R-CMD Check: no visible binding for global variable

[the-mayer]

Overview

Be explicit in all function calls. Utilize rlang::.data as appropriate, checking functions off the list as they have been updated.

Function List

• BinaryDomainNetwork: no visible binding for global variable ‘id’
• BinaryDomainNetwork: no visible binding for global variable ‘size’
• BinaryDomainNetwork: no visible binding for global variable ‘width’
• GenContextNetwork: no visible binding for global variable ‘size’
• GenContextNetwork: no visible binding for global variable ‘width’
• LineagePlot: no visible binding for global variable ‘GenContext’
• LineagePlot: no visible binding for global variable ‘Lineage’
• LineagePlot: no visible binding for global variable ‘Query’
• LineagePlot: no visible binding for global variable ‘ReducedLin’
• LineagePlot: no visible binding for global variable ‘Kingdom’
• add_leaves: no visible binding for global variable ‘x1’
• add_leaves: no visible binding for global variable ‘AccNum’
• add_leaves: no visible binding for global variable ‘Alignment’
• add_leaves: no visible binding for global variable ‘Species’
• add_leaves: no visible binding for global variable ‘Lineage’
• add_leaves: no visible binding for global variable ‘Kingdom’
• add_leaves: no visible binding for global variable ‘Phylum’
• add_leaves: no visible binding for global variable ‘Genus’
• add_leaves: no visible binding for global variable ‘Spp’
• add_leaves: no visible binding for global variable ‘Leaf’
• add_leaves: no visible binding for global variable ‘Leaf_Acc’
• add_lins: no visible global function definition for ‘:=’
• add_name: no visible binding for global variable ‘Kingdom’
• add_name: no visible binding for global variable ‘Phylum’
• add_name: no visible binding for global variable ‘Genus’
• add_name: no visible binding for global variable ‘Spp’
• add_tax: no visible global function definition for ‘is.data.table’
• add_tax: no visible global function definition for ‘:=’
• add_tax: no visible binding for global variable ‘AccNum.noV’
• add_tax: no visible global function definition for ‘merge.data.table’
• all_non_n_cols_to_char: no visible global function definition for ‘matches’
• clean_clust_file: no visible binding for global variable ‘X1’
• clean_clust_file: no visible binding for global variable ‘colnames.op_ins_cls’
• clean_clust_file: no visible binding for global variable ‘AccNum’
• cleanup_clust: no visible binding for global variable ‘ClustName’
• combine_files: no visible global function definition for ‘col_character’
• convert_aln2fa: no visible global function definition for ‘data.table’
• count_bycol: no visible binding for global variable ‘freq’
• create_lineage_lookup: no visible binding for global variable ‘kingdom’
• create_lineage_lookup: no visible binding for global variable ‘Lineage’
• create_one_col_params: no visible binding for global variable ‘.’
• create_one_col_params: no visible binding for global variable ‘ids’
• create_one_col_params: no visible binding for global variable ‘parents’
• create_one_col_params: no visible binding for global variable ‘values’
• create_one_col_params: no visible binding for global variable ‘hovertext’
• df_iprscan_domains2fasta: no visible binding for global variable ‘seq_domain’
• df_iprscan_domains2fasta: no visible binding for global variable ‘id_domain’
• domain_network: no visible binding for global variable ‘DomArch.ntwrk’
• domain_network: no visible binding for global variable ‘words’
• domain_network: no visible binding for global variable ‘freq’
• domain_network: no visible global function definition for ‘V<-’
• domain_network: no visible global function definition for ‘E<-’
• domain_network : <anonymous>: no visible global function definition for ‘E<-’
• filter_freq: no visible binding for global variable ‘freq’
• find_paralogs: no visible binding for global variable ‘Lineage’
• find_paralogs: no visible binding for global variable ‘GCA_ID’
• find_paralogs: no visible binding for global variable ‘DomArch’
• find_paralogs : : no visible binding for global variable ‘GCA_ID’
• find_paralogs: no visible binding for global variable ‘Species’
• find_paralogs: no visible binding for global variable ‘Count’
• find_top_acc: no visible binding for global variable ‘PcPositive’
• find_top_acc: no visible binding for global variable ‘AccNum’
• format_job_args: no visible binding for global variable ‘tags’
• format_job_args : : no visible binding for global variable ‘fields_metadata’
• format_job_args : : no visible binding for global variable ‘tags’
• gc_undirected_network: no visible binding for global variable ‘totallin’
• gc_undirected_network: no visible global function definition for ‘V<-’
• gc_undirected_network: no visible global function definition for ‘E<-’
• gc_undirected_network : : no visible global function definition for ‘E<-’
• generate_fa2tre: no visible binding for global variable ‘tre_path’
• generate_fa2tre: no visible binding for global variable ‘prot’
• generate_fa2tre: no visible global function definition for ‘midpoint’
• generate_msa: possible error in readAAStringSet(path = fa_file, format = "fasta"): unused argument (path = fa_file)
• generate_msa: no visible global function definition for ‘kalign’
• getJobsWithStates: no visible binding for global variable ‘state’
• get_proc_medians : : no visible global function definition for ‘median’
• ipg2lin: no visible binding for global variable ‘Protein’
• ipg2lin: no visible binding for global variable ‘mergedTax’
• ipg2lin: no visible binding for global variable ‘gca_ipg_dt’
• ipg2lin: no visible binding for global variable ‘assembly_path’
• ipg2lin: no visible binding for global variable ‘Lineage’
• ipr2viz: no visible binding for global variable ‘iprscan_cols’
