Re: [R-pkg-devel] [Error] data length differs from size of matrix

[Max Turgeon]

Hi Tiago,

Which version of R are you using? You will probably need to use the R-devel 
version to reproduce the error AND set a flag, as described here: 
https://cran.r-project.org/

Best,


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



From: R-package-devel  on behalf of 
Tiago Olivoto 
Sent: Thursday, June 3, 2021 7:56 PM
To: R Package Devel 
Subject: [R-pkg-devel] [Error] data length differs from size of matrix


Caution: This message was sent from outside the University of Manitoba.


Dear all,
I have received an email from the CRAN team to fix a problem with my R
package metan > to safely retain it on CRAN.

The error is given at 
and seems to be related to data different from size of matrix.

The question is that and I cannot reproduce the error locally and thus not
able to fix anything. By googling the error I've seen similar issues with a
lot of other packages. Could be this be a temporary issue?

Thanks in advance!
Tiago

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Re: [R-pkg-devel] [Error] data length differs from size of matrix

[Max Turgeon]

I apologize for the wrong link below; as described here: 
https://cran.r-project.org/doc/manuals/r-devel/NEWS.html



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



From: R-package-devel  on behalf of Max 
Turgeon 
Sent: Friday, June 4, 2021 9:35 AM
To: Tiago Olivoto ; R Package Devel 

Subject: Re: [R-pkg-devel] [Error] data length differs from size of matrix


Caution: This message was sent from outside the University of Manitoba.


Hi Tiago,

Which version of R are you using? You will probably need to use the R-devel 
version to reproduce the error AND set a flag, as described here: 
https://cran.r-project.org/

Best,


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



From: R-package-devel  on behalf of 
Tiago Olivoto 
Sent: Thursday, June 3, 2021 7:56 PM
To: R Package Devel 
Subject: [R-pkg-devel] [Error] data length differs from size of matrix


Caution: This message was sent from outside the University of Manitoba.


Dear all,
I have received an email from the CRAN team to fix a problem with my R
package metan > to safely retain it on CRAN.

The error is given at 
and seems to be related to data different from size of matrix.

The question is that and I cannot reproduce the error locally and thus not
able to fix anything. By googling the error I've seen similar issues with a
lot of other packages. Could be this be a temporary issue?

Thanks in advance!
Tiago

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Re: [R-pkg-devel] [Error] data length differs from size of matrix

[Bill Dunlap]

That log file includes the line
using R Under development (unstable) (2021-05-30 r80413)
and later says

The error most likely occurred in:

> ### Name: path_coeff
> ### Title: Path coefficients with minimal multicollinearity
> ### Aliases: path_coeff path_coeff_mat
>
> ### ** Examples
>
> ## No test:
> library(metan)
>
> # Using KW as the response variable and all other ones as predictors
> pcoeff <- path_coeff(data_ge2, resp = KW)
Error in matrix(value, n, p) :
  data length differs from size of matrix: [196 != 1 x 14]
Calls: path_coeff -> [<- -> [<-.data.frame -> matrix
Execution halted

In the current R-devel the matrix command matrix(value, nrow, ncol)
complains if length(value)>nrow*ncol, so you need to truncate 'value'.
(Previously matrix() would silently truncate value.)


-Bill


On Thu, Jun 3, 2021 at 5:57 PM Tiago Olivoto  wrote:

> Dear all,
> I have received an email from the CRAN team to fix a problem with my R
> package metan  > to safely retain it on CRAN.
>
> The error is given at <
> https://www.stats.ox.ac.uk/pub/bdr/donttest/metan.out>
> and seems to be related to data different from size of matrix.
>
> The question is that and I cannot reproduce the error locally and thus not
> able to fix anything. By googling the error I've seen similar issues with a
> lot of other packages. Could be this be a temporary issue?
>
> Thanks in advance!
> Tiago
>
> [[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] [Error] data length differs from size of matrix

[Bill Dunlap]

The offending line in path_coeff seems to be
   betas[i, 2:nvar] <- t(solve_svd(cor.x2, cor.y))
where i is a single integer, nvar is 15, and the right hand side is a 14 by
14 matrix.  What is this line trying to do?  Did it ever give the correct
result?

