Hi,

I'm trying to install the bioconductor package, but am unable to load the libraries xcms, mzR, and CAMERA. I am also unable to install the latest versions of the packages Rmpi and RODBC when I try to ugrade to the latest version of Bioconductor using biocLite("BiocUpgrade"), and these are required for CAMERA.

I am running R 3.2.3 on a Mac with El Capitan, and updated to the latest version of R before installing bioconductor. I need to run the packages xcms and CAMERA for some of my analyses.

When I try to load xcms, mzR, or CAMERA, I get a *** caught segfault *** error because "memory not mapped" (details of output are below). Suspecting that it might be because some packages aren't up to date, I tried to upgrade to the latest bioconductor version using

library(BiocInstaller); biocLite("BiocUpgrade")

whereupon I am offered to upgrade to version 2.14 (I'm currently running 2.13). I'm then asked to install the packages Rmpi and RODBC from source, but then I get configuration errors because it can't find the mpi.h header file, and can't find the ODBC headers sql.h and sqlext.h, so I can't upgrade these two packages.

I'll paste the full output I'm getting below, but first is the sessionInfo() output:

R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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_3.2.3

When trying to load xcms I get the following:

library(xcms)
Loading required package: mzR
Loading required package: Rcpp

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: .Call(symbol)
 2: Module(m, pkg, mustStart = TRUE)
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch({    mod <- Module(m, pkg, mustStart = TRUE)    if (isTRUE(direct)) {        populate(mod, ns)    }    else {        forceAssignInNamespace(m, mod, ns)    }    assign(.moduleMetaName(m), mod, envir = ns)}, error = function(e) {    stop(sprintf("failed to load module %s from package %s\n%s",         m, pkg, conditionMessage(e)))})
 7: loadRcppModules()
 8: fun(libname, pkgname)
 9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch(fun(libname, pkgname), error = identity)
13: runHook(".onLoad", env, package.lib, package)
14: loadNamespace(package, c(which.lib.loc, lib.loc))
15: doTryCatch(return(expr), name, parentenv, handler)
16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: tryCatchList(expr, classes, parentenv, handlers)
18: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        msg <- conditionMessage(e)        sm <- strsplit(msg, "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && identical(getOption("show.error.messages"),         TRUE)) {        cat(msg, file = stderr())        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
19: try({    ns <- loadNamespace(package, c(which.lib.loc, lib.loc))    env <- attachNamespace(ns, pos = pos, deps)})
20: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,     quietly = quietly)
21: .getRequiredPackages2(pkgInfo, quietly = quietly)
22: library(xcms)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
 

With mzR I get the following:

library(mzR)
Loading required package: Rcpp

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: .Call(symbol)
 2: Module(m, pkg, mustStart = TRUE)
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch({    mod <- Module(m, pkg, mustStart = TRUE)    if (isTRUE(direct)) {        populate(mod, ns)    }    else {        forceAssignInNamespace(m, mod, ns)    }    assign(.moduleMetaName(m), mod, envir = ns)}, error = function(e) {    stop(sprintf("failed to load module %s from package %s\n%s",         m, pkg, conditionMessage(e)))})
 7: loadRcppModules()
 8: fun(libname, pkgname)
 9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch(fun(libname, pkgname), error = identity)
13: runHook(".onLoad", env, package.lib, package)
14: loadNamespace(package, c(which.lib.loc, lib.loc))
15: doTryCatch(return(expr), name, parentenv, handler)
16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: tryCatchList(expr, classes, parentenv, handlers)
18: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        msg <- conditionMessage(e)        sm <- strsplit(msg, "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && identical(getOption("show.error.messages"),         TRUE)) {        cat(msg, file = stderr())        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
19: try({    ns <- loadNamespace(package, c(which.lib.loc, lib.loc))    env <- attachNamespace(ns, pos = pos, deps)})
20: library(mzR)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
 

With CAMERA I get the following:

library(CAMERA)

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:stats’:

    xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist

Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: xcms
Loading required package: mzR
Loading required package: Rcpp

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: .Call(symbol)
 2: Module(m, pkg, mustStart = TRUE)
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch({    mod <- Module(m, pkg, mustStart = TRUE)    if (isTRUE(direct)) {        populate(mod, ns)    }    else {        forceAssignInNamespace(m, mod, ns)    }    assign(.moduleMetaName(m), mod, envir = ns)}, error = function(e) {    stop(sprintf("failed to load module %s from package %s\n%s",         m, pkg, conditionMessage(e)))})
 7: loadRcppModules()
 8: fun(libname, pkgname)
 9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch(fun(libname, pkgname), error = identity)
13: runHook(".onLoad", env, package.lib, package)
14: loadNamespace(package, c(which.lib.loc, lib.loc))
15: doTryCatch(return(expr), name, parentenv, handler)
16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: tryCatchList(expr, classes, parentenv, handlers)
18: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        msg <- conditionMessage(e)        sm <- strsplit(msg, "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && identical(getOption("show.error.messages"),         TRUE)) {        cat(msg, file = stderr())        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
19: try({    ns <- loadNamespace(package, c(which.lib.loc, lib.loc))    env <- attachNamespace(ns, pos = pos, deps)})
20: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,     quietly = quietly)
21: .getRequiredPackages2(pkgInfo, quietly = quietly)
22: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,     quietly = quietly)
23: .getRequiredPackages2(pkgInfo, quietly = quietly)
24: library(CAMERA)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
 

I'd be very grateful for advice on how I can get these packages to work.

Thanks in advance,

Patrick