Question

Install CRISPRseek packageand get documentation

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susobhanbaidya • 0

@susobhanbaidya-13780

Last seen 7.3 years ago

I have installed my R studio and installed Bioconductor version 3.6 , but when I want to run the command biocLite(CRISPRseek). It is not working

> biocLite(CRISPRseek)
Error in "BiocUpgrade" %in% pkgs : object 'CRISPRseek' not found
>

Even after that I tried to upgrade

> biocLite("BiocUpgrade")
Error: Bioconductor version 3.6 cannot be upgraded with R version 3.4.1

Sir Please help me to install this CRISPRseek pack

software error • 1.2k views

ADD COMMENT • link updated 7.3 years ago by Martin Morgan 25k • written 7.3 years ago by susobhanbaidya • 0

score 0 · Answer 1 · 2017-08-18

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Martin Morgan 25k

@martin-morgan-1513

Last seen 4 months ago

United States

The argument to bicoLite() must be a character vector e.g., biocLite("CRISPRseek"); note the quotation marks.

ADD COMMENT • link 7.3 years ago Martin Morgan 25k

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Thank you Sir,

Now I am am unable to execute the following commands.

inputFile1Path <- system.file("extdata", "rs362331C.fa", package = "CRISPRseek")
> inputFile2Path <- system.file("extdata", "rs362331T.fa", package = "CRISPRseek")

> seqs <- compare2Sequences(inputFile1Path, inputFile2Path,
+ outputDir = outputDir , REpatternFile = REpatternFile,
+ overwrite = TRUE)
Error in file.path(outputDir, paste(basename(inputFile1Path), format(Sys.time(), :
object 'outputDir' not found

Please guide me to set the input path.

ADD REPLY • link 7.3 years ago susobhanbaidya • 0

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Are you familiar with R? If not I recommend that you spend a few hours working through one of the many introductory R tutorials available on the web.

ADD REPLY • link 7.3 years ago Martin Morgan 25k

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Please set outputDir <- getwd() Per Martin's recommendation, you will benefit greatly from the following sites.http://www.r-tutor.com/r-introduction http://www.r-tutor.com/r-introduction/data-frame/data-import Best wishes, Julie Sent from my iPhone On Aug 18, 2017, at 6:31 AM, susobhanbaidya [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User susobhanbaidya<https: support.bioconductor.org="" u="" 13780=""/> wrote Comment: Install CRISPRseek packageand get documentation<https: support.bioconductor.org="" p="" 99379="" #99389="">: Thank you Sir, Now I am am unable to execute the following commands. > seqs <- compare2Sequences(, inputFile2Path, + outputDir = outputDir , REpatternFile = REpatternFile, + overwrite = TRUE) Error in file.path(outputDir, paste(basename(inputFile1Path), format(Sys.time(), : object 'outputDir' not found Please guide me set the input path. ________________________________ Post tags: software error You may reply via email or visit C: Install CRISPRseek packageand get documentation

ADD REPLY • link 7.3 years ago Julie Zhu ★ 4.3k