Erroe when using makeOrgPackageFromNCBI()
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Patadù ▴ 10
@ff20d7e7
Last seen 9 days ago
The Netherlands

Hello everybody,

I have analysed my RNAseq dataset with RStudio and DESeq2. Now, I would like to use the output of DESeq2 to perform GO analysis. I am working with Verticillium dahlaie and I have understood that I have first to "make my organism package" using '''makeOrgPackageFromNCBI()'''. I have tried to run the code I found in the '''AnnotationForge''' vignette but, after extracting data from '''gene2go''' I get an error. Here is the code I am using at the error I get:

BiocManager::install("AnnotationForge")

library(AnnotationForge)

makeOrgPackageFromNCBI(version = "0.1",
                       author = "schoch2@ncbi.nlm.nih.gov",
                       maintainer = "schoch2@ncbi.nlm.nih.gov",
                       outputDir = "path/to/folder",
                       tax_id = "498257 ",
                       genus = "Verticillium",
                       species = "dahliae")



  '''If files are not cached locally this may take awhile to assemble a 33 GB cache databse in the NCBIFilesDir directory. Subsequent calls to this function should be faster (seconds). The cache will try to rebuild once per day.Please also see AnnotationHub for some pre-builtOrgDb downloads
preparing data from NCBI ...
starting download for 
[1] gene2pubmed.gz
[2] gene2accession.gz
[3] gene2refseq.gz
[4] gene_info.gz
[5] gene2go.gz
getting data for gene2pubmed.gz
rebuilding the cache
extracting data for our organism from : gene2pubmed
getting data for gene2accession.gz
rebuilding the cache
extracting data for our organism from : gene2accession
getting data for gene2refseq.gz
rebuilding the cache
extracting data for our organism from : gene2refseq
getting data for gene_info.gz
rebuilding the cache
extracting data for our organism from : gene_info
getting data for gene2go.gz
rebuilding the cache
extracting data for our organism from : gene2go
processing gene2pubmed
processing gene_info: chromosomes
processing gene_info: description
processing alias data
processing refseq data
processing accession data
processing GO data
    Error in (function (cond)  : 
    error during  the evaluation of the argument 'table' in the selection of a method for the function '%in%': there is no package called 'biomaRt'
    In addition: Warning message:
    call dbDisconnect() when finished working with a connection'''

Do I need to install the biomaRt package or is something else?

Luigi

AnnotationForge • 144 views
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Guido Hooiveld ★ 4.0k
@guido-hooiveld-2020
Last seen 2 days ago
Wageningen University, Wageningen, the …

Yes, that error indeed indicates that the required package biomaRt is not installed.

I also noticed that you did not correctly follow the naming convention for specifying the author and maintainer; the mail should be between < and >. See ?makeOrgPackageFromNCBI, that tells you to do that like this:

author = "Some One <so@someplace.org>",
maintainer = "Some One <so@someplace.org>",

Lastly, to prevent downloading again all files from the NCBI, you may want to delete the created, but incomplete file/database NBCI.sqlite from your working directory, and then set rebuildCache = FALSE in your function call. See e.g. the recent remark of James here: Error for AnnotationForge makeOrgPackageFromNCBI function

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Thanks a lot Guido, now it is running smoothly.

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