Lori, Thank you for the clarification. I will try it.
Yasir From: Shepherd, Lori [mailto:lori.sheph...@roswellpark.org] Sent: Thursday, April 26, 2018 6:14 AM To: Rahmatallah, Yasir; joris.m...@ugent.be Cc: bioc-devel Subject: Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist " The packages will not be rejected for this WARNING, but please see the suggestion in the previous response that also might help clear them up. 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=DwQFAg&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=RbKe4MFAcV0_xq_8rPWdvqLRpwGo928zxC03xVPDNLU&s=6dH_sMZpCoB-KuxO9R71HqnXe_adTLdH4CpO5hxfSj4&e=> Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on behalf of Joris Meys <joris.m...@ugent.be<mailto:joris.m...@ugent.be>> Sent: Thursday, April 26, 2018 4:30:08 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=DwMFAg&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=RbKe4MFAcV0_xq_8rPWdvqLRpwGo928zxC03xVPDNLU&s=Mv-R1qX6544OBh7KthjZO_bsy4Vi1k7I8cQ4lcxDVN4&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=DwMFAg&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=RbKe4MFAcV0_xq_8rPWdvqLRpwGo928zxC03xVPDNLU&s=6dH_sMZpCoB-KuxO9R71HqnXe_adTLdH4CpO5hxfSj4&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=DwMFAg&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=RbKe4MFAcV0_xq_8rPWdvqLRpwGo928zxC03xVPDNLU&s=loZl-moADbYBJHjxIwCU5MzqJc2uYVLPa0i7psS3eg0&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://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium&entry=gmail&source=g<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=DwMFAg&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=RbKe4MFAcV0_xq_8rPWdvqLRpwGo928zxC03xVPDNLU&s=QSWViXuwYYvEn6WF5YrpBto4G4ZMR6ttt4MawMBQHQY&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=DwMFAg&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=RbKe4MFAcV0_xq_8rPWdvqLRpwGo928zxC03xVPDNLU&s=tsZNdiaIdge721aSMDbb6kng_thI5yJ9yZkPLi2vC0A&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=DwMFAg&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=RbKe4MFAcV0_xq_8rPWdvqLRpwGo928zxC03xVPDNLU&s=Ujb3PrFAWnKo6BPgi4vHnw8R3GTcKOcR_LgqmGYm3go&e=> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwMFAg&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=M-Ft62y7wSZB9rIGEFhwBvnNEaDz1z36pR5qqwuFMuI&m=RbKe4MFAcV0_xq_8rPWdvqLRpwGo928zxC03xVPDNLU&s=-5Lyh_VCaWQqLFiNZF7vnbulWW4nCKT3n0uOMJlXx8s&e=> This email message may contain legally privileged and/or confidential information. 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