Re: [Rd] install_github and survival
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." To: "r-devel@r-project.org" Subject: [Rd] install_github and survival Message-ID: <771925$cbi...@ironport10.mayo.edu> Content-Type: text/plain; charset="utf-8" I treat CRAN as the main repository for survival, but I have also had a github (therneau/survival) version for a couple of years. It has a vignette2 directory, for instance, that contains extra vignettes that either take too long to run or depend on other packages. It also gets updated more often than CRAN (though those updates mght not be as well tested yet). In any case, since it is there, people will of course run install_github against it. I've added a config script to do the one extra step necessary, but when I try install_github it fails. I'm clearly doing something wrong. If someone were willing to contribute a fix I would be most grateful. survival3.1-0 is almost ready for CRAN, by the way. Reverse dependency checks of hdnom turned up one last thing to repair... Terry Therneau [[alternative HTML version deleted]] -- Subject: Digest Footer ___ R-devel@r-project.org mailing list DIGESTED https://stat.ethz.ch/mailman/listinfo/r-devel -- End of R-devel Digest, Vol 199, Issue 6 *** __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [EXTERNAL] RE: install_github and survival
Yes, that is exactly the problem. The code found in the "config" script is never run. But why doesn't it get run? On 9/6/19 5:44 AM, Georgi Boshnakov wrote: > I cloned therneau/survival and the installation failed since there is no > definition for exported function survfit(). > A file seems to be missing - there is survfit0() and survfit0.R but, compared > to CRAN, no survfit.R. > > Georgi Boshnakov > > > -- > > Message: 1 > Date: Thu, 05 Sep 2019 12:53:11 -0500 > From: "Therneau, Terry M., Ph.D." > To: "r-devel@r-project.org" > Subject: [Rd] install_github and survival > Message-ID: <771925$cbi...@ironport10.mayo.edu> > 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 > > ___ > R-devel@r-project.org mailing list DIGESTED > https://stat.ethz.ch/mailman/listinfo/r-devel > > > -- > > End of R-devel Digest, Vol 199, Issue 6 > *** [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [EXTERNAL] RE: install_github and survival
On Fri, 6 Sep 2019 at 14:08, Therneau, Terry M., Ph.D. via R-devel 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Cryptic error message from namespaceExport
Dear all,
Today I got this error message (R 3.6.1) when installing my package:
Error: package or namespace load failed for ‘inlatools’ in
namespaceExport(ns, exports):
undefined exports: .__C__inla
My package was using setOldClass("inla") and exported the "inla" class via
the NAMESPACE. It imports functions from the INLA package. Older versions
of the INLA package did not export the "inla" class. Hence the use of
setOldClass().
The current version of the INLA package does export the "inla" class
through it NAMESPACE. This triggered the error described above.
Is the possible to improve this error message? The current message is
misleading as neither packages contain the string ".__C__inla"
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be
///
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///
[[alternative HTML version deleted]]
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Re: [Rd] Cryptic error message from namespaceExport
Just to clarify, your package is exporting a class that is not
defined? Or is it exporting a class that is defined by a dependency
and then masked by setOldClass()? A simple reproducible example would
help.
On Fri, Sep 6, 2019 at 7:48 AM Thierry Onkelinx via R-devel
wrote:
>
> Dear all,
>
> Today I got this error message (R 3.6.1) when installing my package:
>
> Error: package or namespace load failed for ‘inlatools’ in
> namespaceExport(ns, exports):
> undefined exports: .__C__inla
>
> My package was using setOldClass("inla") and exported the "inla" class via
> the NAMESPACE. It imports functions from the INLA package. Older versions
> of the INLA package did not export the "inla" class. Hence the use of
> setOldClass().
> The current version of the INLA package does export the "inla" class
> through it NAMESPACE. This triggered the error described above.
