I am testing the
mzR package with some mzIdentML data following the instructions in section 3.2 of the vignette. When trying to extract the scores of each psm R crashes (see the relevant code below). When using the sample data used in the vignette (
Tandem.mzid.gz in the
msdata package) everything works as expected. My mzIdentML data was exported using Scaffold 4.4.5 (linux version).
> library(mzR) Loading required package: Rcpp > sessionInfo() R version 3.2.1 (2015-06-18) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.4 (Yosemite) locale:  C/UTF-8/C/C/C/C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  mzR_2.2.1 Rcpp_0.11.6 loaded via a namespace (and not attached):  ProtGenerics_1.0.0 parallel_3.2.1 Biobase_2.28.0  codetools_0.2-11 BiocGenerics_0.14.0 > x <- openIDfile("150602Nakai_mus.mzid.gz") > x Identification file handle. Filename: foo.mzid.gz Number of psms: 1150 > scr <- score(x) *** caught segfault *** address 0xf1000013, cause 'memory not mapped' Traceback: 1: .External(list(name = "CppMethod__invoke_notvoid", address = , dll = list(name = "Rcpp", path = "/Library/Frameworks/R.framework/Versions/3.2_R/Resources/library/Rcpp/libs/Rcpp.so", dynamicLookup = TRUE, handle = , info = ), numParameters = -1L), , , .pointer) 2: x@backend$getScore() 3: .local(x, ...) 4: score(x) 5: score(x) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace