Re: [Rd] RIOT 2020

2020-04-07 Thread Stepan 
After carefully considering the current situation regarding COVID-19, we 
decided to cancel this year's RIOT workshop.


Best regards,
Stepan

On 25. 02. 20 17:38, Stepan wrote:
I hope you don’t mind us using this mailing list for a small 
advertisement, but we think it is most relevant for this group:


We'd like to invite you to RIOT 2020 - the 5rd workshop on R 
Implementation, Optimization and Tooling [1]. It will take place 
co-located with, and during, useR! 2020 in St. Louis on July 8th. RIOT 
is an excellent venue for deep technical discussions about R 
implementations, tools, optimizations and R extension, and will be very 
interesting for anyone interested in what’s under the hood of R.


Regards,
Stepan Sindelar, Lukas Stadler (Oracle Labs), Jan Vitek (Northeastern), 
Alexander Bertram (BeDataDriven)


[1] 
http://riotworkshop.github.io 



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[Rd] Hard memory limit of 16GB under Windows?

2020-04-07 Thread Samuel Granjeaud IR/Inserm 
Hi,
I am not not sure whether this topic belongs to this mail list, but I 
feel the subscribers here should be the right audience.
I noticed that the memory limit reported under Windows is 16 GB. I am 
wondering how to increase it. I didn't found anything in Rprofile.site 
nor .Rprofile. Is this limit hard coded at compilation?
Best,
Samuel
[[alternative HTML version deleted]]

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Re: [Rd] Hard memory limit of 16GB under Windows?

2020-04-07 Thread Tomas Kalibera 

Hi Samuel,

could you please provide more information? Where do you see the limit 
reported or how did you trigger it, what version of Windows do you have, 
are you using 64-bit build of R (sessionInfo())


Please check help("Memory-limits") and section 8 of R Admin manual

Best,
Tomas

On 4/7/20 1:35 PM, Samuel Granjeaud IR/Inserm wrote:

Hi,
I am not not sure whether this topic belongs to this mail list, but I
feel the subscribers here should be the right audience.
I noticed that the memory limit reported under Windows is 16 GB. I am
wondering how to increase it. I didn't found anything in Rprofile.site
nor .Rprofile. Is this limit hard coded at compilation?
Best,
Samuel
[[alternative HTML version deleted]]

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Re: [Rd] Hard memory limit of 16GB under Windows?

2020-04-07 Thread Samuel Granjeaud IR/Inserm 

Hi Tomas,

Many thanks for your answer.

Here is a copy of a fresh session under RStudio, and after a copy under 
Rgui.
Strangely enough the result of memory.limit() is not the same. Without 
your question I would not have looked to RGui, being used to work with 
RStudio.


The value under RGui sounds to correspond to the total RAM of the 
computer. It makes me noticing that the value is in MB.


The value under Rstudio was so huge (1.759219e+13) that I just 
interpreted it as GB. But I was totally wrong. So in fact I don't know 
what it refers to. The documentation says "For a 64-bit versions of R 
under 64-bit Windows the limit is currently 8Tb.", but it looks like 
being 16TB, which my computer don't have of course.


I still have to understand why my colleague has a problem of memory 
allocation (cannot allocate vector of size 12.6 Gb).


Sorry for the wrong interpretation, but thanks for the help,
Samuel

--- RStudio

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.

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.

> memory.limit()
[1] 1.759219e+13
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
LC_MONETARY=French_France.1252 LC_NUMERIC=C

[5] LC_TIME=French_France.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_3.6.3 tools_3.6.3
>

--- RGui

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.

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.

> ls()
character(0)
> memory.limit()
[1] 32627
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
LC_MONETARY=French_France.1252

[4] LC_NUMERIC=C   LC_TIME=French_France.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_3.6.3
>

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Re: [Rd] Hard memory limit of 16GB under Windows?

2020-04-07 Thread Tomas Kalibera 

Hi Samuel,

please also have a look at ?memory.limit. You can set this limit at R 
startup. It is in megabytes. Maybe R Studio sets it at runtime.


Best
Tomas

On 4/7/20 3:57 PM, Samuel Granjeaud IR/Inserm wrote:

Hi Tomas,

Many thanks for your answer.

Here is a copy of a fresh session under RStudio, and after a copy 
under Rgui.
Strangely enough the result of memory.limit() is not the same. Without 
your question I would not have looked to RGui, being used to work with 
RStudio.