-Bill


On Fri, Jun 4, 2021 at 7:39 AM Bill Dunlap  wrote:

> That log file includes the line
> using R Under development (unstable) (2021-05-30 r80413)
> and later says
>
> The error most likely occurred in:
>
> > ### Name: path_coeff
> > ### Title: Path coefficients with minimal multicollinearity
> > ### Aliases: path_coeff path_coeff_mat
> >
> > ### ** Examples
> >
> > ## No test:
> > library(metan)
> >
> > # Using KW as the response variable and all other ones as predictors
> > pcoeff <- path_coeff(data_ge2, resp = KW)
> Error in matrix(value, n, p) :
>   data length differs from size of matrix: [196 != 1 x 14]
> Calls: path_coeff -> [<- -> [<-.data.frame -> matrix
> Execution halted
>
> In the current R-devel the matrix command matrix(value, nrow, ncol) complains 
> if length(value)>nrow*ncol, so you need to truncate 'value'.  (Previously 
> matrix() would silently truncate value.)
>
>
> -Bill
>
>
> On Thu, Jun 3, 2021 at 5:57 PM Tiago Olivoto 
> wrote:
>
>> Dear all,
>> I have received an email from the CRAN team to fix a problem with my R
>> package metan > > to safely retain it on CRAN.
>>
>> The error is given at <
>> https://www.stats.ox.ac.uk/pub/bdr/donttest/metan.out>
>> and seems to be related to data different from size of matrix.
>>
>> The question is that and I cannot reproduce the error locally and thus not
>> able to fix anything. By googling the error I've seen similar issues with
>> a
>> lot of other packages. Could be this be a temporary issue?
>>
>> Thanks in advance!
>> Tiago
>>
>> [[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] [Error] data length differs from size of matrix

[Tiago Olivoto]

Thanks, Bill and Max for your suggestions.
I was using R 4.1.0. After updating to R-devel I was able to reproduce the
error, which was just fixed by using solve() instead solve_svd() in the
line suggested by Bill.

Best regards,
Tiago

Em sex., 4 de jun. de 2021 às 12:41, Bill Dunlap 
escreveu:

> The offending line in path_coeff seems to be
>betas[i, 2:nvar] <- t(solve_svd(cor.x2, cor.y))
> where i is a single integer, nvar is 15, and the right hand side is a 14
> by 14 matrix.  What is this line trying to do?  Did it ever give the
> correct result?
>
> -Bill
>
>
> On Fri, Jun 4, 2021 at 7:39 AM Bill Dunlap 
> wrote:
>
>> That log file includes the line
>> using R Under development (unstable) (2021-05-30 r80413)
>> and later says
>>
>> The error most likely occurred in:
>>
>> > ### Name: path_coeff
>> > ### Title: Path coefficients with minimal multicollinearity
>> > ### Aliases: path_coeff path_coeff_mat
>> >
>> > ### ** Examples
>> >
>> > ## No test:
>> > library(metan)
>> >
>> > # Using KW as the response variable and all other ones as predictors
>> > pcoeff <- path_coeff(data_ge2, resp = KW)
>> Error in matrix(value, n, p) :
>>   data length differs from size of matrix: [196 != 1 x 14]
>> Calls: path_coeff -> [<- -> [<-.data.frame -> matrix
>> Execution halted
>>
>> In the current R-devel the matrix command matrix(value, nrow, ncol) 
>> complains if length(value)>nrow*ncol, so you need to truncate 'value'.  
>> (Previously matrix() would silently truncate value.)
>>
>>
>> -Bill
>>
>>
>> On Thu, Jun 3, 2021 at 5:57 PM Tiago Olivoto 
>> wrote:
>>
>>> Dear all,
>>> I have received an email from the CRAN team to fix a problem with my R
>>> package metan >> > to safely retain it on CRAN.
>>>
>>> The error is given at <
>>> https://www.stats.ox.ac.uk/pub/bdr/donttest/metan.out>
>>> and seems to be related to data different from size of matrix.
>>>
>>> The question is that and I cannot reproduce the error locally and thus
>>> not
>>> able to fix anything. By googling the error I've seen similar issues
>>> with a
>>> lot of other packages. Could be this be a temporary issue?
>>>
>>> Thanks in advance!
>>> Tiago
>>>
>>> [[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] [Error] data length differs from size of matrix

[Bill Dunlap]

solve_svd's second argument is 'tolerance', a small scalar value, not the
right hand side of X %*% beta == Y.  It returns the [approximate] inverse
of X, not beta.

solve_svd(cor.x2,cor.y) should probably be solve_svd(cor.x2)%*%cor.y (or
just solve(cor.x2,cor.y)).

