I tried to use the eCBS package, which calls .Fortran() in a function gev_mle. When I used one of the functions estcpt, it gave me this error:
Error in .Fortran("estcpt", n = as.integer(current.n), x = as.double(current.genomdat), :
"estcpt" not available for .Fortran() for package "eCBS"
The package was manually unpacked and installed with R CMD INSTALL and placed in "/Users/pgweb/Library/R/3.3/library/eCBS". I check the Fortran subroutine scripts are not in this folder, while the the unzipped package contains a src folder which contains the *.f files. But even when I move this unzipped folder also into the library directory, the same error occurs.
I tried to do R CMD SHLIB to create shared object, and also tried to use dyn.load() to load the script. Neither helped. I checked the R code and tried to find if it loaded the function (before calling .Fortran()), which doesn't seem so:
function (genomdati, chromi, uchrom, data.type = "logratio",
alpha = 0.01, nperm, verbose = 1)
{
skew <- sum((genomdati - mean(genomdati))^3)/((length(genomdati) -
1) * sd(genomdati)^3)
kurt <- sum((genomdati - mean(genomdati))^4)/((length(genomdati) -
1) * sd(genomdati)^4)
genomdat.new <- NULL
for (ic in uchrom) {
genomdat = genomdati[chromi == ic]
n <- length(genomdat)
seg.end <- c(0, n)
k <- length(seg.end)
change.loc <- NULL
min.width = 10
while (k > 1) {
current.n <- seg.end[k] - seg.end[k - 1]
if (current.n >= 2 * min.width) {
current.genomdat <- genomdat[(seg.end[k - 1] +
1):seg.end[k]]
current.genomdat <- current.genomdat - mean(current.genomdat)
current.tss <- sum(current.genomdat^2)
gev_parameter <- c(0, 0, 0)
if (current.n <= 10000) {
gev_parameter <- gev(current.n, skew, kurt)
}
zzz <- .Fortran("estcpt", n = as.integer(current.n),
x = as.double(current.genomdat), tss = as.double(current.tss),
px = double(current.n), sx = double(current.n),
nperm = as.integer(nperm), cpval = as.double(alpha),
ncpt = integer(1), icpt = integer(2), ibin = as.logical(data.type ==
"binary"), al0 = as.integer(min.width), gev_p = as.double(gev_parameter),
PACKAGE = "eCBS")
}
else {
zzz <- list()
zzz$ncpt <- 0
}
if (zzz$ncpt == 0) {
change.loc <- c(change.loc, seg.end[k])
}
seg.end <- switch(1 + zzz$ncpt, seg.end[-k], c(seg.end[1:(k -
1)], seg.end[k - 1] + zzz$icpt[1], seg.end[k]),
c(seg.end[1:(k - 1)], seg.end[k - 1] + zzz$icpt,
seg.end[k]))
k <- length(seg.end)
}
seg.ends <- rev(change.loc)
nseg <- length(seg.ends)
lseg <- diff(c(0, seg.ends))
genomdatj <- genomdat
ll <- uu <- 0
for (i in 1:length(lseg)) {
uu <- uu + lseg[i]
genomdatj[(ll + 1):uu] <- genomdat[(ll + 1):uu] -
mean(genomdat[(ll + 1):uu])
ll <- uu
}
genomdat.new <- c(genomdat.new, genomdatj)
}
gev_mle <- NULL
gev_mle[1] <- sum((genomdat.new - mean(genomdat.new))^3)/((length(genomdat.new) -
1) * sd(genomdat.new)^3)
gev_mle[2] <- sum((genomdat.new - mean(genomdat.new))^4)/((length(genomdat.new) -
1) * sd(genomdat.new)^4)
gev_mle
}
<environment: namespace:eCBS>
