BSgenome package building
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@oussamabadad-17646
Last seen 2.9 years ago

Hi all,

i am trying to build a BSgenome package for olea europea for some Medipseq analysis , i run the first command

library(BSgenome)
> forgeBSgenomeDataPkg("path/to/my/seed")

it working and creating the single_sequences.2bit

the when i run the second command

R CMD build /scratch/obadad/BSgenome.Oeuropaea.IOGC.v1./  it checks the DESCRIPTION file but then gives me this error .

(medip) [obadad@bigdawg BSgenome.Oeuropaea.IOGC.v1.]$ R CMD build /scratch/obadad/BSgenome.Oeuropaea.IOGC.v1./
* checking for file ‘/scratch/obadad/BSgenome.Oeuropaea.IOGC.v1./DESCRIPTION’ ... OK
* preparing ‘BSgenome.Oeuropaea.IOGC.v1.’:
* checking DESCRIPTION meta-information ... ERROR
Malformed package name

Malformed package version.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.

here is my DESCRIPTION FILE

Package: BSgenome.Oeuropaea.IOGC.v1.
Title: Full genome sequences for Olea Europaea var. sylvestris (IOGC version 1).
Description: Full genome sequences for Olea Europaea var. sylvestris (olive) as provided by IOGC (v1, 2017) and stored in olea europaea genome $
Version: 1.0.
Author: The Bioconductor Dev Team
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
Depends: BSgenome (>= 1.48.0)
Imports: BSgenome
Suggests:
License: Artistic-2.0
organism: Olea Europaea var.sylvestris.
common_name: Olive.
provider: IOGC.
provider_version: v1.
release_date: 2017.
release_name: OE1.0.
source_url: http://olivegenome.org/genome_datasets/Olea_europaea_chromosome.fa.gz.
biocViews: AnnotationData, Genetics, BSgenome, Olea_europaea.

i have tried to read the 'The DESCRIPTION file' in the 'Writing R Extensions'
manual. but couldnt figure out the ERROR message .

i would really appreciate some help

thank you

oussama

 

bsgenome • 620 views
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@james-w-macdonald-5106
Last seen 2 days ago
United States

The version is malformed because 1.0. isn't a version (you cannot end with a period). And the package name is malformed for the same reason. You might want to remove all the trailing periods, as they aren't necessary and may be messing things up.

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Entering edit mode

Yep. And don't fix the DESCRIPTION file. Fix the seed file instead and re-generate the package with forgeBSgenomeDataPkg("path/to/my/seed"). Also show us your seed file if things are still not working. Thanks!

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