Re: [R-pkg-devel] function name conflict problem

[Hugh Parsonage]

Package karon is the problem. Is that package in your depends or imports?
Does that package use Depends?

On Wed, 5 Feb 2020 at 8:24 am,  wrote:

> In trying to develop a package to be submitted to CRAN, when I do Install
> and Reload or devtools::check(), I get the warning:
>
>
>
> Warning: replacing previous import 'ellipse::pairs' by 'graphics::pairs'
> when loading 'karon'
>
> Warning: replacing previous import 'MVN::mvn' by 'mgcv::mvn' when loading
> 'karon'
>
>
>
> I need one function each from the packages ellipse and mgcv (I do not need
> pairs from ellipse and mvn from mgcv).  To restrict to the function that I
> need, I have used the commands
>
> @importFrom  ellipse  ellipse
>
> @importFrom  mgcv  in.out
>
>
>
> NAMESPACE includes the lines
>
> importFrom(ellipse,ellipse)
>
> importFrom(mgcv,in.out)
>
>
>
> However, DESCRIPTION does not restrict the functions imported from ellipse
> and mgcv; it has
>
> Imports: MVN, MASS, scatterplot3d, rgl, mgcv, randomForest, rpart,
> partykit,
> Formula, ellipse,..
>
>
>
> Do these warnings need to be solved before submitting to CRAN?
>
> Is it necessary to edit DESCRIPTION  If so, what should be done?
>
> Is there some other potential solution?
>
>
>
> Thanks!
>
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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[Bioc-devel] DeMixT issue

[py11]

Hi Bioconductor team,

I just pushed DeMixT package from 1.3.3 to 1.3.4 into level branch and 1.2.3 to 
1.2.4 into release branch since I found a bug in the package.

Since I am very new to git, may I know how can I verify the change of log?

Besides, is there anyway that I can notice the change to users?

Thanks,

Peng

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Re: [R-pkg-devel] Warning: parse error in file 'Rraven-Ex.R'

[Jeff Newmiller]

In your examples.

On February 4, 2020 5:53:08 PM PST, Marcelo Araya Salas  
wrote:
>Hi all
>
>I got this error from CRAN tests:
>
>Warning: parse error in file 'Rraven-Ex.R':
>'\.' is an unrecognized escape in character string starting ""\."
>
>However, I can't find the original file where the error is found. I
>have
>try unsuccessfully for several hours :(
>
>any suggestions on how to find it?
>
>thanks!
>
>Marcelo
>
>
>
>El mar., 4 feb. 2020 a las 8:34, Dirk Eddelbuettel ()
>escribió:
>
>>
>> On 4 February 2020 at 08:15, Marcelo Araya Salas wrote:
>> | I found it here:
>> |
>> | ftp://cran.r-project.org/incoming/archive/
>> |
>> | not sure what that's suppose to mean
>>
>> "It's dead."
>>
>> It generally means you will have gotten an email with the reasoning. 
>But
>> whatever is in archive/ is no longer processed.
>>
>> Dirk
>>
>> --
>> http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>>
>
>   [[alternative HTML version deleted]]
>
>__
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-- 
Sent from my phone. Please excuse my brevity.

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[R-pkg-devel] Warning: parse error in file 'Rraven-Ex.R'

[Marcelo Araya Salas]

Hi all

I got this error from CRAN tests:

Warning: parse error in file 'Rraven-Ex.R':
'\.' is an unrecognized escape in character string starting ""\."

However, I can't find the original file where the error is found. I have
try unsuccessfully for several hours :(

any suggestions on how to find it?

thanks!

Marcelo



El mar., 4 feb. 2020 a las 8:34, Dirk Eddelbuettel ()
escribió:

>
> On 4 February 2020 at 08:15, Marcelo Araya Salas wrote:
> | I found it here:
> |
> | ftp://cran.r-project.org/incoming/archive/
> |
> | not sure what that's suppose to mean
>
> "It's dead."
>
> It generally means you will have gotten an email with the reasoning.  But
> whatever is in archive/ is no longer processed.
>
> Dirk
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>

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Re: [R-pkg-devel] function name conflict problem

[sierrastew]

Thanks.  I had seen this but it didn't register.  I made this change to all
the potential conflicts (the packages ellipse and mgcv are never in an
@import statement), but I still get the conflict messages.  John Karon

 

From: Max Turgeon  
Sent: Tuesday, February 4, 2020 3:10 PM
To: sierras...@mindspring.com; r-package-devel@r-project. org

Subject: Re: [R-pkg-devel] function name conflict problem

 

I find it's well explained in the book by Hadley Wickham:

http://r-pkgs.had.co.nz/namespace.html#imports

 

If package ellipse is in Imports (in your DESCRIPTION file), then
install.packages will make sure it's available on the user's system when
installing your own package. Therefore you can write ellipse::ellipse
without requiring importFrom(ellipse,ellipse) in your NAMESPACE.

 

Max Turgeon
Assistant Professor

Department of Statistics
Department of Computer Science
University of Manitoba

  maxturgeon.ca

 

  _  

From: R-package-devel mailto:r-package-devel-boun...@r-project.org> > on behalf of
sierras...@mindspring.com mailto:sierras...@mindspring.com> >
Sent: February 4, 2020 3:48:16 PM
To: r-package-devel@r-project. org
Subject: [R-pkg-devel] function name conflict problem 

 

Thanks Duncan.  Please clarify: if I use ellipse::ellipse in code, do I need
to have @importFrom ellipse eliipse in the Roxygen code.

-Original Message-
From: Duncan Murdoch < 
murdoch.dun...@gmail.com> 
Sent: Tuesday, February 4, 2020 2:45 PM
To:   sierras...@mindspring.com
Subject: Re: [R-pkg-devel] function name conflict problem

If you call it via ellipse::ellipse, you don't need to mention it in
NAMESPACE.

I can't tell what's going wrong in your NAMESPACE file, but that's where the
problem is that leads to the errors you saw.

In future, please don't write privately, post to the list.