>
> Is the possible to improve this error message? The current message is
> misleading as neither packages contain the string ".__C__inla"
>
> Best regards,
>
> ir. Thierry Onkelinx
> Statisticus / Statistician
>
> Vlaamse Overheid / Government of Flanders
> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
> FOREST
> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> thierry.onkel...@inbo.be
> Havenlaan 88 bus 73, 1000 Brussel
> www.inbo.be
>
> ///
> To call in the statistician after the experiment is done may be no more
> than asking him to perform a post-mortem examination: he may be able to say
> what the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
> ///
>
>
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
--
Michael Lawrence
Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
micha...@gene.com
Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
__
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Re: [Rd] Cryptic error message from namespaceExport
Dear Michael,
my package has setOldClass("inla") and the NAMESPACE
contains exportClasses(inla) and importFrom(INLA, inla.posterior.sample)
the old version of INLA uses the S3 class "inla" but does not export it.
the new version of INLA has setOldClass("inla") and the NAMESPACE
contains exportClasses(inla)
installing my package in combination with an older INLA version works
install.packages("
https://inla.r-inla-download.org/R/stable/src/contrib/INLA_18.07.12.tar.gz";,
repos = NULL)
remotes::install_github("inbo/inlatools", upgrade = FALSE, force = TRUE)
installing my package with a recent INLA versions yields the error
install.packages("
https://inla.r-inla-download.org/R/stable/src/contrib/INLA_19.09.03.tar.gz";,
repos = NULL)
remotes::install_github("inbo/inlatools", upgrade = FALSE, force = TRUE)
Warning: INLA is a very large package. The old version is 87 MB, the new
one 250 MB
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be
///
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///
Op vr 6 sep. 2019 om 17:16 schreef Michael Lawrence <
lawrence.mich...@gene.com>:
> Just to clarify, your package is exporting a class that is not
> defined? Or is it exporting a class that is defined by a dependency
> and then masked by setOldClass()? A simple reproducible example would
> help.
>
> On Fri, Sep 6, 2019 at 7:48 AM Thierry Onkelinx via R-devel
> wrote:
> >
> > Dear all,
> >
> > Today I got this error message (R 3.6.1) when installing my package:
> >
> > Error: package or namespace load failed for ‘inlatools’ in
> > namespaceExport(ns, exports):
> > undefined exports: .__C__inla
> >
> > My package was using setOldClass("inla") and exported the "inla" class
> via
> > the NAMESPACE. It imports functions from the INLA package. Older versions
> > of the INLA package did not export the "inla" class. Hence the use of
> > setOldClass().
> > The current version of the INLA package does export the "inla" class
> > through it NAMESPACE. This triggered the error described above.
> >
> > Is the possible to improve this error message? The current message is
> > misleading as neither packages contain the string ".__C__inla"
> >
> > Best regards,
> >
> > ir. Thierry Onkelinx
> > Statisticus / Statistician
> >
> > Vlaamse Overheid / Government of Flanders
> > INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
> AND
> > FOREST
> > Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> > thierry.onkel...@inbo.be
> > Havenlaan 88 bus 73, 1000 Brussel
> > www.inbo.be
> >
> >
> ///
> > To call in the statistician after the experiment is done may be no more
> > than asking him to perform a post-mortem examination: he may be able to
> say
> > what the experiment died of. ~ Sir Ronald Aylmer Fisher
> > The plural of anecdote is not data. ~ Roger Brinner
> > The combination of some data and an aching desire for an answer does not
> > ensure that a reasonable answer can be extracted from a given body of
> data.
> > ~ John Tukey
> >
> ///
> >
> >
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
> --
> Michael Lawrence
> Scientist, Bioinformatics and Computational Biology
> Genentech, A Member of the Roche Group
> Office +1 (650) 225-7760
> micha...@gene.com
>
> Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
>
[[alternative HTML version deleted]]
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Re: [Rd] [EXTERNAL] Re: RE: install_github and survival
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 > 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 [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