• ipr2viz: no visible binding for global variable ‘Name’
• ipr2viz: no visible binding for global variable ‘Lineage_short’
• ipr2viz: no visible binding for global variable ‘QueryName’
• ipr2viz: no visible binding for global variable ‘PcPositive’
• ipr2viz: no visible binding for global variable ‘AccNum’
• ipr2viz: no visible binding for global variable ‘StartLoc’
• ipr2viz: no visible binding for global variable ‘StopLoc’
• ipr2viz: no visible binding for global variable ‘Analysis’
• ipr2viz: no visible binding for global variable ‘lookup_table_cols’
• ipr2viz: no visible binding for global variable ‘ShortName’
• ipr2viz: no visible global function definition for ‘unit’
• ipr2viz: no visible binding for global variable ‘SLength’
• ipr2viz: no visible global function definition for ‘as.formula’
• ipr2viz_web: no visible binding for global variable ‘lookup_table_cols’
• ipr2viz_web: no visible binding for global variable ‘Name’
• ipr2viz_web: no visible binding for global variable ‘AccNum’
• ipr2viz_web: no visible binding for global variable ‘StartLoc’
• ipr2viz_web: no visible binding for global variable ‘StopLoc’
• ipr2viz_web: no visible binding for global variable ‘Analysis’
• ipr2viz_web: no visible binding for global variable ‘ShortName’
• ipr2viz_web: no visible global function definition for ‘unit’
• ipr2viz_web: no visible binding for global variable ‘SLength’
• ipr2viz_web: no visible global function definition for ‘as.formula’
• lineage.DA.plot: no visible binding for global variable ‘Lineage’
• lineage.DA.plot: no visible binding for global variable ‘totalcount’
• lineage.domain_repeats.plot: no visible binding for global variable ‘query.DAdoms’
• lineage.domain_repeats.plot: no visible binding for global variable ‘DomArch.norep’
• lineage.domain_repeats.plot: no visible binding for global variable ‘Lineage’
• lineage.domain_repeats.plot: no visible binding for global variable ‘GenContext.norep’
• lineage.domain_repeats.plot: no visible binding for global variable ‘SIG.TM.LADB’
• lineage.domain_repeats.plot: no visible binding for global variable ‘GenContext’
• lineage.domain_repeats.plot: no visible binding for global variable ‘AccNum’
• lineage.domain_repeats.plot: no visible binding for global variable ‘domains’
• lineage.neighbors.plot: no visible binding for global variable ‘lincount’
• lineage_sunburst: no visible global function definition for ‘d3_nest’
• lineage_sunburst: no visible binding for global variable ‘cpcols’
• lineage_sunburst: no visible global function definition for ‘sund2b’
• make_accnums_unique: no visible binding for global variable ‘accnum’
• make_accnums_unique: no visible binding for global variable ‘suffix’
• make_accnums_unique: no visible binding for global variable ‘accnum_adjusted’
• make_df_iprscan_domains: no visible binding for global variable ‘Analysis’
• make_df_iprscan_domains: no visible binding for global variable ‘AccNum’
• make_df_iprscan_domains: no visible binding for global variable ‘StartLoc’
• make_df_iprscan_domains: no visible binding for global variable ‘StopLoc’
• make_df_iprscan_domains: no visible binding for global variable ‘id_domain’
• pick_longer_duplicate: no visible binding for global variable ‘AccNum’
• pick_longer_duplicate: no visible binding for global variable ‘row.orig’
• plot_estimated_walltimes : get_powerset : : no visible global function definition for ‘combn’
• plot_estimated_walltimes: no visible binding for global variable ‘n_inputs’
• plot_estimated_walltimes: no visible binding for global variable ‘est_walltime’
• plot_estimated_walltimes: no visible binding for global variable ‘advanced_opts’
• remove_tails: no visible binding for global variable ‘domains_keep’
• repeat2s: no visible binding for global variable ‘.’
• stacked_lin_plot: no visible binding for global variable ‘cpcols’
• stacked_lin_plot: no visible global function definition for ‘unit’
• summ.DA: no visible binding for global variable ‘DomArch’
• summ.DA: no visible binding for global variable ‘totallin’
• summ.DA: no visible binding for global variable ‘totalcount’
• summ.DA.byLin: no visible binding for global variable ‘DomArch’
• summ.DA.byLin: no visible binding for global variable ‘Lineage’
• summ.GC: no visible binding for global variable ‘GenContext’
• summ.GC: no visible binding for global variable ‘DomArch’
• summ.GC: no visible binding for global variable ‘Lineage’
• summ.GC: no visible binding for global variable ‘totalcount’
• summ.GC: no visible binding for global variable ‘totalDA’
• summ.GC: no visible binding for global variable ‘totallin’
• summ.GC.byDALin: no visible binding for global variable ‘GenContext’
• summ.GC.byDALin: no visible binding for global variable ‘DomArch’
• summ.GC.byDALin: no visible binding for global variable ‘Lineage’
• summ.GC.byLin: no visible binding for global variable ‘GenContext’
• summ.GC.byLin: no visible binding for global variable ‘DomArch’
• summ.GC.byLin: no visible binding for global variable ‘Lineage’
• total_counts: no visible binding for global variable ‘totalcount’
• total_counts: no visible binding for global variable ‘CumulativePercent’
• upset.plot: no visible binding for global variable ‘Words’
• upset.plot: no visible binding for global variable ‘AccNum’
• upset.plot: no visible binding for global variable ‘Lineage’
• upset.plot: no visible global function definition for ‘par’
• wordcloud2_element: no visible binding for global variable ‘freq’
• wordcloud2_element: no visible binding for global variable ‘words’
• wordcloud2_element: no visible binding for global variable ‘label’
• words2wc: no visible binding for global variable ‘words’
• words2wc: no visible binding for global variable ‘freq’
• write_proc_medians_table: no visible binding for global variable ‘median_seconds’

