Re: [Rd] italic font on cairo devices in R 3.4

[Paul Murrell]

Hi

Do you have the 'fonts-texgyre' (Debian) package installed?
If not, does installing that help?

Paul

On 07/07/17 20:30, Ilia Kats wrote:

[cross-post from R-help]

Hi all,

I have the following problem: Since R 3.4.0, italic fonts rendered on 
Cairo devices appear pixelated. Here's a minimal example:

cairo_pdf('test.pdf')
plot(1:10, ylab=expression(italic(test)))
dev.off()

The same problem occurs with bolditalic, but not bold. I am using Debian 
Stretch. Several friends tried the same on their machines, another 
Debian machine has the same problem. On MacOSX the output was not 
pixelated, but it wasn't italic either. Ubuntu 16.04.2 xenial works 
fine. My impression is that R somehow can't find the proper font to use 
and falls back to something weird. Ideas?


Note that I'm not subscribed to the list, so please CC me in replies.

Cheers, Ilia

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--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
p...@stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/

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Re: [Rd] Background session with R

[Norm Matloff]

My Rdsm package will do what you want, 

https://cran.r-project.org/web/packages/Rdsm/index.html

Norm Matloff

> Message: 4
> Date: Mon, 10 Jul 2017 17:12:57 +
> From: "Stravs, Michael" 
> To: "r-devel@r-project.org" 
> Cc: "shiny-disc...@googlegroups.com" 
> Subject: [Rd] Background session with R
> Message-ID:
>   <9dd73f68ac266d4aa329e07b678177b191e37...@ee-mbx3.ee.emp-eaw.ch>
> Content-Type: text/plain; charset="UTF-8"
> 
> Hi,
> 
> I am working on some code to have a background R process running that I can 
> submit data to, check computation progress, and retrieve results later. I am 
> aware that "parallel" does a lot of that - however, "parallel" shuts down the 
> nodes when I quit the master process. On the contrary, I would want these 
> nodes to continue running, so I can fire up R again later and reconnect to 
> the nodes to retrieve the results.
> 
> The use case is Shiny apps, where I want a thin frontend as a GUI, workflow 
> launcher and result viewer, and launch background computation that isn't 
> dependent on the Shiny script staying alive.
> 
> Has this been done already, and/or are there simple modifications of 
> parallel/snow/etc that allow this? My current WIP thing uses Rserve.
> 
> (shiny-discuss cc'd).
> 
> Michael Stravs
> Eawag
> Umweltchemie
> BU E 23
> ?berlandstrasse 133
> 8600 D?bendorf
> +41 58 765 6742

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Re: [Rd] Solaris SPARC testbed

[Prof Brian Ripley]

On 11/07/2017 16:48, Avraham Adler wrote:

I've looked at some package testing results and I'm not seeing Solaris
SPARC. Has that test-bed been deprecated for package testing?


Are you talking about CRAN's check results?

The Sparc hardware used for CRAN died during an unplanned power outage, 
and it seems unlikely it can be resurrected.


But questions about CRAN should be sent to CRAN, and you should give 
credit where it is due if you discuss such services in public fora.


--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

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[Rd] Solaris SPARC testbed

[Avraham Adler]

I've looked at some package testing results and I'm not seeing Solaris
SPARC. Has that test-bed been deprecated for package testing?

Thanks,

Avi

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Re: [R-pkg-devel] MAP-DP Clustering Algorithm package

[Sarah Goslee]

A complete sentence ends in a period.



On Tue, Jul 11, 2017 at 4:19 AM, Thorsten Wagner
 wrote:
> Hi,
>
> I’ve implemented the MAP-DP clustering algorithm in R  following MatLab 
> scripts of this paper:
> http://journals.plos.org/plosone/article/citation?id=10.1371/journal.pone.0162259
>
> Here is the repository:
> https://github.com/thorstenwagner/R-ClustMAPDP
>
> I would like to add the package to CRAN but something seems to be wrong with 
> my description file:
> "Malformed Description field: should contain one or more complete sentences.”
>
> I would be happy if someone could tell me the reason.
>
> Best,
> Thorsten
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-- 
Sarah Goslee
http://www.functionaldiversity.org

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Re: [Rd] write.csv

[Uwe Ligges]

This is a bit difficult:

R binaries (both for R base and R packages) are still built with Windows 
Server 2008 and my desktop machine is Windows 7, hence at least 
currently such a check would not get executed on the machines R core / 
CRAN use ...


Best,
Uwe

On 11.07.2017 00:59, Nathan Sosnovske via R-devel wrote:

As a follow up to this, Martin Maechler suggested that I write a small script 
that allows this to be tested on Windows from R. The attached script 
demonstrates creating and mounting a very small (4 MiB) VHD to a path on the 
system (in this case c:/smallmount) and then calling write.csv with a large 
dataframe to the newly mounted path.

