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Bioconductor / AnnotationForge

Tools for building SQLite-based annotation data packages
https://bioconductor.org/packages/AnnotationForge
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Package from AnnotationForge is not available for this version of R #53

Closed phancanhtrinh closed 1 year ago

phancanhtrinh commented 1 year ago

Hi, Is there any person get this problem? I generated a database from AnnotationForge for GO term. Then I could not install it because of this error:

Warning in install.packages :   package ‘org.CalbicansSC5314V63.eg.sqlite’ is not available for this version of R  A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
--

library(AnnotationForge)
makeOrgPackage(gene_info=fSym, go=fGO,
               version="0.1",
               maintainer="",
               author="",
               outputDir = ".",
               tax_id="",
               genus="Candida",
               species="albicansSC5314V63",
               goTable="go")

## then you can call install.packages based on the return value
install.packages("org.CalbicansSC5314V63.eg.sqlite")

image

I also did install the package that I generated last year. It had the same problem. I think this came from new version of R?

I hope some people can help me. Thak you very much!

jmacdon commented 1 year ago

You should post questions like this on the support site (support.bioconductor.org) rather than here, as this is a misunderstanding on your part rather than an issue with the package.

The answer is

install.packages("org.CalbicansSC5324V63.eg.db", repos = NULL)
## or if on Windows
install.packages("org.CalbicansSC5324V63.eg.db", repos = NULL, type = "source")
phancanhtrinh commented 1 year ago

Thank you very much for your support!

On Fri, 23 Jun 2023 at 18:09, James W. MacDonald @.***> wrote:

You should post questions like this on the support site ( support.bioconductor.org) rather than here, as this is a misunderstanding on your part rather than an issue with the package.

The answer is

install.packages("org.CalbicansSC5324V63.eg.db", repos = NULL)

or if on Windows

install.packages("org.CalbicansSC5324V63.eg.db", repos = NULL, type = "source")

— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/AnnotationForge/issues/53#issuecomment-1604499032, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOUK72CXHWK2LCO63UHEGXLXMW5S3ANCNFSM6AAAAAAZRX5NRU . You are receiving this because you authored the thread.Message ID: @.***>