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Question: BSgenome package building
gravatar for oussama.badad
4 months ago by
oussama.badad0 wrote:

Hi all,

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

> 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'


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 <>
Depends: BSgenome (>= 1.48.0)
Imports: BSgenome
License: Artistic-2.0
organism: Olea Europaea var.sylvestris.
common_name: Olive.
provider: IOGC.
provider_version: v1.
release_date: 2017.
release_name: OE1.0.
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



bsgenome • 156 views
ADD COMMENTlink modified 4 months ago by James W. MacDonald49k • written 4 months ago by oussama.badad0
Answer: BSgenome package building
gravatar for James W. MacDonald
4 months ago by
United States
James W. MacDonald49k wrote:

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.

ADD COMMENTlink written 4 months ago by James W. MacDonald49k

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!

ADD REPLYlink written 4 months ago by Hervé Pagès ♦♦ 13k
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