Re: [R-pkg-devel] Two packages with the same name

[Peter Carbonetto]

Thanks, Dirk and Uwe, for your helpful replies.

I have learned from this situation that there is some risk involved in
depending on a package that is not available in CRAN or on Bioconductor.

Peter

On Mon, Nov 28, 2022 at 1:18 PM Uwe Ligges 
wrote:

>
>
> On 28.11.2022 19:36, Dirk Eddelbuettel wrote:
> >
> > On 28 November 2022 at 12:15, Peter Carbonetto wrote:
> > | I maintain the mashr R package (
> https://cran.r-project.org/package=mashr),
> > | which has been on CRAN a little over 2 years. The mashr package
> depends on
> > | another package, flashr, which is available from an external repository
> > | (via *Additional_repositories*).
> > |
> > | Very recently, we have found ourselves in the awkward situation that
> there
> > | are now two flashr packages:
> > |
> > | https://cran.r-project.org/package=flashr
> > |
> > | (mashr is listed as one of the reverse dependencies of this package,
> which
> > | is incorrect.)
> > |
> > | Does anyone have any suggestions for how to navigate this awkward
> > | situation? The problem needs to be fixed by Dec 7 otherwise mashr will
> be
> > | taken off CRAN. On the other hand, the new "flashr" seems like a nice
> > | package, and I don't see any reason why it shouldn't exist on CRAN.
> >
> > Yikes. My tendency would be to work with what is under your control and
> have
> > your 'flashr' package renamed in its 'additional repository'. Also keep
> the
> > existing one (for existing users), and new one (say, 'flashr2' or any
> other
> > name, maybe even 'flashr4mashr'), upload to the 'additional repository'
> and
> > then update 'mashr'.
> >
> > As far as CRAN is concerned, there is really only one 'flashr'.
>
> Indeed, and CRAN makes sure that a new package does not take a name from
> CRAN nor BioC, which are what we call mainstream repositories.
> In order to prevent what happened, choose a rather unique name - and
> perhaps consider to submit that to CRAN, too.
>
> We see "flashr" and similar names are also used in other projects, so
> one more point for a new name.
>
> Best,
> Uwe Ligges
>
> > Hth,  Dirk
> >
>

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[R-pkg-devel] Two packages with the same name

[Peter Carbonetto]

Hi All,

I maintain the mashr R package (https://cran.r-project.org/package=mashr),
which has been on CRAN a little over 2 years. The mashr package depends on
another package, flashr, which is available from an external repository
(via *Additional_repositories*).

Very recently, we have found ourselves in the awkward situation that there
are now two flashr packages:

https://cran.r-project.org/package=flashr

(mashr is listed as one of the reverse dependencies of this package, which
is incorrect.)

Does anyone have any suggestions for how to navigate this awkward
situation? The problem needs to be fixed by Dec 7 otherwise mashr will be
taken off CRAN. On the other hand, the new "flashr" seems like a nice
package, and I don't see any reason why it shouldn't exist on CRAN.

Any helpful advice would be greatly appreciated.

Thank you,

Peter Carbonetto
Computational Scientist, Statistics & Genetics,
Research Computing Center & Dept. of Human Genetics
University of Chicago

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Re: [R-pkg-devel] clang: error: unsupported option '-fopenmp'

[Peter Carbonetto]

Have you seen this note (from https://cran.r-project.org/bin/macosx/)?

Important: this release uses Clang 7.0.0 and GNU Fortran 6.1, neither of
which is supplied by Apple. If you wish to compile R packages from sources,
you will need to download and install those tools - see the tools
directory.

Peter Carbonetto
Computational Scientist, Statistics & Genetics,
Research Computing Center & Dept. of Human Genetics
University of Chicago

On Fri, May 3, 2019 at 9:36 AM Maxime Turgeon 
wrote:

