Search
Question: BSgenome package building
0
gravatar for oussama.badad
8 weeks 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

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

 

ADD COMMENTlink modified 8 weeks ago by James W. MacDonald48k • written 8 weeks ago by oussama.badad0
2
gravatar for James W. MacDonald
8 weeks ago by
United States
James W. MacDonald48k 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 8 weeks ago by James W. MacDonald48k

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 8 weeks ago by Hervé Pagès ♦♦ 13k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 234 users visited in the last hour