Re: [R] Off-topic: ChatGPT Code Interpreter

2023-07-17 Thread Rui Barradas

Às 00:23 de 18/07/2023, Jim Lemon escreveu:

I haven't really focused on the statistical capabilities of AI, that
marriage of massive memory and associative learning. I am impressed by
its ability to perform text-to-image conversion, something I have
recently needed. My artistic ability is that of the average three year
old, yet I can employ AI to translate my mental images into realistic
pictures. Perhaps we really are learning about how we think. As far as
I am aware, it just does what we tell it to do. Like other tools, it
is as good or bad as the user.

Jim

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Hello,

Also off-topic but the date is fun:


A system is not a head.
Furniture is not people.
All processes and all devices,
will be useless for organizations,
if the heads of the individuals who employ them,
are not properly organized.
And these heads will be organized,
if the same part of the boss's body that directs them
is properly organized.
Just like you can write nonsense
with a latest model typewriter,
nonsense can also be done
with the most perfect systems and devices
meant to help you not to.
Systems, processes, furniture, machines,
are purely auxiliary elements.
The real process is to think.
The fundamental machine is intelligence.

Fernando Pessoa, 1926

Revista de Comércio e Contabilidade, nº 4. Lisboa, 25-4-1926.
(Magazine of Commerce and Accounting, nº 4. Lisbon, 25-4-1926)


Rui Barradas

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Re: [R] how to change the y-axis to logarithmic in a barplot ggplot

2023-07-17 Thread Kimmo Elo
Hi,

Have you tried:

scale_y_continuous(trans='log10')

HTH,

Kimmo

Lähettäjä: Maria Lathouri via R-help 
Lähetetty: maanantai 17. heinäkuuta 2023 23.01.57
Vastaanottaja: Maria Lathouri via R-help; Ivan Krylov
Aihe: Re: [R] how to change the y-axis to logarithmic in a barplot ggplot

Hi Ivan,

yes you are right. I have many values close to zero and if I use log, they are 
instantly transformed to negative values and then the bars show above. The sqrt 
trans worked ok but when I used the pseudo_log_trans, it did the work!

Many thanks.

Kind regards,
Maria






Στις Δευτέρα 17 Ιουλίου 2023 στις 04:43:59 π.μ. GMT+1, ο χρήστης Ivan Krylov 
 έγραψε:





On Sun, 16 Jul 2023 21:51:10 + (UTC)

Maria Lathouri via R-help  wrote:

> As you can see, the values range from 0 to 400. I want it to plot it
> in bars; when I am plotting it as you can imagine the values near
> zero don't show at all.


A logarithmic scale won't work when the range of numbers to display
includes 0. It would have worked if it was some small non-zero
quantity, but an actual zero is infinitely far down; it won't fit.

There is a number of transformations described in
help(scale_y_continuous). You may find trans="pseudo_log" or
trans="sqrt" useful.

help(geom_bar) recommends geom_col() instead of geom_bar() to represent
values (not counts of occurrences).

We could help you more efficiently if you clarified the relationship
between your data (with columns `ID`, `values`, `databases`) and your
code (which mentions `Temp`, `mean`, `Glass`).

--
Best regards,
Ivan

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Re: [R] Off-topic: ChatGPT Code Interpreter

2023-07-17 Thread Jim Lemon
I haven't really focused on the statistical capabilities of AI, that
marriage of massive memory and associative learning. I am impressed by
its ability to perform text-to-image conversion, something I have
recently needed. My artistic ability is that of the average three year
old, yet I can employ AI to translate my mental images into realistic
pictures. Perhaps we really are learning about how we think. As far as
I am aware, it just does what we tell it to do. Like other tools, it
is as good or bad as the user.

Jim

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Re: [R] how to change the y-axis to logarithmic in a barplot ggplot

2023-07-17 Thread Maria Lathouri via R-help
Hi Ivan, 

yes you are right. I have many values close to zero and if I use log, they are 
instantly transformed to negative values and then the bars show above. The sqrt 
trans worked ok but when I used the pseudo_log_trans, it did the work!

Many thanks. 