The value under RGui sounds to correspond to the total RAM of the 
computer. It makes me noticing that the value is in MB.


The value under Rstudio was so huge (1.759219e+13) that I just 
interpreted it as GB. But I was totally wrong. So in fact I don't know 
what it refers to. The documentation says "For a 64-bit versions of R 
under 64-bit Windows the limit is currently 8Tb.", but it looks like 
being 16TB, which my computer don't have of course.


I still have to understand why my colleague has a problem of memory 
allocation (cannot allocate vector of size 12.6 Gb).


Sorry for the wrong interpretation, but thanks for the help,
Samuel

--- RStudio

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.

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.

> memory.limit()
[1] 1.759219e+13
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252 
LC_MONETARY=French_France.1252 LC_NUMERIC=C

[5] LC_TIME=French_France.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods base

loaded via a namespace (and not attached):
[1] compiler_3.6.3 tools_3.6.3
>

--- RGui

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.

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.

> ls()
character(0)
> memory.limit()
[1] 32627
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252 
LC_MONETARY=French_France.1252

[4] LC_NUMERIC=C   LC_TIME=French_France.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods base

loaded via a namespace (and not attached):
[1] compiler_3.6.3
>



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Re: [Rd] Hard memory limit of 16GB under Windows?

2020-04-07 Thread Marc Schwartz via R-devel 
Hi Samuel,

You may already be aware, but if not, RStudio has their own support mechanisms 
here:

  https://support.rstudio.com/hc/en-us

If this does turn out to be RStudio specific, you may wish to check there for 
additional insights.

Regards,

Marc Schwartz


> On Apr 7, 2020, at 10:24 AM, Tomas Kalibera  wrote:
> 
> Hi Samuel,
> 
> please also have a look at ?memory.limit. You can set this limit at R 
> startup. It is in megabytes. Maybe R Studio sets it at runtime.
> 
> Best
> Tomas
> 
> On 4/7/20 3:57 PM, Samuel Granjeaud IR/Inserm wrote:
>> Hi Tomas,
>> 
>> Many thanks for your answer.
>> 
>> Here is a copy of a fresh session under RStudio, and after a copy under Rgui.
>> Strangely enough the result of memory.limit() is not the same. Without your 
>> question I would not have looked to RGui, being used to work with RStudio.
>> 
>> The value under RGui sounds to correspond to the total RAM of the computer. 
>> It makes me noticing that the value is in MB.
>> 
>> The value under Rstudio was so huge (1.759219e+13) that I just interpreted 
>> it as GB. But I was totally wrong. So in fact I don't know what it refers 
>> to. The documentation says "For a 64-bit versions of R under 64-bit Windows 
>> the limit is currently 8Tb.", but it looks like being 16TB, which my 
>> computer don't have of course.
>> 
>> I still have to understand why my colleague has a problem of memory 
>> allocation (cannot allocate vector of size 12.6 Gb).
>> 
>> Sorry for the wrong interpretation, but thanks for the help,
>> Samuel
>> 
>> --- RStudio
>> 
>> R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
>> 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.
>> 
>> 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.
>> 
>> > memory.limit()
>> [1] 1.759219e+13
>> > sessionInfo()
>> R version 3.6.3 (2020-02-29)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> Running under: Windows 10 x64 (build 18363)
>> 
>> Matrix products: default
>> 
>> locale:
>> [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252 
>> LC_MONETARY=French_France.1252 LC_NUMERIC=C
>> [5] LC_TIME=French_France.1252
>> 
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods base
>> 
>> loaded via a namespace (and not attached):
>> [1] compiler_3.6.3 tools_3.6.3
>> >
>> 
>> --- RGui
>> 
>> R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
>> 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.
>> 
>> 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.
>> 
>> > ls()
>> character(0)
>> > memory.limit()
>> [1] 32627
>> > sessionInfo()
>> R version 3.6.3 (2020-02-29)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> Running under: Windows 10 x64 (build 18363)
>> 
>> Matrix products: default
>> 
>> locale:
>> [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252 
>> LC_MONETARY=French_France.1252
>> [4] LC_NUMERIC=C   LC_TIME=French_France.1252
>> 
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods base
>> 
>> loaded via a namespace (and not attached):
>> [1] compiler_3.6.3
>> >
>> 
> 
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Re: [Rd] Rtools and R 4.0.0?

