msmsWorkflow(..., readMethod="peaklist") throwing an error

[sneumann]

Hi Erik, The RMBXCMS vignette currently has the last section "commented out" via <<eval=FALSE>>=

The code there fails with

> msmsPeaklist <- newMsmsWorkspace()
> msmsPeaklist@files <- list.files(system.file("spectra.Glucolesquerellin",
+                                              package = "RMassBankData"),
+                                  "Glucolesquerellin.*csv", full.names=TRUE)
> msmsPeaklist <- msmsWorkflow(msmsPeaklist, steps=1:8,
+                              mode="mH", readMethod="peaklist")
Error in handSpec[, 1] : incorrect number of dimensions
> 
> msmsPeaklist@files
[1] "/vol/R/R-3.0.0/lib/R/library-bioc213/RMassBankData/spectra.Glucolesquerellin/Glucolesquerellin_2184_1.csv"
[2] "/vol/R/R-3.0.0/lib/R/library-bioc213/RMassBankData/spectra.Glucolesquerellin/Glucolesquerellin_2184_2.csv"

Yours, Steffen

[ermueller]

Fixed in my branch.

[sneumann]

Hi, unfortunately I still get that error here after merging b758b7369b1a4409f8b3cdd398908a5823bcbad3 . Can you remove the <<eval=FALSE>>= in RMassBankXCMS.Rnw and run R CMD Sweave RMassBankXCMS.Rnw to double check ?

Yours, Steffen

[ermueller]

Works just fine when I do it. I have no idea :(