Answer: When R builds the vignettes for PTXQC, it needs to download a test dataset from a public PRIDE repository. On rare occasions, the server might not be reachable. Either wait a little until it comes back up and try again, OR simply skip building the vignettes using
install_github("cbielow/PTXQC", build_vignettes = FALSE, dependencies = TRUE)
This omits the part where the error occurs. Downside: no offline vignettes for PTXQC – but you can always look them up on GitHub.
Alternatively, use CRAN:
Answer: One common error is that the CRAN mirror hosting the R packages is incomplete/buggy and installation of packages fails. This could look like this:
Error in XXXX(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open the connection In addition: Warning messages: ... or
Warning message: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 228962 != reported length 229751
Try another CRAN mirror (type
chooseCRANmirror()) and then re-run the failed command.
If you’re still stuck, please open a ticket (see ‘Bug Reporting’ on the main PTXQC homepage for the details you should provide).
Answer: PTXQC uses the mqpar.xml file from MaxQuant to extract certain parameters (like mass accuracy search tolerances) automatically. By default the mqpar.xml is created by MaxQuant in the root folder of each analysis (where the Raw files reside). The warning now tells you to copy this mqpar.xml into the combined/txt/ folder, where PTXQC can read it.
The reason why PTXQC does not directly use the mqpar.xml from the root folder is two-fold:
Answer: Most metrics and figures are described in the publication (see ‘Citation’ on the main homepage of PTXQC). Updated and new metrics will be described in the documentation of the package. A short description of each plot and the scoring function is given in each Html report (click the “Show Help” box just below each section heading). See [examples][https://github.com/cbielow/PTXQC/tree/master/inst/examples] for more.