2020-04-07 Thread Dirk Eddelbuettel 


There appears to have been some progress on this matter:

-Note that @command{g++} 4.9.x (as used for @R{} on Windows up to 3.6.x)
+Note that @command{g++} 4.9.x (as used on Windows prior to @R{} 4.0.0)

See SVN commit r78169 titled 'anticipate change in Windows toolchain', or the
mirrored git commit at 
https://github.com/wch/r-source/commit/bd674e2b76b2384169424e3d899fbfb5ac174978

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [Rd] Hard memory limit of 16GB under Windows?

2020-04-07 Thread Thierry Onkelinx via R-devel 
Dear Samuel,

The most important information from your mail was the actual error message:
"cannot allocate vector of size 12.6 Gb".

You'll need to know what code generated this error message. And then figure
out if the code does something sensible. Often that is not the case when
you get a similar error message.

Best regards,

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

///
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///




Op di 7 apr. 2020 om 16:16 schreef Samuel Granjeaud IR/Inserm <
samuel.granje...@inserm.fr>:

> Hi Tomas,
>
> Many thanks for your answer.
>
> Here is a copy of a fresh session under RStudio, and after a copy under
> Rgui.
> Strangely enough the result of memory.limit() is not the same. Without
> your question I would not have looked to RGui, being used to work with
> RStudio.
>
> The value under RGui sounds to correspond to the total RAM of the
> computer. It makes me noticing that the value is in MB.
>
> The value under Rstudio was so huge (1.759219e+13) that I just
> interpreted it as GB. But I was totally wrong. So in fact I don't know
> what it refers to. The documentation says "For a 64-bit versions of R
> under 64-bit Windows the limit is currently 8Tb.", but it looks like
> being 16TB, which my computer don't have of course.
>
> I still have to understand why my colleague has a problem of memory
> allocation (cannot allocate vector of size 12.6 Gb).
>
> Sorry for the wrong interpretation, but thanks for the help,
> Samuel
>
> --- RStudio
>
> R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
> 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.
>
> 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.
>
>  > memory.limit()
> [1] 1.759219e+13
>  > sessionInfo()
> R version 3.6.3 (2020-02-29)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 18363)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
> LC_MONETARY=French_France.1252 LC_NUMERIC=C
> [5] LC_TIME=French_France.1252
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] compiler_3.6.3 tools_3.6.3
>  >
>
> --- RGui
>
> R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
> 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.
>
> 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.
>
>  > ls()
> character(0)
>  > memory.limit()
> [1] 32627
>  > sessionInfo()
> R version 3.6.3 (2020-02-29)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 18363)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
> LC_MONETARY=French_France.1252
> [4] LC_NUMERIC=C   LC_TIME=French_France.1252
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] compiler_3.6.3
>  >
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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Re: [Rd] Rtools and R 4.0.0?

2020-04-07 Thread Kevin Ushey 
That's great to see, although I suspect it's still a speculative
change and could be backed out if any non-trivial issues were
encountered.

Regardless, I would like to thank R core, CRAN, and Jeroen for all of
the time that has gone into creating and validating this new
toolchain. This is arduous work at an especially arduous time, so I'd
like to voice my appreciation for all the time and energy they have
spent on making this possible.

Best,
Kevin

On Tue, Apr 7, 2020 at 7:47 AM Dirk Eddelbuettel  wrote:
>
>
> There appears to have been some progress on this matter:
>
> -Note that @command{g++} 4.9.x (as used for @R{} on Windows up to 3.6.x)
> +Note that @command{g++} 4.9.x (as used on Windows prior to @R{} 4.0.0)
>
> See SVN commit r78169 titled 'anticipate change in Windows toolchain', or the
> mirrored git commit at
> https://github.com/wch/r-source/commit/bd674e2b76b2384169424e3d899fbfb5ac174978
>
> Dirk
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>
> __
> R-devel@r-project.org mailing list
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Re: [Rd] [SPAM] Hard memory limit of 16GB under Windows?

2020-04-07 Thread Michael Dewey 

Dear Samuel

Does the FAQ for Windows section 2.9 help you here?

