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 m
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 https://github.com/r-lib/devtools/issues/700#
issuecomment-235127291) .
I don't know how install.package
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 use
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)
biocLite("GenomicAlignments
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
https://github.com/r-lib/devtools/issues/700#issueco
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
Mi
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 Biostatisti
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
Uni
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 .libPaths() perhaps it is picking up th
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 l
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
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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’, ‘images/benchmark
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:
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 at
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':
‘
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
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___
Bio
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
Camperdow
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
Good day,
I created a minimalist package that demonstrates the issue and it is attached
to this letter. After using R CMD build, the subsequent R CMD check process
emits one warning.
--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
Tester
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