[jananiravi]

@SunSummoner, this might be a good place to start. @the-mayer has started working on this for now.

[SunSummoner]

@jananiravi @the-mayer I will start with this. Thanks!

[valentina-buoro]

Hi @jananiravi , can I work on this?

[jananiravi]

yes, please! coordinate with @SunSummoner via github/slack to see if she's started some work already.

[SunSummoner]

@jananiravi I talked with @valentina-buoro and we were thinking of dividing some of the functions after getting the PR reviewed for changes.

[the-mayer]

Splitting the remainder (roughly) by function(s), so that multiple people may participate!

Note, most of these errors come from how R handles Non Standard Evaluation. Resolving these issues does not actually change code functionality. It will however, clear a R CMD warning, which will be important for when MolEvolvR is submitted for review. Consider the following example:

filter_function <- function(data, filter_value) {
  data %>%
    filter(numeric_column_in_data < filter_value)
  }

R knows that numeric_column_in_data can be found within the data object. But, if this code were to be written in an R package, when running devtools:check() a warning would be produced:

filter_function: no visible binding for global variable 'numeric_column_in_data'

rlang, the package that helps with NSE offers a way to deal with this, by making the function code (within a package) more explicit. By refactoring to include a .data prefix, we can clear the warning:

filter_function <- function(data, filter_value) {
  data %>%
    filter(.data$numeric_column_in_data < filter_value)
  }

Please take the comments that follow, convert to an issue, then follow the contributing guidelines and create a new branch containing your changes. Commit your work, and submit a PR when ready for review.

