Re: [R-sig-phylo] NAMESPACE issue

[Liam J. Revell]

Hi Kevin.

Sorry, this is pretty much all my fault. The definition of the S3 method 
/rescale/ now lives in /phytools/. /rescale/ is still exported by the 
namespace of /geiger/ on CRAN, so I suspect you're working with the 
GitHub version.

The easiest thing to do is add /phytools (>1.5-1)/ to *Depends:* in your 
DESCRIPTION file and /importFrom(phytools, rescale)/ to NAMESPACE. (This 
should work immediately because currently on CRAN /rescale/ is defined & 
exported by both /phytools/ and /geiger/.)

Please let me know if that works.

All the best, Liam

Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
Book: Phylogenetic Comparative Methods in R 
<https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r> 
(/Princeton University Press/, 2022)


On 2/28/2023 9:33 AM, Kevin Arbuckle wrote:
> CAUTION: EXTERNAL SENDER
>
> Hi Emmanuel,
>
> Strangely enough it was a Windows machine I used to check it and it runs 
> fine. The log files from the checks all come back fine except for the note in 
> my original email, but as the info in the log file only say what the problem 
> is but gives no indication how to address it in this case I'm struggling with 
> it. I assume it is something to do with the NAMESPACE file (or, plausibly, 
> the DESCRIPTION file) but as I can't figure out what's going on and nothing 
> has changed with imported functions from the geiger package I was hoping 
> someone might be able to spot issues in those files, or maybe has come across 
> a similar issue and knows how to resolve it.
>
> Cheers,
> Kev
>
> Dr Kevin Arbuckle
> Athro Cyswllt (Darllenydd) mewn Biowyddorau (Bioleg Esblygiadol) / Associate 
> Professor (Reader) in Biosciences (Evolutionary Biology)
> Adran Biowyddorau / Department of Biosciences
> Cyfadran Gwyddoniaeth a Pheirianneg / Faculty of Science and Engineering
> Prifysgol Abertawe  / Swansea University
> Abertawe / Swansea
> SA2 8PP
> UK
>
> Rhowch wybod i ni os hoffech dderbyn eich gohebiaeth yn Gymraeg. Rydym yn 
> croesawu gohebiaeth yn Gymraeg neu yn Saesneg. Ni fydd gohebu yn Gymraeg yn 
> arwain at oedi.
>
> -Original Message-
> From: Emmanuel Paradis
> Sent: 28 February 2023 11:03
> To: Kevin Arbuckle
> Cc: r-sig-phylo
> Subject: Re: [R-sig-phylo] NAMESPACE issue
>
> Hi Kevin,
>
> Do you run the checks of a new version of windex on this site:
>
> win-builder.r-project.org/
>
> ? It runs the checks both on Debian and Windowns with several choices of R 
> versions, and you can access the detailed log files.
>
> Best,
>
> Emmanuel
>
> - Le 28 Fév 23, à 17:38, arbucklekevin.arbuc...@swansea.ac.uk  a écrit :
>
>> Hi all,
>>
>> I realise this might not be strictly a phylogeny-related issue, but it
>> might be as it relates to geiger and in any case the CRAN Core Team
>> have left me at an impasse trying to get an update to windex through
>> to CRAN (just repeating the error message then ignoring messages
>> asking for clarification or advice on fixing it). Hopefully it's relevant 
>> enough to this list to be OK.
>>
>> When trying to submit an update to the package, all Debian checks are
>> coming back fine, but there is one note in the Windows checks that is
>> stopping the process. The note reads:-
>>
>> "windex: no visible global function definition for 'rescale'
>> Undefined global functions or variables:
>>   rescale"
>>
>> However, geiger (the package which contains rescale) is listed as a
>> dependency in the DESCRIPTION and is imported in the NAMESPACE, so
>> rescale should definitely be there. Combined with the lack of issue
>> flagged by Debian checks (which presumably would also check basic
>> things like 'do the functions exist') and the fact that this issue
>> hasn't occurred in previous version submitted to CRAN (nothing has
>> changed with respect to the use of the rescale function), I am at a loss.
>>
>> In case it helps, the contents of the DESCRIPTION and NAMESPACE files
>> are as
>> follows:-
>>
>> DESCRIPTION file:
>> Package: windex
>> Type: Package
>> Title: Analysing Convergent Evolution using the Wheatsheaf Index
>> Version: 2.0.4
>> Date: 2023-02-23
>> Author: Kevin Arbuckle and Amanda Minter
>> Maintainer: Kevin Arbuckle
>> kevin.arbuc...@swansea.ac.uk<mailto:kevin.arbuc...@swansea.ac.uk>
>> Description: Analysing convergent evolution using the Wheatsheaf
>> index, described in Arbuckle et al. (2014) > 10./2041-210X.12195>, and some other unrelated but perhaps useful 
>> functions.
>> License: GPL-2

