I am trying to use topGO, but when I want to load this package, I have gotten the following error:
biocLite("topGO") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2. Installing package(s) 'topGO' trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/topGO_2.14.0.tar.gz' Content type 'application/x-gzip' length 1288615 bytes (1.2 Mb) opened URL ================================================== downloaded 1.2 Mb * installing *source* package ‘topGO’ ... ** R ** data ** inst ** preparing package for lazy loading Error : .onLoad failed in loadNamespace() for 'GO.db', details: call: match.arg(synchronous, c("off", "normal", "full")) error: 'arg' must be NULL or a character vector Error : package ‘GO.db’ could not be loaded ERROR: lazy loading failed for package ‘topGO’ * removing ‘/home/vjimenez/R/i686-pc-linux-gnu-library/3.0/topGO’ The downloaded source packages are in ‘/tmp/RtmpHaAZrQ/downloaded_packages’ Warning message: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘topGO’ had non-zero exit status > biocValid() [1] TRUE > sessionInfo() R version 3.0.2 (2013-09-25) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.12.1 loaded via a namespace (and not attached): [1] tools_3.0.2
Suggestions?
biocLite("topGO")
would have included an attempt to load the package, and I guess that was successfulor similar. So it is strange that your attempt to load topGO fails. I guess this is because you are using different versions of R, or have different
.libPaths()
in the two sessions, or you have several versions of the RSQLite package installed.You indicated that you reinstalled R. Did you re-install the latest version of R, version 3.1.2? Then it should not be necessary to install a special version of RSQLite. Also, try
source("http://bioconductor.org/biocLite.R"); biocLite()
with no arguments (to update all packages to their current version), andbiocValid()
to see if there are package incompatibilities.If you are using R-3.1.2, not only is it not necessary to install an older version of RSQLite, but things will not work if you do. You will need version 1.0.0 (or higher).