[Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

[Rahmatallah, Yasir]

Thanks for your help Joris.

Yasir

From: Joris Meys [mailto:Joris.Meys at ugent.be]
Sent: Thursday, April 26, 2018 3:30 AM
To: Rahmatallah, Yasir
Cc: bioc-devel
Subject: Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "



On Wed, Apr 25, 2018 at 11:52 PM, Rahmatallah, Yasir <YRahmatallah at uams.edu<mailto:YRahmatallah at uams.edu>> wrote:
Dear all,

Build report show that many packages still have check warnings due to missing file links (cross referencing pages from other packages) under windows. The issue happens because there are different man pages for different operating systems. My package (GSAR) shows the same warning under Windows in the build report, although it locally passes R CMD build and R CMD check without warnings. Although not a perfect solution, substituting the linking in the .Rd file \code{\link[pkg:bar]{foo}} with \code{\link{foo}} or \code{\link[pkg]{foo}} was suggested in a recent discussion
https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013315.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2018-2DApril_013315.html&d=DwMFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=hG-MFl6NNsIiCaUiwkfOS4KlZn8xfbfEA-yqRSD3yZ0&s=DDXtfchBh56PcZyl9YISltZcOndbYAP-yjS1mqb_Z6k&e=>

Actually, that is the correct solution. As per "Writing R Extensions", \link[pkg]{name} searches for a html file with the name name.html in package pkg. In a number of cases the name of the html help file is not the same as the function you want to point to. For example, ppois and qpois etc are discussed in a page called Poisson. Also in "Writing R Extensions" they mention that if you want to use another name as a link, you should do \link[pkg:name]{foo}. In our example: \link[stats:Poisson]{ppois}

https://cran.r-project.org/doc/manuals/R-exts.html#Cross_002dreferences<https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_doc_manuals_R-2Dexts.html-23Cross-5F002dreferences&d=DwMFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=hG-MFl6NNsIiCaUiwkfOS4KlZn8xfbfEA-yqRSD3yZ0&s=xbdzuTPB1-qSmMRcc1Kgy0tLRCK9gQJDVpNRSg_9hl4&e=>

I understood that although a check warning is produced (under Windows only), it will be accepted (considered as advice) and packages that currently show it will proceed to Bioc release. Is that correct? There are still many packages showing this warning in yesterday's report
http://bioconductor.org/checkResults/3.7/bioc-LATEST/#show=warnings<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_3.7_bioc-2DLATEST_-23show-3Dwarnings&d=DwMFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=hG-MFl6NNsIiCaUiwkfOS4KlZn8xfbfEA-yqRSD3yZ0&s=NtMolhjVyChrcF-xyTE1D18QVa4pJWaVr98V13Hdx2s&e=>

As this is the case for even recommended packages like the survival package, I don't see how this would be a reason to reject a package. But it still makes sense to adapt your links in the way it is specified in the official R manual.
Cheers
Joris

--
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
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