You'll need to add a cran repository as SUSE might not have the most
 up-to-date version of R.
 
 This is the code for Ubuntu I assume it's the same, just change the distro
 and keyserver:
 
 sudo apt-get update
 sudo add-apt-repository 'deb
 http://cran.ma.imperial.ac.uk/bin/linux/ubuntu oneiric/'
 gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
 gpg -a --export E084DAB9 | sudo apt-key add -
 
 
 
 You may also want to get Sun java, again, change distro and keyserver:
 
 sudo add-apt-repository ppa:ferramroberto/java
 sudo apt-key adv --recv-key --keyserver keyserver.ubuntu.comB725097B3ACC3965
 sudo apt-get update
 sudo apt-get install sun-java6-jdk sun-java6-plugin
 
 Then run:
 
 
 sudo apt-get install r-base r-base-dev
 sudo R CMD javareconf
 
 Cheers,
 
 Gavin.
 
 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
 On Behalf Of Matthew Pettis
 Sent: 13 January 2012 16:43
 To: r-help@r-project.org
 Subject: [R] Problem Installing R to SuSE 10 via RPM
 
 Hi,
 
 I'm trying to install R from an rpm locally to my account (the reason I'm
 not doing it through yast/yast2/zypper is that the sys admin isn't yet
 willing to install it, and doesn't want to support it, but will help me
 support it if I install it locally -- in short, policy problems rather than
 technical).  Below is the SuSE version, Kernel version, and rpm install
 error I'm getting, as well as the error...
 
 Can anyone help me with the error?  I'm trying to install R-base 2.14.1,
 but it is telling me that I need R-base version 2.14.1 as a dependency.  Am
 I using the wrong rpm for an installation starting from scratch?
 
 I got the rpm from:
 
 http://download.opensuse.org/repositories/devel:/languages:/R:/base/SLE_10/x86_64/
 
 Thanks,
 Matt
 
 
 
 
 pettis@swat:~/bin cat /etc/*-release
 SUSE Linux Enterprise Server 10 (x86_64)
 VERSION = 10
 PATCHLEVEL = 2
 
 pettis@swat:~/bin uname -a
 Linux swat 2.6.16.60-0.34-smp #1 SMP Fri Jan 16 14:59:01 UTC 2009 x86_64
 x86_64 x86_64 GNU/Linux
 
 pettis@swat:~/bin rpm -ivh R-base-devel-2.14.1-30.1.x86_64.rpm
 warning: R-base-devel-2.14.1-30.1.x86_64.rpm: Header V3 DSA signature:
 NOKEY, key ID 793371fe
 error: Failed dependencies:
   R-base = 2.14.1 is needed by R-base-devel-2.14.1-30.1.x86_64

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problem Installing R to SuSE 10 via RPM

[Ken Hutchison]

apt-get wont run on Suse unless you have aptitude, also your distribution won't 
compile a deb without some intervention. You won't be able to query the package 
regardless of key if your local proxy settings won't let you because of admin. 
Perhaps see if there is a tool to convert the deb package to rpm locally to 
install after downloading the deb, although building from source shouldn't be 
that challenging unless you have ridiculous Fortran compiler problems like I do 
with Linux.
 Hope that helps,
   Ken 


On Jan 13, 2012, at 1:13 PM, Marc Schwartz marc_schwa...@me.com wrote:

 Two things:
 
 1. Looking at the sizes of the RPMs at the URL provided, the 'R-base-devel' 
 RPM is only 84k. So as with other Linux distros, that is likely to contain R 
 header files and other such things to enable compilation of CRAN packages 
 during their installation using the source tarballs. The 'R-base' RPM is 
 33Mb, so that is your primary install for R. You will want both.
 
 2. I don't know about the configuration of the RPMs on SUSE, but presume that 
 as with RH/Fedora, the RPMs can be created in such a fashion that they are 
 not relocatable. That means that they are configured to be only installed 
 'system-wide', not to a specific user's directory tree. You may have issues 
 trying to install them without root access on your computer, thus may get 
 other permission related errors when you get the correct RPM. Whether they 
 are or are not relocatable would be a question for the SUSE maintainer for 
 the R package. If they are, there are 'rpm' command line arguments that are 
 relevant. So use 'man rpm' for more details. If the RPMs are not relocatable, 
 you will be left with the option of building R from source in order to 
 install R locally and will want to read the R Installation and Administration 
 manual for details.
 