Michael

On 07/04/2020 12:35, Samuel Granjeaud IR/Inserm wrote:

Hi,
I am not not sure whether this topic belongs to this mail list, but I
feel the subscribers here should be the right audience.
I noticed that the memory limit reported under Windows is 16 GB. I am
wondering how to increase it. I didn't found anything in Rprofile.site
nor .Rprofile. Is this limit hard coded at compilation?
Best,
Samuel
[[alternative HTML version deleted]]

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http://www.dewey.myzen.co.uk/home.html

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Re: [Rd] Hard memory limit of 16GB under Windows?

2020-04-07 Thread Hervé Pagès 
Agreed. I don't see any evidence of a "hard limit" here. It just looks 
like the code you're running has exhausted the memory of your machine. 
It doesn't require creating a lot of 12.6 Gb vectors to do that, even on 
a machine with a lot of memory ;-)


H.

On 4/7/20 08:05, Thierry Onkelinx via R-devel wrote:

Dear Samuel,

The most important information from your mail was the actual error message:
"cannot allocate vector of size 12.6 Gb".

You'll need to know what code generated this error message. And then figure
out if the code does something sensible. Often that is not the case when
you get a similar error message.

Best regards,

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.inbo.be&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=r6WLJ5dXWo2qb7mQwONaCxYeeWgKwycd3y89JoqY-oY&s=VNmTfuiByvneqd4lcQS0o961TZa3ygo2Rdp7AtiGnk0&e=

///
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///




Op di 7 apr. 2020 om 16:16 schreef Samuel Granjeaud IR/Inserm <
samuel.granje...@inserm.fr>:


Hi Tomas,

Many thanks for your answer.

Here is a copy of a fresh session under RStudio, and after a copy under
Rgui.
Strangely enough the result of memory.limit() is not the same. Without
your question I would not have looked to RGui, being used to work with
RStudio.

The value under RGui sounds to correspond to the total RAM of the
computer. It makes me noticing that the value is in MB.

The value under Rstudio was so huge (1.759219e+13) that I just
interpreted it as GB. But I was totally wrong. So in fact I don't know
what it refers to. The documentation says "For a 64-bit versions of R
under 64-bit Windows the limit is currently 8Tb.", but it looks like
being 16TB, which my computer don't have of course.

I still have to understand why my colleague has a problem of memory
allocation (cannot allocate vector of size 12.6 Gb).

Sorry for the wrong interpretation, but thanks for the help,
Samuel

--- RStudio

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.

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.

  > memory.limit()
[1] 1.759219e+13
  > sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_3.6.3 tools_3.6.3
  >

--- RGui

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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.

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.

  > ls()
character(0)
  > memory.limit()
[1] 32627
  > sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Runni

[Rd] ASAN

2020-04-07 Thread Therneau, Terry M., Ph.D. via R-devel 
I'm trying to chase down a possible issue with the survival package, and 
so was trying to resurrect my ASAN version of r-devel.   I added the 
lines to config.site for CC, CFLAGS and MAIN_LDFLAGS per section 4.3.3 
of the  'packages' documentation, and lines to ~/.R/Makevars.

I followed that with  svn up,  tools/rsync-recommended, make distclean, 
./configure, then make.

It fails on the rebuild of MASS with the message

==15755==ASan runtime does not come first in initial library list; you 
should either link runtime to your application or manually preload it 
with LD_PRELOAD.
ERROR: loading failed
* removing ‘/usr/local/src/R-devel/library/MASS’

It's not quite clear to me what to do next.

Terry Therneau



[[alternative HTML version deleted]]

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Re: [Rd] Plotmath on Fedora 31 broken with with pango >= 1.44 - workarounds?

2020-04-07 Thread Paul Murrell 



The R-symfam branch (r78176) is now working, for my basic tests, on ...

Ubuntu (pango < 1.44)
Ubuntu (no pango)
Fedora (pango > 1.44)
Windows

I need help to confirm that this builds on macOS and that the basic 
tests work ...


https://github.com/pmur002/R-symfam-testing

Brian has been helping with the build, but I am still looking for 
someone who can run the tests please.  Happy to be fed PDF files to 
scrutinize myself;  it's generating the PDF files on macOS that I need 
help with.


Paul

On 6/04/20 2:59 pm, Paul Murrell wrote:

Hi

The R branch ...

https://svn.r-project.org/R/branches/R-symfam/

... is now set up so that it works "out of the box" on Fedora by setting 
the default to be 'symbolfamily=cairoSymbolFont(family, usePUA=FALSE)' 
when grSoftVersion()["pango"] is greater than "1.44".


