Question: I can not load a fasta file in Rstudio
0
gravatar for apl00028
12 months ago by
apl0002870
apl0002870 wrote:

I can not load a fasta file because when I try to load this file I see this message:

          cmv3_genome =readDNAStringSet("cmv3.fasta")

      Error in readDNAStringSet("cmv3.fasta") : could not find function "readDNAStringSet"

So, I installed its package:

                    source("http://bioconductor.org/biocLite.R")  
                    biocLite("Biostrings")

and I update all files;

after to do that I activate this package:

                    library(Biostrings)

and I see this message:

               Loading required package: XVector
               Error: package ‘IRanges’ 2.14.12 is loaded, but >= 2.15.12 is required by ‘XVector’
                In addition: Warning message:
                package ‘Biostrings’ was built under R version 3.5.2

So, I install IRanges package; library(BiocManager) BiocManager::install("IRanges")

And I tried to activate the package again and I got the same message:

             > library(Biostrings)
             Loading required package: XVector
             Error: package ‘IRanges’ 2.14.12 is loaded, but >= 2.15.12 is required by ‘XVector’
             In addition: Warning message:
             package ‘Biostrings’ was built under R version 3.5.2

I need a solution, thanks a lot!

sequence R • 678 views
ADD COMMENTlink written 12 months ago by apl0002870
1
gravatar for apl00028
12 months ago by
apl0002870
apl0002870 wrote:

The solution was remove IRanges package

removepackage(IRanges);

and installed the latest IRanges version installing BiocManager, due to this package include IRanges package:

install.packages("BiocManager")
ADD COMMENTlink modified 12 months ago by WouterDeCoster43k • written 12 months ago by apl0002870
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