Re: [R-sig-phylo] NAMESPACE issue

[Kevin Arbuckle]

Hi Emmanuel,

Strangely enough it was a Windows machine I used to check it and it runs fine. 
The log files from the checks all come back fine except for the note in my 
original email, but as the info in the log file only say what the problem is 
but gives no indication how to address it in this case I'm struggling with it. 
I assume it is something to do with the NAMESPACE file (or, plausibly, the 
DESCRIPTION file) but as I can't figure out what's going on and nothing has 
changed with imported functions from the geiger package I was hoping someone 
might be able to spot issues in those files, or maybe has come across a similar 
issue and knows how to resolve it.

Cheers,
Kev

Dr Kevin Arbuckle
Athro Cyswllt (Darllenydd) mewn Biowyddorau (Bioleg Esblygiadol) / Associate 
Professor (Reader) in Biosciences (Evolutionary Biology)
Adran Biowyddorau / Department of Biosciences
Cyfadran Gwyddoniaeth a Pheirianneg / Faculty of Science and Engineering
Prifysgol Abertawe  / Swansea University 
Abertawe / Swansea
SA2 8PP
UK

Rhowch wybod i ni os hoffech dderbyn eich gohebiaeth yn Gymraeg. Rydym yn 
croesawu gohebiaeth yn Gymraeg neu yn Saesneg. Ni fydd gohebu yn Gymraeg yn 
arwain at oedi.

-Original Message-
From: Emmanuel Paradis  
Sent: 28 February 2023 11:03
To: Kevin Arbuckle 
Cc: r-sig-phylo 
Subject: Re: [R-sig-phylo] NAMESPACE issue

Hi Kevin,

Do you run the checks of a new version of windex on this site:

win-builder.r-project.org/

? It runs the checks both on Debian and Windowns with several choices of R 
versions, and you can access the detailed log files.

Best,

Emmanuel

- Le 28 Fév 23, à 17:38, Arbuckle kevin.arbuc...@swansea.ac.uk a écrit :

> Hi all,
> 
> I realise this might not be strictly a phylogeny-related issue, but it 
> might be as it relates to geiger and in any case the CRAN Core Team 
> have left me at an impasse trying to get an update to windex through 
> to CRAN (just repeating the error message then ignoring messages 
> asking for clarification or advice on fixing it). Hopefully it's relevant 
> enough to this list to be OK.
> 
> When trying to submit an update to the package, all Debian checks are 
> coming back fine, but there is one note in the Windows checks that is 
> stopping the process. The note reads:-
> 
> "windex: no visible global function definition for 'rescale'
> Undefined global functions or variables:
>  rescale"
> 
> However, geiger (the package which contains rescale) is listed as a 
> dependency in the DESCRIPTION and is imported in the NAMESPACE, so 
> rescale should definitely be there. Combined with the lack of issue 
> flagged by Debian checks (which presumably would also check basic 
> things like 'do the functions exist') and the fact that this issue 
> hasn't occurred in previous version submitted to CRAN (nothing has 
> changed with respect to the use of the rescale function), I am at a loss.
> 
> In case it helps, the contents of the DESCRIPTION and NAMESPACE files 
> are as
> follows:-
> 
> DESCRIPTION file:
> Package: windex
> Type: Package
> Title: Analysing Convergent Evolution using the Wheatsheaf Index
> Version: 2.0.4
> Date: 2023-02-23
> Author: Kevin Arbuckle and Amanda Minter
> Maintainer: Kevin Arbuckle
> kevin.arbuc...@swansea.ac.uk<mailto:kevin.arbuc...@swansea.ac.uk>
> Description: Analysing convergent evolution using the Wheatsheaf 
> index, described in Arbuckle et al. (2014)  10./2041-210X.12195>, and some other unrelated but perhaps useful 
> functions.
> License: GPL-2
> Depends: phytools, geiger (>= 2.0), ape (>= 4.0), phangorn, 
> scatterplot3d, utils, methods, R (>= 3.0.0)
> Packaged: 2023-02-23 12:36:50 UTC; karbuckle
> 
> NAMESPACE file:
> exportPattern("^[^\\.]")
> import(ape,utils,scatterplot3d)
> importFrom("graphics", "abline", "hist", "legend", "points", "arrows",
> "plot","text","polygon")
> importFrom("stats", "dist", "quantile", "sd", "var", "AIC", "BIC", 
> "logLik", "na.omit", "pchisq", "shapiro.test","model.frame","density")
> importFrom("methods", "is")
> importFrom("phytools", "findMRCA", "nodeHeights") importFrom("geiger", 
> "rescale", "ratematrix", "sim.char") importFrom("phangorn", "CI", 
> "as.phyDat", "Children", "Descendants")
> 
> 
> Any advice on how to resolve this would be welcome. Note that 
> originally I had imported geiger (and phangorn) as import rather than 
> importFrom in the NAMESPACE, but the current v

