ACers do not work on species level

[dernesa]

Hi gosling Team,

I have one more: I get an error, when trying to provide a Acylceramide string.

Thank you for your help!

library(rgoslin)


# Working
parseLipidNames("Cer 36:1;2")[[1]]
#> [1] "Cer 36:1;O2"
parseLipidNames("Cer 67:2;2")[[1]]
#> [1] "Cer 67:2;O2"
# Not working
parseLipidNames("ACer 67:2;2")[[1]]
#> Encountered an error while parsing 'ACer 67:2;2': Expecting a single string value: [type=character; extent=4].
#> [1] NA

^{Created on 2022-05-25 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     2022-05-25
#>  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)
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#>  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     * 1.0.1   2022-05-20 [1] Github (lifs-tools/rgoslin@b449c41)
#>  rlang         1.0.2   2022-03-04 [2] CRAN (R 4.1.1)
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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 Mathias,

Thank you very much for your support and pinpointing of issues :-) I will take care of that.

Cheers,
Dominik

[dernesa]

Hi Dominik,
any progress on this issue?
Thank you!
Mathias

[nilshoffmann]

Hi Mathias, the changes should already be available in the repository. I will add some more tests to cover ACers. We haven‘t pushed the changes to Bioconductor yet, but you should be able to install the updated package from github directly. Best regards Nils

…

Am 16.06.2022 um 15:56 schrieb Mathias Gerl ***@***.***>:  Hi Dominik, any progress on this issue? Thank you! Mathias — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.

[dominik-kopczynski]

Hi Mathias,
sorry forgot completely to look at the issue. At first glance, I see that you are writing ACer 67:2;2. This corresponds to the old nomenclature, where we didn't support ACers. When you use the new nomenclature, i.e., ACer(FA) 67:2;O2 or simply ACer 67:2;O2, it should work. When using the new nomenclature is no option for you, of course, I would implement ACers into the old nomenclature.
Cheers,
Dominik

[dernesa]

Hi Dominik and Nils,
Thank you for the fix!
I installed from Github and I can work with this now! :-)

[dominik-kopczynski]

That's great :-) Thank you once again for the support. Cheers