The method I attached has two limitations.

1) It will only work if run as administrator. This is a limitation of the OS.
2) It will only work on Windows 8.1/Server 2012R2 or higher, as it uses 
powershell commands that only exist on those operating systems. I believe it 
could be made to work on Windows 7, but it would need to be written using the 
windows C apis at that point.

If a regression test is created for this issue I would be more than happy to 
integrate this method into that if there is interest and if it would work in 
the environment where automated builds/tests for windows are run.

-Original Message-
From: Nathan Sosnovske
Sent: Tuesday, July 4, 2017 8:02 AM
To: 'Duncan Murdoch' ; Jim Hester 

Cc: r-devel@r-project.org; Lipatz Jean-Luc 
Subject: RE: [Rd] write.csv

The best way to test on Windows would probably be creating a small virtual hard 
disk (via CreateVirtualDisk), mounting it, and writing to the mounted location. 
I believe the drive could even be mounted to an arbitrary location on the 
filesystem (instead of a drive letter) so that drive letter conflicts don't 
come into play.

-Original Message-
From: R-devel [mailto:r-devel-boun...@r-project.org] On Behalf Of Duncan Murdoch
Sent: Tuesday, July 4, 2017 7:53 AM
To: Jim Hester 
Cc: r-devel@r-project.org; Lipatz Jean-Luc 
Subject: Re: [Rd] write.csv

On 04/07/2017 10:01 AM, Jim Hester wrote:

On linux at least you can use `/dev/full` [1] to test writing to a full device.

 > echo 'foo' > /dev/full
 bash: echo: write error: No space left on device


Unfortunately, I get a permission denied error if I try to write there from 
MacOS.  I don't know if Windows has an equivalent.

I've taken a look at the code.  Essentially it comes down to a call to the C 
function vfprintf, which is supposed to return the number of bytes written, or 
a negative value for an error. This return value is often not checked; in 
particular, write.table and friends don't check it.

I'll add code to signal an error if there's a negative value.

I don't think it's feasible to check the number of bytes (formatted text with 
possible translation to a different encoding could have any number of bytes) if 
it's positive.  So hopefully all of our file systems will correctly signal an 
error, and not just report how many bytes were successfully written.



Although that won't be a perfect test for this case where part of the
file is written successfully.

An alternative suggestion for testing this is to create and mount a
loop device [2] with a small file.

[1]:
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wi
kipedia.org%2Fwiki%2F%2Fdev%2Ffull=02%7C01%7Cnsosnov%40microsoft.
com%7Cb97a7371538b4dbe9a7308d4c2ec5aa0%7C72f988bf86f141af91ab2d7cd011d
b47%7C1%7C0%7C636347767773809248=Cb2oduozc2IDCLvXZGG1C4i4hQA7FPs
5jHmnFYbk7zQ%3D=0
[2]:
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstack
overflow.com%2Fa%2F16044420%2F2055486=02%7C01%7Cnsosnov%40microso
ft.com%7Cb97a7371538b4dbe9a7308d4c2ec5aa0%7C72f988bf86f141af91ab2d7cd0
11db47%7C1%7C0%7C636347767773809248=%2BWPfqD0nUS%2F30DUNDqQU79lR
EJh02ZX0yik9HXiY5kg%3D=0


Loop devices sound ideal, but seem to be Linux-only (at least with that recipe).

Duncan




On Tue, Jul 4, 2017 at 3:38 PM, Duncan Murdoch  wrote:

On 04/07/2017 8:40 AM, Lipatz Jean-Luc wrote:


I would really like the bug fixed. At least this one, because I know
people in my institute using this function.
I understand your arguments about open source, but I also saw in
this mail list a proposal for a fix for this bug for which there
were no answer from the people who are able to include it in the
distribution. It looks like if there were interesting bugs and the other ones.



Please post a link to that, and I'll look.  Bug reports should be
posted to the bug list.  It's unfortunate that it is currently so
difficult to do so, but if they are only posted here, they are often overlooked.


I don't understand the other arguments : the example was reproduced
with a simple USB key and you cannot state that a disk will
eternally be empty enough, specially when it has several users.



I am not 

[R-pkg-devel] MAP-DP Clustering Algorithm package

[Thorsten Wagner]

Hi,

I’ve implemented the MAP-DP clustering algorithm in R  following MatLab scripts 
of this paper:
http://journals.plos.org/plosone/article/citation?id=10.1371/journal.pone.0162259

Here is the repository:
https://github.com/thorstenwagner/R-ClustMAPDP

I would like to add the package to CRAN but something seems to be wrong with my 
description file:
"Malformed Description field: should contain one or more complete sentences.”

I would be happy if someone could tell me the reason.

Best,
Thorsten
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