readChromatogram not working in xic mode (Windows 11)

[Heriette]

Hi, for some reason, I can't get readChromatogram to return XICs. I've found a similar issue here, but the cause of the error there doesn't apply to me. Here is what I get:

> library(rawrr)
> rawfile <- './data/IS268_Lumos18_HeLa050ng_80IS_HCD-OT_DDA_240807_01.raw'
> cr <- readChromatogram(rawfile, mass = 487.25, tmpdir = './tmp')
failed to catch configfile and itol
Error accessing RAWFileReader library! - Input string was not in a correct format.

Memory Usage:
   Before 16108 kb, After 147896 kb, Extra 131788 kb
Error in .rawrrSystem2Source(rawfile, input = mass, rawrrArgs = sprintf("xic %f %s",  : 
  Rcode file to parse does not exist. 'C:\Users\435328\AppData\Local/R/cache/R/rawrr/rawrrassembly/rawrr.exe' failed for an unknown reason.
Please check the debug files:
	./tmp\file13a853623f2.stderr
	./tmp\file13a81b204b85.stdout
and the System Requirements

And the sessionInfo:

R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=Czech_Czechia.utf8  LC_CTYPE=Czech_Czechia.utf8    LC_MONETARY=Czech_Czechia.utf8 LC_NUMERIC=C                  
[5] LC_TIME=Czech_Czechia.utf8    

time zone: Europe/Prague
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rawrr_1.10.2

loaded via a namespace (and not attached):
 [1] utf8_1.2.4          R6_2.5.1            codetools_0.2-19    xfun_0.46           tidyselect_1.2.1    magrittr_2.0.3      glue_1.7.0         
 [8] tibble_3.2.1        knitr_1.48          parallel_4.3.3      pkgconfig_2.0.3     dplyr_1.1.4         generics_0.1.3      lifecycle_1.0.4    
[15] cli_3.6.3           fansi_1.0.6         vctrs_0.6.5         pkgload_1.4.0       compiler_4.3.3      highr_0.11          rstudioapi_0.16.0  
[22] tools_4.3.3         evaluate_0.24.0     pillar_1.9.0        rlang_1.1.4         BiocParallel_1.36.0

TIC and BPC work with no issues, do you have an idea why the XIC could be failing?
Thanks a lot!

[tobiasko]

Hi @Heriette,

could you try

> readChromatogram(rawfile = sampleFilePath(), mass = 487.25)
[[1]]
$filter
[1] "ms"

$ppm
[1] 10

$mass
[1] 487.25

$times
 [1] 0.001619751 0.031642766 0.061663615 0.091651065 0.121640750 0.151644970 0.181667770
 [8] 0.211526280 0.241284530 0.271307600 0.301222200 0.331145000 0.361147270 0.391168050
[15] 0.421057700 0.450970250 0.481045180 0.510989030 0.540955750 0.570893130 0.600724580
[22] 0.630620300 0.660428770 0.690318400 0.720320350 0.750197620 0.780105920

$intensities
 [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

attr(,"filename")
[1] "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rawrr/extdata/sample.raw"
attr(,"type")
[1] "xic"
attr(,"class")
[1] "rawrrChromatogram"

attr(,"filter")
[1] "ms"
attr(,"filename")
[1] "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rawrr/extdata/sample.raw"
attr(,"type")
[1] "xic"
attr(,"tol")
[1] 10
attr(,"class")
[1] "rawrrChromatogramSet"

What do you get?