Duncan Murdoch

On 04/02/2020 4:40 p.m.,  
sierras...@mindspring.com wrote:
> Thanks very much for the quick reply.  Here is the entire set of import
commands from NAMESPACE.  Also, when I use the function ellipse, I code it
as ellipse::ellipse; similarly for using in.out.  I don't see any request
for anything but ellipse from the package ellipse, and in.out from mgcv:
> 
> import(Formula)
> import(MASS)
> import(assertthat)
> import(corrplot)
> import(grDevices)
> import(graphics)
> import(missForest)
> import(nortest)
> import(partykit)
> import(qqtest)
> import(randomForest)
> import(rpart)
> import(scatterplot3d)
> import(stats)
> importFrom(MVN,mvn)
> importFrom(ellipse,ellipse)
> importFrom(graphics,pairs)
> importFrom(mgcv,in.out)
> importFrom(rgl,rgl.postscript)
> 
> -Original Message-
> From: Duncan Murdoch < 
murdoch.dun...@gmail.com>
> Sent: Tuesday, February 4, 2020 2:31 PM
> To:   sierras...@mindspring.com;
r-package-devel@r-project. org 
> <  r-package-devel@r-project.org>
> Subject: Re: [R-pkg-devel] function name conflict problem
> 
> On 04/02/2020 4:21 p.m.,  
sierras...@mindspring.com wrote:
>> In trying to develop a package to be submitted to CRAN, when I do 
>> Install and Reload or devtools::check(), I get the warning:
>>
>>
>>
>> Warning: replacing previous import 'ellipse::pairs' by 'graphics::pairs'
>> when loading 'karon'
>>
>> Warning: replacing previous import 'MVN::mvn' by 'mgcv::mvn' when 
>> loading 'karon'
>>
>>
>>
>> I need one function each from the packages ellipse and mgcv (I do not 
>> need pairs from ellipse and mvn from mgcv).  To restrict to the 
>> function that I need, I have used the commands
>>
>> @importFrom  ellipse  ellipse
>>
>> @importFrom  mgcv  in.out
>>
>>
>>
>> NAMESPACE includes the lines
>>
>> importFrom(ellipse,ellipse)
>>
>> importFrom(mgcv,in.out)
>>
>>
>>
>> However, DESCRIPTION does not restrict the functions imported from 
>> ellipse and mgcv; it has
>>
>> Imports: MVN, MASS, scatterplot3d, rgl, mgcv, randomForest, rpart, 
>> partykit, Formula, ellipse,..
>>
>>
>>
>> Do these warnings need to be solved before submitting to CRAN?
>>
>> Is it necessary to edit DESCRIPTION  If so, what should be done?
>>
>> Is there some other potential solution?
> 
> I don't know if they *must* be fixed, but they should be.  Something in
your NAMESPACE file (derived from some comment in your code by roxygen2) is
importing ellipse::pairs, even though you say you don't want to do that.
You should fix that.
> 
>   From what we can see, your DESCRIPTION file is fine.  The problem lies
in NAMESPACE.
> 
> Duncan Murdoch
> 

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Re: [R-pkg-devel] function name conflict problem

[Max Turgeon]

I find it's well explained in the book by Hadley Wickham: 
http://r-pkgs.had.co.nz/namespace.html#imports


If package ellipse is in Imports (in your DESCRIPTION file), then 
install.packages will make sure it's available on the user's system when 
installing your own package. Therefore you can write ellipse::ellipse without 
requiring importFrom(ellipse,ellipse) in your NAMESPACE.


Max Turgeon
Assistant Professor
Department of Statistics
Department of Computer Science
University of Manitoba
maxturgeon.ca



From: R-package-devel  on behalf of 
sierras...@mindspring.com 
Sent: February 4, 2020 3:48:16 PM
To: r-package-devel@r-project. org
Subject: [R-pkg-devel] function name conflict problem

Thanks Duncan.  Please clarify: if I use ellipse::ellipse in code, do I need to 
have @importFrom ellipse eliipse in the Roxygen code.

-Original Message-
From: Duncan Murdoch 
Sent: Tuesday, February 4, 2020 2:45 PM
To: sierras...@mindspring.com
Subject: Re: [R-pkg-devel] function name conflict problem

If you call it via ellipse::ellipse, you don't need to mention it in NAMESPACE.

I can't tell what's going wrong in your NAMESPACE file, but that's where the 
problem is that leads to the errors you saw.

In future, please don't write privately, post to the list.

Duncan Murdoch

On 04/02/2020 4:40 p.m., sierras...@mindspring.com wrote:
> Thanks very much for the quick reply.  Here is the entire set of import 
> commands from NAMESPACE.  Also, when I use the function ellipse, I code it as 
> ellipse::ellipse; similarly for using in.out.  I don't see any request for 
> anything but ellipse from the package ellipse, and in.out from mgcv:
>
> import(Formula)
> import(MASS)
> import(assertthat)
> import(corrplot)
> import(grDevices)
> import(graphics)
> import(missForest)
> import(nortest)
> import(partykit)
> import(qqtest)
> import(randomForest)
> import(rpart)
> import(scatterplot3d)
> import(stats)
> importFrom(MVN,mvn)
> importFrom(ellipse,ellipse)
> importFrom(graphics,pairs)
> importFrom(mgcv,in.out)
> importFrom(rgl,rgl.postscript)
>
> -Original Message-
> From: Duncan Murdoch 
> Sent: Tuesday, February 4, 2020 2:31 PM
> To: sierras...@mindspring.com; r-package-devel@r-project. org
> 
> Subject: Re: [R-pkg-devel] function name conflict problem
>
> On 04/02/2020 4:21 p.m., sierras...@mindspring.com wrote:
>> In trying to develop a package to be submitted to CRAN, when I do
>> Install and Reload or devtools::check(), I get the warning:
>>
>>
>>
>> Warning: replacing previous import 'ellipse::pairs' by 'graphics::pairs'
>> when loading 'karon'
>>
>> Warning: replacing previous import 'MVN::mvn' by 'mgcv::mvn' when
>> loading 'karon'
>>
>>
>>
>> I need one function each from the packages ellipse and mgcv (I do not
>> need pairs from ellipse and mvn from mgcv).  To restrict to the
>> function that I need, I have used the commands
>>
>> @importFrom  ellipse  ellipse
>>
>> @importFrom  mgcv  in.out
>>
>>
>>
>> NAMESPACE includes the lines
>>
>> importFrom(ellipse,ellipse)
>>
>> importFrom(mgcv,in.out)
>>
>>
>>
>> However, DESCRIPTION does not restrict the functions imported from
>> ellipse and mgcv; it has
>>
>> Imports: MVN, MASS, scatterplot3d, rgl, mgcv, randomForest, rpart,
>> partykit, Formula, ellipse,..
>>
>>
>>
>> Do these warnings need to be solved before submitting to CRAN?
>>
>> Is it necessary to edit DESCRIPTION  If so, what should be done?
>>
>> Is there some other potential solution?
>
> I don't know if they *must* be fixed, but they should be.  Something in your 
> NAMESPACE file (derived from some comment in your code by roxygen2) is 
> importing ellipse::pairs, even though you say you don't want to do that.  You 
> should fix that.
>
>   From what we can see, your DESCRIPTION file is fine.  The problem lies in 
> NAMESPACE.
>
> Duncan Murdoch
>

