Re: [R-pkg-devel] NOTE in r-devel-linux-x86_64-fedora-clang
On 8/7/20 8:35 PM, Duncan Murdoch wrote: On 07/08/2020 6:53 p.m., Helmut Schütz wrote: Hi Duncan, Duncan Murdoch wrote on 2020-08-07 21:55: On 07/08/2020 3:22 p.m., Helmut Schütz wrote: I see. However, the HTML-source states This manual is for R, version 4.1.0 Under development (2020-08-06). I was relying on the PDF-version (4.0.2 of 2020-06-22) which does *not* contain this sentence. Hence, I fell into the trap. Should be stated in the PDF as well, IMHO. Oh, c'mon. It will be a new requirement in R 4.1.0 It's not a requirement in 4.0.2, and you didn't get a NOTE about it there, you only got the note in one of the r-devel platforms. Yep, but why are the others not configured in the same way (with setenv _R_CHECK_SUGGESTS_ONLY_ false)? Doesn't sound consistent to me. What has this got to do with your suggestion that changes that will be released in R 4.1.0 next year should be documented in R 4.0.2? Duncan Murdoch I agree that package developers should always be reading the very most recent version of the docs. But I also agree that it gets confusing when the settings for different r-devel platforms on CRAN are different/inconsistent in ways that don't seem required by intrinsic between-platform differences ... The general way things work in R is that changes get announced well in advance of release *by putting them in R-devel*. That's why you're asked to check your package against R-devel before submitting: so that it meets upcoming announced changes to requirements as well as ones that are in the current release. Of course, we checked the package on winbuilder... Are you suggesting to set up a multi-boot system for all those OSs? Even if one -- not us -- would aim at that: Where to get Solaris v10? Buy a Mac to run checks on maxOS? At least I understand now the differences between r-devel-linux-x86_64-debian-gcc and r-devel-linux-x86_64-debian-gcc (given in the last line there: https://www.stats.ox.ac.uk/pub/bdr/Rconfig/r-devel-linux-x86_64-fedora-gcc). Helmut __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE in r-devel-linux-x86_64-fedora-clang
On 07/08/2020 6:53 p.m., Helmut Schütz wrote: Hi Duncan, Duncan Murdoch wrote on 2020-08-07 21:55: On 07/08/2020 3:22 p.m., Helmut Schütz wrote: I see. However, the HTML-source states This manual is for R, version 4.1.0 Under development (2020-08-06). I was relying on the PDF-version (4.0.2 of 2020-06-22) which does *not* contain this sentence. Hence, I fell into the trap. Should be stated in the PDF as well, IMHO. Oh, c'mon. It will be a new requirement in R 4.1.0 It's not a requirement in 4.0.2, and you didn't get a NOTE about it there, you only got the note in one of the r-devel platforms. Yep, but why are the others not configured in the same way (with setenv _R_CHECK_SUGGESTS_ONLY_ false)? Doesn't sound consistent to me. What has this got to do with your suggestion that changes that will be released in R 4.1.0 next year should be documented in R 4.0.2? Duncan Murdoch The general way things work in R is that changes get announced well in advance of release *by putting them in R-devel*. That's why you're asked to check your package against R-devel before submitting: so that it meets upcoming announced changes to requirements as well as ones that are in the current release. Of course, we checked the package on winbuilder... Are you suggesting to set up a multi-boot system for all those OSs? Even if one -- not us -- would aim at that: Where to get Solaris v10? Buy a Mac to run checks on maxOS? At least I understand now the differences between r-devel-linux-x86_64-debian-gcc and r-devel-linux-x86_64-debian-gcc (given in the last line there: https://www.stats.ox.ac.uk/pub/bdr/Rconfig/r-devel-linux-x86_64-fedora-gcc). Helmut __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE in r-devel-linux-x86_64-fedora-clang
Hi Duncan, Duncan Murdoch wrote on 2020-08-07 21:55: On 07/08/2020 3:22 p.m., Helmut Schütz wrote: I see. However, the HTML-source states This manual is for R, version 4.1.0 Under development (2020-08-06). I was relying on the PDF-version (4.0.2 of 2020-06-22) which does *not* contain this sentence. Hence, I fell into the trap. Should be stated in the PDF as well, IMHO. Oh, c'mon. It will be a new requirement in R 4.1.0 It's not a requirement in 4.0.2, and you didn't get a NOTE about it there, you only got the note in one of the r-devel platforms. Yep, but why are the others not configured in the same way (with setenv _R_CHECK_SUGGESTS_ONLY_ false)? Doesn't sound consistent to me. The general way things work in R is that changes get announced well in advance of release *by putting them in R-devel*. That's why you're asked to check your package against R-devel before submitting: so that it meets upcoming announced changes to requirements as well as ones that are in the current release. Of course, we checked the package on winbuilder... Are you suggesting to set up a multi-boot system for all those OSs? Even if one -- not us -- would aim at that: Where to get Solaris v10? Buy a Mac to run checks on maxOS? At least I understand now the differences between r-devel-linux-x86_64-debian-gcc and r-devel-linux-x86_64-debian-gcc (given in the last line there: https://www.stats.ox.ac.uk/pub/bdr/Rconfig/r-devel-linux-x86_64-fedora-gcc). Helmut -- Ing. Helmut Schütz BEBAC – Consultancy Services for Bioequivalence and Bioavailability Studies Neubaugasse 36/11 1070 Vienna, Austria E helmut.schu...@bebac.at W https://bebac.at/ F https://forum.bebac.at/ __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE in r-devel-linux-x86_64-fedora-clang
