Some GSL Classes do not work

[dernesa]

Hi Rgoslin Team,

some of the GSL classes below do not work for me.
They are listed in the supplement table of your publication:

Kopczynski, Dominik, Nils Hoffmann, Bing Peng, Gerhard Liebisch, Friedrich Spener, and Robert Ahrends. “Goslin 2.0 Implements the Recent Lipid Shorthand Nomenclature for MS-Derived Lipid Structures.” Analytical Chemistry, April 11, 2022. https://doi.org/10.1021/acs.analchem.1c05430.

They should work, right?

Thank you and cheers,

Mathias

library(rgoslin)

# Working
parseLipidNames("SM 36:1;2")[[1]]
#> [1] "SM 36:1;O2"
parseLipidNames("GM3 36:1;2")[[1]]
#> [1] "GM3 36:1;O2"

# Working
parseLipidNames("GD3 36:1;2")[[1]]
#> [1] "GD3 36:1;O2"
# Not working
parseLipidNames("GD1 36:1;2")[[1]]
#> Encountered an error while parsing 'GD1 36:1;2': Expecting a single string value: [type=character; extent=4].
#> [1] NA
parseLipidNames("GD2 36:1;2")[[1]]
#> Encountered an error while parsing 'GD2 36:1;2': Expecting a single string value: [type=character; extent=4].
#> [1] NA

# Working
parseLipidNames("GM3 36:1;2")[[1]]
#> [1] "GM3 36:1;O2"
parseLipidNames("GM1 36:1;2")[[1]]
#> [1] "GM1 36:1;O2"
# Not working
parseLipidNames("GM2 36:1;2")[[1]]
#> Encountered an error while parsing 'GM2 36:1;2': Expecting a single string value: [type=character; extent=4].
#> [1] NA

# Not working
parseLipidNames("GT1 36:1;2")[[1]]
#> Encountered an error while parsing 'GT1 36:1;2': Expecting a single string value: [type=character; extent=4].
#> [1] NA
parseLipidNames("GT2 36:1;2")[[1]]
#> Encountered an error while parsing 'GT2 36:1;2': Expecting a single string value: [type=character; extent=4].
#> [1] NA
parseLipidNames("GT2 36:1;2")[[1]]
#> Encountered an error while parsing 'GT2 36:1;2': Expecting a single string value: [type=character; extent=4].
#> [1] NA

^{Created on 2022-05-18 by the reprex package (v2.0.1)}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.1.3 (2022-03-10)
#>  os       macOS Monterey 12.4
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Europe/Berlin
#>  date     2022-05-18
#>  pandoc   2.17.1.1 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
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#>  cli           3.3.0   2022-04-25 [2] CRAN (R 4.1.1)
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#>  dplyr         1.0.9   2022-04-28 [2] CRAN (R 4.1.1)
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#>  magrittr      2.0.3   2022-03-30 [2] CRAN (R 4.1.1)
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#>  reprex        2.0.1   2021-08-05 [2] CRAN (R 4.1.1)
#>  rgoslin     * 0.99.12 2022-04-12 [1] Github (lifs-tools/rgoslin@2634716)
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#> 
#>  [1] /Users/gerl/Library/R/arm64/4.1/library
#>  [2] /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

[dominik-kopczynski]

Hi Matthias, thanks for the hint, will have a look at it and let you know when this is fixed. Cheers

[dominik-kopczynski]

Hi Matthias, please make a fresh pull from the rgoslin repository and try once again. It should work now. Cheers

[dernesa]

Hi Dominik and Nils,
Thanks for the fix! It now works!
Cheers