Re: [R-pkg-devel] Warnings and error message in CRAN Package Check Results

2018-03-24 Thread Wenchao Ma 

Hi Joshua and Peter,

Thank you so much for your help. Yes, it's definitely my mistake in 
mixing R and c++ function calls...


I think I can fix the problems now.

Thank you once again,
Wenchao

On 3/24/2018 7:31 PM, peter dalgaard wrote:




On 25 Mar 2018, at 00:42 , Wenchao Ma  wrote:

arma::vec Pj = Calc_Pj(par = par, designMj = designMj, linkfunc = linkfunc, 
boundary = boundary, eps = eps);


I was never any good at C++, but that syntax looks like R code. Does C++ allow tag=value 
argument specification? Aren't all the subexpressions of type "par = par" just 
assignments??



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Re: [R-pkg-devel] Warnings and error message in CRAN Package Check Results

2018-03-24 Thread peter dalgaard 


> On 25 Mar 2018, at 00:42 , Wenchao Ma  wrote:
> 
>arma::vec Pj = Calc_Pj(par = par, designMj = designMj, linkfunc = 
> linkfunc, boundary = boundary, eps = eps);

I was never any good at C++, but that syntax looks like R code. Does C++ allow 
tag=value argument specification? Aren't all the subexpressions of type "par = 
par" just assignments??

-- 
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Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
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Office: A 4.23
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Re: [R-pkg-devel] Warnings and error message in CRAN Package Check Results

2018-03-24 Thread Joshua Ulrich 
On Sat, Mar 24, 2018 at 6:42 PM, Wenchao Ma  wrote:
> Dear Duncan,
>
> Thank you. I really appreciate your help!
>
> Yes, the Fedora warning is self explanatory, but I'm still quite confused.
> Below are part of my Mstep.cpp file (both functions are in the same file).
> The fedora warned me that, among others,
> Mstep.cpp:62:69: warning: explicitly assigning value of variable of type
> 'int' to itself [-Wself-assign]
> arma::vec Pj = Calc_Pj(par = par, designMj = designMj, linkfunc =
> linkfunc, boundary = boundary, eps = eps);
> ^
> 
>
> So, basically, I called Calc_Pj function from Calc_Pj_jac function, but not
> sure why this is not allowed.
>
The compiler isn't complaining about the function call. It's warning
about all the assignments you make in the function call.

Like Duncan said, the compiler thinks you have something like "i = i"
in your code.  Which you do, for every argument to the function.

You seem to confuse calling functions in R with calling functions in
C++.  C++ function arguments do not have names. They are matched by
position.  Note that none of the other function calls in the file use
"named arguments".

> 
>
> // [[Rcpp::depends(RcppArmadillo)]]
> #include 
> using namespace Rcpp;
> using namespace arma;
> // [[Rcpp::export]]
> arma::vec Calc_Pj(const arma::vec  par, const arma::mat  designMj,
> const int & linkfunc,int boundary = 0,const double  eps = 1e-16){
>   arma::vec Pj;
>   if(linkfunc==1){ //identity
> Pj = designMj*par;
>   }else if(linkfunc==2){//logit
> Pj = exp(designMj*par)/(1 + exp(designMj*par));
>   }else if(linkfunc==3){//log
> Pj = exp(designMj*par);
>   }
>   if(boundary==1){
> Pj.elem(find(Pj Pj.elem(find(Pj>1-eps)).fill(1-eps);
>   }
>   return Pj;
> }
>
> // [[Rcpp::export]]
> arma::mat Calc_Pj_jac(arma::vec  par,
>   arma::mat designMj,
>   int & linkfunc,
>   int boundary = 0,
>   double eps = 1e-16){
>   arma::mat ret = designMj;
>   if(linkfunc>1){
> arma::vec Pj = Calc_Pj(par = par, designMj = designMj, linkfunc =
> linkfunc, boundary = boundary, eps = eps);
> if(linkfunc==2){//logit
>   ret.each_col() %= Pj%(1-Pj);
> }else if(linkfunc==3){//log
>   ret.each_col() %= Pj;
> }
>   }
>   return ret;
>
> }
>
> On 3/24/2018 6:18 PM, Duncan Murdoch wrote:
>>
>> On 24/03/2018 9:28 AM, Wenchao Ma wrote:
>>>
>>> Dear all,
>>>
>>> I just submitted a package to CRAN. It went well on my computer and
>>> winbuilder, but produced warning and error messages on some linux and
>>> solaris systems, as shown here:
>>> https://cran.r-project.org/web/checks/check_results_GDINA.html
>>>
>>> Does anyone know what is going on here?
>>
>>
>> The compilers on those systems are set up to be more sensitive to coding
>> problems than yours.
>>
>> The Solaris error comes from your code
>>
>>   arma::umat B = arma::ones(K,pow(2,K)-K-1);
>>
>> The library you're using has no function definition for pow() that takes 2
>> integers.  If a float or double result is okay, you could use pow(2.0, K).
>> If you really need an int in that argument, you'll need to typecast or write
>> your own pow() function.
>>
>> The Fedora warning seems self explanatory:
>>
>> Mstep.cpp:62:69: warning: explicitly assigning value of variable of type
>> 'int' to itself [-Wself-assign]
>>
>> Take a look at that line (and the other similar ones) and see why the
>> compiler thinks you've got something like
>>
>> i = i;
>>
>> in your code.
>>
>> Duncan Murdoch
>
>
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Re: [R-pkg-devel] Warnings and error message in CRAN Package Check Results