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Re: [R-pkg-devel] function name conflict problem

[Duncan Murdoch]

On 04/02/2020 4:21 p.m., sierras...@mindspring.com wrote:

In trying to develop a package to be submitted to CRAN, when I do Install
and Reload or devtools::check(), I get the warning:

  


Warning: replacing previous import 'ellipse::pairs' by 'graphics::pairs'
when loading 'karon'

Warning: replacing previous import 'MVN::mvn' by 'mgcv::mvn' when loading
'karon'

  


I need one function each from the packages ellipse and mgcv (I do not need
pairs from ellipse and mvn from mgcv).  To restrict to the function that I
need, I have used the commands

@importFrom  ellipse  ellipse

@importFrom  mgcv  in.out

  


NAMESPACE includes the lines

importFrom(ellipse,ellipse)

importFrom(mgcv,in.out)

  


However, DESCRIPTION does not restrict the functions imported from ellipse
and mgcv; it has

Imports: MVN, MASS, scatterplot3d, rgl, mgcv, randomForest, rpart, partykit,
Formula, ellipse,..

  


Do these warnings need to be solved before submitting to CRAN?

Is it necessary to edit DESCRIPTION  If so, what should be done?

Is there some other potential solution?


I don't know if they *must* be fixed, but they should be.  Something in 
your NAMESPACE file (derived from some comment in your code by roxygen2) 
is importing ellipse::pairs, even though you say you don't want to do 
that.  You should fix that.


From what we can see, your DESCRIPTION file is fine.  The problem lies 
in NAMESPACE.


Duncan Murdoch

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[R-pkg-devel] function name conflict problem

[sierrastew]

In trying to develop a package to be submitted to CRAN, when I do Install
and Reload or devtools::check(), I get the warning:

 

Warning: replacing previous import 'ellipse::pairs' by 'graphics::pairs'
when loading 'karon'

Warning: replacing previous import 'MVN::mvn' by 'mgcv::mvn' when loading
'karon'

 

I need one function each from the packages ellipse and mgcv (I do not need
pairs from ellipse and mvn from mgcv).  To restrict to the function that I
need, I have used the commands

@importFrom  ellipse  ellipse

@importFrom  mgcv  in.out

 

NAMESPACE includes the lines

importFrom(ellipse,ellipse)

importFrom(mgcv,in.out)

 

However, DESCRIPTION does not restrict the functions imported from ellipse
and mgcv; it has

Imports: MVN, MASS, scatterplot3d, rgl, mgcv, randomForest, rpart, partykit,
Formula, ellipse,..

 

Do these warnings need to be solved before submitting to CRAN?

Is it necessary to edit DESCRIPTION  If so, what should be done?

Is there some other potential solution?

 

Thanks!


[[alternative HTML version deleted]]

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Re: [Rd] Stroring and extracting AICs from an ARIMA model using a nested loop

[ismael ismael via R-devel]

I does help! Thank you for clarifications!


Sent from my iPhone

> On Feb 4, 2020, at 9:36 AM, Rui Barradas  wrote:
> 
> Hello,
> 
> Don't worry, we've seen worst questions :).
> Inline.
> 
> Às 13:20 de 04/02/20, ismael ismael escreveu:
>> I am now aware that I should not post this type of questions on this group. 
>> However, I would like to have some clarifications related to the response 
>> you've already provided. The code you provided yields accurate results, 
>> however I still have issues grasping the loop process in case 1 & 2.
>> In case 1, the use of "p+1" and "q+1" is still blurry to me? 
> 
> 1. R indexes starting from 1, both your orders p and q are 0:3. So to assign 
> the results to the results matrix, add 1 and get indices 1:4.
> You could also set the row and column names after, to make it more clear:
> 
> dimnames(storage1) <- list(paste0("p", 0:3), paste0("q", 0:3))
> 
> 2. 0L is an integer, just 0 is a floating-point corresponding to the C 
> language double.
> 
> class(0L)   # "integer"
> class(0)# "numeric"
> 
> typeof(0L)  # "integer"
> typeof(0)   # "double"
> 
> Indices are integers, so I used integers and added 1L every iteration through 
> the inner loop.
> 
> This also means that in point 1. I should have indexed the matrix with p + 1L 
> and q + 1L, see the output of
> 
> class(0:3)
> 
> 
> Hope this helps,
> 
> Rui Barradas
> 
> Likewise
>> "0L" and " i + 1L" in case 2.
>> Can you please provide explanations on the loop mechanisms you've used.
>> Le lundi 3 février 2020 à 03:47:20 UTC−6, Rui Barradas 
>>  a écrit :
>> Hello,
>> You can solve the problem in two different ways.
>> 1. Redefine storage1 as a matrix and extract the aic *in* the loop.
>> storage1 <- matrix(0, 4, 4)
>> for(p in 0:3){
>>   for(q in 0:3){
>> storage1[p + 1, q + 1] <- arima(etc)$aic
>>   }
>> }
>> 2. define storage1 as a list.
>> storage1 <- vector("list", 16)
>> i <- 0L
>> for(p in 0:3){
>>   for(q in 0:3){
>> i <- i + 1L
>> storage1[[i]] <- arima(etc)
>>   }
>> }
>> lapply(storage1, '[[', "aic")  # get the aic's.
>> Maybe sapply is better it will return a vector.
>> Hope this helps,
>> Rui Barradas
>> Às 06:23 de 03/02/20, ismael ismael via R-devel escreveu:
>> > Hello
>> > I am trying to extract AICs from an ARIMA estimation with different
>> > combinations of p & q ( p =0,1,2,3
>> > and q=0,1.2,3). I have tried using the following code unsucessfully. Can
>> > anyone help?
>> >
>> > code:
>> > storage1 <- numeric(16)
>> > for (p in 0:3){
>> >
>> >  for (q in 0:3){
>> >
>> >  storage1[p]  <- arima(x,order=c(p,0,q), method="ML")}
>> > }
>> > storage1$aic
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > __
>> > R-devel@r-project.org  mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-devel
>> >

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Re: [R-pkg-devel] 转发: [CRAN-pretest-archived] CRAN submission BAREB 1.0

[Duncan Murdoch]

The 00install.out file has this error message:

 unable to load shared object 
‘/srv/hornik/tmp/CRAN/BAREB.Rcheck/00LOCK-BAREB/00new/BAREB/libs/BAREB.so’:


/srv/hornik/tmp/CRAN/BAREB.Rcheck/00LOCK-BAREB/00new/BAREB/libs/BAREB.so: 
undefined symbol: dpotrf_


That name dpotrf_ looks like something from LAPACK, but it is not listed 
in the README for included LAPACK routines in


https://svn.r-project.org/R/trunk/src/modules/lapack/README

However, dpotrf2 is listed there, so perhaps you can modify your source 
to use that instead.


