I have an Rstudio project that I've been working on. Since I last updated Rstudio to 1.0.143 - Mac OS X 10.6+ (64-bit) the project fails to start up. I think it might be linked to a package that was automatically loading on start-up and for whatever reason has not decided to stop working with R/Rstudio. XLConnect...
I've tried removing .RData, .Rhistory and .Rproj.user from the directory. Only removing .RData worked and Rstudio started up without issues. I don't seem to have any .RProfile files in the directory, my home directory or a site-wide file either.
Right now I can't even open the Rstudio session because it crashes with an error
R encountered a fatal error. The session was terminated.
I can open other Rstudio sessions without a problem.
When I open a separate R session (no R studio) and try to
load('path/to/.RData')
I get the following error message:
* caught segfault * address 0x18, cause 'memory not mapped'
Traceback: 1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
4: asNamespace(ns)
5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
6: loadNamespace(name)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(loadNamespace(name), error = function(e) { warning(gettextf("namespace %s is not available and has been
replaced\nby .GlobalEnv when processing object %s", sQuote(name)[1L], sQuote(where)), domain = NA, call. = >FALSE, immediate. = TRUE) .GlobalEnv})
11: ..getNamespace(c("openxlsx", "4.0.17"), "uwc.sel.book")
12: load("./Dropbox/OxfordTT2017/DNAextraction_26052017/ColWork2017/Fielddata_04052016/.RData")
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
So I'm looking for a way to stop the Rstudio session from loading the packages on startup (I'm not sure why it does this in the first place as I don't remember setting any kind of RProfile..).
So this is what I did to solve the problem:
Everything below is at the directory which containes the *.RProj file.
First, I 'hid' the .RData file by running this in the terminal.
mv .RData ./.RData_old
Next, I ran this in an R session (not Rstudio):
remove.packages('XLConnect', 'XLConnectJars')
Then I closed the R session and opened the Rstudio project to make sure it would open fine without the RData file.
After that I got my RData file back
mv .RData_old ./.RData
Finally I opened the project file again and presto!
It complains about packages not installed but at least I know which packages are required. Moreover, my data and results aren't lost.