2018-03-24 Thread Wenchao Ma 

Dear Duncan,

Thank you. I really appreciate your help!

Yes, the Fedora warning is self explanatory, but I'm still quite 
confused. Below are part of my Mstep.cpp file (both functions are in the 
same file). The fedora warned me that, among others,
Mstep.cpp:62:69: warning: explicitly assigning value of variable of type 
'int' to itself [-Wself-assign]
arma::vec Pj = Calc_Pj(par = par, designMj = designMj, linkfunc = 
linkfunc, boundary = boundary, eps = eps);
    ^ 



So, basically, I called Calc_Pj function from Calc_Pj_jac function, but 
not sure why this is not allowed.




// [[Rcpp::depends(RcppArmadillo)]]
#include 
using namespace Rcpp;
using namespace arma;
// [[Rcpp::export]]
arma::vec Calc_Pj(const arma::vec  par, const arma::mat  designMj,
const int & linkfunc,int boundary = 0,const double  eps = 1e-16){
  arma::vec Pj;
  if(linkfunc==1){ //identity
Pj = designMj*par;
  }else if(linkfunc==2){//logit
Pj = exp(designMj*par)/(1 + exp(designMj*par));
  }else if(linkfunc==3){//log
Pj = exp(designMj*par);
  }
  if(boundary==1){
Pj.elem(find(Pj1-eps)).fill(1-eps);
  }
  return Pj;
}

// [[Rcpp::export]]
arma::mat Calc_Pj_jac(arma::vec  par,
  arma::mat designMj,
  int & linkfunc,
  int boundary = 0,
  double eps = 1e-16){
  arma::mat ret = designMj;
  if(linkfunc>1){
arma::vec Pj = Calc_Pj(par = par, designMj = designMj, linkfunc = 
linkfunc, boundary = boundary, eps = eps);

if(linkfunc==2){//logit
  ret.each_col() %= Pj%(1-Pj);
}else if(linkfunc==3){//log
  ret.each_col() %= Pj;
}
  }
  return ret;
}

On 3/24/2018 6:18 PM, Duncan Murdoch wrote:

On 24/03/2018 9:28 AM, Wenchao Ma wrote:

Dear all,

I just submitted a package to CRAN. It went well on my computer and
winbuilder, but produced warning and error messages on some linux and
solaris systems, as shown here:
https://cran.r-project.org/web/checks/check_results_GDINA.html

Does anyone know what is going on here?


The compilers on those systems are set up to be more sensitive to coding 
problems than yours.


The Solaris error comes from your code

  arma::umat B = arma::ones(K,pow(2,K)-K-1);

The library you're using has no function definition for pow() that takes 
2 integers.  If a float or double result is okay, you could use pow(2.0, 
K).  If you really need an int in that argument, you'll need to typecast 
or write your own pow() function.


The Fedora warning seems self explanatory:

Mstep.cpp:62:69: warning: explicitly assigning value of variable of type 
'int' to itself [-Wself-assign]


Take a look at that line (and the other similar ones) and see why the 
compiler thinks you've got something like


i = i;

in your code.

Duncan Murdoch


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Re: [R-pkg-devel] Warnings and error message in CRAN Package Check Results

2018-03-24 Thread Duncan Murdoch 

On 24/03/2018 9:28 AM, Wenchao Ma wrote:

Dear all,

I just submitted a package to CRAN. It went well on my computer and
winbuilder, but produced warning and error messages on some linux and
solaris systems, as shown here:
https://cran.r-project.org/web/checks/check_results_GDINA.html

Does anyone know what is going on here?


The compilers on those systems are set up to be more sensitive to coding 
problems than yours.


The Solaris error comes from your code

 arma::umat B = arma::ones(K,pow(2,K)-K-1);

The library you're using has no function definition for pow() that takes 
2 integers.  If a float or double result is okay, you could use pow(2.0, 
K).  If you really need an int in that argument, you'll need to typecast 
or write your own pow() function.


The Fedora warning seems self explanatory:

Mstep.cpp:62:69: warning: explicitly assigning value of variable of type 
'int' to itself [-Wself-assign]


Take a look at that line (and the other similar ones) and see why the 
compiler thinks you've got something like


i = i;

in your code.

Duncan Murdoch

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