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rformassspectrometry / MsBackendTimsTof

Spectra backend supporting TimsTOF data files using the opentimsr package.
https://rformassspectrometry.github.io/MsBackendTimsTof/
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Cannot open connection #23

Closed chufz closed 5 months ago

chufz commented 5 months ago

Hi Johannes,

Tested on a Linux computer, the current version reveals the following error:

library(Spectra)
library(MsBackendTimsTof)
fl <- system.file("ddaPASEF.d", package = "MsBackendTimsTof")
sps <- Spectra(fl, backend=MsBackendTimsTof())

Error: BiocParallel errors 1 remote errors, element index: 1 0 unevaluated and other errors first remote error: Error in file(con, "r"): cannot open the connection

While everything works fine for the direct use of opentimsr:

ot <- opentimsr::OpenTIMS(fl)

Any idea what can be the issue?

jorainer commented 5 months ago

could you please provide the output of your sessionInfo()?

jorainer commented 5 months ago

Or, try setting source = MsBackendTimsTof() instead of backend = MsBackendTimsTof(). That fixes the error for my installation (Spectra 1.12.0, MsBackendTimsTof 0.1.5)

chufz commented 5 months ago

oh yes, that solves it for me as well :) Thank you, Johannes.