Duncan Murdoch

On 04/02/2020 11:48 a.m., Yuliang Li wrote:

Hi all,

I am trying to submit my R package to CRAN. However, I keep getting an error in 
the second link, saying my package could not be installed. But the package 
works perfectly fine in my personal computer. I would really appreciate it if 
you could provide some possible solution.

Thanks in advance!

Best wishes,
Yuliang




发件人: lig...@statistik.tu-dortmund.de 
发送时间: 2020年2月4日 13:07
收件人: Yuliang Li
抄送: cran-submissi...@r-project.org
主题: [CRAN-pretest-archived] CRAN submission BAREB 1.0

Dear maintainer,

package BAREB_1.0.tar.gz does not pass the incoming checks automatically, 
please see the following pre-tests:
Windows: 

Status: 5 WARNINGs, 8 NOTEs
Debian: 

Status: 1 ERROR, 1 WARNING, 2 NOTEs



Please fix all problems and resubmit a fixed version via the webform.
If you are not sure how to fix the problems shown, please ask for help on the 
R-package-devel mailing list:

If you are fairly certain the rejection is a false positive, please reply-all 
to this message and explain.

More details are given in the directory:

The files will be removed after roughly 7 days.

No strong reverse dependencies to be checked.

Best regards,
CRAN teams' auto-check service


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[R-pkg-devel] 转发: [CRAN-pretest-archived] CRAN submission BAREB 1.0

[Yuliang Li]

Hi all,

I am trying to submit my R package to CRAN. However, I keep getting an error in 
the second link, saying my package could not be installed. But the package 
works perfectly fine in my personal computer. I would really appreciate it if 
you could provide some possible solution.

Thanks in advance!

Best wishes,
Yuliang




发件人: lig...@statistik.tu-dortmund.de 
发送时间: 2020年2月4日 13:07
收件人: Yuliang Li
抄送: cran-submissi...@r-project.org
主题: [CRAN-pretest-archived] CRAN submission BAREB 1.0

Dear maintainer,

package BAREB_1.0.tar.gz does not pass the incoming checks automatically, 
please see the following pre-tests:
Windows: 

Status: 5 WARNINGs, 8 NOTEs
Debian: 

Status: 1 ERROR, 1 WARNING, 2 NOTEs



Please fix all problems and resubmit a fixed version via the webform.
If you are not sure how to fix the problems shown, please ask for help on the 
R-package-devel mailing list:

If you are fairly certain the rejection is a false positive, please reply-all 
to this message and explain.

More details are given in the directory:

The files will be removed after roughly 7 days.

No strong reverse dependencies to be checked.

Best regards,
CRAN teams' auto-check service
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
Check: CRAN incoming feasibility, Result: NOTE
  Maintainer: 'Yuliang Li '
  
  New submission
  
  Non-FOSS package license (Johns Hopkins University)
  
  Possibly mis-spelled words in DESCRIPTION:
BAREB (3:8, 9:220, 9:380)
Biclustering (3:36)
DPP (9:264)
biclustering (9:35)
biclusters (9:311)
determinantal (9:235)
faciliate (9:325)
interpretability (9:349)
  
  The Title field starts with the package name.
  
  Size of tarball: 15969613 bytes

Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
Check: package dependencies, Result: NOTE
  Package in Depends/Imports which should probably only be in LinkingTo: 
'RcppArmadillo'

Flavor: r-devel-windows-ix86+x86_64
Check: DESCRIPTION meta-information, Result: WARNING
  Non-standard license specification:
Johns Hopkins University
  Standardizable: FALSE

Flavor: r-devel-windows-ix86+x86_64
Check: top-level files, Result: NOTE
  Non-standard files/directories found at top level:
'BAREB_1.0.pdf' 'gfortran-4.8.2-darwin13.tar.bz2'

Flavor: r-devel-windows-ix86+x86_64
Check: S3 generic/method consistency, Result: WARNING
  update:
function(object, ...)
  update.theta.beta:
function(theta, tau, Beta, sig)
  
  update:
function(object, ...)
  update.theta.gamma:
function(theta, tau, Gamma, S, Ds, sig)
  
  See section 'Generic functions and methods' in the 'Writing R
  Extensions' manual.
  
  Found the following apparent S3 methods exported but not registered:
update.theta.beta update.theta.gamma
  See section 'Registering S3 methods' in the 'Writing R Extensions'
  manual.

Flavor: r-devel-windows-ix86+x86_64
Check: R code for possible problems, Result: NOTE
  update.theta.beta: no visible global function definition for 'rnorm'
  update.theta.beta: no visible global function definition for 'dnorm'
  update.theta.beta: no visible global function definition for 'runif'
  update.theta.gamma: no visible global function definition for 'rnorm'
  update.theta.gamma: no visible global function definition for 'dnorm'
  update.theta.gamma: no visible global function definition for 'runif'
  update_RJ: no visible binding for global variable 'E'
  update_RJ: no visible binding for global variable 'tau'
  update_RJ: no visible binding for global variable 'm'
  update_RJ: no visible binding for global variable 'T0'
  update_sigma_squre: no visible global function definition for 'na.omit'
  update_sigma_squre: no visible global function definition for 'rgamma'
  update_w: no visible global function definition for 'rgamma'
  update_w_beta: no visible global function definition for 'rgamma'
  Undefined global functions or variables:
E T0 dnorm m na.omit rgamma rnorm runif tau
  Consider adding
importFrom("stats", "dnorm", "na.omit", "rgamma", "rnorm", "runif")
  to your NAMESPACE file.

Flavor: r-devel-windows-ix86+x86_64
Check: Rd line widths, Result: NOTE
  Rd file 'updateBeta.Rd':
\usage lines wider than 90 characters:
   updateBeta(X, Y, Z, delta, Beta, Gamma, E, R, S, Ds, mustar, mu, sigma, 
c, C, step, runif, n, m, T0, p, q, D, theta,tau)
  
  Rd file 'updateE.Rd':
\usage lines wider than 90 characters:
   updateE( Beta, Gamma,w, X, Y, Z, delta,E, R, S, Ds, mu, mustar, sigma, 
c, n, m, T0, p, q, D)
  
  Rd file 'updateGamma.Rd':
\usage lines wider than 90 characters:
   

Re: [R-pkg-devel] Suggests in a Package

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Thanks.  And thanks for the tip.