On 07/08/2020 3:22 p.m., Helmut Schütz wrote: Hi Duncan, Duncan Murdoch wrote on 2020-08-07 18:39: You're reading the wrong version of the manual. This is in the R-devel manual: "Packages referred to by these ‘other forms’ should be declared in the DESCRIPTION file, in the ‘Depends’, ‘Imports’, ‘Suggests’ or ‘Enhances’ fields. " This is at the end of section 2.5 in https://cran.r-project.org/doc/manuals/r-devel/R-exts.html. I see. However, the HTML-source states This manual is for R, version 4.1.0 Under development (2020-08-06). I was relying on the PDF-version (4.0.2 of 2020-06-22) which does *not* contain this sentence. Hence, I fell into the trap. Should be stated in the PDF as well, IMHO. Oh, c'mon. It will be a new requirement in R 4.1.0 It's not a requirement in 4.0.2, and you didn't get a NOTE about it there, you only got the note in one of the r-devel platforms. The general way things work in R is that changes get announced well in advance of release *by putting them in R-devel*. That's why you're asked to check your package against R-devel before submitting: so that it meets upcoming announced changes to requirements as well as ones that are in the current release. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE in r-devel-linux-x86_64-fedora-clang
Hi Duncan, Duncan Murdoch wrote on 2020-08-07 18:39: You're reading the wrong version of the manual. This is in the R-devel manual: "Packages referred to by these ‘other forms’ should be declared in the DESCRIPTION file, in the ‘Depends’, ‘Imports’, ‘Suggests’ or ‘Enhances’ fields. " This is at the end of section 2.5 in https://cran.r-project.org/doc/manuals/r-devel/R-exts.html. I see. However, the HTML-source states This manual is for R, version 4.1.0 Under development (2020-08-06). I was relying on the PDF-version (4.0.2 of 2020-06-22) which does *not* contain this sentence. Hence, I fell into the trap. Should be stated in the PDF as well, IMHO. Helmut -- Ing. Helmut Schütz BEBAC – Consultancy Services for Bioequivalence and Bioavailability Studies Neubaugasse 36/11 1070 Vienna, Austria E helmut.schu...@bebac.at W https://bebac.at/ F https://forum.bebac.at/ __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE in r-devel-linux-x86_64-fedora-clang
On 07/08/2020 11:02 a.m., Brian G. Peterson wrote: On Fri, 2020-08-07 at 15:46 +0100, Gábor Csárdi wrote: If you want to link to a package in the documentation, you'll have to add it to Suggests. This doesn't make any sense. If you don't use the code from that package anywhere, then a cross-reference to that package should not require the extra dependency in Suggests. Cross references should be able to point to other functionality that might be useful to the user, or might add extra depth of understanding to a concept. If the user doesn't have the package installed, no worries, it is just a cross reference. The requirement you are suggesting is also not discussed in Writing R Extensions: https://cran.r-project.org/doc/manuals/r-patched/R-exts.html#Cross_002dreferences In fact, it explicitly allows links to potentially uninstalled packages. You're reading the wrong version of the manual. This is in the R-devel manual: "Packages referred to by these ‘other forms’ should be declared in the DESCRIPTION file, in the ‘Depends’, ‘Imports’, ‘Suggests’ or ‘Enhances’ fields. " This is at the end of section 2.5 in https://cran.r-project.org/doc/manuals/r-devel/R-exts.html. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE in r-devel-linux-x86_64-fedora-clang
The whole point of the Suggests package relationship is that you don't actually have to have it installed to use the package. It does have to be installed to check the package, which allows the link to be tested at least once before being released. On August 7, 2020 8:02:47 AM PDT, "Brian G. Peterson" wrote: > >On Fri, 2020-08-07 at 15:46 +0100, Gábor Csárdi wrote: >> If you want to link to a package in the documentation, you'll have to >> add it to Suggests. > >This doesn't make any sense. If you don't use the code from that >package anywhere, then a cross-reference to that package should not >require the extra dependency in Suggests. > >Cross references should be able to point to other functionality that >might be useful to the user, or might add extra depth of understanding >to a concept. If the user doesn't have the package installed, no >worries, it is just a cross reference. > >The requirement you are suggesting is also not discussed in Writing R >Extensions: > >https://cran.r-project.org/doc/manuals/r-patched/R-exts.html#Cross_002dreferences > >In fact, it explicitly allows links to potentially uninstalled >packages. > >Regards, > >Brian > >__ >R-package-devel@r-project.org mailing list >https://stat.ethz.ch/mailman/listinfo/r-package-devel -- Sent from my phone. Please excuse my brevity. __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE in r-devel-linux-x86_64-fedora-clang