 HTH,
 
 Marc Schwartz
 
 On Jan 13, 2012, at 11:00 AM, Matthew Pettis wrote:
 
 Thanks, will do!  I thought devel included base, but evidently, that's not
 the case...
 
 On Fri, Jan 13, 2012 at 10:58 AM, Gavin Blackburn 
 gavin.blackb...@strath.ac.uk wrote:
 
 I think it's saying you need to install R-base before R-base-devel.
 
 You'll need to add a cran repository as SUSE might not have the most
 up-to-date version of R.
 
 This is the code for Ubuntu I assume it's the same, just change the distro
 and keyserver:
 
 sudo apt-get update
 sudo add-apt-repository 'deb
 http://cran.ma.imperial.ac.uk/bin/linux/ubuntu oneiric/'
 gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
 gpg -a --export E084DAB9 | sudo apt-key add -
 
 
 
 You may also want to get Sun java, again, change distro and keyserver:
 
 sudo add-apt-repository ppa:ferramroberto/java
 sudo apt-key adv --recv-key --keyserver keyserver.ubuntu.comB725097B3ACC3965
 sudo apt-get update
 sudo apt-get install sun-java6-jdk sun-java6-plugin
 
 Then run:
 
 
 sudo apt-get install r-base r-base-dev
 sudo R CMD javareconf
 
 Cheers,
 
 Gavin.
 
 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
 On Behalf Of Matthew Pettis
 Sent: 13 January 2012 16:43
 To: r-help@r-project.org
 Subject: [R] Problem Installing R to SuSE 10 via RPM
 
 Hi,
 
 I'm trying to install R from an rpm locally to my account (the reason I'm
 not doing it through yast/yast2/zypper is that the sys admin isn't yet
 willing to install it, and doesn't want to support it, but will help me
 support it if I install it locally -- in short, policy problems rather than
 technical).  Below is the SuSE version, Kernel version, and rpm install
 error I'm getting, as well as the error...
 
 Can anyone help me with the error?  I'm trying to install R-base 2.14.1,
 but it is telling me that I need R-base version 2.14.1 as a dependency.  Am
 I using the wrong rpm for an installation starting from scratch?
 
 I got the rpm from:
 
 http://download.opensuse.org/repositories/devel:/languages:/R:/base/SLE_10/x86_64/
 
 Thanks,
 Matt
 
 
 
 
 pettis@swat:~/bin cat /etc/*-release
 SUSE Linux Enterprise Server 10 (x86_64)
 VERSION = 10
 PATCHLEVEL = 2
 
 pettis@swat:~/bin uname -a
 Linux swat 2.6.16.60-0.34-smp #1 SMP Fri Jan 16 14:59:01 UTC 2009 x86_64
 x86_64 x86_64 GNU/Linux
 
 pettis@swat:~/bin rpm -ivh R-base-devel-2.14.1-30.1.x86_64.rpm
 warning: R-base-devel-2.14.1-30.1.x86_64.rpm: Header V3 DSA signature:
 NOKEY, key ID 793371fe
 error: Failed dependencies:
  R-base = 2.14.1 is needed by R-base-devel-2.14.1-30.1.x86_64
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide

Re: [R] Problem Installing R to SuSE 10 via RPM

[peter dalgaard]

On Jan 13, 2012, at 17:43 , Matthew Pettis wrote:

 Hi,
 
 I'm trying to install R from an rpm locally to my account (the reason I'm
 not doing it through yast/yast2/zypper is that the sys admin isn't yet
 willing to install it, and doesn't want to support it, but will help me
 support it if I install it locally -- in short, policy problems rather than
 technical).  Below is the SuSE version, Kernel version, and rpm install
 error I'm getting, as well as the error...

