More than one package document with the same name

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Guest User ★ 13k

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Last seen 9.7 years ago

Hi, A suggestion. Typically a Bioconductor package provides documentation of two types, one or more vignettes and a reference manual; and they have the same file name, PackageName.pdf. When downloaded some file name manipulation is required, or accept PackageName(1).pdf. I suggest the documents be given different names, for example the reference manual could be named PackageNameRefMan.pdf. Package checking could enforce the rule. -- output of sessionInfo(): R version 3.1.1 (2014-07-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GLAD_2.28.1 BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] tools_3.1.1 > -- Sent via the guest posting facility at bioconductor.org.

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ADD COMMENT • link updated 9.8 years ago by Julian Gehring ★ 1.3k • written 9.8 years ago by Guest User ★ 13k

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Julian Gehring ★ 1.3k

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Last seen 5.0 years ago

Hi Jerry, Within the structure of the installed package, the vignette(s) and compiled manual pages live in different directories and have different file extensions, so they can be distinguished. The changes you are describing are general to R packages, and would have to be enforced by the R core. Best wishes Julian On 05.08.2014 09:25, Jerry Davison [guest] wrote: > Hi, > > A suggestion. Typically a Bioconductor package provides documentation of two types, one or more vignettes and a reference manual; and they have the same file name, PackageName.pdf. When downloaded some file name manipulation is required, or accept PackageName(1).pdf. > > I suggest the documents be given different names, for example the reference manual could be named PackageNameRefMan.pdf. Package checking could enforce the rule. >

ADD COMMENT • link 9.8 years ago Julian Gehring ★ 1.3k

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----- Original Message ----- > From: "Julian Gehring" <julian.gehring at="" embl.de=""> > To: bioconductor at stat.math.ethz.ch > Sent: Tuesday, August 5, 2014 1:27:32 PM > Subject: Re: [BioC] More than one package document with the same name > > Hi Jerry, > > Within the structure of the installed package, the vignette(s) and > compiled manual pages live in different directories and have > different > file extensions, so they can be distinguished. The changes you are > describing are general to R packages, and would have to be enforced > by > the R core. I'm not sure this is true. The vignette can be named whatever the package author wants, as long as it has the appropriate file extension. So BiocCheck could suggest that it be named package-vignette.Rnw instead of package.Rnw. And the compiled (PDF) reference manual doesn't exist in a source package. So (this is probably better than my previous suggestion) BioC could rename the compiled manuals on the package landing pages to be (e.g.) package-manual.pdf instead of package.pdf. Dan > > Best wishes > Julian > > > On 05.08.2014 09:25, Jerry Davison [guest] wrote: > > Hi, > > > > A suggestion. Typically a Bioconductor package provides > > documentation of two types, one or more vignettes and a reference > > manual; and they have the same file name, PackageName.pdf. When > > downloaded some file name manipulation is required, or accept > > PackageName(1).pdf. > > > > I suggest the documents be given different names, for example the > > reference manual could be named PackageNameRefMan.pdf. Package > > checking could enforce the rule. > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >

ADD REPLY • link 9.8 years ago Dan Tenenbaum ★ 8.2k

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Hi, For the BiocCheck of the vignette name, one could also check that the vignette file name is not 'package.[Rnw|Rmd]'. This would give more flexibility, and avoid a fixed naming scheme. Since the issue affects all R packages - bioc or not -, I still think it is worth trying to address this at the R level. Best wishes Julian On 05.08.2014 10:36, Dan Tenenbaum wrote: > > I'm not sure this is true. The vignette can be named whatever the package author wants, as long as it has the appropriate file extension. > So BiocCheck could suggest that it be named package-vignette.Rnw instead of package.Rnw. > And the compiled (PDF) reference manual doesn't exist in a source package. So (this is probably better than my previous suggestion) BioC could rename the compiled manuals on the package landing pages to be (e.g.) package-manual.pdf instead of package.pdf. > > Dan >

ADD REPLY • link 9.8 years ago Julian Gehring ★ 1.3k

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