This means that on Fedora 31 (at least on the Docker container I am 
testing on) "sans"->"NimubusSans" is used as the symbol font by default 
and R converts Adobe Symbol Encoding code points to non-PUA UTF8 code 
points.  This is not the prettiest result, but it is a lot better than 
the page full of missing glyphs that we had.


The default on less "bleeding edge" systems, e.g., my Ubuntu 18.04, 
remains 'symbolfamily="Symbol"'.


The default on other platforms is supposed to be the same as it was, but 
I need help to confirm that.  I have set up a github repo ...


https://github.com/pmur002/R-symfam-testing

... that describes how to test this on macOS and Windows if anyone has 
time to do so.


I will start trying to set up a Windows test unless someone beats me to it.

Paul

On 30/03/20 3:24 pm, Paul Murrell wrote:

Hi

I have created an R branch that contains a potential fix ...

https://svn.r-project.org/R/branches/R-symfam/

This allows, for example, ...

cairo_pdf(symbolfamily="OpenSymbol")

... to specify that the OpenSymbol family should be used as the 
"symbol" font (e.g., for "plotmath") in R.


This is just a separate branch for now because, while I have tested it 
under Unbuntu 18.04 and Fedora 31, I cannot even build R for Windows 
(right now) or Mac (ever) and I do not want to drop a bomb on R-devel 
at this stage of the release process for R 4.0.0.


The attached file contains at least an outline of steps required to do 
a minimal test if anyone wants to try the fix on Linux.


cc'ing Simon and Jeroen in case they are able to help with checking 
that this builds and works on Mac and/or Windows.


NOTEs:
- 'symbolfamily' can only be specified when a graphics device is 
opened, and it is then fixed for that device.
- on Windows, for cairo-based devices, the "symbol" font is still 
hard-coded as "Standard Symbols L"


Paul

On 30/03/20 8:15 am, Paul Murrell wrote:

Hi

Thanks for your input on this Iñaki and Nicolas.

I am starting testing an R fix for this problem today.

As suggested, the plan is to allow the R user to specify a font 
family other than "symbol" for plotmath output (or, more generally, 
in R parlance, for 'font=5' or 'fontface=5') on a Cairo-based 
graphics device.


Paul


On 27/03/20 11:30 pm, Iñaki Ucar wrote:

On Wed, 25 Mar 2020 at 12:25, Nicolas Mailhot
 wrote:




R brought this all on itself by hardcoding a Windows-only “Symbol” 
font
family name in its default conf. Linux systems are UTF-8 by default 
for

~20 years now, they don’t need the forcing of magic font families to
handle symbols not present in the 8-bit legacy Windows encodings.

The actual effect of this conf is not the selection of font files with
special and unusual symbols. It is to priorize fonts that match the
"Symbol" magic name. And those fonts are few and crumbling on Linux
systems, because no one has needed to bother with them since Linux
switched to UTF-8 last millenium.

Just stop using “Symbol” in R and things will work a lot better.
Alternatively, prepare to maintain the “Symbol” aliasing stack in
fontconfig (and fight with wine for it), because *no* *one* *else*
*cares* about this legacy Windows-specific stuff.


So, in the light of Nicolas' input (thanks!), I think that font
selection should be fixed upstream in R. I'd be happy to put all this
together in R's bugzilla, but I don't have an account. Could someone
please invite me?

Iñaki

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Department of Statistics
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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] Plotmath on Fedora 31 broken with with pango >= 1.44 - workarounds?

2020-04-07 Thread Gabriel Becker 
Paul et al,

I will try to do this tonight or tomorrow, though it will not be built with
th system tools because I have yet to get that tto work locally (spent a
good chunk of this morning trying).

I will send a separate messaage regarding those difficulties as well so
that we can at least confirm that they are due to a malconfiguration on my
part.

