Adducts "ammonium"

[AndreaCa96]

Describe the bug I cannot start the "inst/scripts/prepare_libraries_adducts.R"

Last error message: objetct'ammonium' doesn't found Last error traceback: prepare_libraries_adducts(str_met = lib_mer_str_met, adducts_masses_list... create_adducts(ms_mode = "pos") tidytable::mutate(tidytable::mutate(masses_table, [1M+(H)3]3+ = (exact... tidytable::mutate(masses_table, [1M+(H)3]3+ = (exact_mass + 3 p... mutate.data.frame(masses_table, [1M+(H)3]3+ = (exact_mass + 3 p... mutate(.df, ..., .by = { { .by } }, .keep = .keep, .befo... mutate.tidytable(.df, ..., .by = { { .by } }, .keep = .k... eval_tidy(dt_expr, .df, dt_env) (~.df)[, :=([1M+(H)4(N)1]1+ = exact_mass + ammonium)] [.data.table(~.df, , :=([1M+(H)4(N)1]1+ = exact_mass + ammoni... eval(jsub, SDenv, parent.frame()) eval(jsub, SDenv, parent.frame()) .handleSimpleError(function (condition) { state$error <- build_mess... h(simpleError(msg, call))

To Reproduce Steps to reproduce the behavior:

1. Go to 'inst/scripts/prepare_libraries_adducts.R'
2. Click on '....'
3. Scroll down to '....'
4. See error: Last error message: objetct'ammonium' doesn't found Last error traceback: prepare_libraries_adducts(str_met = lib_mer_str_met, adducts_masses_list... create_adducts(ms_mode = "pos") tidytable::mutate(tidytable::mutate(masses_table, [1M+(H)3]3+ = (exact... tidytable::mutate(masses_table, [1M+(H)3]3+ = (exact_mass + 3 p... mutate.data.frame(masses_table, [1M+(H)3]3+ = (exact_mass + 3 p... mutate(.df, ..., .by = { { .by } }, .keep = .keep, .befo... mutate.tidytable(.df, ..., .by = { { .by } }, .keep = .k... eval_tidy(dt_expr, .df, dt_env) (~.df)[, :=([1M+(H)4(N)1]1+ = exact_mass + ammonium)] [.data.table(~.df, , :=([1M+(H)4(N)1]1+ = exact_mass + ammoni... eval(jsub, SDenv, parent.frame()) eval(jsub, SDenv, parent.frame()) .handleSimpleError(function (condition) { state$error <- build_mess... h(simpleError(msg, call))

Expected behavior Installation of adducts library

Screenshots If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: windows
• Browser chrome
• Version [e.g. 22]

Add any other context about the problem here.

[Adafede]

Hi @AndreaCa96!

I am missing some context to be able to help you. Are you running the latest version? If not, please remove any old version and do a clean pull/install.

Are you trying to achieve some particular intermediate library or just running the default pipeline?

Happy to help further!

[AndreaCa96]

Hi @AndreaCa96!

I am missing some context to be able to help you. Are you running the latest version? If not, please remove any old version and do a clean pull/install.

Are you trying to achieve some particular intermediate library or just running the default pipeline?

Happy to help further!

Hi i'm download the new version but i'm have always the same problem concerning the adducts. Yes is the default pipeline, and the browser is edge not chrome sorry.

here it is a screenshot ✖ errored target lib_add ✖ errored pipeline [16.03 seconds] Warning: Error in : Error running targets::tar_make() Error messages: targets::tar_meta(fields = error, complete_only = TRUE) Debugging guide: https://books.ropensci.org/targets/debugging.html How to ask for help: https://books.ropensci.org/targets/help.html Last error message: oggetto 'ammonium' non trovato Last error traceback: prepare_libraries_adducts(str_met = lib_mer_str_met, adducts_masses_list... create_adducts(ms_mode = "pos") tidytable::mutate(tidytable::mutate(masses_table, [1M+(H)3]3+ = (exact... tidytable::mutate(masses_table, [1M+(H)3]3+ = (exact_mass + 3 p... mutate.data.frame(masses_table, [1M+(H)3]3+ = (exact_mass + 3 p... mutate(.df, ..., .by = { { .by } }, .keep = .keep, .befo... mutate.tidytable(.df, ..., .by = { { .by } }, .keep = .k... eval_tidy(dt_expr, .df, dt_env) (~.df)[, :=([1M+(H)4(N)1]1+ = exact_mass + ammonium)] [.data.table(~.df, , :=([1M+(H)4(N)1]1+ = exact_m [... truncated] 5: shiny::runApp 4: eval [inst/scripts/run_app.R#14] 3: eval 1: source

[Adafede]

Could you try running

Rscript inst/scripts/install.R

and then

Rscript inst/scripts/run_app.R

again and tell me if it solved the issue?

I suspect you still have some leftovers of a previous version, could this be? Else we'll probably have to investigate further.

[AndreaCa96]

Thank you, it is something about my leftovers of a previous version! Thank you very much for your prompt reply!

Andrea