As others have said, installing from RPM outside the system folders could be a 
no-go. Another option is to install from source, this works fine if you have 
all the relevant packages installed (compilers, libraries, header files...). If 
you don't already have them get your sysadm to install them (say, one per day 
over a couple of weeks, until he sees the error of his ways...).

But really, the painless option for both of you is just to install it from the 
official SUSE sources with yast, keep it updated automagically, and keep all 
add-on packages in your own home directory. The sysadmin workload for R on SUSE 
(and most other Linuxen) should be essentially nil. 

 
 Can anyone help me with the error?  I'm trying to install R-base 2.14.1,
 but it is telling me that I need R-base version 2.14.1 as a dependency.  Am
 I using the wrong rpm for an installation starting from scratch?
 
 I got the rpm from:
 http://download.opensuse.org/repositories/devel:/languages:/R:/base/SLE_10/x86_64/
 
 Thanks,
 Matt
 
 
 
 
 pettis@swat:~/bin cat /etc/*-release
 SUSE Linux Enterprise Server 10 (x86_64)
 VERSION = 10
 PATCHLEVEL = 2
 
 pettis@swat:~/bin uname -a
 Linux swat 2.6.16.60-0.34-smp #1 SMP Fri Jan 16 14:59:01 UTC 2009 x86_64
 x86_64 x86_64 GNU/Linux
 
 pettis@swat:~/bin rpm -ivh R-base-devel-2.14.1-30.1.x86_64.rpm
 warning: R-base-devel-2.14.1-30.1.x86_64.rpm: Header V3 DSA signature:
 NOKEY, key ID 793371fe
 error: Failed dependencies:
R-base = 2.14.1 is needed by R-base-devel-2.14.1-30.1.x86_64
 
   [[alternative HTML version deleted]]
 
 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem in R

[iliketurtles]

data-matrix(rnorm(10))
data[c(1,4,6)]-NA
print(data)
data-matrix(data[!is.na(data)])
print(data)

-


Isaac
Research Assistant
Quantitative Finance Faculty, UTS
--
View this message in context: 
http://r.789695.n4.nabble.com/problem-in-R-tp4260254p4260976.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem in R

[R. Michael Weylandt]

I'm not a huge fan of this sort of solution because it doesn't make
sense for non-vector-shaped (i.e., matrix or data.frame) data. It only
works here because the matrix produced is a special 1xN case.

E.g.,

# Set up some data (and yes, I realize I'm using the trick I'm
speaking out against, but c'est la vie)
testData - matrix(rnorm(20), 5)
testData[c(3,6,7)] - NA

testData[!is.na(testData)] # No longer a matrix so any information
stored in the shape is lost

# I'd prefer something like
testData[complete.cases(testData), ]

or perhaps these sorts of helper functions:

completeRows - function(x){
x[rowSums(is.na(x)) == 0L, ]
}

completeCols - function(x){
x[, colSums(is.na(x)) == 0L]
}

both of which I believe will work for matrices  data.frames. With a
little work, one could make them work for regular vectors as well to
have a general solution.

In general, however, you'll need to figure out what the correct
treatment of NA's for your problem is: some functions like lm(), sum()
etc. can deal with NAs so you don't need to pre-change your input.
(Protip: with lm(), I find people almost always prefer na.exclude to
the default na.omit)

Michael

On Wed, Jan 4, 2012 at 6:01 AM, iliketurtles isaacm...@gmail.com wrote:
 data-matrix(rnorm(10))
 data[c(1,4,6)]-NA
 print(data)
 data-matrix(data[!is.na(data)])
 print(data)

 -
 

 Isaac
 Research Assistant
 Quantitative Finance Faculty, UTS
 --
 View this message in context: 
 http://r.789695.n4.nabble.com/problem-in-R-tp4260254p4260976.html
 Sent from the R help mailing list archive at Nabble.com.

 __
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] problem in R

[iliketurtles]

Michael, thank you for your post, I learned a lot.

Why is it that people prefer na.exclude to na.omit?

-


Isaac
Research Assistant
Quantitative Finance Faculty, UTS
--
View this message in context: 
http://r.789695.n4.nabble.com/problem-in-R-tp4260254p4263119.html
Sent from the R help mailing list archive at Nabble.com.

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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