fixes for github actions

- remove metfrag_source (old version, not functioning)
- add options to skip cmd check and bioccheck in actions
- update some documentation

.github/workflows/check-bioc.yml

@@ -216,6 +216,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Run CMD check
+        if: env.cmd_check == 'true'
         env:
           _R_CHECK_CRAN_INCOMING_: false
           DISPLAY: 99.0
@@ -241,6 +242,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Run BiocCheck
+        if: env.has_bioc_check == 'true'
         env:
           DISPLAY: 99.0
         run: |

DESCRIPTION

@@ -53,9 +53,6 @@ Collate:
     'BiocFileCache_database_class.R'
     'CompoundDb_source_class.R'
     'MTox700plus_database_class.R'
-    'annotation_table_class.R'
-    'lcms_table_class.R'
-    'MetFrag_source_class.R'
     'MetMashR-package.R'
     'PathBank_metabolite_database_class.R'
     'add_columns_class.R'
@@ -64,9 +61,11 @@ Collate:
     'annotation_histogram_class.R'
     'annotation_histogram2d_class.R'
     'annotation_pie_chart.R'
+    'annotation_table_class.R'
     'annotation_venn_chart.R'
     'calc_ppm_diff_class.R'
     'calc_rt_diff_class.R'
+    'lcms_table_class.R'
     'cd_source_class.R'
     'rest_api_parsers.R'
     'rest_api_class.R'

NAMESPACE

@@ -24,7 +24,6 @@ export(BiocFileCache_database)
 export(CompoundDb_source)
 export(GO_database)
 export(MTox700plus_database)
-export(MetFrag_source)
 export(PathBank_metabolite_database)
 export(add_columns)
 export(add_labels)

R/MTox700plus_database_class.R

@@ -58,7 +58,7 @@ MTox700plus_database <- function(version = "latest",
                 "The version number of the MTox700+ database to import. ",
                 "Available versions are listed here: ",
                 "[https://github.com/michabohealthscience/MTox700plus/releases].",
-                ' `version` should match the tag of thr release e.g. `"v1.0"`.',
+                ' `version` should match the tag of the release e.g. `"v1.0"`.',
                 ' For convenience `version = "latest"` will always retrieve ',
                 "the most recent release. To prevent unecessary downloads ",
                 "`BiocFileCache` is used to store a local copy."

R/cd_source_class.R

@@ -1,5 +1,5 @@
 #' @eval get_description('cd_source')
-#' @include annotation_source_class.R
+#' @include annotation_source_class.R lcms_table_class.R
 #' @family {annotation sources}
 #' @family {annotation tables}
 #' @rawNamespace import(dplyr, except = as_data_frame)