Kind regards,
Maria






Στις Δευτέρα 17 Ιουλίου 2023 στις 04:43:59 π.μ. GMT+1, ο χρήστης Ivan Krylov 
 έγραψε: 





On Sun, 16 Jul 2023 21:51:10 + (UTC)

Maria Lathouri via R-help  wrote:

> As you can see, the values range from 0 to 400. I want it to plot it
> in bars; when I am plotting it as you can imagine the values near
> zero don't show at all.


A logarithmic scale won't work when the range of numbers to display
includes 0. It would have worked if it was some small non-zero
quantity, but an actual zero is infinitely far down; it won't fit.

There is a number of transformations described in
help(scale_y_continuous). You may find trans="pseudo_log" or
trans="sqrt" useful.

help(geom_bar) recommends geom_col() instead of geom_bar() to represent
values (not counts of occurrences).

We could help you more efficiently if you clarified the relationship
between your data (with columns `ID`, `values`, `databases`) and your
code (which mentions `Temp`, `mean`, `Glass`).

-- 
Best regards,
Ivan

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Re: [R] how to change the y-axis to logarithmic in a barplot ggplot

2023-07-17 Thread Maria Lathouri via R-help
Dear Bert, 

Thank you very much for the tip. The reason that I took the initiative to write 
here is because I receive here as well questions about ggplot. Next time I will 
use the ggplot help. 

Maria






Στις Δευτέρα 17 Ιουλίου 2023 στις 12:20:25 π.μ. GMT+1, ο χρήστης Bert Gunter 
 έγραψε: 





Maria,

ggplot is part of the Posit -- formerly RStudio -- assortment of contributed 
packages. They have their own support site here , which you *may* find useful 
for such questions, also. Though ggplot queries *are* frequently posted and 
answered on R-Help.

Cheers,
Bert

On Sun, Jul 16, 2023 at 3:58 PM Maria Lathouri via R-help 
 wrote:
> I will find the ggplot help. 
> 
> But I have tried everything, including what you have suggested and nothing 
> works.
> 
> Kind regards,
> Maria
> 
> 
> 
> 
> 
> 
> Στις Κυριακή 16 Ιουλίου 2023 στις 11:22:36 μ.μ. GMT+1, ο χρήστης CALUM 
> POLWART  έγραψε: 
> 
> 
> 
> 
> 
> Try adding
> 
> scale_y_log10()
> 
> This is a general R help list. It's not a ggplot list and you are likely to 
> be chased off to ggplot's package maintainers nominated support pages.
> 
> But really a Google search should surely have found this?
> 
> 
> 
> On Sun, 16 Jul 2023, 22:51 Maria Lathouri via R-help,  
> wrote:
>> Dear all, 
>> 
>> ggplot(fc, aes(x = Temp, y = mean, fill = Glass)) + 
>> geom_bar(stat = "identity", position = "dodge", aes(y=log(mean))) 
>> + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = 
>> element_blank()) + theme(legend.position = c(0.45, 0.85), legend.title = 
>> element_blank()) 
>> + scale_fill_brewer(palette = "Dark2") + scale_color_brewer(palette = 
>> "Dark2") +
>> 
> scale_y_log10()
> 
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
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> and provide commented, minimal, self-contained, reproducible code.
> 

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Re: [R] Obtaining R-squared from All Possible Combinations of Linear Models Fitted

2023-07-17 Thread John C Frain
MuMln is a package designed to select optimum models mainly based on
information criteria.  R-squared is not a suitable criterion for this
purpose.   As far as I can see is not covered in this package.  (I presume
you already know that R-squared for the model with all possible regressors
is at least as great as R with any subset of the regressors).

If you want to calculate all these R-squared's it should be easy to write a
small routine to estimate them.  I am very curious as to why you wish to do
this.


