install_github and survival

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install_github and survival

R devel mailing list
I treat CRAN as the main repository for survival, but I have also had a github
(therneau/survival) version for a couple of years.  It has a vignette2 directory, for
instance, that contains extra vignettes that either take too long to run or depend on
other packages.  It also gets updated more often than CRAN (though those updates mght not
be as well tested yet).

In any case, since it is there, people will of course run install_github against it.  
I've added a config script to do the one extra step necessary, but when I try
install_github it fails.   I'm clearly doing something wrong.  If someone were willing to
contribute a fix I would be most grateful.

survival3.1-0 is almost ready for CRAN, by the way.   Reverse dependency checks of hdnom
turned up one last thing to repair...


Terry Therneau


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Re: install_github and survival

Georgi Boshnakov
I cloned therneau/survival and the installation failed since there is no definition for exported function survfit().
A file seems to be missing - there is survfit0() and survfit0.R but, compared to CRAN, no survfit.R.

Georgi Boshnakov


----------------------------------------------------------------------

Message: 1
Date: Thu, 05 Sep 2019 12:53:11 -0500
From: "Therneau, Terry M., Ph.D." <[hidden email]>
To: "[hidden email]" <[hidden email]>
Subject: [Rd] install_github and survival
Message-ID: <771925$[hidden email]>
Content-Type: text/plain; charset="utf-8"

I treat CRAN as the main repository for survival, but I have also had a github
(therneau/survival) version for a couple of years.  It has a vignette2 directory, for
instance, that contains extra vignettes that either take too long to run or depend on
other packages.  It also gets updated more often than CRAN (though those updates mght not
be as well tested yet).

In any case, since it is there, people will of course run install_github against it.  
I've added a config script to do the one extra step necessary, but when I try
install_github it fails.   I'm clearly doing something wrong.  If someone were willing to
contribute a fix I would be most grateful.

survival3.1-0 is almost ready for CRAN, by the way.   Reverse dependency checks of hdnom
turned up one last thing to repair...


Terry Therneau


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Re: install_github and survival

Farid Moussaoui
In reply to this post by R devel mailing list

You got the same error 2 years ago. It seems some data files are missing.
https://github.com/therneau/survival/issues/12
F.

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Re: [EXTERNAL] RE: install_github and survival

R devel mailing list
In reply to this post by Georgi Boshnakov
Yes, that is exactly the problem.  The code found in the "config" script is never run. 
But why doesn't it get run?

On 9/6/19 5:44 AM, Georgi Boshnakov wrote:

> I cloned therneau/survival and the installation failed since there is no definition for exported function survfit().
> A file seems to be missing - there is survfit0() and survfit0.R but, compared to CRAN, no survfit.R.
>
> Georgi Boshnakov
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 05 Sep 2019 12:53:11 -0500
> From: "Therneau, Terry M., Ph.D." <[hidden email]>
> To: "[hidden email]" <[hidden email]>
> Subject: [Rd] install_github and survival
> Message-ID: <771925$[hidden email]>
> Content-Type: text/plain; charset="utf-8"
>
> I treat CRAN as the main repository for survival, but I have also had a github
> (therneau/survival) version for a couple of years.  It has a vignette2 directory, for
> instance, that contains extra vignettes that either take too long to run or depend on
> other packages.  It also gets updated more often than CRAN (though those updates mght not
> be as well tested yet).
>
> In any case, since it is there, people will of course run install_github against it.
> I've added a config script to do the one extra step necessary, but when I try
> install_github it fails.   I'm clearly doing something wrong.  If someone were willing to
> contribute a fix I would be most grateful.
>
> survival3.1-0 is almost ready for CRAN, by the way.   Reverse dependency checks of hdnom
> turned up one last thing to repair...
>
>
> Terry Therneau
>
>
> [[alternative HTML version deleted]]
>
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> [hidden email] mailing list  DIGESTED
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
> ------------------------------
>
> End of R-devel Digest, Vol 199, Issue 6
> ***************************************


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Re: [EXTERNAL] RE: install_github and survival

Iñaki Ucar
On Fri, 6 Sep 2019 at 14:08, Therneau, Terry M., Ph.D. via R-devel
<[hidden email]> wrote:
>
> Yes, that is exactly the problem.  The code found in the "config" script is never run.
> But why doesn't it get run?

It should be called "configure", not "config".

Iñaki

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Re: [EXTERNAL] Re: RE: install_github and survival

R devel mailing list
Many thanks.  Something obvious is sometimes the hardest thing for me to see.

Terry


On 9/6/19 7:10 AM, Iñaki Ucar wrote:
> On Fri, 6 Sep 2019 at 14:08, Therneau, Terry M., Ph.D. via R-devel
> <[hidden email]> wrote:
>> Yes, that is exactly the problem.  The code found in the "config" script is never run.
>> But why doesn't it get run?
> It should be called "configure", not "config".
>
> Iñaki


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Re: install_github and survival

Jim Hester
In reply to this post by R devel mailing list
I just sent a PR that makes a few small changes to the package and
fixes the installation with `install_github()` (and also `R CMD
INSTALL`) and other ways of installing the package.

https://github.com/therneau/survival/pull/84

Jim

On Thu, Sep 5, 2019 at 1:53 PM Therneau, Terry M., Ph.D. via R-devel
<[hidden email]> wrote:

>
> I treat CRAN as the main repository for survival, but I have also had a github
> (therneau/survival) version for a couple of years.  It has a vignette2 directory, for
> instance, that contains extra vignettes that either take too long to run or depend on
> other packages.  It also gets updated more often than CRAN (though those updates mght not
> be as well tested yet).
>
> In any case, since it is there, people will of course run install_github against it.
> I've added a config script to do the one extra step necessary, but when I try
> install_github it fails.   I'm clearly doing something wrong.  If someone were willing to
> contribute a fix I would be most grateful.
>
> survival3.1-0 is almost ready for CRAN, by the way.   Reverse dependency checks of hdnom
> turned up one last thing to repair...
>
>
> Terry Therneau
>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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