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:  LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252  LC_NUMERIC=C LC_TIME=English_Australia.1252 attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods base other attached packages:  AnnotationDbi_1.28.2 Biobase_2.26.0 Rsamtools_1.18.3 Biostrings_2.34.1 XVector_0.6.0  airway_1.0.0 GenomicRanges_1.18.4 GenomeInfoDb_1.2.4 IRanges_2.0.1 S4Vectors_0.4.0  BiocGenerics_0.12.1 BiocInstaller_1.16.2 loaded via a namespace (and not attached):  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.