John C Frain.
3 Aranleigh Park
Rathfarnham
Dublin 14
Ireland
www.tcd.ie/Economics/staff/frainj/home.html
https://jcfrain.wordpress.com/
https://jcfraincv19.wordpress.com/

mailto:fra...@tcd.ie
mailto:fra...@gmail.com


On Mon, 17 Jul 2023 at 18:25, Paul Bernal  wrote:

> Dear friends,
>
> I need to automatically fit all possible linear regression models (with all
> possible combinations of regressors), and found the MuMIn package, which
> has the dredge function.
>
> This is the dataset  I am working with:
> > dput(final_frame)
> structure(list(y = c(41.9, 44.5, 43.9, 30.9, 27.9, 38.9, 30.9,
> 28.9, 25.9, 31, 29.5, 35.9, 37.5, 37.9), x1 = c(6.6969, 8.7951,
> 9.0384, 5.9592, 4.5429, 8.3607, 5.898, 5.6039, 4.9176, 6.2712,
> 5.0208, 5.8282, 5.9894, 7.5422), x4 = c(1.488, 1.82, 1.5, 1.121,
> 1.175, 1.777, 1.24, 1.501, 0.998, 0.975, 1.5, 1.225, 1.256, 1.69
> ), x8 = c(22, 50, 23, 32, 40, 48, 51, 32, 42, 30, 62, 32, 40,
> 22), x2 = c(1.5, 1.5, 1, 1, 1, 1.5, 1, 1, 1, 1, 1, 1, 1, 1.5),
> x7 = c(3, 4, 3, 3, 3, 4, 3, 3, 4, 2, 4, 3, 3, 3)), class =
> "data.frame", row.names = c(NA,
> -14L))
>
> I started with the all regressor model, which I called globalmodel as
> follows:
> #Fitting Regression model with all possible combinations of regressors
> options(na.action = "na.fail") # change the default "na.omit" to prevent
> models
> globalmodel <- lm(y~., data=final_frame)
>
> Then, the following code provides the different coefficients (for
> regressors and the intercept) for each of the possible model combinations:
> combinations <- dredge(globalmodel)
> print(combinations)
>  I would like to retrieve  the R-squared generated by each combination, but
> have not been able to get it thus far.
>
> Any guidance on how to retrieve the R-squared from all linear model
> combinations would be greatly appreciated.
>
> Kind regards,
> Paul
>
> [[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] Off-topic: ChatGPT Code Interpreter

2023-07-17 Thread Ebert,Timothy Aaron
This seems spot on, given that Paul Bernal just posted a request to fit all 
possible models and compare them using r-squared. The all models approach does 
not promote understanding about what your model is saying about the data and 
how the system works. Nor does it facilitate fitting the methods to best 
address the research goals.
Tim

-Original Message-
From: R-help  On Behalf Of Bert Gunter
Sent: Monday, July 17, 2023 2:46 PM
To: R-help 
Subject: [R] Off-topic: ChatGPT Code Interpreter

[External Email]

This is an **off-topic** post about the subject line, that I thought might be 
of interest to the R Community. I hope this does not offend anyone.

The widely known ChatGPT software now offers what  is called a "Code 
Interpreter," that, among other things, purports to do "data analysis."  
(Search for articles with details.) One quote, from the
(online) NY Times, is:

"Arvind Narayanan, a professor of computer science at Princeton University, 
cautioned that people should not become overly reliant on code interpreter for 
data analysis as A.I. still produces inaccurate results and misinformation.

'Appropriate data analysis requires just a lot of critical thinking about the 
data," he said.' "

Amen. ... Maybe.

(As this is off-topic, if you wish to reply to me, probably better to do so 
privately).

Cheers to all,
Bert

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Re: [R] Off-topic: ChatGPT Code Interpreter

2023-07-17 Thread Spencer Graves
	  I don't know about ChatGPT, but Daniel Kahneman won the 2002 Nobel 
Memorial Prize in Economics,[1] even though he's not an economist, for 
his leadership in creating a new subfield in the intersection of human 
psychology and economics now called "behavioral economics".[2] Then in 
2009 Kahneman and Gary Klein published an article on, "Conditions for 
intuitive expertise: a failure to disagree", which concluded that expert 
intuition is learned from frequent, rapid, high-quality feedback. 
People you do not learn from frequent, rapid, high-quality feedback can 
be beaten by simple heuristics developed by intelligent lay people.[3] 
That includes most professions, which Kahneman Sibony and Sunstein call 
"respect-experts".