[the-mayer]

• generate_fa2tre: no visible binding for global variable ‘tre_path’
• generate_fa2tre: no visible binding for global variable ‘prot’
• generate_fa2tre: no visible global function definition for ‘midpoint’

Note, in addition to undefined global variables, this function will need to declare an import for midpoint

[the-mayer]

• getJobsWithStates: no visible binding for global variable ‘state’
• get_proc_medians : : no visible global function definition for ‘median’
• ipg2lin: no visible binding for global variable ‘Protein’
• ipg2lin: no visible binding for global variable ‘mergedTax’
• ipg2lin: no visible binding for global variable ‘gca_ipg_dt’
• ipg2lin: no visible binding for global variable ‘assembly_path’
• ipg2lin: no visible binding for global variable ‘Lineage’

[the-mayer]

• ipr2viz: no visible binding for global variable ‘iprscan_cols’
• ipr2viz: no visible binding for global variable ‘Name’
• ipr2viz: no visible binding for global variable ‘Lineage_short’
• ipr2viz: no visible binding for global variable ‘QueryName’
• ipr2viz: no visible binding for global variable ‘PcPositive’
• ipr2viz: no visible binding for global variable ‘AccNum’
• ipr2viz: no visible binding for global variable ‘StartLoc’
• ipr2viz: no visible binding for global variable ‘StopLoc’
• ipr2viz: no visible binding for global variable ‘Analysis’
• ipr2viz: no visible binding for global variable ‘lookup_table_cols’
• ipr2viz: no visible binding for global variable ‘ShortName’
• ipr2viz: no visible global function definition for ‘unit’
• ipr2viz: no visible binding for global variable ‘SLength’
• ipr2viz: no visible global function definition for ‘as.formula’
• ipr2viz_web: no visible binding for global variable ‘lookup_table_cols’
• ipr2viz_web: no visible binding for global variable ‘Name’
• ipr2viz_web: no visible binding for global variable ‘AccNum’
• ipr2viz_web: no visible binding for global variable ‘StartLoc’
• ipr2viz_web: no visible binding for global variable ‘StopLoc’
• ipr2viz_web: no visible binding for global variable ‘Analysis’
• ipr2viz_web: no visible binding for global variable ‘ShortName’
• ipr2viz_web: no visible global function definition for ‘unit’
• ipr2viz_web: no visible binding for global variable ‘SLength’
• ipr2viz_web: no visible global function definition for ‘as.formula’

[the-mayer]

• lineage.DA.plot: no visible binding for global variable ‘Lineage’
• lineage.DA.plot: no visible binding for global variable ‘totalcount’
• lineage.domain_repeats.plot: no visible binding for global variable ‘query.DAdoms’
• lineage.domain_repeats.plot: no visible binding for global variable ‘DomArch.norep’
• lineage.domain_repeats.plot: no visible binding for global variable ‘Lineage’
• lineage.domain_repeats.plot: no visible binding for global variable ‘GenContext.norep’
• lineage.domain_repeats.plot: no visible binding for global variable ‘SIG.TM.LADB’
• lineage.domain_repeats.plot: no visible binding for global variable ‘GenContext’
• lineage.domain_repeats.plot: no visible binding for global variable ‘AccNum’
• lineage.domain_repeats.plot: no visible binding for global variable ‘domains’

[the-mayer]

• lineage.neighbors.plot: no visible binding for global variable ‘lincount’
• lineage_sunburst: no visible global function definition for ‘d3_nest’
• lineage_sunburst: no visible binding for global variable ‘cpcols’
• lineage_sunburst: no visible global function definition for ‘sund2b’
• make_accnums_unique: no visible binding for global variable ‘accnum’
• make_accnums_unique: no visible binding for global variable ‘suffix’
• make_accnums_unique: no visible binding for global variable ‘accnum_adjusted’
• make_df_iprscan_domains: no visible binding for global variable ‘Analysis’
• make_df_iprscan_domains: no visible binding for global variable ‘AccNum’
• make_df_iprscan_domains: no visible binding for global variable ‘StartLoc’
• make_df_iprscan_domains: no visible binding for global variable ‘StopLoc’
• make_df_iprscan_domains: no visible binding for global variable ‘id_domain’

[the-mayer]

