Laboratoire ICAR » Plateforme TXM

The FactoMineR package cannot be loaded with the library(FactoMineR) R command and TXM crashes.

*** caught segfault ***
address 0x5, 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(package, c(which.lib.loc, lib.loc))
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers) 

Hypothesis¶

TXM R package path is broken or TXM dynamic libraries path is broken (R path or package specific path) or the two are broken: there are version mismatch between packages or dynamic libraries.

diagnostic¶

Hypothesis: A so library is loaded from a wrong library directory.

Call the R commands within /usr/lib/TXM/R :

library.dynam()
.libPaths()
find.package() 

Note: Windows 10: all the dynamic library paths point to TXM R installation directory.

Solution¶

Some paths of the /usr/lib/TXM/R/etc/Renviron point to either the R system packages and the user R system packages but should only poin to TXM R packages.

To stop point to either the R system packages and the user R system packages:

• fix: Comment the 43th and 49th line of the /usr/lib/TXM/R/etc/Renviron file
• if TXM R loads its own packages, it will load its own dynamic libraries