	  Kahneman Sibony and Sunstein further report that with a little data, 
a regression model can outperform a simple heuristic, and with massive 
amounts of data, artificial intelligence can outperform regression 
models.[4]



	  An extreme but real example of current reality was describe in an 
article on "Asylum roulette":  With asylum judges in the same 
jurisdiction with cases assigned at random, one judge approved 5 percent 
of cases while another approved 88 percent.[5] However, virtually all 
"respect-experts" are influenced in their judgements by time of day and 
whether their favorite sports team won or lost the previous day.  That 
level of noise can be reduced dramatically by use of appropriate 
artificial intelligence.



  Comments?
  Spencer Graves


[1]


https://en.wikipedia.org/wiki/Daniel_Kahneman


[2]


https://en.wikipedia.org/wiki/Behavioral_economics


[3]


https://www.researchgate.net/publication/26798603_Conditions_for_Intuitive_Expertise_A_Failure_to_Disagree


[4]


Daniel Kahneman; Olivier Sibony; Cass Sunstein (2021). Noise: A Flaw in 
Human Judgment (Little, Brown and Company).



[5]


https://en.wikipedia.org/wiki/Refugee_roulette


On 7/17/23 1:46 PM, Bert Gunter wrote:

This is an **off-topic** post about the subject line, that I thought
might be of interest to the R Community. I hope this does not offend
anyone.

The widely known ChatGPT software now offers what  is called a "Code
Interpreter," that, among other things, purports to do "data
analysis."  (Search for articles with details.) One quote, from the
(online) NY Times, is:

"Arvind Narayanan, a professor of computer science at Princeton
University, cautioned that people should not become overly reliant on
code interpreter for data analysis as A.I. still produces inaccurate
results and misinformation.

'Appropriate data analysis requires just a lot of critical thinking
about the data,” he said.' "

Amen. ... Maybe.

(As this is off-topic, if you wish to reply to me, probably better to
do so privately).

Cheers to all,
Bert

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[R] Off-topic: ChatGPT Code Interpreter

2023-07-17 Thread Bert Gunter
This is an **off-topic** post about the subject line, that I thought
might be of interest to the R Community. I hope this does not offend
anyone.

The widely known ChatGPT software now offers what  is called a "Code
Interpreter," that, among other things, purports to do "data
analysis."  (Search for articles with details.) One quote, from the
(online) NY Times, is:

"Arvind Narayanan, a professor of computer science at Princeton
University, cautioned that people should not become overly reliant on
code interpreter for data analysis as A.I. still produces inaccurate
results and misinformation.

'Appropriate data analysis requires just a lot of critical thinking
about the data,” he said.' "

Amen. ... Maybe.

(As this is off-topic, if you wish to reply to me, probably better to
do so privately).

Cheers to all,
Bert

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


[R] Obtaining R-squared from All Possible Combinations of Linear Models Fitted

2023-07-17 Thread Paul Bernal
Dear friends,

I need to automatically fit all possible linear regression models (with all
possible combinations of regressors), and found the MuMIn package, which
has the dredge function.

This is the dataset  I am working with:
> dput(final_frame)
structure(list(y = c(41.9, 44.5, 43.9, 30.9, 27.9, 38.9, 30.9,
28.9, 25.9, 31, 29.5, 35.9, 37.5, 37.9), x1 = c(6.6969, 8.7951,
9.0384, 5.9592, 4.5429, 8.3607, 5.898, 5.6039, 4.9176, 6.2712,
5.0208, 5.8282, 5.9894, 7.5422), x4 = c(1.488, 1.82, 1.5, 1.121,
1.175, 1.777, 1.24, 1.501, 0.998, 0.975, 1.5, 1.225, 1.256, 1.69
), x8 = c(22, 50, 23, 32, 40, 48, 51, 32, 42, 30, 62, 32, 40,
22), x2 = c(1.5, 1.5, 1, 1, 1, 1.5, 1, 1, 1, 1, 1, 1, 1, 1.5),
x7 = c(3, 4, 3, 3, 3, 4, 3, 3, 4, 2, 4, 3, 3, 3)), class =
"data.frame", row.names = c(NA,
-14L))

I started with the all regressor model, which I called globalmodel as
follows:
#Fitting Regression model with all possible combinations of regressors
options(na.action = "na.fail") # change the default "na.omit" to prevent
models
globalmodel <- lm(y~., data=final_frame)

Then, the following code provides the different coefficients (for
regressors and the intercept) for each of the possible model combinations:
combinations <- dredge(globalmodel)
print(combinations)
 I would like to retrieve  the R-squared generated by each combination, but
have not been able to get it thus far.

