Seurat: Error in MeanVarPlot R 3.4.0 on Ubuntu

[psavas]

Hi,

I just updated to R 3.4.0 on my Ubuntu Xenial box and recompiled Seurat. It was working perfectly in exactly the some environment on R 3.3.1. Now MeanVarPlot fails with the error:

Error in linbin2D(x, gpoints1, gpoints2) : object 'F_lbtwod' not found

After examining the source code and doing a bit of testing, I traced the problem to line 4547 in seurat.R, which calls the smoothScatter function from the R 'graphics' library. Running smoothScatter directly causes the same error. Looking at smoothScatter in more detail, the problematic function is KernSmooth::bkde2D, which is called by grDevices:::.smoothScatterCalcDensity inside smoothScatter. A similar bug has been reported: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=860876

The culprit in KernSmooth is the linbin2D function (line 579 https://github.com/cran/KernSmooth/blob/master/R/all.R), which contains the Fortran call:

out <- .Fortran(F_lbtwod, as.double(X), as.integer(n),
                    as.double(a1), as.double(a2), as.double(b1), as.double(b2),
                    as.integer(M1), as.integer(M2), double(M1*M2))

One work around is to set do.plot = FALSE in MeanVarPlot.

This is probably a compiler issue with the latest R on Ubuntu rather than Seurat, but thought I would post it in case anyone else gets this somewhat cryptic error.

[psavas]

Also, installing KernSmooth from CRAN fixes this problem without having to reinstall Seurat.

[andrewwbutler]

Thanks for posting this! We did notice this error on Ubuntu after upgrading to R 3.4.0 and had been recommending reverting to R 3.3.3. We'll link to this solution from the install page in case others are having similar issues.