Best,
~G

On Tue, Apr 7, 2020 at 7:25 PM Paul Murrell 
wrote:

>
> The R-symfam branch (r78176) is now working, for my basic tests, on ...
>
> Ubuntu (pango < 1.44)
> Ubuntu (no pango)
> Fedora (pango > 1.44)
> Windows
>
> I need help to confirm that this builds on macOS and that the basic
> tests work ...
>
> https://github.com/pmur002/R-symfam-testing
>
> Brian has been helping with the build, but I am still looking for
> someone who can run the tests please.  Happy to be fed PDF files to
> scrutinize myself;  it's generating the PDF files on macOS that I need
> help with.
>
> Paul
>
> On 6/04/20 2:59 pm, Paul Murrell wrote:
> > Hi
> >
> > The R branch ...
> >
> > https://svn.r-project.org/R/branches/R-symfam/
> >
> > ... is now set up so that it works "out of the box" on Fedora by setting
> > the default to be 'symbolfamily=cairoSymbolFont(family, usePUA=FALSE)'
> > when grSoftVersion()["pango"] is greater than "1.44".
> >
> > This means that on Fedora 31 (at least on the Docker container I am
> > testing on) "sans"->"NimubusSans" is used as the symbol font by default
> > and R converts Adobe Symbol Encoding code points to non-PUA UTF8 code
> > points.  This is not the prettiest result, but it is a lot better than
> > the page full of missing glyphs that we had.
> >
> > The default on less "bleeding edge" systems, e.g., my Ubuntu 18.04,
> > remains 'symbolfamily="Symbol"'.
> >
> > The default on other platforms is supposed to be the same as it was, but
> > I need help to confirm that.  I have set up a github repo ...
> >
> > https://github.com/pmur002/R-symfam-testing
> >
> > ... that describes how to test this on macOS and Windows if anyone has
> > time to do so.
> >
> > I will start trying to set up a Windows test unless someone beats me to
> it.
> >
> > Paul
> >
> > On 30/03/20 3:24 pm, Paul Murrell wrote:
> >> Hi
> >>
> >> I have created an R branch that contains a potential fix ...
> >>
> >> https://svn.r-project.org/R/branches/R-symfam/
> >>
> >> This allows, for example, ...
> >>
> >> cairo_pdf(symbolfamily="OpenSymbol")
> >>
> >> ... to specify that the OpenSymbol family should be used as the
> >> "symbol" font (e.g., for "plotmath") in R.
> >>
> >> This is just a separate branch for now because, while I have tested it
> >> under Unbuntu 18.04 and Fedora 31, I cannot even build R for Windows
> >> (right now) or Mac (ever) and I do not want to drop a bomb on R-devel
> >> at this stage of the release process for R 4.0.0.
> >>
> >> The attached file contains at least an outline of steps required to do
> >> a minimal test if anyone wants to try the fix on Linux.
> >>
> >> cc'ing Simon and Jeroen in case they are able to help with checking
> >> that this builds and works on Mac and/or Windows.
> >>
> >> NOTEs:
> >> - 'symbolfamily' can only be specified when a graphics device is
> >> opened, and it is then fixed for that device.
> >> - on Windows, for cairo-based devices, the "symbol" font is still
> >> hard-coded as "Standard Symbols L"
> >>
> >> Paul
> >>
> >> On 30/03/20 8:15 am, Paul Murrell wrote:
> >>> Hi
> >>>
> >>> Thanks for your input on this Iñaki and Nicolas.
> >>>
> >>> I am starting testing an R fix for this problem today.
> >>>
> >>> As suggested, the plan is to allow the R user to specify a font
> >>> family other than "symbol" for plotmath output (or, more generally,
> >>> in R parlance, for 'font=5' or 'fontface=5') on a Cairo-based
> >>> graphics device.
> >>>
> >>> Paul
> >>>
> >>>
> >>> On 27/03/20 11:30 pm, Iñaki Ucar wrote:
>  On Wed, 25 Mar 2020 at 12:25, Nicolas Mailhot
>   wrote:
> >
> > 
> >
> > R brought this all on itself by hardcoding a Windows-only “Symbol”
> > font
> > family name in its default conf. Linux systems are UTF-8 by default
> > for
> > ~20 years now, they don’t need the forcing of magic font families to
> > handle symbols not present in the 8-bit legacy Windows encodings.
> >
> > The actual effect of this conf is not the selection of font files
> with
> > special and unusual symbols. It is to priorize fonts that match the
> > "Symbol" magic name. And those fonts are few and crumbling on Linux
> > systems, because no one has needed to bother with them since Linux
> > switched to UTF-8 last millenium.
> >
> > Just stop using “Symbol” in R and things will work a lot better.
> > Alternatively, prepare to maintain the “Symbol” aliasing stack in
> > fontconfig (and fight with wine for it), because *no* *one* *else*
> > *cares* about this legacy Windows-specific stuff.
> 
>  So, in the light of Nicolas' input (thanks!), I t