Any guidance on how to retrieve the R-squared from all linear model
combinations would be greatly appreciated.

Kind regards,
Paul

[[alternative HTML version deleted]]

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[R] Dates and location for useR! 2024

2023-07-17 Thread Heather Turner
Dear All,

We are pleased to announce that useR! 2024 will be a hybrid conference, taking 
place 8-11 July in Salzburg, Austria.

The conference website is yet to be set up. In the meantime, you can keep 
up-to-date the following ways:

useR! LinkedIn Page: https://www.linkedin.com/company/user-conf
useR! Twitter: https://twitter.com/_useRconf
R Foundation Mastodon: https://fosstodon.org/@R_Foundation (we will likely set 
up a Mastodon account for useR! in due course)

Best wishes,

Heather
On behalf of the R Foundation Conference Committee

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Re: [R] how to change the y-axis to logarithmic in a barplot ggplot

2023-07-17 Thread Kimmo Elo
Hi,

try:

scale_y_continuous(trans='log10')

HTH,

Kimmo
17. heinäk. 2023, 1.58, Maria Lathouri via R-help 
mailto:r-help@r-project.org>> kirjoitti:

I will find the ggplot help.

But I have tried everything, including what you have suggested and nothing 
works.

Kind regards,
Maria






Στις Κυριακή 16 Ιουλίου 2023 στις 11:22:36 μ.μ. GMT+1, ο χρήστης CALUM POLWART 
 έγραψε:





Try adding

scale_y_log10()

This is a general R help list. It's not a ggplot list and you are likely to be 
chased off to ggplot's package maintainers nominated support pages.

But really a Google search should surely have found this?



On Sun, 16 Jul 2023, 22:51 Maria Lathouri via R-help,  
wrote:
 Dear all,

 ggplot(fc, aes(x = Temp, y = mean, fill = Glass)) +
 geom_bar(stat = "identity", position = "dodge", aes(y=log(mean)))
 + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = 
element_blank()) + theme(legend.position = c(0.45, 0.85), legend.title = 
element_blank())
 + scale_fill_brewer(palette = "Dark2") + scale_color_brewer(palette = "Dark2") 
+

scale_y_log10()



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[[alternative HTML version deleted]]

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Re: [R] nlmixr2 installation problems

2023-07-17 Thread Ivan Krylov
On Mon, 17 Jul 2023 08:23:19 +0200
Troels Ring  wrote:

> install.packages("openssl",dependencies=TRUE,type="source") and
> likewise for sass resulted in a lengthy compilation and installation
> process ending happily, however, after which
> 
> install.packages("nlmixr2",dependencies=TRUE)
> 
> appeared to do as expected
> 
> Strange only, that RStudio doesn't suggest the type="source" by itself

It sounds like R was using utils::askYesNo() to confirm whether you'd
like to install newer source packages, but the pop-up window was lost
behind the RStudio window. Unfortunately, this doesn't seem to be
something that an R front-end could handle on its end.

Glad you solved the problem anyway.

-- 
Best regards,
Ivan

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Re: [R] nlmixr2 installation problems

2023-07-17 Thread Troels Ring

Problem solved, I think:

issuing

install.packages("openssl",dependencies=TRUE,type="source") and likewise 
for sass resulted in a lengthy compilation and installation process 
ending happily, however, after which


install.packages("nlmixr2",dependencies=TRUE)

appeared to do as expected

Strange only, that RStudio doesn't suggest the type="source" by itself

Best wishes

Troels

Den 17-07-2023 kl. 07:54 skrev Troels Ring:

