Trying to install bioClite 3.2 onto R 3.2.2 using
biocLite("tgirke/systemPipeR", build_vignettes=TRUE, dependencies=TRUE)
this appears to install all the packages then fails as
* checking for file 'C:...\Temp\Rtmpmm0BY2\devtools278c2297552f\tgirke-systemPipeR-4b48c46/DESCRIPTION' ... OK * preparing 'systemPipeR': * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes Warning: running command '"C:/PROGRA~1/R/R-32~1.2/bin/x64/Rcmd.exe" INSTALL -l "C:....\Temp\RtmpYF4EL9\Rinst1e543dcb4481" --no-multiarch "C:/..../Temp/RtmpYF4EL9/Rbuild1e544bb64e5d/systemPipeR"' had status 1 ----------------------------------- ERROR: dependency 'GO.db' is not available for package 'systemPipeR' * removing 'C:/..../Temp/RtmpYF4EL9/Rinst1e543dcb4481/systemPipeR'
biocValid() finds only the the R-package curl is possibly out of date the curl version is 0.9.7 given as built under R version 3.2.5, I am running R 3.2.2
> traceback() 14: stop("Command failed (", status, ")", call. = FALSE) 13: fun(r, args = args, env_vars = env_vars, path = path, ...) 12: R(cmd, path, quiet = quiet) 11: force(code) 10: withr::with_temp_libpaths(R(cmd, path, quiet = quiet)) 9: build(pkg, tempdir(), vignettes = build_vignettes, quiet = quiet) 8: install(source, ..., quiet = quiet, metadata = metadata) 7: FUN(X[[i]], ...) 6: vapply(remotes, install_remote, ..., FUN.VALUE = logical(1)) 5: install_remotes(remotes, quiet = quiet, ...) 4: devtools::install_github(doing, ...) 3: .githubInstall(todo, ...) 2: .biocLiteInstall(pkgs, ask = ask, siteRepos = siteRepos, suppressUpdates = suppressUpdates, ...) 1: biocLite("tgirke/systemPipeR", build_vignettes = TRUE, dependencies = TRUE)
Any suggestions would be appreciated.
Presumably this is actually a problem with
GO.db
or one if its dependencies. Do you get an error message when you install it directly?