Unconditional use of package `rms`

spatialEco only Suggests the package rms, but R CMD check fails without this package installed since it is called unconditionally in the examples of logistic.regression. Maybe you would consider wrapping the example in a condition that ensures that it only runs if rms is present?

The same goes for tabularaster and exactextractr. I'm setting up a new reverse dependency checker for the spatstat family of packages and that is why I'm noticing these. If you don't want to wrap these examples in conditionals it is not a big issue for me. I just wanted to let you know.

Ege, Thank you for pointing this how, I always appreciate feedback. I was given specific direction by CRAN that dependencies that only a single function requires should be included in “suggests” and not “depends”. In the first line of code of the logistic.regression function I have a package check. The same check is included for the polygon.extract (tabularaster dependency) and zonal.stats (exactextractr dependency). Why do you think that this is failing on the build? if(!any(which(utils::installed.packages()[,1] %in% "rms"))) stop("please install rms package before running this function") Best, Jeff Jeffrey S. Evans, Ph.D., | Senior Landscape Ecologist & Biometrician The Nature Conservancy | Global Protect Science Visiting Professor | University of Wyoming | Zoology & Physiology Laramie, WY | ***@***.******@***.***> | (970) 672-6766<tel:(970)%20672-6766> From: Ege Rubak ***@***.***> Sent: Thursday, January 20, 2022 5:31 AM To: jeffreyevans/spatialEco ***@***.***> Cc: Subscribed ***@***.***> Subject: [jeffreyevans/spatialEco] Unconditional use of package `rms` (Issue #40) spatialEco only Suggests the package rms, but R CMD check fails without this package installed since it is called unconditionally in the examples of logistic.regression. Maybe you would consider wrapping the example in a condition that ensures that it only runs if rms is present? — Reply to this email directly, view it on GitHub<#40>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACLKH74JPROAXTAPJD4LOSLUW756RANCNFSM5MMTY53Q>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.******@***.***>>

It is happening when the checker goes through the examples of the package on a system that doesn't have e.g. rms installed. So you for example need to replace require(rms) with if(requireNamespace(rms, quietly = TRUE)){ here:

spatialEco/R/logistic.regression.R

Line 62 in 6caf8ec

#' require(rms)

and then a } towards the end of the examples section when rms is no longer necessary.

OK, I was being dense but I get what you mean in regard to failure of examples. Probably being overly cautious and verbose here but, I am wrapping the relevant function examples in: p = c("sp", "spdep", "rms") if(any(!unlist(lapply(p, requireNamespace, quietly=TRUE)))) { m = which(!unlist(lapply(p, requireNamespace, quietly=TRUE))) stop("Can't run examples, please install ", paste(p[m], collapse = " ")) } else { invisible(lapply(p, require, character.only=TRUE)) # run example code… } I want to be informative if it bails out because of a missing package so am printing an error and which package(s) is missing. Probably easier to just add the packages back to dependencies but, I am trying to follow CRAN guidelines. Best, Jeff From: Ege Rubak ***@***.***> Sent: Thursday, January 20, 2022 10:55 AM To: jeffreyevans/spatialEco ***@***.***> Cc: Jeffrey Evans ***@***.***>; Comment ***@***.***> Subject: Re: [jeffreyevans/spatialEco] Unconditional use of package `rms` (Issue #40) It is happening when the checker goes through the examples of the package on a system that doesn't have e.g. rms installed. So you for example need to replace require(rms) with if(requireNamespace(rms, quietly = TRUE)){ here: https://github.com/jeffreyevans/spatialEco/blob/6caf8ec919963497d4651c1171d1609a2140ef5d/R/logistic.regression.R#L62<https://github.com/jeffreyevans/spatialEco/blob/6caf8ec919963497d4651c1171d1609a2140ef5d/R/logistic.regression.R#L62> and then a } towards the end of the examples section when rms is no longer necessary. — Reply to this email directly, view it on GitHub<#40 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACLKH75KYOCBIODO3D5B7MLUXBEA7ANCNFSM5MMTY53Q>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you commented.Message ID: ***@***.******@***.***>>

In terms of automatic checking of examples it would be better if the example doesn't generate the error stop("Can't run examples, please install ", paste(p[m], collapse = " ")) when missing suggested package(s). Could you replace the stop with a message or something like that so it doesn't generate an error and stop further processing of examples?

Anyway, it is just a suggestion and by now I have installed the suggested packages on my reverse dependency checker so it doesn't cause problems for me any more.

Best,
Ege