Closed ekemmler closed 9 years ago
Hi Emanuel,
does mzR-version 2.2.1 still work?
best regards, Gunnar
Hi Gunnar,
unfortunately, with 2.2.1 there is the same Error. With mzR 2.0.0 it is still working.
kind regards
Thanks for telling me!
I'm going to update my R-packages and see if I can reproduce and fix the bug.
thanks, Gunnar
Unfortunately https://github.com/sneumann/mzR/blob/master/NEWS is a bit sketchy about the changes between 2.0.0 and 2.2.1 Emmanuel is currently writing a unit test based on mtbls2
This could be the beginning of a unitTest:
library(xcms)
library(IPO)
data("mtbls2")
# Workaround: should actually happen in mtbls2/R/zzz.R
attr(mtbls2Set, "filepaths") <- file.path(find.package("mtbls2"), gsub("/", .Platform$file.sep, attr(mtbls2Set, "filepaths")))
nSlaves <- 4
outdir <- tempdir()
retcor_parameter <- getDefaultRetGroupStartingParams()
resultRG <- optimizeRetGroup(xset=mtbls2Set,
params = retcor_parameter,
nSlaves = nSlaves,
subdir = outdir)
It is a namespace issue:
Attaching package: ‘igraph’
The following object is masked from ‘package:rsm’:
star
The following object is masked from ‘package:xcms’:
groups
A first workaround is to load "igraph" FIRST in every script:
library(igraph)
library(xcms)
library(IPO)
Proper fix will come later, and needs to go to xcms.
Hi,
by using optimizeRetGroup() with mzR 2.3.1 (devel version) I get an Error:
Traceback:
kind regards, Emanuel