-Roy

> On Feb 4, 2020, at 10:20 AM, Duncan Murdoch  wrote:
> 
> On 04/02/2020 1:13 p.m., Roy Mendelssohn - NOAA Federal via R-package-devel 
> wrote:
>> Hi All:
>> I still get a little confused on what it means if a package is listed in 
>> "Suggest" in my package.  I have been working to try and keep dependencies 
>> down.  One of my packages produces maps with data, and I have been asked if 
>> the maps can be made interactive.  It turns out this can be done very easily 
>> using "plotly" and I want to include something about that in the vignette. 
>> What my question is if I Suggest "plotly" in the package,  does a user have 
>> to have "plotly" installed in order to install and run the package?  My 
>> understanding is not,  so someone who doesn't want to do this doesn't need 
>> to install "plotly" but I wanted to double-check.
> 
> Your understanding is correct:  someone who doesn't have plotly installed 
> should still be able to install and run your package.
> 
> You should make sure that any functions that need plotly check for it first.  
> The recommended way to do that is to use a requireNamespace("plotly") test, 
> e.g. something like
> 
>  if (requireNamespace("plotly")) {
> plotly::plotly(...)
>  } else
> stop("This function requires the 'plotly' package")
> 
> Your tests that use such a function should only be run if 
> requireNamespace("plotly") returns TRUE.
> 
> Duncan Murdoch

**
"The contents of this message do not reflect any position of the U.S. 
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

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Re: [R-pkg-devel] Suggests in a Package

[Duncan Murdoch]

On 04/02/2020 1:13 p.m., Roy Mendelssohn - NOAA Federal via 
R-package-devel wrote:

Hi All:

I still get a little confused on what it means if a package is listed in "Suggest" in my package.  I have been working 
to try and keep dependencies down.  One of my packages produces maps with data, and I have been asked if the maps can be made 
interactive.  It turns out this can be done very easily using "plotly" and I want to include something about that in 
the vignette. What my question is if I Suggest "plotly" in the package,  does a user have to have "plotly" 
installed in order to install and run the package?  My understanding is not,  so someone who doesn't want to do this doesn't need 
to install "plotly" but I wanted to double-check.


Your understanding is correct:  someone who doesn't have plotly 
installed should still be able to install and run your package.


You should make sure that any functions that need plotly check for it 
first.  The recommended way to do that is to use a 
requireNamespace("plotly") test, e.g. something like


  if (requireNamespace("plotly")) {
 plotly::plotly(...)
  } else
 stop("This function requires the 'plotly' package")

Your tests that use such a function should only be run if 
requireNamespace("plotly") returns TRUE.


Duncan Murdoch

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Re: [Bioc-devel] Problems on BiocCredentials account_activation

[Danrley Fernandes]

Sorry but i still unable to access git bioconductor credentials. I've asked
for a password reset but the reset email didn't came in more than 48h. And
if i try login with the account you send me i receive the message:

"Your email and password didn't match. Have you activated your account? If
yes, please check the spelling and try again.

   - Please enter a correct email address and password. Note that both
   fields may be case-sensitive."


Em ter, 28 de jan de 2020 15:43, Danrley Fernandes 
escreveu:

> Hi,
> I'm the developer of the package rSWeeP, and I'm trying to activate my
> account at Bioconductor Git Credentials (
> https://git.bioconductor.org/BiocCredentials/account_activation/)
> and I keep receiving the message " danrle...@gmail.com is not associated
> with a maintainer of a Bioconductor package. Please check the spelling or
> contact bioc-devel@r-project.org for help". But both the account of the
> GitHub that submitted the package and the maintainer's email on the
> description are  danrle...@gmail.com.
> does someone know how I should proceed?
>

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[R-pkg-devel] Suggests in a Package

[Roy Mendelssohn - NOAA Federal via R-package-devel]

Hi All:

I still get a little confused on what it means if a package is listed in 
"Suggest" in my package.  I have been working to try and keep dependencies 
down.  One of my packages produces maps with data, and I have been asked if the 
maps can be made interactive.  It turns out this can be done very easily using 
"plotly" and I want to include something about that in the vignette. What my 
question is if I Suggest "plotly" in the package,  does a user have to have 
"plotly" installed in order to install and run the package?  My understanding 
is not,  so someone who doesn't want to do this doesn't need to install 
"plotly" but I wanted to double-check.

Thanks,

-Roy



**
"The contents of this message do not reflect any position of the U.S. 
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

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Re: [R-pkg-devel] r-hub status

[brian knaus]

Thank  you Gabor! I've posted an issue.

https://github.com/r-hub/rhub/issues/338

Thank you Bill! I think the solution for this may be simple. But I wanted
to make sure I could reproduce the warning so that I can validate that my
fix resolves the issue.

And thank you Uwe for all the work you do helping package developers!

Brian

On Tue, Feb 4, 2020 at 9:32 AM Uwe Ligges 
wrote:

>
>
> On 04.02.2020 18:21, William Dunlap wrote:
> > CRAN's check gives a warning
> >
> > checking Rd \usage sections ... WARNING
> > Documented arguments not in \usage in documentation object 'Process
> chromR
> > objects':
> >‘...’
> >
> >
> > and man/proc_chromR.Rd on github does list '...' in the \arguments
> section
> > but no function listed in the \usage section uses '...'.
> >
> > The question is why you don't always get that warning.
>
> Because there was a bug in R that the warnings was not produced for a
> long time, and this is now fixed in recent verisons of R-devel. Hence ou
> only get it here.
>
> Best,
> Uwe Ligges
>
>
>
> > Bill Dunlap
> > TIBCO Software
> > wdunlap tibco.com
> >
> >
> > On Tue, Feb 4, 2020 at 8:47 AM brian knaus 
> wrote:
> >
> >> Does anyone know the current status of r-hub? My package (
> >> https://github.com/knausb/vcfR) is throwing warnings on R-devel (
> >> https://cran.r-project.org/web/checks/check_results_vcfR.html) and CRAN
> >> has
> >> asked me to fix it. Tried r-hub but it failed.
> >>
> >>
> >>
> https://builder.r-hub.io/status/vcfR_1.9.0.9000.tar.gz-ad6bc014056941a58d94765de3134c4e
> >>
> >>
> >>
> https://builder.r-hub.io/status/vcfR_1.9.0.9000.tar.gz-f673df2011864365ae5f7f66b4d16bf3
> >>
> >> My interpretation is that this is not due to my package. Is anyone else
> >> having issues with r-hub?
> >>
> >> Thanks!
> >> Brian
> >>
> >>  [[alternative HTML version deleted]]
> >>
> >> __
> >> R-package-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>

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Re: [R-pkg-devel] r-hub status

[Uwe Ligges]

On 04.02.2020 18:21, William Dunlap wrote:

CRAN's check gives a warning

checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'Process chromR
objects':
   ‘...’


and man/proc_chromR.Rd on github does list '...' in the \arguments section
but no function listed in the \usage section uses '...'.

