Error in forging Casuarina genome in BSgenome Package
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@66ce6032
Last seen 20 months ago
India

Im a beginner in R and I want to forge Casuarina equistifolia genome in BSgenome package as it is not available as inbuilt package. After spending so much time in solving errors but still I couldn't solve one error. Kindly help me to solve the below error.

Seed File I have used

Package: BSgenome.Cequisetifolia.NCBI.ASM379533v1

Title: Full genome sequences for Casuarina equisetifolia incana (ASM379533v1)

Description: Full genome sequences for Casuarina equisetifolia incana as provided by NCBI (assembly ASM379533v1, assembly accession GCA_003795335.1) and stored in Biostrings objects

Version: 1.5.0

organism: Casuarina equisetifolia incana

common_name: Pine

genome: ASM379533v1

provider: NCBI

release_date: 2018/11/19

source_url: https://www.ncbi.nlm.nih.gov/assembly/GCA_003795335.1

organism_biocview: Casuarina_equisetifolia_incana

BSgenomeObjname: Cequisetifolia

circ_seqs: character(0)

SrcDataFiles: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/795/335/GCA_003795335.1_ASM379533v1/

PkgExamples: genome[["chr1"]]

seqs_srcdir: C:/Users/manoj/OneDrive/Desktop/genomepackage/seqs_srcdir

seqfile_name: ASM379533v1.2bit

Error Im getting

> forgeBSgenomeDataPkg("BSgenome.Cequisetifolia.NCBI.ASM379533v1-seed")
Creating package in ./BSgenome.Cequisetifolia.NCBI.ASM379533v1 
Copying 'C:/Users/manoj/OneDrive/Desktop/genomepackage/seqs_srcdir/ASM379533v1.2bit' to './BSgenome.Cequisetifolia.NCBI.ASM379533v1/inst/extdata/single_sequences.2bit' ... DONE

Warning message:
In readLines(infile, n = 25000L) :

  incomplete final line found on 'BSgenome.Cequisetifolia.NCBI.ASM379533v1-seed'
BSgenome.Cequisetifolia.NCBI • 619 views
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@james-w-macdonald-5106
Last seen 3 days ago
United States

That's not an error, it's a warning. And what it means is what it says - your final line is incomplete, meaning it has no carriage return. As a simple example, consider

> cat("line1\nline2\nline3", file = "tmp.txt")
> readLines("tmp.txt")
[1] "line1" "line2" "line3"
Warning message:
In readLines("tmp.txt") : incomplete final line found on 'tmp.txt'
> cat("line1\nline2\nline3\n", file = "tmp.txt")
> readLines("tmp.txt")
[1] "line1" "line2" "line3"

The only difference being that I am missing the terminal carriage return for the third line, but it gets read in without problem regardless.

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Thanks a lot sir. I knew that you @james-w-macdonald-5106 will be the first person to solve the above post. Even I wanted to mail you personally but couldn't get your mail address.

Thank you once again.

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