Error with "library("GenomicFeatures")" - "there is no package called ‘XML’"
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Entering edit mode
@gregmulhearn-7639
Last seen 4.3 years ago
Australia

I am a new user to Bioconductor and R, so please excuse my inexperience.

I installed R and Biconductor (on a Windows-7, 64-bit system), as per the instructions on the Bioconductor website.

I am now trying to follow the instructions in the workflow document:  "RNA-Seq workflow: gene-level exploratory analysis and differential expression" from the website.  All was going well until I got to the step in the workflow: "library("GenomicFeatures")".

I got the following error message:

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

The previous steps in the workflow had all worked as per the workflow document.

Below I have pasted the results I got when I tried this step.  Is anyone able to shed any light on what is happening here.

>
> library("GenomicFeatures")
Welcome to Bioconductor

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

Attaching package: ‘AnnotationDbi’

The following object is masked from ‘package:GenomeInfoDb’:

species

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘XML’
Error: package or namespace load failed for ‘GenomicFeatures’
>
>
>
> traceback()
2: stop(gettextf("package or namespace load failed for %s", sQuote(package)),
call. = FALSE, domain = NA)
1: library("GenomicFeatures")
>
>
>
> sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C                       LC_TIME=English_Australia.1252

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] AnnotationDbi_1.28.2 Biobase_2.26.0       Rsamtools_1.18.3     Biostrings_2.34.1    XVector_0.6.0
[6] airway_1.0.0         GenomicRanges_1.18.4 GenomeInfoDb_1.2.4   IRanges_2.0.1        S4Vectors_0.4.0
[11] BiocGenerics_0.12.1  BiocInstaller_1.16.2

loaded via a namespace (and not attached):
[1] bitops_1.0-6    DBI_0.3.1       RCurl_1.95-4.5  RSQLite_1.0.0   tools_3.1.3     zlibbioc_1.12.0
>
>

As a separate issue, whenever I try to "Search" for anything in the list of previous posts, it always comes back with "No Results found".   Do I need to do anything special to search through previous posts.

Thanks, Greg

genomicfeatures xml loadnamespace • 6.3k views
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@james-w-macdonald-5106
Last seen 2 hours ago
United States

Whenever you get an error that says something like

there is no package called ‘XML’

it means that you are missing a package called XML, so you need to install it.

library(BiocInstaller)
biocLite("XML")
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Entering edit mode
@gregmulhearn-7639
Last seen 4.3 years ago
Australia

Thanks James for your prompt reply which has fixed the problem.  I installed XML as per your instructions, and I was able to proceed with the workflow.

Interestingly, when I did the previous step of installing the workflow as per these instructions:

> source("http://bioconductor.org/workflows.R")

Bioconductor version 3.0 (BiocInstaller 1.16.2), ?biocLite for help

> workflowInstall("rnaseqGene")

Installing package into ‘C:/Users/gmul3410/Documents/R/win-library/3.1’

(as ‘lib’ is unspecified)

I took note that it said XML had been successfully unpacked (is that the same as being installed ?).  But when I went back and checked again after your response, I noticed that there was a "warning" message after the line saying that XML had been unpacked.  Below is a capture of a few lines of output around this message:

package ‘colorspace’ successfully unpacked and MD5 sums checked

package ‘mime’ successfully unpacked and MD5 sums checked

package ‘XML’ successfully unpacked and MD5 sums checked

Warning: unable to move temporary installation ‘C:\Users\gmul3410\Documents\R\win-library\3.1\file379455a521fc\XML’ to ‘C:\Users\gmul3410\Documents\R\win-library\3.1\XML’

package ‘Formula’ successfully unpacked and MD5 sums checked

package ‘acepack’ successfully unpacked and MD5 sums checked

I have now progressed through the "RNA-Seq workflow: gene-level exploratory analysis and differential expression" workflow, but now have another problem with it not displaying the graphical output of some plots and heat maps.  I will start a new question regarding this, so that I can put a meaningful title around it.