GEOquery problem in calling the function in Rstudio
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Entering edit mode
jemaatita • 0
@jemaatita-13557
Last seen 4.0 years ago

Hello I'm a university student from Indonesia and i'm using Rstudio for a test and I need to use GEOquery to analyze GDS54523.

I'm using the library(Biobase) and library (GEOquery) function, but when i run the GEOquery one the response that i received is:

>library(Biobase) 

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap,
    parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call,
    duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unlist, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite
    Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.

>library(GEOquery)

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘XML’
Error: package or namespace load failed for ‘GEOquery’

It was all fine in the morning when I used it but when I tried to continue my work in the night it seems there is something wrong with the package, I have tried to close and reopening Rstudio and restarting my computer even updated my Rstudio to the latest release but the response is still the same.

Do you mind helping me? Because I need to finish the project by 30th of July. Thanks

R software error biobase geoquery • 1.0k views
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2
Entering edit mode
@james-w-macdonald-5106
Last seen 7 hours ago
United States

It appears you have lost your XML package. Does

library(BiocInstaller)

biocLite("XML")

fix the problem?

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0
Entering edit mode

Thank you it fix my problem and just wanted to know if i should just put all the check mark on the user library to use it? thank you again

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Entering edit mode

because when I click the check mark on the box from each package it says:

> library("MASS", lib.loc="~/R/win-library/3.2")
Warning message:
package ‘MASS’ was built under R version 3.2.5 

 

is this alright?

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