Re: [Bioc-devel] Unexpected Warning About Cross-Reference Without Package Specification

On 05/11/2018 06:00 PM, Dario Strbenac wrote: Good day, limma was installed using biocLite, so it would be built before R CMD check was run. I could summarise all of the relevant information and send to R-package-devel mailing list to check if it is a bug. the 'relevant information' needs

Re: [Bioc-devel] Unexpected Warning About Cross-Reference Without Package Specification

Good day, limma was installed using biocLite, so it would be built before R CMD check was run. I could summarise all of the relevant information and send to R-package-devel mailing list to check if it is a bug. -- Dario Strbenac University of Sydney

[Bioc-devel] BSGenome submission.

Hello. I got two BSGenome packages using the BSGenome and I´d like to distribute them. Please, could anyone give me some information on how to submit them to the AnnotationHub? Thanks, Jose [[alternative HTML version deleted]] ___

Re: [Bioc-devel] Vignette warnings/errors

On 05/11/2018 01:37 PM, Kenneth Condon wrote: Hi all, I'm hoping to submit my package soon. But I am having issues with the vignette. R CMD check results0 errors | 1 warning | 0 noteschecking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc':

Re: [Bioc-devel] Fwd: Vignette warnings/errors

add something like this vignette: > %\VignetteIndexEntry{[your index entry]} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} to your vignette YAML ... see 1.4.2 of https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Writing-package-vignettes On Fri, May 11, 2018

[Bioc-devel] Fwd: Vignette warnings/errors

I forgot to add the YAML header of my .rmd file. --- title: "User Guide" author: "Kenneth Condon" date: "`r Sys.Date()`" output: html_document: number_sections: true theme: cerulean highlight: default toc: TRUE toc_depth: 3 toc_float:

[Bioc-devel] Vignette warnings/errors

Hi all, I'm hoping to submit my package soon. But I am having issues with the vignette. R CMD check results0 errors | 1 warning | 0 noteschecking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘UserGuide.Rmd’, ‘UserGuide.html’,

Re: [Bioc-devel] CRAN R 3.5 binary - where is it?

Hi, I have managed to navigate through the dependency issues on my work desktop. Over the weekend I will mess about on my own laptop to follow your suggestions to get the 2.5 binary installed form from launchpad. Thank you all, Kenneth [[alternative HTML version deleted]]

Re: [Bioc-devel] Unexpected Warning About Cross-Reference Without Package Specification

I'm not really sure about this, but Writing R Extensions says about these forms of \link that they are seldom needed, except when linking to "not-yet-installed packages". I think if you were to have installed limma without first building it (e.g., R CMD INSTALL limma rather than R CMD INSTALL

Re: [Bioc-devel] biocValid() and package version

yes that was the pb. I have to remove.packages from the wrong libraries. Thank you so much. Nicolas 2018-05-11 7:56 GMT-04:00 Shepherd, Lori : > Not sure if this could be the case - but do you have the package installed > in multiple locations / multiple

Re: [Bioc-devel] Unexpected Warning About Cross-Reference Without Package Specification

Good day, Indeed, it is in the Suggests component of the dependency specification. I didn't find any extra requirements for this case in the Cross-references section of Writing R Extensions, so I'm unsure of where to read about the rule. -- Dario Strbenac

Re: [Bioc-devel] biocValid() and package version

Not sure if this could be the case - but do you have the package installed in multiple locations / multiple .libPaths() perhaps it is picking up the package version that is in a different location? Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of

Re: [Bioc-devel] Unexpected Warning About Cross-Reference Without Package Specification

On 05/11/2018 01:00 AM, Dario Strbenac wrote: Good day, I have documented a parameter that is linked to lmFit's documentation. \item{...}{Optional settings that are passed to \code{\link{lmFit}}.} The package checking process displays a warning. * checking Rd cross-references ... WARNING

Re: [Bioc-devel] BiocInstaller: next generation

On 05/11/2018 03:33 AM, Lluís Revilla wrote: Dear Bioconductor team, Bioconductor packages can be installed via install.packages when they are a dependency of another package if there is in the DESCRIPTION file a "biocViews:" section (see

Re: [Bioc-devel] BiocInstaller: next generation

Good day, The features of the proposed package seem a lot like BiocInstaller. Once I have upgraded R and have the newest BiocInstaller installed using the bootstrapping technique of source("https://bioconductor.org/biocLite.R;), I typically do library(BiocInstaller)

Re: [Bioc-devel] limma Suggests:statmod vs Imports:statmod

hi Ryan, thanks for the clarification. robert. On 05/11/2018 09:08 AM, Ryan Thompson wrote: Hi Robert, My understanding is that the "requireNamespace" trick, combined with listing the package in "Suggests" is the standard way to implement optional dependencies. Users of limma that never

Re: [Bioc-devel] limma Suggests:statmod vs Imports:statmod

Hi Robert, My understanding is that the "requireNamespace" trick, combined with listing the package in "Suggests" is the standard way to implement optional dependencies. Users of limma that never use duplicateCorrelation or other functions that require statmod will never need to install it. For

[Bioc-devel] limma Suggests:statmod vs Imports:statmod

hi, this is a question for limma developers. at every new fresh installation of BioC and limma i get this message when i use 'duplicateCorrelation()': "statmod package required but is not installed" i just install 'statmod' and problem solved. this, however, triggers questions from some of

Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17

Dear Pijush, Once a package has been accepted to Bioconductor, a copy is made in Bioconductor's own git repository and this is the source from which the packages are made available to users. Any change you make in Github won't be automatically reflected there, you have to explicitly make the