> Hi Spencer,
>
> I remember having a similar error a few years ago when trying to compile R
> (and its recommended packages, e.g. mgcv) from source. I was using clang as
> a compiler (this is what Hadley recommends in his book "R packages"), and I
> solved the issue by going back to g++. This can be done in your
> ".R/Makevars" file. Alternatively, you could switch to a version of clang
> that supports OpenMP.
>
> Best,
> Max
> 
> From: R-package-devel  on behalf
> of Spencer Graves 
> Sent: May 3, 2019 10:18 AM
> To: List r-package-devel
> Subject: [R-pkg-devel] clang: error: unsupported option '-fopenmp'
>
> Hello, All:
>
>
>I'm getting "clang: error: unsupported option '-fopenmp'" when
> trying to build "https://github.com/helske/bssm; under macOS 10.14.14
> with R 3.6.0;  see below.
>
>
>What do you suggest?
>
>
>Thanks,
>Spencer Graves
>
>
> p.s.  I assume I have to install compiler(s).  However, I've so far been
> unable to find instructions that are sufficiently current to convince me
> I might not do more harm than good following them.
>
>
>  > R CMD build bssm
> * checking for file ‘bssm/DESCRIPTION’ ... OK
> * preparing ‘bssm’:
> * checking DESCRIPTION meta-information ... OK
> * cleaning src
> * installing the package to build vignettes
>---
> * installing *source* package ‘bssm’ ...
> ** using staged installation
> ** libs
> clang++ -std=gnu++11
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include"
>
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include"
>
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include"
>
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/ramcmc/include"
>
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sitmo/include"
> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> -I/usr/local/include -fopenmp -fPIC  -Wall -g -O2  -c R_approx.cpp -o
> R_approx.o
> clang: error: unsupported option '-fopenmp'
> make: *** [R_approx.o] Error 1
> ERROR: compilation failed for package ‘bssm’
> * removing
>
> ‘/private/var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T/RtmppA2gBg/Rinst24427c5cbfeb/bssm’
>---
> ERROR: package installation failed
>
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Re: [R-pkg-devel] List of reverse dependencies, including archived packages

[Peter Carbonetto]

That works quite well! Thank you for the suggestion.

Peter

On Tue, Feb 26, 2019 at 1:45 AM Iñaki Ucar  wrote:

> On Tue, 26 Feb 2019 at 05:29, Peter Carbonetto
>  wrote:
> >
> > I'm wondering if there is a way to get a list of reverse dependencies on
> > CRAN that includes archived packages.
> >
> > I am asking because "ashr", an R package I maintain, was recently removed
> > from CRAN, and now it is back after I fixed the critical problem.
> However,
> > some of the downstream packages that were affected by this removal are no
> > longer listed as a reverse dependency.
>
> I think that the easiest way is to use Microsoft's CRAN time machine
> [1]. Simply set the session's repo to the day before the archiving
> date, and then you can get the complete list using regular procedures.
>
> [1] https://mran.microsoft.com/timemachine
>
> Iñaki
>

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[R-pkg-devel] List of reverse dependencies, including archived packages

[Peter Carbonetto]

I'm wondering if there is a way to get a list of reverse dependencies on
CRAN that includes archived packages.

I am asking because "ashr", an R package I maintain, was recently removed
from CRAN, and now it is back after I fixed the critical problem. However,
some of the downstream packages that were affected by this removal are no
longer listed as a reverse dependency.

For example, the CorShrink package (
https://cran.r-project.org/package=CorShrink) imports ashr, and was
therefore removed when ashr was removed. But as you can see from the ashr
page (https://cran.r-project.org/package=ashr), CorShrink is no longer
listed as a reverse dependency.

I would like to notify all the maintainers of the packages that depend on
ashr---including maintainers of the packages that were removed---so that
they can take appropriate action.

I suspect that I am not the first one to confront this situation, but I
couldn't find anything in the R-pkg-devel archives that was relevant.

Thank you,

Peter Carbonetto
Computational Scientist, Statistics & Genetics,
Research Computing Center & Dept. of Human Genetics
University of Chicago

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Re: [R-pkg-devel] Where do demos fit in?

[Peter Carbonetto]

Hi Neal,

Re-using demos for your package tests is a great idea, and should be done
more often.

However, I tend to agree with Iñaki---I generally prefer vignettes to demos.

I wanted to point out that you could take a similar strategy to what you
suggested, but using a vignette instead of a demo. The code is slightly
more complicated but seems to work. See here for an example:

https://raw.githubusercontent.com/pcarbo/varbvs/test_vignette/varbvs-R/tests/testthat/test_vignette.R

(Anyone, please reply if you know of a better way to implement this!)

Peter

On Fri, Oct 20, 2017 at 1:18 AM, Iñaki Úcar  wrote:

> 2017-10-20 5:42 GMT+02:00 Neal Fultz :
> > A graduate student just asked me (copied below), in response to a bug I
> > wrote (
> > https://github.com/DeclareDesign/estimatr/pull/38/commits/
> 99e82e253979d1307714632e9dc05d2e2c9c66df
> > ):
> >
> > How do demos normally relate to tests and vignettes? Is the purpose
> simply
> >> to have manually run tests that check the things work in the global
> >> environment?
>
> There is a good definition and description here:
> http://r-pkgs.had.co.nz/misc.html
>
> Personally, I'm not a fan of demos, because I prefer to copy
> from vignettes as I read and understand the different parts of the
> problem in question.
>
> Iñaki
>
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