Open AndreasReinecke opened 6 months ago
Hi, xcmsSet
is quite deprecated, without any recent developments and in case we find issues with it, we are rather going to remove it than to fix it. So we encourage you to look at the newer classes and functions in the vignette.
Back to your issue, this looks like something with parallelisation, so first check would be to disable that:
xset <- xcmsSet(files=files, mzdiff=0.2, fwhm=5, step=0.1, snthresh=5, BPPARAM=SerialParam())
If that fixes things, you need to check your BiocParallel installation.
Yours, Steffen
Thanks Steffen! ..., BPPARAM=SerialParam() ) helped. But instead I get "invalid class “xcmsPeaks” object: superclass "mMatrix" not defined in the environment of the object's class". The BiocParallel installation is 1.36.0. I admit that I am - although quite experienced with GC-MS - new to processing the data with R. Sorry for bothering. Best wishes andreas
Hi, great, that identifies the parallelisation as underlying cause. If you need a speedup because you run large studies on the laptop, you'll need to troubleshoot the BiocParallel stuff.
Please search the issues here about the Matrix issue, iirc you need a newer Matrix package.
Yours, Steffen
Note: the Matrix
error/issue seems to get fixed by a re-installation of the Matrix
and xcms
packages from source:
BiocManager::install(c("Matrix", "xcms"), type = "source", force = TRUE)
at least that fixed this error in issue #733
Hi, thanks for the hint! Unfortunately it didn't resolve my issue. When executing the forced installation the error message further down was displayed. Could this be related to R-Studio using a 'User Library' and a 'System Library'? In the meantime I used exactly the same script on a Windows PC with most the most recent R-Version installed and it worked fine. The issue therefore seems to be MAC specific. Best wishes
the error you get here is because you have no compiler installed on your macOS - you would need to install the "command line tools" from apple. Maybe you can find some information on the official R page https://cloud.r-project.org/
Hi, when running the following command line on a MAC M1 / MOC OS 14.3 with R 4.3.3 , BiocManager 1.30.22 and xcms 4.0.2 I get the error messages below: I'd be grateful for any hint. Best andreas