The question is why you don't always get that warning.


Because there was a bug in R that the warnings was not produced for a 
long time, and this is now fixed in recent verisons of R-devel. Hence ou 
only get it here.


Best,
Uwe Ligges




Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Tue, Feb 4, 2020 at 8:47 AM brian knaus  wrote:


Does anyone know the current status of r-hub? My package (
https://github.com/knausb/vcfR) is throwing warnings on R-devel (
https://cran.r-project.org/web/checks/check_results_vcfR.html) and CRAN
has
asked me to fix it. Tried r-hub but it failed.


https://builder.r-hub.io/status/vcfR_1.9.0.9000.tar.gz-ad6bc014056941a58d94765de3134c4e


https://builder.r-hub.io/status/vcfR_1.9.0.9000.tar.gz-f673df2011864365ae5f7f66b4d16bf3

My interpretation is that this is not due to my package. Is anyone else
having issues with r-hub?

Thanks!
Brian

 [[alternative HTML version deleted]]

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Re: [R-pkg-devel] r-hub status

[William Dunlap]

CRAN's check gives a warning

checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'Process chromR
objects':
  ‘...’


and man/proc_chromR.Rd on github does list '...' in the \arguments section
but no function listed in the \usage section uses '...'.

The question is why you don't always get that warning.

Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Tue, Feb 4, 2020 at 8:47 AM brian knaus  wrote:

> Does anyone know the current status of r-hub? My package (
> https://github.com/knausb/vcfR) is throwing warnings on R-devel (
> https://cran.r-project.org/web/checks/check_results_vcfR.html) and CRAN
> has
> asked me to fix it. Tried r-hub but it failed.
>
>
> https://builder.r-hub.io/status/vcfR_1.9.0.9000.tar.gz-ad6bc014056941a58d94765de3134c4e
>
>
> https://builder.r-hub.io/status/vcfR_1.9.0.9000.tar.gz-f673df2011864365ae5f7f66b4d16bf3
>
> My interpretation is that this is not due to my package. Is anyone else
> having issues with r-hub?
>
> Thanks!
> Brian
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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Re: [R-pkg-devel] CXX14 not defined on Windows

[Dirk Eddelbuettel]

On 4 February 2020 at 17:51, Guido Kraemer wrote:
| I am testing building a package on Windows. The package requires C++14. 

You will have to wait.

The current Rtools is at g++ 4.9.3 which (barely) supports C++11.  We all
keep our fingers crossed as the replacement Rtools would bring g++ 8.*.  This
may happen with R 4.0.0 in April but I have no more details either.

Dirk

-- 
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Re: [R-pkg-devel] r-hub status

[Gábor Csárdi]

This is the R-hub issue tracker:
https://github.com/r-hub/rhub/issues

Gabor

On Tue, Feb 4, 2020 at 4:47 PM brian knaus  wrote:
>
> Does anyone know the current status of r-hub? My package (
> https://github.com/knausb/vcfR) is throwing warnings on R-devel (
> https://cran.r-project.org/web/checks/check_results_vcfR.html) and CRAN has
> asked me to fix it. Tried r-hub but it failed.
>
> https://builder.r-hub.io/status/vcfR_1.9.0.9000.tar.gz-ad6bc014056941a58d94765de3134c4e
>
> https://builder.r-hub.io/status/vcfR_1.9.0.9000.tar.gz-f673df2011864365ae5f7f66b4d16bf3
>
> My interpretation is that this is not due to my package. Is anyone else
> having issues with r-hub?
>
> Thanks!
> Brian
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

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[R-pkg-devel] CXX14 not defined on Windows

[Guido Kraemer]

I am testing building a package on Windows. The package requires C++14. 
I have installed the latest versions of R (3.6.2), RTools (3.5), and 
RStudio. The package builds fine under Linux.

I get the following error:

> devtools::install_github("gdkrmr/zarr-R")
   ...
  C++14 standard requested but CXX14 is not defined
   ...


I have also set `~/.R/Makevars.win` as suggested in the manual "Writing 
R extensions", Section 1.2.5 "Using C++14 code". When typing `R CMD 
config CXX14` in the RStudio terminal, I get a reply 
("c:/Rtools/mingw_64/bin/g++"). When trying to install the package 
manually with `R CMD INSTALL ...` from the RStudio terminal, I get the 
same error.


What am I doing wrong?

Thanks!

Guido

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[R-pkg-devel] r-hub status

[brian knaus]

Does anyone know the current status of r-hub? My package (
https://github.com/knausb/vcfR) is throwing warnings on R-devel (
https://cran.r-project.org/web/checks/check_results_vcfR.html) and CRAN has
asked me to fix it. Tried r-hub but it failed.

https://builder.r-hub.io/status/vcfR_1.9.0.9000.tar.gz-ad6bc014056941a58d94765de3134c4e

https://builder.r-hub.io/status/vcfR_1.9.0.9000.tar.gz-f673df2011864365ae5f7f66b4d16bf3

My interpretation is that this is not due to my package. Is anyone else
having issues with r-hub?

Thanks!
Brian

[[alternative HTML version deleted]]

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[Rd] document base::`[[.data.frame`

[Jan Gorecki]

Dear R-devel,

Looking at source of base::`[[.data.frame` we can see a mysterious
handling of subsetting rows and columns at the same time. That does
not seems to be dcoumented anywhere in `[[`. Could we extend
documentation for such data.frame use cases? Or if it is meant to be
used only internally, then maybe better to put that into own internal
function?

Best regards,
Jan Gorecki

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Re: [Rd] Stroring and extracting AICs from an ARIMA model using a nested loop

[Rui Barradas]

Hello,

Don't worry, we've seen worst questions :).
Inline.

Às 13:20 de 04/02/20, ismael ismael escreveu:
I am now aware that I should not post this type of questions on this 
group. However, I would like to have some clarifications related to the 
response you've already provided. The code you provided yields accurate 
results, however I still have issues grasping the loop process in case 1 
& 2.


In case 1, the use of "p+1" and "q+1" is still blurry to me? 


1. R indexes starting from 1, both your orders p and q are 0:3. So to 
assign the results to the results matrix, add 1 and get indices 1:4.

You could also set the row and column names after, to make it more clear:

dimnames(storage1) <- list(paste0("p", 0:3), paste0("q", 0:3))

2. 0L is an integer, just 0 is a floating-point corresponding to the C 
language double.


class(0L)   # "integer"
class(0)# "numeric"

typeof(0L)  # "integer"
typeof(0)   # "double"

Indices are integers, so I used integers and added 1L every iteration 
through the inner loop.


