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R-CMD Check: summarizeDomArch, summarizeDomArch_ByLineage, summarizeGenContext, summarizeGenContext_ByDomArchLineage, summarizeGenContext_ByLineage #116

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Klangina opened this issue Oct 28, 2024 · 0 comments · Fixed by #117
Closed
17 tasks

R-CMD Check: summarizeDomArch, summarizeDomArch_ByLineage, summarizeGenContext, summarizeGenContext_ByDomArchLineage, summarizeGenContext_ByLineage #116

Klangina opened this issue Oct 28, 2024 · 0 comments · Fixed by #117

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@Klangina
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Klangina commented Oct 28, 2024 •
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  • summ.DA summarizeDomArch: no visible binding for global variable ‘DomArch’
  • summ.DA summarizeDomArch: no visible binding for global variable ‘totallin’
  • summ.DA summarizeDomArch: no visible binding for global variable ‘totalcount’
  • summ.DA summarizeDomArch_ByLineage: no visible binding for global variable ‘DomArch’
  • summ.DA summarizeDomArch_ByLineage: no visible binding for global variable ‘Lineage’
  • summ.GC summarizeGenContext: no visible binding for global variable ‘GenContext’
  • summ.GC summarizeGenContext: no visible binding for global variable ‘DomArch’
  • summ.GC summarizeGenContext: no visible binding for global variable ‘Lineage’
  • summ.GC summarizeGenContext: no visible binding for global variable ‘totalcount’
  • summ.GC summarizeGenContext: no visible binding for global variable ‘totalDA’
  • summ.GC summarizeGenContext: no visible binding for global variable ‘totallin’
  • summ.GC.byDALinsummarizeGenContext_ByDomArchLineage : no visible binding for global variable ‘GenContext’
  • summ.GC.byDALinsummarizeGenContext_ByDomArchLineage: no visible binding for global variable ‘DomArch’
  • summ.GC.byDALinsummarizeGenContext_ByDomArchLineage: no visible binding for global variable ‘Lineage’
  • summ.GC.byLin summarizeGenContext_ByLineage: no visible binding for global variable ‘GenContext’
  • summ.GC.byLin summarizeGenContext_ByLineage: no visible binding for global variable ‘DomArch’
  • summ.GC.byLin summarizeGenContext_ByLineage: no visible binding for global variable ‘Lineage’

Originally posted by @the-mayer in #4 (comment)
Klangina added a commit to Klangina/MolEvolvR that referenced this issue Oct 28, 2024
@Klangina
[FIXED][JRaviLab#116]:
4df6053 
summarizeDomArch: no visible binding for global variable ‘DomArch’
  summarizeDomArch: no visible binding for global variable ‘totallin’
  summarizeDomArch: no visible binding for global variable ‘totalcount’

[Changes]

    Added @importFrom rlang .data to import the .data pronoun.
    Used .data$DomArch, .data$count, .data$totallin, and .data$totalcount to refer to the columns within dplyr functions.
    Added desc to the @importFrom dplyr list as it's used in the arrange function.
    Updated the example in the documentation to show that the function expects an argument.
Klangina added a commit to Klangina/MolEvolvR that referenced this issue Oct 28, 2024
@Klangina
[FIXED] [JRaviLab#116]
b632df0 
summarizeDomArch_ByLineage: no visible binding for global variable
    ‘DomArch’
  summarizeDomArch_ByLineage: no visible binding for global variable
    ‘Lineage’

[CHANGES]

Added @importFrom rlang .data to import the .data pronoun.
    Used .data$DomArch and .data$Lineage to refer to the columns within dplyr functions.
Updated the example in the documentation to show that the function expects an argument.
Klangina added a commit to Klangina/MolEvolvR that referenced this issue Oct 28, 2024
@Klangina
[Fixed] [JRaviLab#116]
2ea9598 
ummarizeGenContext: no visible binding for global variable
    ‘GenContext’
  summarizeGenContext: no visible binding for global variable ‘DomArch’
  summarizeGenContext: no visible binding for global variable ‘Lineage’
  summarizeGenContext: no visible binding for global variable
    ‘totalcount’
  summarizeGenContext: no visible binding for global variable ‘totalDA’
  summarizeGenContext: no visible binding for global variable ‘totallin’

  [Changed]
Added @importFrom rlang .data to import the .data pronoun.
    Used .data$GenContext, .data$DomArch, .data$Lineage, and .data$count to refer to the columns within dplyr functions.
    Used .data$totalcount, .data$totalDA, and .data$totallin in the arrange function.
    Updated the function documentation to reflect that a count column is expected in the input data.
    Updated the example in the documentation to show that the function expects an argument.
Klangina added a commit to Klangina/MolEvolvR that referenced this issue Oct 28, 2024
@Klangina
[FIXED] [JRaviLab#116]
5d9eb0f 
summarizeGenContext_ByDomArchLineage: no visible binding for global
     variable ‘GenContext’
   summarizeGenContext_ByDomArchLineage: no visible binding for global
     variable ‘DomArch’
   summarizeGenContext_ByDomArchLineage: no visible binding for global
     variable ‘Lineage’
   summarizeGenContext_ByLineage: no visible binding for global variable
     ‘GenContext’
   summarizeGenContext_ByLineage: no visible binding for global variable
     ‘DomArch’
   summarizeGenContext_ByLineage: no visible binding for global variable
     ‘Lineage’
[Changes]
Added @importFrom rlang .data to import the .data pronoun.
    Used .data$GenContext, .data$DomArch, .data$Lineage, and .data$count to refer to the columns within dplyr functions.
    Updated the examples and documentation.
@the-mayer the-mayer linked a pull request Nov 1, 2024 that will close this issue
Fixes Issue #116 #117
Merged
11 tasks
the-mayer added a commit that referenced this issue Nov 1, 2024
@the-mayer
Merge pull request #117 from Klangina/Issue-116
aacda7d 
Fixes Issue #116
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Fixes Issue #116 Klangina/MolEvolvR
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@Klangina