Hello,

I keep having the same issue with the first step of msmsworkflow (RMassBank):

> w <- msmsWorkflow(w, mode = "mH", steps = c(1:4), archivename = "PFAS_labelled")
msmsWorkflow: Step 1. Acquire all MSMS spectra from files
Error in msmsRead(w = w, files = w@files, readMethod = readMethod, mode = mode,  : 
  Please supply the cpdids corresponding to the files in the filetable or the filenames

The IDs are on the compound list as well as on the mzML files name (separated with _ ). When loading the list, I have no problems:

> loadList("./PFAS_list.csv")
Loaded compoundlist successfully

When loading RMassBank I have this message (and am wondering if related):

> library(RMassBank)
Loading required package: Rcpp
Warning message:
In fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.2)
than is installed on your system (1.0.3). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.

I re-installed BiocManager but did not managed to check mzR:

> BiocManager::valid() 
[1] TRUE
> library(BiocManager)
Bioconductor version 3.10 (BiocManager 1.30.10), ?BiocManager::install for help
> biocLite("mzR")
Error in biocLite("mzR") : could not find function "biocLite"
> source("http://bioconducor.org/biocLite.R")
Error in file(filename, "r", encoding = encoding) : 
  cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  cannot open URL 'http://bioconducor.org/biocLite.R': HTTP status was '404 Not Found'

Here are the session information:

> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=Swedish_Sweden.1252  LC_CTYPE=Swedish_Sweden.1252    LC_MONETARY=Swedish_Sweden.1252
[4] LC_NUMERIC=C                    LC_TIME=Swedish_Sweden.1252    
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] BiocManager_1.30.10
loaded via a namespace (and not attached):
[1] compiler_3.6.2 tools_3.6.2 

I'll take any suggestions. Cheers Jean