This also means that in point 1. I should have indexed the matrix with p 
+ 1L and q + 1L, see the output of


class(0:3)


Hope this helps,

Rui Barradas

Likewise

"0L" and " i + 1L" in case 2.

Can you please provide explanations on the loop mechanisms you've used.





Le lundi 3 février 2020 à 03:47:20 UTC−6, Rui Barradas 
 a écrit :



Hello,

You can solve the problem in two different ways.

1. Redefine storage1 as a matrix and extract the aic *in* the loop.

storage1 <- matrix(0, 4, 4)
for(p in 0:3){
   for(q in 0:3){
     storage1[p + 1, q + 1] <- arima(etc)$aic
   }
}


2. define storage1 as a list.

storage1 <- vector("list", 16)
i <- 0L
for(p in 0:3){
   for(q in 0:3){
     i <- i + 1L
     storage1[[i]] <- arima(etc)
   }
}

lapply(storage1, '[[', "aic")  # get the aic's.

Maybe sapply is better it will return a vector.


Hope this helps,

Rui Barradas




Às 06:23 de 03/02/20, ismael ismael via R-devel escreveu:
 > Hello
 > I am trying to extract AICs from an ARIMA estimation with different
 > combinations of p & q ( p =0,1,2,3
 > and q=0,1.2,3). I have tried using the following code unsucessfully. Can
 > anyone help?
 >
 > code:
 > storage1 <- numeric(16)
 > for (p in 0:3){
 >
 >      for (q in 0:3){
 >
 >      storage1[p]  <- arima(x,order=c(p,0,q), method="ML")}
 > }
 > storage1$aic

 >
 >     [[alternative HTML version deleted]]
 >
 > __
 > R-devel@r-project.org  mailing list
 > https://stat.ethz.ch/mailman/listinfo/r-devel

 >


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Re: [R-pkg-devel] new package processing time

[Duncan Murdoch]

On 04/02/2020 9:15 a.m., Marcelo Araya Salas wrote:

Thanks

I found it here:

ftp://cran.r-project.org/incoming/archive/

not sure what that's suppose to mean


That generally means that it has been rejected.  The usual sequence of 
events is:


You submit it, and an email comes to the maintainer asking for 
confirmation of the submission.  If that confirmation doesn't come, it 
could end up in archive.


Then CRAN runs automatic tests on Windows and Debian.  If those have 
sufficiently severe issues (I don't know what the exact cutoff is, but 
certainly ERRORs are severe enough, and probably WARNINGs too) then an 
email is sent to the maintainer, and it is moved to archive.  The last 
time I got one of those emails the header had


From: lig...@statistik.tu-dortmund.de
Reply-To: cran-submissi...@r-project.org
To: murd...@stats.uwo.ca
Cc: cran-submissi...@r-project.org
Subject: [CRAN-pretest-archived] CRAN submission rgl 0.100.40

so maybe you can check your spam folder for a message like that.

If it passes the automatic test, it probably gets some manual testing; 
problems there would also lead to archiving, generally with a message 
from whoever did the testing.


Duncan Murdoch



Marcelo

El mar., 4 feb. 2020 a las 8:12, Dirk Eddelbuettel ()
escribió:



On 4 February 2020 at 10:28, Helmut Schütz wrote:
| Possibly it went unnoticed.

A follow-up email may be a good idea.

| My first new package took two days from submission to acceptance
| including answering questions in July last year.

It is _much_ more clogged now as you can tell via a quick 'ls -lR' on the
incoming/ directory (and its subdirectories) will tell you. [1]

My RcppSimdJson package has been sitting there since Jan 26 but is slowly
bubbling to the top but there is still well over a done ahead of it. And
newbies/ contains more than _two screenfuls_ here...

Dirk

[1] Many ftp clients let you do that, I use a one-line wrapper around
ncftp;
or if you can't there is the Locke shiny app).

--
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Re: [R-pkg-devel] new package processing time

[Dirk Eddelbuettel]

On 4 February 2020 at 08:15, Marcelo Araya Salas wrote:
| I found it here:
| 
| ftp://cran.r-project.org/incoming/archive/
| 
| not sure what that's suppose to mean

"It's dead."

It generally means you will have gotten an email with the reasoning.  But
whatever is in archive/ is no longer processed.

Dirk

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Re: [R-pkg-devel] new package processing time

[Ben Bolker]

  Also a vote for the foghorn::cran_incoming() function.

  "archive" means your package was rejected.  If you don't know
why/didn't receive an e-mail, you might have to e-mail CRAN maintainers
for clarification.

• Hornik, Ligges and Zeileis. "Changes on CRAN: 2017-12-01 to
  2018-06-30", R Journal 10(1), July 2018. https://journal.r-project.org/archive/2018-1/cran.pdf>

  • Maëlle Salmon, Locke Data, Stephanie Locke, Mitchell
  O'Hara-Wild, Hugo Gruson. "CRAN incoming dashboard", https://cransays.itsalocke.com/articles/dashboard.html>


On 2020-02-04 9:15 a.m., Marcelo Araya Salas wrote:
> Thanks
> 
> I found it here:
> 
> ftp://cran.r-project.org/incoming/archive/
> 
> not sure what that's suppose to mean
> 
> Marcelo
> 
> El mar., 4 feb. 2020 a las 8:12, Dirk Eddelbuettel ()
> escribió:
> 
>>
>> On 4 February 2020 at 10:28, Helmut Schütz wrote:
>> | Possibly it went unnoticed.
>>
>> A follow-up email may be a good idea.
>>
>> | My first new package took two days from submission to acceptance
>> | including answering questions in July last year.
>>
>> It is _much_ more clogged now as you can tell via a quick 'ls -lR' on the
>> incoming/ directory (and its subdirectories) will tell you. [1]
>>
>> My RcppSimdJson package has been sitting there since Jan 26 but is slowly
>> bubbling to the top but there is still well over a done ahead of it. And
>> newbies/ contains more than _two screenfuls_ here...
>>
>> Dirk
>>
>> [1] Many ftp clients let you do that, I use a one-line wrapper around
>> ncftp;
>> or if you can't there is the Locke shiny app).
>>
>> --
>> http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>>
> 
>   [[alternative HTML version deleted]]
> 
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Re: [R-pkg-devel] new package processing time

[Marcelo Araya Salas]

Thanks

I found it here:

ftp://cran.r-project.org/incoming/archive/

not sure what that's suppose to mean

Marcelo

El mar., 4 feb. 2020 a las 8:12, Dirk Eddelbuettel ()
escribió:

