Error reported when creating Masked BSgenome

[Song-10-YF]

Hi,

I'm just using BSgenome and not yet very skilled. The following error occurred when I created masked BSgenome in R. "Error in forgeMaskedBSgenomeDataPkg(y, masks_srcdir = masks_srcdir, destdir = destdir, : values for symbols PKGVERSION are not single strings" My seed file is as follows： "RefPkgname: BSgenome.Psubhirtella.MengLi.ps1 source_url: organism_biocview: Prunus_subhirtella nmask_per_seq: 2 SrcDataFiles: AGAPS masks:F:\NFU\P_subhirtella_genome\Psub_V1.0.mask.agp RM masks: F:\NFU\P_subhirtella_genome\Psub.mask.fa.out masks_srcdir: F:\NFU\P_subhirtella_genome\mask"

Looking forward to your response.

Best, Yanfeng

[hpages]

Your seed file looks so incomplete! It lacks plenty of mandatory fields like Package, Title, Description, Version, Author, etc...

Please refer to the "How to forge a BSgenome data package" vignette in the BSgenome package for how to prepare a seed file for a masked BSgenome data package.

Also please note that the regular BSgenome data package (BSgenome.Psubhirtella.MengLi.ps1 in your case) is usually all what is needed as it covers 99% of the use cases. So make you sure that you really need BSgenome.Psubhirtella.MengLi.ps1.masked before trying to forge it.

Best, H.

[Song-10-YF]

Hi,

This is the complete seed file (as shown below). Sorry, I just intercepted the problematic part.

Yes, my BSgenome.Psubhirtella.MengLi.ps1 has been successfully installed in R.

Package: BSgenome.Psubhirtella.MengLi.ps1.masked Title: Full masked genome sequences for Prunus subhirtella Description: Full masked genome sequences for Prunus subhirtella (Higan cherry) as provided by MengLi (PS1, July. 2022) and stored in Biostrings objects. RefPkgname: BSgenome.Psubhirtella.MengLi.ps1 source_url: organism_biocview: Prunus_subhirtella nmask_per_seq: 2 SrcDataFiles: AGAPS masks:F:\NFU\P_subhirtella_genome\Psub_V1.0.mask.agp                 RM masks: F:\NFU\P_subhirtella_genome\Psub.mask.fa.out masks_srcdir: F:\NFU\P_subhirtella_genome\mask

Best, Yanfeng

------------------ 原始邮件 ------------------ 发件人: "Bioconductor/BSgenome" @.>; 发送时间: 2023年2月15日(星期三) 中午1:21 @.>; @.**@.>; 主题: Re: [Bioconductor/BSgenome] Error reported when creating Masked BSgenome (Issue #66)

Your seed file looks so incomplete! It lacks plenty of mandatory fields like Package, Title, Description, Version, Author, etc...

Please refer to the "How to forge a BSgenome data package" in the BSgenome package for how to prepare a seed file for a masked BSgenome data package.

Also please note that the regular BSgenome data package (BSgenome.Psubhirtella.MengLi.ps1 in your case) is usually all what is needed as it covers 99% of the use cases. So make you sure that you really need BSgenome.Psubhirtella.MengLi.ps1.masked before trying to forge it.

Best, H.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[hpages]

Sorry but I still don't see the Version field in your seed file!

Again, please take the time to read carefully the "How to forge a BSgenome data package" vignette in the BSgenome package for how to prepare a seed file for a masked BSgenome data package.

[Song-10-YF]

Hi, I still encounter the following reported error：

In the masks_srcdir: ./mask directory, I put only masked genome files in fasta format, and I also prepared .2bit format files with the same name, as follows:

Also, I have also converted the masked genome to .agp and provided the RM .out file. Looking forward to your reply, thank you!

------------------ 原始邮件 ------------------ 发件人: "Bioconductor/BSgenome" @.>; 发送时间: 2023年2月16日(星期四) 凌晨3:28 @.>; @.**@.>; 主题: Re: [Bioconductor/BSgenome] Error reported when creating Masked BSgenome (Issue #66)

Sorry but I still don't see the Version field in your seed file!

Again, please take the time to read carefully the "How to forge a BSgenome data package" vignette in the BSgenome package for how to prepare a seed file for a masked BSgenome data package.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[hpages]

In the masks_srcdir: ./mask directory, I put only masked genome files in fasta format, and I also prepared .2bit format files with the same name, as follows:

Note that "as follows:" is not followed by anything in your post above.

Anyways that's not what we put in the masks/ folder. Please refer to the "How to forge a BSgenome data package" vignette for what to put there.

[hpages]

@Song-10-YF Were you able to sort this out? Is it ok to close the issue? Thanks