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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MetaboDynamics
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* checking for file ‘MetaboDynamics/DESCRIPTION’ ... OK
* preparing ‘MetaboDynamics’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MetaboDynamics.Rmd’ using rmarkdown
2025-09-03 16:54:29.240 R[69303:156943632] XType: Using static font registry.
metabolite_modules       package:MetaboDynamics        R Documentation

_K_E_G_G _Q_u_e_r_y _R_e_s_u_l_t_s _o_f _e_x_p_e_r_i_m_e_n_t_a_l _m_e_t_a_b_o_l_i_t_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Using the package KEGGREST
     (https://www.bioconductor.org/packages/release/bioc/html/KEGGREST.html)
     all experimental metabolites (see data("intra")) were queried with
     there KEGG-IDs and all functional modules recorded to which the
     metabolite is annotated in the KEGG-database.

_U_s_a_g_e:

     data("metabolite_modules")
     
_F_o_r_m_a_t:

     A data frame with 348 observations on the following 8 variables.

     '...1' row number of the dataframe

     'metabolite' name of the experimental metabolite

     'KEGG' KEGG ID of the experimental metabolite

     'module_id' ID of the KEGG module to which the metabolite is
          annotated

     'module_name' name of the KEGG module to which the metabolite is
          annotated

     'upper_hierarchy' name of the highest hierachy level of module
          organisation

     'middle_hierarchy' name of the middle hierachy = functional
          module, p.e. "Amino acid metabolism"

     'lower_hierarchy' name of the lowest level of modules, this often
          contain only a couple pathways p.e. "Arginine and proline
          metabolism"

_S_o_u_r_c_e:

     https://www.genome.jp/kegg/module.html

_S_e_e _A_l_s_o:

     modules_compounds


modules_compounds        package:MetaboDynamics        R Documentation

_B_a_c_k_g_r_o_u_n_d _K_E_G_G _Q_u_e_r_y _R_e_s_u_l_t_s _O_f _F_u_n_c_t_i_o_n_a_l _M_o_d_u_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Using the package KEGGREST
     (https://www.bioconductor.org/packages/release/bioc/html/KEGGREST.html)
     a list of all KEGG-modules (KeggList("module")) including their
     upper, middle and lower hierachy as given by the KEGG-database and
     the corresponding annotated metabolites was queried.

_U_s_a_g_e:

     data("modules_compounds")
     
_F_o_r_m_a_t:

     A data frame with 1988 observations on the following 6 variables.

     'KEGG' KEGG ID of a metabolite annotated to a functional module

     'upper_hierarchy' name of the highest hierachy level of module
          organisation

     'middle_hierarchy' name of the middle hierachy = functional
          module, p.e. "Amino acid metabolism"

     'lower_hierarchy' name of the lowest level of modules, this often
          contain only a couple pathways p.e. "Arginine and proline
          metabolism"

     'module_id' the ID of the KEGG functional module

     'module_name' name of the KEGG module

_S_o_u_r_c_e:

     https://www.genome.jp/kegg/module.html

_S_e_e _A_l_s_o:

     metabolite_modules



Quitting from MetaboDynamics.Rmd:469-475 [unnamed-chunk-19]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `data.frame()`:
! arguments imply differing number of rows: 1, 0
---
Backtrace:
    ▆
 1. └─MetaboDynamics::compare_dynamics(...)
 2.   └─base::data.frame(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MetaboDynamics.Rmd' failed with diagnostics:
arguments imply differing number of rows: 1, 0
--- failed re-building ‘MetaboDynamics.Rmd’

--- re-building ‘MetaboDynamics_dataframes.Rmd’ using rmarkdown
--- finished re-building ‘MetaboDynamics_dataframes.Rmd’

SUMMARY: processing the following file failed:
  ‘MetaboDynamics.Rmd’

Error: Vignette re-building failed.
Execution halted