[Bioc-devel] Help with R CMD check NOTEs
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> 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
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