R/zzz.R

In Rhtslib: HTSlib high-throughput sequencing library as an R package

### There should be a much better way to do this.
.getRconfig <- function(VAR, default=NULL)
{
    cmd <- file.path(R.home(), "bin", "R")
    args <- c("CMD", "config", VAR)
    val <- suppressWarnings(system2(cmd, args=args, stdout=TRUE))
    status <- attr(val, "status")
    ok <- is.null(attr(val, "errmsg")) && (is.null(status) || status == 0)
    if (!ok)
        val <- default
    val
}

pkgconfig <- function(opt=c("PKG_LIBS", "PKG_CPPFLAGS"))
{
    opt <- match.arg(opt)
    if (opt == "PKG_LIBS") {
        usrlib_dir <- Sys.getenv(
            "RHTSLIB_RPATH",
            system.file("usrlib", package="Rhtslib", mustWork=TRUE)
        )
        platform <- Sys.info()[["sysname"]]
        if (platform == "Windows") {
            r_arch <- .Platform[["r_arch"]]
            usrlib_dir <- file.path(usrlib_dir, r_arch)
        }
        usrlib_path <- sprintf("'%s'", file.path(usrlib_dir, "libhts.a"))
        if (platform == "Windows") {
            LOCAL_SOFT <- .getRconfig("LOCAL_SOFT", default="C:/extsoft")
            ## See how PKG_LIBS is defined in Rhtslib/src/Makevars.win
            ## and make sure to produce the same value here.
            libs <- c("curl", "rtmp", "ssl", "ssh2", "crypto",
                      "gdi32", "z", "ws2_32", "wldap32", "winmm")
            if (r_arch == "i386")
                libs <- c(libs, "idn")
            libs <- paste(sprintf("-l%s", libs), collapse=" ")
            libs <- sprintf("-L%s/lib/%s %s", LOCAL_SOFT, r_arch, libs)
        } else {
            ## See how PKG_LIBS is defined in Rhtslib/src/Makevars
            ## and make sure to produce the same value here.
            libs <- "-lcurl"
        }
        config <- paste(usrlib_path, libs)
    } else {
        ## See how PKG_CPPFLAGS is defined in Rhtslib/src/Makevars.common
        ## and make sure to produce the same value here.
        config <- "-D_FILE_OFFSET_BITS=64"
        ## Packages that link to Rhtslib should have Rhtslib in their
        ## LinkingTo field so the preprocessor option below will automatically
        ## be added. There is no need to add it again here.
        #include_dir <- system.file("include", package="Rhtslib")
        #config <- paste(config, sprintf("-I'%s'", include_dir))
    }
    cat(config)
}

htsVersion <- function()
{
    vers <- .Call("Rhtslib_htslib_version", PACKAGE="Rhtslib")
    message(vers)
}

.onAttach <- function(...)
{
    vers <- .Call("Rhtslib_htslib_version", PACKAGE="Rhtslib")
    packageStartupMessage("Rhtslib htslib version ", vers)
}