Re: [R-pkg-devel] win-builder 3.3.3 libcurl error + NOTE
Given that R-oldrelease will become 3.4.4 when we branch for 3.5.0 on Monday, perhaps you could just wait it out? -pd > On 23 Mar 2018, at 17:59 , Tyler wrote: > > I am getting a NOTE only on R-oldrelease when checking my package on > win-builder: > > * checking CRAN incoming feasibility ... NOTE > Maintainer: 'Tyler Morgan-Wall ' > > Found the following (possibly) invalid URLs: > URL: http://github.com/tylermorganwall/skpr >From: DESCRIPTION >Status: Error >Message: libcurl error code 35 > error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert > protocol version > URL: http://github.com/tylermorganwall/skpr/issues >From: DESCRIPTION >Status: Error >Message: libcurl error code 35 > error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert > protocol version > > I checked the version of the package currently on the CRAN that passed > without any libcurl errors or NOTEs back in January, and it too displayed > this NOTE, which again only occurred on R-oldrelease. Is there a way to > prevent this or should I just mention this NOTE in my CRAN submission > comment? > > Tyler > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] win-builder 3.3.3 libcurl error + NOTE
Sorry, I forgot: We don't switch until _release_ of 3.5.0, four weeks further down the line. Still, it doesn't seem worth it making much of a fuss about 3.3.3. -pd > On 24 Mar 2018, at 10:10 , peter dalgaard wrote: > > Given that R-oldrelease will become 3.4.4 when we branch for 3.5.0 on Monday, > perhaps you could just wait it out? > > -pd > >> On 23 Mar 2018, at 17:59 , Tyler wrote: >> >> I am getting a NOTE only on R-oldrelease when checking my package on >> win-builder: >> >> * checking CRAN incoming feasibility ... NOTE >> Maintainer: 'Tyler Morgan-Wall ' >> >> Found the following (possibly) invalid URLs: >> URL: http://github.com/tylermorganwall/skpr >> From: DESCRIPTION >> Status: Error >> Message: libcurl error code 35 >> error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert >> protocol version >> URL: http://github.com/tylermorganwall/skpr/issues >> From: DESCRIPTION >> Status: Error >> Message: libcurl error code 35 >> error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert >> protocol version >> >> I checked the version of the package currently on the CRAN that passed >> without any libcurl errors or NOTEs back in January, and it too displayed >> this NOTE, which again only occurred on R-oldrelease. Is there a way to >> prevent this or should I just mention this NOTE in my CRAN submission >> comment? >> >> Tyler >> >> [[alternative HTML version deleted]] >> >> __ >> R-package-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-package-devel > > -- > Peter Dalgaard, Professor, > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Office: A 4.23 > Email: pd@cbs.dk Priv: pda...@gmail.com > > > > > > > > > -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] win-builder 3.3.3 libcurl error + NOTE
This is more likely an issue with the win-builder server than an issue with 3.3.3, as I uploaded a prior version of my package that previously (in January) had a clean check and it returned the same NOTE. I believe this error stems from GitHub discontinuing support on Feb 22nd for the cryptographically weak TLS 1.0 & 1.1 protocols and only supporting connections with the TLS 1.2 protocol. https://githubengineering.com/crypto-removal-notice/ This could probably be fixed with upgrading/updating the SSL software on the win-builder server (to whatever version the 3.4.4 and 3.5.0 servers have). On Sat, Mar 24, 2018 at 5:21 AM, peter dalgaard wrote: > Sorry, I forgot: We don't switch until _release_ of 3.5.0, four weeks > further down the line. Still, it doesn't seem worth it making much of a > fuss about 3.3.3. > > -pd > > > On 24 Mar 2018, at 10:10 , peter dalgaard wrote: > > > > Given that R-oldrelease will become 3.4.4 when we branch for 3.5.0 on > Monday, perhaps you could just wait it out? > > > > -pd > > > >> On 23 Mar 2018, at 17:59 , Tyler wrote: > >> > >> I am getting a NOTE only on R-oldrelease when checking my package on > >> win-builder: > >> > >> * checking CRAN incoming feasibility ... NOTE > >> Maintainer: 'Tyler Morgan-Wall ' > >> > >> Found the following (possibly) invalid URLs: > >> URL: http://github.com/tylermorganwall/skpr > >> From: DESCRIPTION > >> Status: Error > >> Message: libcurl error code 35 > >> error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert > >> protocol version > >> URL: http://github.com/tylermorganwall/skpr/issues > >> From: DESCRIPTION > >> Status: Error > >> Message: libcurl error code 35 > >> error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert > >> protocol version > >> > >> I checked the version of the package currently on the CRAN that passed > >> without any libcurl errors or NOTEs back in January, and it too > displayed > >> this NOTE, which again only occurred on R-oldrelease. Is there a way to > >> prevent this or should I just mention this NOTE in my CRAN submission > >> comment? > >> > >> Tyler > >> > >> [[alternative HTML version deleted]] > >> > >> __ > >> R-package-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/r-package-devel > > > > -- > > Peter Dalgaard, Professor, > > Center for Statistics, Copenhagen Business School > > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > > Phone: (+45)38153501 > > Office: A 4.23 > > Email: pd@cbs.dk Priv: pda...@gmail.com > > > > > > > > > > > > > > > > > > > > -- > Peter Dalgaard, Professor, > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Office: A 4.23 > Email: pd@cbs.dk Priv: pda...@gmail.com > > > > > > > > > > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Warnings and error message in CRAN Package Check Results
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? Thanks a lot, Wenchao __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Warnings and error message in CRAN Package Check Results
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 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Warnings and error message in CRAN Package Check Results
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
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Warnings and error message in CRAN Package Check Results
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
>
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
--
Joshua Ulrich | about.me/joshuaulrich
FOSS Trading | www.fosstrading.com
R/Finance 2018 | www.rinfinance.com
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Warnings and error message in CRAN Package Check Results
> 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?? -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Warnings and error message in CRAN Package Check Results
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?? __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
