Question: Problem in installing bioconductor
0
gravatar for nosheenfaiz09
22 months ago by
nosheenfaiz090 wrote:

 I am trying to install bioconductor through source("http://bioconductor.org/biocLite.R") but I am getting this message

"Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help"

thats why its difficult to run the code further.  Please give me suggestion

Thanks

package installation • 859 views
ADD COMMENTlink modified 22 months ago • written 22 months ago by nosheenfaiz090
Answer: Problem in installing bioconductor
1
gravatar for Laurent Gatto
22 months ago by
Laurent Gatto1.1k
United Kingdom
Laurent Gatto1.1k wrote:

The message you show looks good - this is exactly what you are supposed to see.

Now, you need to decide what package to use depending on the type of data you have and analysis you want to do.

 


 

ADD COMMENTlink written 22 months ago by Laurent Gatto1.1k

Thank you 

I want to use Biostrings it gives this messsage and somtimes says that biostrings package not found.

> biocLite("Biostrings")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.1 (2017-06-30).
Installing package(s) ‘Biostrings’
Warning: package ‘Biostrings’ is in use and will not be installed

ADD REPLYlink written 22 months ago by nosheenfaiz090

Restart and R and install it from a clean R session.

The message tells you that Biostrings is already loaded and it doesn't want to install a new version over it while it's in use.

ADD REPLYlink written 22 months ago by Steve Lianoglou12k

I did but even afer installing Biostring i am getting this message

> ?biostrings
No documentation for ‘biostrings’ in specified packages and libraries:
you could try ‘??biostrings’

ADD REPLYlink written 22 months ago by nosheenfaiz090

There is no function called biostrings, so you won't get a help page. What exactly are you expecting ?biostrings to do for you?

ADD REPLYlink written 22 months ago by James W. MacDonald50k

 myrawfile <- readRNAStringSet("abc.fasta")
Error in .Call2("new_input_filexp", filepath, PACKAGE = "XVector") : 
  cannot open file 'abc.fasta'

Thats why I am not able to read fasta file in R

ADD REPLYlink written 22 months ago by nosheenfaiz090

That's the error you get if you try to open a file that isn't there:

> readRNAStringSet("theresnofilehere.fasta")
Error in .Call2("new_input_filexp", filepath, PACKAGE = "XVector") :
  cannot open file 'theresnofilehere.fasta'

This doesn't prove anything. The following does, and should work for you:

> filepath1 <- system.file("extdata", "someORF.fa", package="Biostrings")
> readDNAStringSet(filepath1)

A DNAStringSet instance of length 7
    width seq                                               names               
[1]  5573 ACTTGTAAATATATCTTTTATTT...CTTATCGACCTTATTGTTGATAT YAL001C TFC3 SGDI...
[2]  5825 TTCCAAGGCCGATGAATTCGACT...AGTAAATTTTTTTCTATTCTCTT YAL002W VPS8 SGDI...
[3]  2987 CTTCATGTCAGCCTGCACTTCTG...TGGTACTCATGTAGCTGCCTCAT YAL003W EFB1 SGDI...
[4]  3929 CACTCATATCGGGGGTCTTACTT...TGTCCCGAAACACGAAAAAGTAC YAL005C SSA1 SGDI...
[5]  2648 AGAGAAAGAGTTTCACTTCTTGA...ATATAATTTATGTGTGAACATAG YAL007C ERP2 SGDI...
[6]  2597 GTGTCCGGGCCTCGCAGGCGTTC...AAGTTTTGGCAGAATGTACTTTT YAL008W FUN14 SGD...
[7]  2780 CAAGATAATGTCAAAGTTAGTGG...GCTAAGGAAGAAAAAAAAATCAC YAL009W SPO7 SGDI...
>
ADD REPLYlink written 22 months ago by James W. MacDonald50k

> filepath1 <- system.file("extdata", "someORF.fa", package="Biostrings")
> readDNAStringSet(filepath1)
Error in readDNAStringSet(filepath1) : 
  could not find function "readDNAStringSet"

I dont know what going wrong. It is also not working. Please guide me I am not good in R thats why.

ADD REPLYlink written 22 months ago by nosheenfaiz090

source("http://bioconductor.org/biocLite.R")
biocLite("Biostrings")
library(Biostrings)
filepath1 <- system.file("extdata", "someORF.fa", package="Biostrings")
readDNAStringSet(filepath1)

I tried this but not working ang says there is no Biostrings package

ADD REPLYlink written 22 months ago by nosheenfaiz090

We need to take a step back here and make sure that Biostrings installs correctly. You also need to provide more of R's error messages instead of your interpreted summary of what you think is going wrong.

For example, your "... says there is no Biostrings package" paraphrasing isn't exactly helpful, because we don't know what the exact error message was, or exactly when it was printed. Those two things are important for us to help you help yourself

So, please restart R so you that have a clean workspace (again) then run the following:

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

Please copy and paste all of the output that follows the biocLite call.

After you copy paste that, please run the following command:

sessionInfo()

And copy and paste all of the output from that.

 

ADD REPLYlink written 22 months ago by Steve Lianoglou12k

This worked out

source("http://bioconductor.org/biocLite.R")
biocLite("Biostrings")
require(Biostrings)
filepath1 <- system.file("extdata", "someORF.fa", package="Biostrings")
readDNAStringSet(filepath1)

Now another problem is 

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

> require(Rsamtools)
Loading required package: Rsamtools
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Rsamtools’

ADD REPLYlink written 22 months ago by nosheenfaiz090
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