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

``` r 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 #> assertthat 0.2.1 2019-03-21 [2] CRAN (R 4.1.0) #> cli 3.3.0 2022-04-25 [2] CRAN (R 4.1.1) #> crayon 1.5.1 2022-03-26 [2] CRAN (R 4.1.1) #> DBI 1.1.2 2021-12-20 [2] CRAN (R 4.1.1) #> digest 0.6.29 2021-12-01 [2] CRAN (R 4.1.1) #> dplyr 1.0.9 2022-04-28 [2] CRAN (R 4.1.1) #> ellipsis 0.3.2 2021-04-29 [2] CRAN (R 4.1.0) #> evaluate 0.15 2022-02-18 [2] CRAN (R 4.1.1) #> fansi 1.0.3 2022-03-24 [2] CRAN (R 4.1.1) #> fastmap 1.1.0 2021-01-25 [2] CRAN (R 4.1.0) #> fs 1.5.2 2021-12-08 [2] CRAN (R 4.1.1) #> generics 0.1.2 2022-01-31 [2] CRAN (R 4.1.1) #> glue 1.6.2 2022-02-24 [2] CRAN (R 4.1.1) #> highr 0.9 2021-04-16 [2] CRAN (R 4.1.0) #> htmltools 0.5.2 2021-08-25 [2] CRAN (R 4.1.1) #> knitr 1.39 2022-04-26 [2] CRAN (R 4.1.1) #> lifecycle 1.0.1 2021-09-24 [2] CRAN (R 4.1.1) #> magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.1.1) #> pillar 1.7.0 2022-02-01 [2] CRAN (R 4.1.1) #> pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.1.0) #> purrr 0.3.4 2020-04-17 [2] CRAN (R 4.1.0) #> R6 2.5.1 2021-08-19 [2] CRAN (R 4.1.1) #> Rcpp 1.0.8.3 2022-03-17 [2] CRAN (R 4.1.1) #> 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) #> rlang 1.0.2 2022-03-04 [2] CRAN (R 4.1.1) #> rmarkdown 2.14 2022-04-25 [2] CRAN (R 4.1.1) #> rstudioapi 0.13 2020-11-12 [2] CRAN (R 4.1.0) #> sessioninfo 1.2.2 2021-12-06 [2] CRAN (R 4.1.1) #> stringi 1.7.6 2021-11-29 [2] CRAN (R 4.1.1) #> stringr 1.4.0 2019-02-10 [2] CRAN (R 4.1.1) #> tibble 3.1.7 2022-05-03 [2] CRAN (R 4.1.1) #> tidyselect 1.1.2 2022-02-21 [2] CRAN (R 4.1.1) #> utf8 1.2.2 2021-07-24 [2] CRAN (R 4.1.0) #> vctrs 0.4.1 2022-04-13 [2] CRAN (R 4.1.1) #> withr 2.5.0 2022-03-03 [2] CRAN (R 4.1.1) #> xfun 0.31 2022-05-10 [2] CRAN (R 4.1.1) #> yaml 2.3.5 2022-02-21 [2] CRAN (R 4.1.1) #> #> [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