From |@wrence@m|ch@e| @end|ng |rom gene@com  Sat Sep 21 20:41:54 2019
From: |@wrence@m|ch@e| @end|ng |rom gene@com (Michael Lawrence)
Date: Sat, 21 Sep 2019 11:41:54 -0700
Subject: [Rd] Cryptic error message from namespaceExport
In-Reply-To: <CAJuCY5yP1RT_OiYRG=1vCnxZZ-d9Xb+1qLxm7g9J_2EF_eyBzA@mail.gmail.com>
References: <CAJuCY5yZe=T=kn0dbwTi=aLNJnfgrGWBo8n0yCH+RY23fBh5ug@mail.gmail.com>
 <CAOQ5Nycz=ObY9uB2XH4AG8bDRPNXVp6_T1+nkma8xVty6cVO4g@mail.gmail.com>
 <CAJuCY5yP1RT_OiYRG=1vCnxZZ-d9Xb+1qLxm7g9J_2EF_eyBzA@mail.gmail.com>
Message-ID: <CAOQ5NyfzpVMVmG=n8mcXaocrvB_m8cgWJSuzJOyw+eioAH39qQ@mail.gmail.com>

Thanks. The error message will now say:

undefined exports: class inla

Will check-in after running more tests.


On Fri, Sep 6, 2019 at 10:19 AM Thierry Onkelinx <thierry.onkelinx at inbo.be>
wrote:

> 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.onkelinx at 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
>
> ///////////////////////////////////////////////////////////////////////////////////////////
>
> <https://www.inbo.be>
>
>
> Op vr 6 sep. 2019 om 17:16 schreef Michael Lawrence <
> lawrence.michael at 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
>> <r-devel at r-project.org> 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.onkelinx at 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
>> >
>> ///////////////////////////////////////////////////////////////////////////////////////////
>> >
>> > <https://www.inbo.be>
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-devel at 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
>> michafla at gene.com
>>
>> Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
>>
>

-- 
Michael Lawrence
Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
michafla at gene.com

Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube

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[Rd] Cryptic error message from namespaceExport
Michael Lawrence