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Bioconductor / BSgenome

Software infrastructure for efficient representation of full genomes and their SNPs
https://bioconductor.org/packages/BSgenome
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Help #54

Closed zhanglp996 closed 1 year ago

zhanglp996 commented 1 year ago

When I forge Brassica rapa BSgenome, I got the problem

forgeBSgenomeDataPkg("./BSgenome.Brassica.rapaV3.0-seed", verbose=TRUE) Creating package in ./BSgenome.BRAD.BrapaV3.0 Copying '/43t/zhanglp/hic/bowtie2_index/Brapa_sequence.2bit' to './BSgenome.BRAD.BrapaV3.0/inst/extdata/single_sequences.2bit' ... Error in .copyTwobitFile(seqfile_name, seqs_srcdir, seqs_destdir, verbose = verbose) : FAILED In addition: Warning message: In file.create(to[okay]) : cannot create file './BSgenome.BRAD.BrapaV3.0/inst/extdata/single_sequences.2bit', reason 'No such file or directory'

The following is seed file: Package: BSgenome.BRAD.BrapaV3.0 Title: Full genome sequences for Brassica rapa (BRAD version Brapa_V3.0) Description: Full genome sequences for Brassica rapa as provided by BRAD (BrapaV3.0) and stored in Biostrings objects. Version: 1.0.0 organism: Brapa common_name: Brapa genome: Brapa provider: BRAD release_date: Feb 2022 source_url: http://39.100.233.196:82/download_genome/Brassica_Genome_data/Brara_Chiifu_V3.0/Brapa_sequence_v3.0.fasta.gz organism_biocview: Brapa rapa BSgenomeObjname: Brapa SrcDataFiles: Brapa_sequence.2bit, transferred by faToTwoBit PkgExamples: genome$1 # same as genome[["1"]]

directory of seed file

seqs_srcdir: /43t/zhanglp/hic/bowtie2_index

name of seed file

seqfile_name: Brapa_sequence.2bit circ_seqs: character(0)

Can you help me?

vjcitn commented 1 year ago

See https://support.bioconductor.org/p/9136141/ ... the error you are reporting seems to relate to the operating system -- you may need to look at your folder permissions or preparation of the files to be written.

hpages commented 1 year ago

@zhanglp996 What system are you on? Can you please provide the output of your sessionInfo()? Note that the process of forging a BSgenome data package is only supported on Linux at the moment, as mentioned in the "How to forge a BSgenome data package" vignette.

Also it's better to ask this type of question on the Bioconductor support site at https://support.bioconductor.org/ (please make sure to read the Posting Guide before you post there). GitHub issues are preferably for reporting bugs.

Finally, note that opening an issue or starting a conversation with the title "Help" is not good practice. Please use a more descriptive title in the future. Thanks!

zhanglp996 commented 1 year ago

Thank you very much! I have solved the problem by changing another linux platform

------------------ 原始邮件 ------------------ 发件人: "Bioconductor/BSgenome" @.>; 发送时间: 2022年11月24日(星期四) 中午11:07 @.>; @.**@.>; 主题: Re: [Bioconductor/BSgenome] Help (Issue #54)

@zhanglp996 What system are you on? Can you please provide the output of your sessionInfo()? Note that the process of forging a BSgenome data package is only supported on Linux at the moment, as mentioned in the "How to forge a BSgenome data package" vignette.

Also it's better to ask this type of question on the Bioconductor support site at https://support.bioconductor.org/ (please make sure to read the Posting Guide before you post there). GitHub issues are preferably for reporting bugs.

Finally, note that opening an issue or starting a conversation with the title "Help" is not good practice. Please use a more descriptive title in the future. Thanks!

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

WANGchuang715 commented 1 year ago

Thank you very much! I have solved the problem by changing another linux platform … ------------------ 原始邮件 ------------------ 发件人: "Bioconductor/BSgenome" @.>; 发送时间: 2022年11月24日(星期四) 中午11:07 @.>; @.**@.>; 主题: Re: [Bioconductor/BSgenome] Help (Issue #54) @zhanglp996 What system are you on? Can you please provide the output of your sessionInfo()? Note that the process of forging a BSgenome data package is only supported on Linux at the moment, as mentioned in the "How to forge a BSgenome data package" vignette. Also it's better to ask this type of question on the Bioconductor support site at https://support.bioconductor.org/ (please make sure to read the Posting Guide before you post there). GitHub issues are preferably for reporting bugs. Finally, note that opening an issue or starting a conversation with the title "Help" is not good practice. Please use a more descriptive title in the future. Thanks! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

I have the same problem on the centos system, may I ask which linux platform you are on without reporting an error？