Hi Herve, Thank you for your response.
>In other words putting everything in Imports can hurt >usability/friendliness. The approach should be more nuanced. It's >good that the 'R CMD check' NOTE reminds us about the Depends vs >Imports trade-off but for Bioconductor packages the choices made >by the developers will not always please 'R CMD check'. I will leave them as dependencies in the Description file. Can you please let me know how to go about the following NOTE. Or if this is something that should be really taken care of for a successful package build and install: * checking re-building of vignette outputs ... NOTE Warnings in re-building vignettes: Warning: file stem ‘/fig2’ is not portable Warning: file stem ‘/fig3’ is not portable @Pariksheet: I am working on the groHMM package. https://github.com/Kraus-Lab/groHMM Thank you, Anusha -------------------- From: Anusha Nagari <anusha.nag...@utsouthwestern.edu> Hi, On 10/18/2017 09:19 AM, Pariksheet Nanda wrote: > Hi Anusha > > On Wed, Oct 18, 2017 at 12:04 PM, Anusha Nagari > <Anusha.Nagari at > utsouthwestern.edu<https://stat.ethz.ch/mailman/listinfo/bioc-devel>> wrote: >> >> Depends: includes the non-default packages: >> ‘MASS’ ‘parallel’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ >> ‘GenomicRanges’ ‘GenomicAlignments’ ‘rtracklayer’ >> Adding so many packages to the search path is excessive and importing >> selectively is preferable. > > Move those to the "Imports" section in your package DESCRIPTION file. It's important to realize that this will remove all the functionalities provided by these packages from the search path e.g. your users will need to explicitly library(MASS) or library(parallel) etc... before they can access things defined in these packages. The code in your examples (man page and vignettes) and possibly in your unit tests will also need to be modified to reflect this. In other words putting everything in Imports can hurt usability/friendliness. The approach should be more nuanced. It's good that the 'R CMD check' NOTE reminds us about the Depends vs Imports trade-off but for Bioconductor packages the choices made by the developers will not always please 'R CMD check'. Cheers, H. > > >> * checking re-building of vignette outputs ... NOTE >> Warnings in re-building vignettes: >> Warning: file stem ‘/fig2’ is not portable >> Warning: file stem ‘/fig3’ is not portable > > Hmm... I think we'll have to look at the exact vignette to see what's > going on. Presumably that's a LaTeX vignette. Can you advise the > package name you are working on and/or link to the the source code? > > >> Anusha > > Pariksheet > > --- > Pariksheet Nanda > PhD Candidate in Genetics and Genomics > System Administrator, Storrs HPC Cluster > University of Connecticut > > _______________________________________________ > Bioc-devel at r-project.org<https://stat.ethz.ch/mailman/listinfo/bioc-devel> > mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Tp7__PT8O8GbCyA7ow-1b8zjttyPnT9vHws3TnbUfSg&s=1ZMs6jKap0uCLdg5FhFAHuKSRe3HF6McPYWj7RWzFAQ&e= > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fredhutch.org<https://stat.ethz.ch/mailman/listinfo/bioc-devel> Phone: (206) 667-5791 Fax: (206) 667-1319 From: Anusha Nagari <anusha.nag...@utsouthwestern.edu> Date: Wednesday, October 18, 2017 at 11:04 AM To: "bioc-devel@r-project.org" <bioc-devel@r-project.org> Subject: Help with R CMD check NOTEs Hello, I am getting the following NOTES at R CMD check step: NOTE1: * checking package dependencies ... NOTE Depends: includes the non-default packages: ‘MASS’ ‘parallel’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’ ‘GenomicAlignments’ ‘rtracklayer’ Adding so many packages to the search path is excessive and importing selectively is preferable. NOTE2: * checking re-building of vignette outputs ... NOTE Warnings in re-building vignettes: Warning: file stem ‘/fig2’ is not portable Warning: file stem ‘/fig3’ is not portable Can anyone suggest how I can fix these? Thanks in advance! Best, Anusha ________________________________ UT Southwestern Medical Center The future of medicine, today. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