On Fri, Aug 7, 2020 at 3:51 PM Helmut Schütz wrote: > > Hi Gábor, > > Gábor Csárdi wrote on 2020-08-07 16:46: > > If you want to link to a package in the documentation, you'll have to > > add it to Suggests. > > THX, will do. Is this documented somewhere? The check is documented in https://cran.r-project.org/doc/manuals/r-devel/R-ints.html You can turn it on with the _R_CHECK_XREFS_PKGS_ARE_DECLARED_ environment variable. > Any why don't the *other* > installations of CRAN complain as well? I don't know if they run a different set of checks on purpose or by accident. G. > Helmut > > -- > Ing. Helmut Schütz > BEBAC – Consultancy Services for > Bioequivalence and Bioavailability Studies > Neubaugasse 36/11 > 1070 Vienna, Austria > T +43 1 2311746 > M +43 699 10792458 > E helmut.schu...@bebac.at > W https://bebac.at/ > C https://bebac.at/Contact.htm > F https://forum.bebac.at/ > GIS 24799386, VAT ATU61115625, DUNS 300370568, EORI ATEOS196209 > GDPR https://bebac.at/Data-Protection.htm > > __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE in r-devel-linux-x86_64-fedora-clang
Hi Gábor, THX again. Case closed. Helmut Gábor Csárdi wrote on 2020-08-07 17:02: On Fri, Aug 7, 2020 at 3:51 PM Helmut Schütz wrote: Hi Gábor, Gábor Csárdi wrote on 2020-08-07 16:46: If you want to link to a package in the documentation, you'll have to add it to Suggests. THX, will do. Is this documented somewhere? The check is documented in https://cran.r-project.org/doc/manuals/r-devel/R-ints.html You can turn it on with the _R_CHECK_XREFS_PKGS_ARE_DECLARED_ environment variable. Any why don't the *other* installations of CRAN complain as well? I don't know if they run a different set of checks on purpose or by accident. G. -- Ing. Helmut Schütz BEBAC – Consultancy Services for Bioequivalence and Bioavailability Studies Neubaugasse 36/11 1070 Vienna, Austria E helmut.schu...@bebac.at W https://bebac.at/ F https://forum.bebac.at/ __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE in r-devel-linux-x86_64-fedora-clang
On Fri, 2020-08-07 at 15:46 +0100, Gábor Csárdi wrote: > If you want to link to a package in the documentation, you'll have to > add it to Suggests. This doesn't make any sense. If you don't use the code from that package anywhere, then a cross-reference to that package should not require the extra dependency in Suggests. Cross references should be able to point to other functionality that might be useful to the user, or might add extra depth of understanding to a concept. If the user doesn't have the package installed, no worries, it is just a cross reference. The requirement you are suggesting is also not discussed in Writing R Extensions: https://cran.r-project.org/doc/manuals/r-patched/R-exts.html#Cross_002dreferences In fact, it explicitly allows links to potentially uninstalled packages. Regards, Brian __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE in r-devel-linux-x86_64-fedora-clang
Hi Brian, you take the words out of my mouth. However, we were slapped in the face... Helmut Brian G. Peterson wrote on 2020-08-07 17:02: On Fri, 2020-08-07 at 15:46 +0100, Gábor Csárdi wrote: If you want to link to a package in the documentation, you'll have to add it to Suggests. This doesn't make any sense. If you don't use the code from that package anywhere, then a cross-reference to that package should not require the extra dependency in Suggests. Cross references should be able to point to other functionality that might be useful to the user, or might add extra depth of understanding to a concept. If the user doesn't have the package installed, no worries, it is just a cross reference. The requirement you are suggesting is also not discussed in Writing R Extensions: https://cran.r-project.org/doc/manuals/r-patched/R-exts.html#Cross_002dreferences In fact, it explicitly allows links to potentially uninstalled packages. Regards, Brian -- Ing. Helmut Schütz BEBAC – Consultancy Services for Bioequivalence and Bioavailability Studies Neubaugasse 36/11 1070 Vienna, Austria E helmut.schu...@bebac.at W https://bebac.at/ F https://forum.bebac.at/ __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE in r-devel-linux-x86_64-fedora-clang
Hi Gábor, Gábor Csárdi wrote on 2020-08-07 16:46: If you want to link to a package in the documentation, you'll have to add it to Suggests. THX, will do. Is this documented somewhere? Any why don't the *other* installations of CRAN complain as well? Helmut -- Ing. Helmut Schütz BEBAC – Consultancy Services for Bioequivalence and Bioavailability Studies Neubaugasse 36/11 1070 Vienna, Austria T +43 1 2311746 M +43 699 10792458 E helmut.schu...@bebac.at W https://bebac.at/ C https://bebac.at/Contact.htm F https://forum.bebac.at/ GIS 24799386, VAT ATU61115625, DUNS 300370568, EORI ATEOS196209 GDPR https://bebac.at/Data-Protection.htm __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] NOTE in r-devel-linux-x86_64-fedora-clang
If you want to link to a package in the documentation, you'll have to
add it to Suggests.