Re: [R-sig-phylo] NAMESPACE issue

[Emmanuel Paradis]

Hi Kevin,

Do you run the checks of a new version of windex on this site:

win-builder.r-project.org/

? It runs the checks both on Debian and Windowns with several choices of R 
versions, and you can access the detailed log files.

Best,

Emmanuel

- Le 28 Fév 23, à 17:38, Arbuckle kevin.arbuc...@swansea.ac.uk a écrit :

> Hi all,
> 
> I realise this might not be strictly a phylogeny-related issue, but it might 
> be
> as it relates to geiger and in any case the CRAN Core Team have left me at an
> impasse trying to get an update to windex through to CRAN (just repeating the
> error message then ignoring messages asking for clarification or advice on
> fixing it). Hopefully it's relevant enough to this list to be OK.
> 
> When trying to submit an update to the package, all Debian checks are coming
> back fine, but there is one note in the Windows checks that is stopping the
> process. The note reads:-
> 
> "windex: no visible global function definition for 'rescale'
> Undefined global functions or variables:
>  rescale"
> 
> However, geiger (the package which contains rescale) is listed as a dependency
> in the DESCRIPTION and is imported in the NAMESPACE, so rescale should
> definitely be there. Combined with the lack of issue flagged by Debian checks
> (which presumably would also check basic things like 'do the functions exist')
> and the fact that this issue hasn't occurred in previous version submitted to
> CRAN (nothing has changed with respect to the use of the rescale function), I
> am at a loss.
> 
> In case it helps, the contents of the DESCRIPTION and NAMESPACE files are as
> follows:-
> 
> DESCRIPTION file:
> Package: windex
> Type: Package
> Title: Analysing Convergent Evolution using the Wheatsheaf Index
> Version: 2.0.4
> Date: 2023-02-23
> Author: Kevin Arbuckle and Amanda Minter
> Maintainer: Kevin Arbuckle
> kevin.arbuc...@swansea.ac.uk
> Description: Analysing convergent evolution using the Wheatsheaf index,
> described in Arbuckle et al. (2014) , and some
> other unrelated but perhaps useful functions.
> License: GPL-2
> Depends: phytools, geiger (>= 2.0), ape (>= 4.0), phangorn, scatterplot3d,
> utils, methods, R (>= 3.0.0)
> Packaged: 2023-02-23 12:36:50 UTC; karbuckle
> 
> NAMESPACE file:
> exportPattern("^[^\\.]")
> import(ape,utils,scatterplot3d)
> importFrom("graphics", "abline", "hist", "legend", "points", "arrows",
> "plot","text","polygon")
> importFrom("stats", "dist", "quantile", "sd", "var", "AIC", "BIC", "logLik",
> "na.omit", "pchisq", "shapiro.test","model.frame","density")
> importFrom("methods", "is")
> importFrom("phytools", "findMRCA", "nodeHeights")
> importFrom("geiger", "rescale", "ratematrix", "sim.char")
> importFrom("phangorn", "CI", "as.phyDat", "Children", "Descendants")
> 
> 
> Any advice on how to resolve this would be welcome. Note that originally I had
> imported geiger (and phangorn) as import rather than importFrom in the
> NAMESPACE, but the current version was an attempt to resolve the issue and
> didn't work in that the same note is coming back every time.
> 
> Best wishes,
> Kev
> 
> Dr Kevin Arbuckle
> Athro Cyswllt (Darllenydd) mewn Biowyddorau (Bioleg Esblygiadol) / Associate
> Professor (Reader) in Biosciences (Evolutionary Biology)
> Adran Biowyddorau / Department of Biosciences
> Cyfadran Gwyddoniaeth a Pheirianneg / Faculty of Science and Engineering
> Prifysgol Abertawe  / Swansea University
> Abertawe / Swansea
> SA2 8PP
> UK
> 
> Rhowch wybod i ni os hoffech dderbyn eich gohebiaeth yn Gymraeg. Rydym yn
> croesawu gohebiaeth yn Gymraeg neu yn Saesneg. Ni fydd gohebu yn Gymraeg yn
> arwain at oedi.
> 
> 
>   [[alternative HTML version deleted]]
> 
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> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
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[R-sig-phylo] NAMESPACE issue

