Question: (Closed) Some packages are not working in the latest version of Bioconductor
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gravatar for laith_mbiologist
17 months ago by
laith_mbiologist0 wrote:

Hi Guys

I am new to R and I have recently downloaded the latest version of R and bioconductor. My aim is to work on analyzing Illumina methylation BeadChipEPIC and also gene expresion. Unfortunately, I finished downloading R, and tried to call the software ChAMP to work, i got the following message:

library(ChAMP)
Loading required package: minfi
Loading required package: GenomicRanges
Error: package ‘IRanges’ required by ‘GenomicRanges’ could not be found
In addition: Warning message:
In read.dcf(file.path(p, "DESCRIPTION"), c("Package", "Version")) :
  cannot open compressed file 'C:/Users/Laith/Documents/R/win-library/3.5/IRanges/DESCRIPTION', probable reason 'No such file or directory'

I am not a computer savvy myself, but it turns out that some packages are not working with the updated R version, is that so ? if yes, how can I counter this problem ?

Any tips /guidelines are appreciated

regards laith

R • 1.6k views
ADD COMMENTlink modified 17 months ago by genomax73k • written 17 months ago by laith_mbiologist0

You need to install IRanges package (and perhaps others).

You could do something like

biocLite("ChAMP", dependencies=TRUE)

to get additional package dependencies you need. Note: Doing it this way may bring down more packages than you may need.

ADD REPLYlink modified 17 months ago • written 17 months ago by genomax73k

Did you try searching/asking the bioconductor support site?

ADD REPLYlink written 17 months ago by RamRS24k

Should be closed here and asked on bioconductor support.

ADD REPLYlink written 17 months ago by Michael Dondrup46k

Hello laith_mbiologist!

We believe that this post does not fit the main topic of this site.

Please ask https://support.bioconductor.org/

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 17 months ago by RamRS24k
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