Thanks a lot - I was not offered the opportunity to recompile - the
system just stopped. Also, today trying


install.packages("sass") Installing package into

‘C:/Users/Admin/AppData/Local/R/win-library/4.3’ (as ‘lib’ is
unspecified) also installing the dependencies ‘digest’, ‘base64enc’,
‘fastmap’, ‘ellipsis’, ‘fs’, ‘htmltools’, ‘rappdirs’ There is a binary
version available but the source version is later: binary source
needs_compilation sass 0.4.6 0.4.7 TRUE - and nothing further - so
definitely not a nlmixr2 issue, right? Best wishes Troels

Den 16-07-2023 kl. 17:21 skrev Rui Barradas:

Às 12:55 de 16/07/2023, Troels Ring escreveu:

Hi friends - Trying to install nlmixr2 caused problems. I'm on windows
with R4.3.1 so made sure to have rtools 4.3 and also reinstalled R
and then

ran

install.packages("nlmixr2",dependencies = TRUE)and got the
responseInstalling package into
‘C:/Users/Admin/AppData/Local/R/win-library/4.3’ (as ‘lib’ is
unspecified) also installing the dependencies ‘fs’, ‘rappdirs’, ‘bit’,
‘prettyunits’, ‘rematch’, ‘askpass’, ‘sass’, ‘commonmark’, ‘proxy’,
‘bit64’, ‘progress’, ‘rootSolve’, ‘lmom’, ‘cellranger’, ‘jsonlite’,
‘mime’, ‘openssl’, ‘htmlwidgets’, ‘ellipsis’, ‘bslib’, ‘fontawesome’,
‘jquerylib’, ‘tinytex’, ‘curl’, ‘markdown’, ‘jpeg’, ‘xml2’, ‘fastmap’,
‘e1071’, ‘generics’, ‘tidyselect’, ‘clipr’, ‘hms’, ‘vroom’, ‘cpp11’,
‘tzdb’, ‘stringi’, ‘purrr’, ‘mvtnorm’, ‘expm’, ‘rstudioapi’, ‘Exact’,
‘gld’, ‘readxl’, ‘httr’, ‘gridExtra’, ‘htmlTable’, ‘viridis’,
‘htmltools’, ‘base64enc’, ‘rmarkdown’, ‘Formula’, ‘bitops’, ‘evaluate’,
‘highr’, ‘xfun’, ‘yaml’, ‘numDeriv’, ‘lazyeval’, ‘optextras’, ‘dparser’,
‘RcppEigen’, ‘StanHeaders’, ‘sitmo’, ‘gridtext’, ‘cachem’,
‘RcppParallel’, ‘RApiSerialize’, ‘stringfish’, ‘classInt’, ‘dplyr’,
‘readr’, ‘stringr’, ‘tidyr’, ‘assertthat’, ‘binom’, ‘Deriv’,
‘DescTools’, ‘Hmisc’, ‘minpack.lm’, ‘pander’, ‘png’, ‘RCurl’,
‘backports’, ‘checkmate’, ‘knitr’, ‘lbfgsb3c’, ‘minqa’, ‘n1qn1’, ‘Rcpp’,
‘rex’, ‘Rvmmin’, ‘symengine’, ‘BH’, ‘RcppArmadillo’, ‘rxode2parse’,
‘rxode2random’, ‘data.table’, ‘digest’, ‘ggtext’, ‘PreciseSums’,
‘inline’, ‘memoise’, ‘sys’, ‘rxode2ll’, ‘rxode2et’, ‘qs’, ‘vpc’, ‘xgxr’,
‘nlmixr2data’, ‘nlmixr2est’, ‘nlmixr2extra’, ‘rxode2’, ‘lotri’,
‘nlmixr2plot’, ‘crayon’ There are binary versions available but the
source versions are later: binary source needs_compilation sass 0.4.6
0.4.7 TRUE openssl 2.0.6 2.1.0 TRUE
- and nothing more happened But when trying to install sass and openssl
individually the same announcement of later source versions appeared
without making it possible to ask for recompilation. All best wishes
Troels

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Hello,

Maybe this [1] is relevant.


[1]
https://community.rstudio.com/t/meaning-of-common-message-when-install-a-package-there-are-binary-versions-available-but-the-source-versions-are-later/2431

Hope this helps,

Rui Barradas

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