-Bill

On Fri, Jun 4, 2021 at 8:41 AM Bill Dunlap  wrote:

> The offending line in path_coeff seems to be
>betas[i, 2:nvar] <- t(solve_svd(cor.x2, cor.y))
> where i is a single integer, nvar is 15, and the right hand side is a 14
> by 14 matrix.  What is this line trying to do?  Did it ever give the
> correct result?
>
> -Bill
>
>
> On Fri, Jun 4, 2021 at 7:39 AM Bill Dunlap 
> wrote:
>
>> That log file includes the line
>> using R Under development (unstable) (2021-05-30 r80413)
>> and later says
>>
>> The error most likely occurred in:
>>
>> > ### Name: path_coeff
>> > ### Title: Path coefficients with minimal multicollinearity
>> > ### Aliases: path_coeff path_coeff_mat
>> >
>> > ### ** Examples
>> >
>> > ## No test:
>> > library(metan)
>> >
>> > # Using KW as the response variable and all other ones as predictors
>> > pcoeff <- path_coeff(data_ge2, resp = KW)
>> Error in matrix(value, n, p) :
>>   data length differs from size of matrix: [196 != 1 x 14]
>> Calls: path_coeff -> [<- -> [<-.data.frame -> matrix
>> Execution halted
>>
>> In the current R-devel the matrix command matrix(value, nrow, ncol) 
>> complains if length(value)>nrow*ncol, so you need to truncate 'value'.  
>> (Previously matrix() would silently truncate value.)
>>
>>
>> -Bill
>>
>>
>> On Thu, Jun 3, 2021 at 5:57 PM Tiago Olivoto 
>> wrote:
>>
>>> Dear all,
>>> I have received an email from the CRAN team to fix a problem with my R
>>> package metan >> > to safely retain it on CRAN.
>>>
>>> The error is given at <
>>> https://www.stats.ox.ac.uk/pub/bdr/donttest/metan.out>
>>> and seems to be related to data different from size of matrix.
>>>
>>> The question is that and I cannot reproduce the error locally and thus
>>> not
>>> able to fix anything. By googling the error I've seen similar issues
>>> with a
>>> lot of other packages. Could be this be a temporary issue?
>>>
>>> Thanks in advance!
>>> Tiago
>>>
>>> [[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] [Error] data length differs from size of matrix

[Tiago Olivoto]

Exactly Bill!
I'll implement your suggestion (solve_svd(cor.x2)%*%cor.y), to return betas.
Best!
Tiago


Em sex., 4 de jun. de 2021 às 15:12, Bill Dunlap 
escreveu:

> solve_svd's second argument is 'tolerance', a small scalar value, not the
> right hand side of X %*% beta == Y.  It returns the [approximate] inverse
> of X, not beta.
>
> solve_svd(cor.x2,cor.y) should probably be solve_svd(cor.x2)%*%cor.y (or
> just solve(cor.x2,cor.y)).
>
> -Bill
>
> On Fri, Jun 4, 2021 at 8:41 AM Bill Dunlap 
> wrote:
>
>> The offending line in path_coeff seems to be
>>betas[i, 2:nvar] <- t(solve_svd(cor.x2, cor.y))
>> where i is a single integer, nvar is 15, and the right hand side is a 14
>> by 14 matrix.  What is this line trying to do?  Did it ever give the
>> correct result?
>>
>> -Bill
>>
>>
>> On Fri, Jun 4, 2021 at 7:39 AM Bill Dunlap 
>> wrote:
>>
>>> That log file includes the line
>>> using R Under development (unstable) (2021-05-30 r80413)
>>> and later says
>>>
>>> The error most likely occurred in:
>>>
>>> > ### Name: path_coeff
>>> > ### Title: Path coefficients with minimal multicollinearity
>>> > ### Aliases: path_coeff path_coeff_mat
>>> >
>>> > ### ** Examples
>>> >
>>> > ## No test:
>>> > library(metan)
>>> >
>>> > # Using KW as the response variable and all other ones as predictors
>>> > pcoeff <- path_coeff(data_ge2, resp = KW)
>>> Error in matrix(value, n, p) :
>>>   data length differs from size of matrix: [196 != 1 x 14]
>>> Calls: path_coeff -> [<- -> [<-.data.frame -> matrix
>>> Execution halted
>>>
>>> In the current R-devel the matrix command matrix(value, nrow, ncol) 
>>> complains if length(value)>nrow*ncol, so you need to truncate 'value'.  
>>> (Previously matrix() would silently truncate value.)
>>>
>>>
>>> -Bill
>>>
>>>
>>> On Thu, Jun 3, 2021 at 5:57 PM Tiago Olivoto 
>>> wrote:
>>>
 Dear all,
 I have received an email from the CRAN team to fix a problem with my R
 package metan > to safely retain it on
 CRAN.