Gabor
On Fri, Aug 7, 2020 at 3:45 PM Helmut Schütz wrote:
>
> Dear all,
>
> I'm struggling to understand this NOTE in
> r-devel-linux-x86_64-fedora-clang (only)
> https://cran.r-project.org/web/checks/check_results_PowerTOST.html
> emmeans is a great package (THX Russell!) but we don't use it anywhere
> in ours.
>
> Only in two man pages we have
> ... obtained via \code{\link[emmeans]{emmeans}} of package \code{emmeans}.
>
> Previously we had plain text and were asked by users for details.
> AFAIK, this is the correct syntax acc. to the REM linking to the man
> page of another package. In the library links work as intended.
>
> Our package is used in a regulated environment where even a NOTE raises
> eyebrows.
> In all other R-versions and operating systems there is no problem. What
> surprises me is that on Fedora the results depends on the C-compiler.
> Strange.
>
> Of course, we could use in NAMESPACE
>importFrom(emmeans, emmeans)
> but that would force users to install a package they might not need at all.
>
>
> Helmut
>
> --
> Ing. Helmut Schütz
> BEBAC – Consultancy Services for
> Bioequivalence and Bioavailability Studies
> Neubaugasse 36/11
> 1070 Vienna, Austria
> E helmut.schu...@bebac.at
> W https://bebac.at/
> F https://forum.bebac.at/
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
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[R-pkg-devel] NOTE in r-devel-linux-x86_64-fedora-clang
Dear all,
I'm struggling to understand this NOTE in
r-devel-linux-x86_64-fedora-clang (only)
https://cran.r-project.org/web/checks/check_results_PowerTOST.html
emmeans is a great package (THX Russell!) but we don't use it anywhere
in ours.
Only in two man pages we have
... obtained via \code{\link[emmeans]{emmeans}} of package \code{emmeans}.
Previously we had plain text and were asked by users for details.
AFAIK, this is the correct syntax acc. to the REM linking to the man
page of another package. In the library links work as intended.
Our package is used in a regulated environment where even a NOTE raises
eyebrows.
In all other R-versions and operating systems there is no problem. What
surprises me is that on Fedora the results depends on the C-compiler.
Strange.
Of course, we could use in NAMESPACE
importFrom(emmeans, emmeans)
but that would force users to install a package they might not need at all.
Helmut
--
Ing. Helmut Schütz
BEBAC – Consultancy Services for
Bioequivalence and Bioavailability Studies
Neubaugasse 36/11
1070 Vienna, Austria
E helmut.schu...@bebac.at
W https://bebac.at/
F https://forum.bebac.at/
__
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Re: [R-pkg-devel] Package can't be imported with Suggests
Hi all,
Thanks for the suggestions and comments. I found a way to allow nimble to work
and avoid the note when checking the package. My solution is to use:
requireNamespace(nimble)
attachNamespace("nimble")
I have a feeling that this may be against the spirit of the check (I believe
that it essentially replicates library()), but it does allow nimble to find its
own functions without any notes.
Cheers,
Simon
Simon Bonner
Assistant Professor of Environmetrics
Department of Statistical and Actuarial Sciences
University of Western Ontario
Office: Western Science Centre rm 276
Email: sbonn...@uwo.ca | Telephone: 519-661-2111 x88205 | Fax: 519-661-3813
Twitter: @bonnerstatslab | Website: http://simon.bonners.ca/bonner-lab/wpblog/
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