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")
Loading required package: AnnotationDbi
Loading required package: Biobase
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

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")

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.

Thanks for your help.