 The error is given at <
 https://www.stats.ox.ac.uk/pub/bdr/donttest/metan.out>
 and seems to be related to data different from size of matrix.

 The question is that and I cannot reproduce the error locally and thus
 not
 able to fix anything. By googling the error I've seen similar issues
 with a
 lot of other packages. Could be this be a temporary issue?

 Thanks in advance!
 Tiago

 [[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] Suggesting gurobi

[Noah Greifer]

Hello,

I have been working on adding an option for my users to use integer
programming (a method of optimization) to enhance the results of a function
in my package. There are several R packages on CRAN that perform integer
programming, including Rglpk and Rsymphony. However, there is a commercial
solver called Gurobi that dramatically outperforms all open-source solvers,
and it comes with an R interface through the gurobi package. I want to
allow my users to use Gurobi to perform the package actions.

A potential issue is that the gurobi package is not on CRAN; it comes with
an installation of the Gurobi software, which requires a license. I am not
sure how to add gurobi to my Description file to satisfy CRAN's
requirements. In CMD CHECK, I get the warning that the package is not
available for checking. However, I have noticed some other packages do use
gurobi just as I want to (i.e., as an option), such as CVXR
 and designmatch
, which put gurobi in
Enhances (though I would have thought it would belong in Suggests). It
seems that neither of these packages passes the CRAN checks, though.

I'm wondering what the best practices are for including gurobi in my
package. To be clear, its use is optional and the package can be functional
without it, but it greatly enhances performance so I want my users to be
able to use it. Thank you!

Noah Greifer

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Re: [R-pkg-devel] Suggesting gurobi

[Balasubramanian Narasimhan]

Suggests" would trigger an attempt to install gurobi, which is not on CRAN.

We used "Enhances" for our CVXR  because

(1) None of the functionality in the package requires gurobi;

(2) Packages in "Enhances" are not required to check the package by CRAN.

Your package mirrors ours in these respects and so I would suggest going 
with "Enhances".


-Naras

On 6/4/21 12:35 PM, Noah Greifer wrote:

Hello,

I have been working on adding an option for my users to use integer
programming (a method of optimization) to enhance the results of a function
in my package. There are several R packages on CRAN that perform integer
programming, including Rglpk and Rsymphony. However, there is a commercial
solver called Gurobi that dramatically outperforms all open-source solvers,
and it comes with an R interface through the gurobi package. I want to
allow my users to use Gurobi to perform the package actions.

A potential issue is that the gurobi package is not on CRAN; it comes with
an installation of the Gurobi software, which requires a license. I am not
sure how to add gurobi to my Description file to satisfy CRAN's
requirements. In CMD CHECK, I get the warning that the package is not
available for checking. However, I have noticed some other packages do use
gurobi just as I want to (i.e., as an option), such as CVXR
 and designmatch
, which put gurobi in
Enhances (though I would have thought it would belong in Suggests). It
seems that neither of these packages passes the CRAN checks, though.

I'm wondering what the best practices are for including gurobi in my
package. To be clear, its use is optional and the package can be functional
without it, but it greatly enhances performance so I want my users to be
able to use it. Thank you!

Noah Greifer

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Re: [R-pkg-devel] Suggesting gurobi

[Dirk Eddelbuettel]

On 4 June 2021 at 16:21, Balasubramanian Narasimhan wrote:
| Suggests" would trigger an attempt to install gurobi, which is not on CRAN.

To my understanding that is not the case. It would only do so if and when
install.packages() is asked to also install packages in Suggests:. And point
of Suggests: is that that is not automagic.

I actually Suggests, together with Additional_Repositories: (for which Noah
may have to set the repo up, I have not checked if gurobi has one) may be the
correct call.

Dirk

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

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