>
> On 4 February 2020 at 10:28, Helmut Schütz wrote:
> | Possibly it went unnoticed.
>
> A follow-up email may be a good idea.
>
> | My first new package took two days from submission to acceptance
> | including answering questions in July last year.
>
> It is _much_ more clogged now as you can tell via a quick 'ls -lR' on the
> incoming/ directory (and its subdirectories) will tell you. [1]
>
> My RcppSimdJson package has been sitting there since Jan 26 but is slowly
> bubbling to the top but there is still well over a done ahead of it. And
> newbies/ contains more than _two screenfuls_ here...
>
> Dirk
>
> [1] Many ftp clients let you do that, I use a one-line wrapper around
> ncftp;
> or if you can't there is the Locke shiny app).
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>

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Re: [R-pkg-devel] Fwd: LICENSE file in package including third party library

[Dirk Eddelbuettel]

On 4 February 2020 at 15:04, GD wrote:
| I have a very specific question regarding the licensing of my R package.
| 
| Here is the details: I have an R package under the MIT license so the
| DESCRIPTION file contains the field `License: MIT + file LICENSE` and
| the LICENSE file contains the following required fields:
| 
| ```
| YEAR: 
| COPYRIGHT HOLDER: xx
| ```
| 
| My problem is that my package includes a third party C++ library also
| under MIT license but with different copyright holder and year
| information (available in its own LICENSE file shipped with the library).

So maybe add a file COPYRIGHTS ?
 
| How can I edit the LICENSE file of my package to have both copyright
| information? Am I supposed to merge them without specifying that I
| developed one package and only included another lib?
| 
| For instance, the package RcppEigen (which has a similar structure with
| an included third party C++ lib) specifies the different copyrights in
| the LICENSE file (but the license is different and not MIT, thus the
| requirement regarding the LICENSE file is not the same).

Did you read what it says?  First two lines are

   Please see the included file COPYRIGHTS for per-file (or per-directory)
   details on licenses as well as copyrights.

and that file is included as it comes from inst/COPYRIGHTS.

Dirk

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Re: [R-pkg-devel] new package processing time

[Dirk Eddelbuettel]

On 4 February 2020 at 10:28, Helmut Schütz wrote:
| Possibly it went unnoticed.

A follow-up email may be a good idea.

| My first new package took two days from submission to acceptance 
| including answering questions in July last year.

It is _much_ more clogged now as you can tell via a quick 'ls -lR' on the
incoming/ directory (and its subdirectories) will tell you. [1]

My RcppSimdJson package has been sitting there since Jan 26 but is slowly
bubbling to the top but there is still well over a done ahead of it. And
newbies/ contains more than _two screenfuls_ here...

Dirk

[1] Many ftp clients let you do that, I use a one-line wrapper around ncftp;
or if you can't there is the Locke shiny app).

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[R-pkg-devel] Fwd: LICENSE file in package including third party library

[GD]

Hi,

I have a very specific question regarding the licensing of my R package.

Here is the details: I have an R package under the MIT license so the
DESCRIPTION file contains the field `License: MIT + file LICENSE` and
the LICENSE file contains the following required fields:

```
YEAR: 
COPYRIGHT HOLDER: xx
```

My problem is that my package includes a third party C++ library also
under MIT license but with different copyright holder and year
information (available in its own LICENSE file shipped with the library).

How can I edit the LICENSE file of my package to have both copyright
information? Am I supposed to merge them without specifying that I
developed one package and only included another lib?

For instance, the package RcppEigen (which has a similar structure with
an included third party C++ lib) specifies the different copyrights in
the LICENSE file (but the license is different and not MIT, thus the
requirement regarding the LICENSE file is not the same).

Thanks in advanced,
Best regards,

-- 
Ghislain Durif
-
Research engineer -- CNRS
Institut Montpelliérain Alexandre Grothendieck (IMAG)
University of Montpellier (France)

Webpage: https://gdurif.perso.math.cnrs.fr
Montpellier Bio-Stats: https://groupes.renater.fr/wiki/montpellier-biostat

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Re: [Rd] Stroring and extracting AICs from an ARIMA model using a nested loop

[ismael ismael via R-devel]

  
I am nowaware that I should not post this type of questions on this group. 
However, Iwould like to have some clarifications related to the response you've 
alreadyprovided. The code you provided yields accurate results, however I still 
haveissues grasping the loop process in case 1 & 2.

In case1, the use of "p+1" and "q+1" is still blurry tome? Likewise "0L" and " 
i + 1L" in case 2.

 

Can youplease provide explanations on the loop mechanisms you've used. 




Le lundi 3 février 2020 à 03:47:20 UTC−6, Rui Barradas 
 a écrit :  
 
 Hello,

You can solve the problem in two different ways.

1. Redefine storage1 as a matrix and extract the aic *in* the loop.

storage1 <- matrix(0, 4, 4)
for(p in 0:3){
  for(q in 0:3){
    storage1[p + 1, q + 1] <- arima(etc)$aic
  }
}


2. define storage1 as a list.

storage1 <- vector("list", 16)
i <- 0L
for(p in 0:3){
  for(q in 0:3){
    i <- i + 1L
    storage1[[i]] <- arima(etc)
  }
}

lapply(storage1, '[[', "aic")  # get the aic's.

Maybe sapply is better it will return a vector.


Hope this helps,

Rui Barradas




Às 06:23 de 03/02/20, ismael ismael via R-devel escreveu:
> Hello
> I am trying to extract AICs from an ARIMA estimation with different
> combinations of p & q ( p =0,1,2,3
> and q=0,1.2,3). I have tried using the following code unsucessfully. Can
> anyone help?
> 
> code:
> storage1 <- numeric(16)
> for (p in 0:3){
> 
>      for (q in 0:3){
>  
>      storage1[p]  <- arima(x,order=c(p,0,q), method="ML")}
> }
> storage1$aic
> 
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> 
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Re: [R-pkg-devel] new package processing time

[Helmut Schütz]

Hi Marcelo,

Marcelo Araya Salas wrote on 2020-02-04 00:56:

I submitted a new package to CRAN a couple of weeks ago. Does anyone know
how long does it take for the package to be processed? New package versions
are usually processed in a few hours so that's why I am wondering if
everything is fine.


Possibly it went unnoticed.
My first new package took two days from submission to acceptance 
including answering questions in July last year.


Cheers,
Helmut

--
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BEBAC – Consultancy Services for
Bioequivalence and Bioavailability Studies
Neubaugasse 36/11
1070 Vienna, Austria
W https://bebac.at/
F https://forum.bebac.at/

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