[Kevin Arbuckle]

Hi all,

I realise this might not be strictly a phylogeny-related issue, but it might be 
as it relates to geiger and in any case the CRAN Core Team have left me at an 
impasse trying to get an update to windex through to CRAN (just repeating the 
error message then ignoring messages asking for clarification or advice on 
fixing it). Hopefully it's relevant enough to this list to be OK.

When trying to submit an update to the package, all Debian checks are coming 
back fine, but there is one note in the Windows checks that is stopping the 
process. The note reads:-

"windex: no visible global function definition for 'rescale'
Undefined global functions or variables:
  rescale"

However, geiger (the package which contains rescale) is listed as a dependency 
in the DESCRIPTION and is imported in the NAMESPACE, so rescale should 
definitely be there. Combined with the lack of issue flagged by Debian checks 
(which presumably would also check basic things like 'do the functions exist') 
and the fact that this issue hasn't occurred in previous version submitted to 
CRAN (nothing has changed with respect to the use of the rescale function), I 
am at a loss.

In case it helps, the contents of the DESCRIPTION and NAMESPACE files are as 
follows:-

DESCRIPTION file:
Package: windex
Type: Package
Title: Analysing Convergent Evolution using the Wheatsheaf Index
Version: 2.0.4
Date: 2023-02-23
Author: Kevin Arbuckle and Amanda Minter
Maintainer: Kevin Arbuckle 
kevin.arbuc...@swansea.ac.uk
Description: Analysing convergent evolution using the Wheatsheaf index, 
described in Arbuckle et al. (2014) , and some 
other unrelated but perhaps useful functions.
License: GPL-2
Depends: phytools, geiger (>= 2.0), ape (>= 4.0), phangorn, scatterplot3d, 
utils, methods, R (>= 3.0.0)
Packaged: 2023-02-23 12:36:50 UTC; karbuckle

NAMESPACE file:
exportPattern("^[^\\.]")
import(ape,utils,scatterplot3d)
importFrom("graphics", "abline", "hist", "legend", "points", "arrows", 
"plot","text","polygon")
importFrom("stats", "dist", "quantile", "sd", "var", "AIC", "BIC", "logLik", 
"na.omit", "pchisq", "shapiro.test","model.frame","density")
importFrom("methods", "is")
importFrom("phytools", "findMRCA", "nodeHeights")
importFrom("geiger", "rescale", "ratematrix", "sim.char")
importFrom("phangorn", "CI", "as.phyDat", "Children", "Descendants")


Any advice on how to resolve this would be welcome. Note that originally I had 
imported geiger (and phangorn) as import rather than importFrom in the 
NAMESPACE, but the current version was an attempt to resolve the issue and 
didn't work in that the same note is coming back every time.

Best wishes,
Kev

Dr Kevin Arbuckle
Athro Cyswllt (Darllenydd) mewn Biowyddorau (Bioleg Esblygiadol) / Associate 
Professor (Reader) in Biosciences (Evolutionary Biology)
Adran Biowyddorau / Department of Biosciences
Cyfadran Gwyddoniaeth a Pheirianneg / Faculty of Science and Engineering
Prifysgol Abertawe  / Swansea University
Abertawe / Swansea
SA2 8PP
UK

Rhowch wybod i ni os hoffech dderbyn eich gohebiaeth yn Gymraeg. Rydym yn 
croesawu gohebiaeth yn Gymraeg neu yn Saesneg. Ni fydd gohebu yn Gymraeg yn 
arwain at oedi.


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