Thanks for your help Joris. Yasir
From: Joris Meys [mailto:joris.m...@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 <yrahmatal...@uams.edu<mailto:yrahmatal...@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 Coupure Links 653, B-9000 Gent (Belgium) <https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.google.com_-3Fq-3DCoupure-2Blinks-2B653-2C-25C2-25A0B-2D9000-2BGent-2C-25C2-25A0Belgium-26entry-3Dgmail-26source-3Dg&d=DwMFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=hG-MFl6NNsIiCaUiwkfOS4KlZn8xfbfEA-yqRSD3yZ0&s=3ckjwnh2aXCV7MnvobE2mAf14rjXzS9hbzlaIFqGhtU&e=> tel: +32 (0)9 264 61 79 ----------- Biowiskundedagen 2017-2018 http://www.biowiskundedagen.ugent.be/<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.biowiskundedagen.ugent.be_&d=DwMFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=hG-MFl6NNsIiCaUiwkfOS4KlZn8xfbfEA-yqRSD3yZ0&s=CMoie5AvHhW_oR_jZ9MyoNR3wuaHhU-O0jjItim_Vs0&e=> ------------------------------- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php<https://urldefense.proofpoint.com/v2/url?u=http-3A__helpdesk.ugent.be_e-2Dmaildisclaimer.php&d=DwMFaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=hG-MFl6NNsIiCaUiwkfOS4KlZn8xfbfEA-yqRSD3yZ0&s=vUuqINgVZvd2Rl0bHibW2XtuwCoxCceXSVXme6yBtWA&e=> ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. 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