• pick_longer_duplicate: no visible binding for global variable ‘AccNum’
• pick_longer_duplicate: no visible binding for global variable ‘row.orig’
• plot_estimated_walltimes : get_powerset : : no visible global function definition for ‘combn’
• plot_estimated_walltimes: no visible binding for global variable ‘n_inputs’
• plot_estimated_walltimes: no visible binding for global variable ‘est_walltime’
• plot_estimated_walltimes: no visible binding for global variable ‘advanced_opts’
• remove_tails: no visible binding for global variable ‘domains_keep’
• repeat2s: no visible binding for global variable ‘.’
• stacked_lin_plot: no visible binding for global variable ‘cpcols’
• stacked_lin_plot: no visible global function definition for ‘unit’

[the-mayer]

• summ.DA: no visible binding for global variable ‘DomArch’
• summ.DA: no visible binding for global variable ‘totallin’
• summ.DA: no visible binding for global variable ‘totalcount’
• summ.DA.byLin: no visible binding for global variable ‘DomArch’
• summ.DA.byLin: no visible binding for global variable ‘Lineage’
• summ.GC: no visible binding for global variable ‘GenContext’
• summ.GC: no visible binding for global variable ‘DomArch’
• summ.GC: no visible binding for global variable ‘Lineage’
• summ.GC: no visible binding for global variable ‘totalcount’
• summ.GC: no visible binding for global variable ‘totalDA’
• summ.GC: no visible binding for global variable ‘totallin’
• summ.GC.byDALin: no visible binding for global variable ‘GenContext’
• summ.GC.byDALin: no visible binding for global variable ‘DomArch’
• summ.GC.byDALin: no visible binding for global variable ‘Lineage’
• summ.GC.byLin: no visible binding for global variable ‘GenContext’
• summ.GC.byLin: no visible binding for global variable ‘DomArch’
• summ.GC.byLin: no visible binding for global variable ‘Lineage’

[the-mayer]

• total_counts: no visible binding for global variable ‘totalcount’
• total_counts: no visible binding for global variable ‘CumulativePercent’
• upset.plot: no visible binding for global variable ‘Words’
• upset.plot: no visible binding for global variable ‘AccNum’
• upset.plot: no visible binding for global variable ‘Lineage’
• upset.plot: no visible global function definition for ‘par’
• wordcloud2_element: no visible binding for global variable ‘freq’
• wordcloud2_element: no visible binding for global variable ‘words’
• wordcloud2_element: no visible binding for global variable ‘label’
• words2wc: no visible binding for global variable ‘words’
• words2wc: no visible binding for global variable ‘freq’
• write_proc_medians_table: no visible binding for global variable ‘median_seconds’

[valentina-buoro]

Splitting the remainder (roughly) by function(s), so that multiple people may participate!

Note, most of these errors come from how R handles Non Standard Evaluation. Resolving these issues does not actually change code functionality. It will however, clear a R CMD warning, which will be important for when MolEvolvR is submitted for review. Consider the following example:

filter_function <- function(data, filter_value) {
  data %>%
    filter(numeric_column_in_data < filter_value)
  }

R knows that numeric_column_in_data can be found within the data object. But, if this code were to be written in an R package, when running devtools:check() a warning would be produced:

filter_function: no visible binding for global variable 'numeric_column_in_data'

rlang, the package that helps with NSE offers a way to deal with this, by making the function code (within a package) more explicit. By refactoring to include a .data prefix, we can clear the warning:

filter_function <- function(data, filter_value) {
  data %>%
    filter(.data$numeric_column_in_data < filter_value)
  }

Please take the comments that follow, convert to an issue, then follow the contributing guidelines and create a new branch containing your changes. Commit your work, and submit a PR when ready for review.

Noted @the-mayer

[valentina-buoro]

• lineage.neighbors.plot: no visible binding for global variable ‘lincount’
• lineage_sunburst: no visible global function definition for ‘d3_nest’
• lineage_sunburst: no visible binding for global variable ‘cpcols’
• lineage_sunburst: no visible global function definition for ‘sund2b’
• make_accnums_unique: no visible binding for global variable ‘accnum’
• make_accnums_unique: no visible binding for global variable ‘suffix’
• make_accnums_unique: no visible binding for global variable ‘accnum_adjusted’
• make_df_iprscan_domains: no visible binding for global variable ‘Analysis’
• make_df_iprscan_domains: no visible binding for global variable ‘AccNum’
• make_df_iprscan_domains: no visible binding for global variable ‘StartLoc’
• make_df_iprscan_domains: no visible binding for global variable ‘StopLoc’
• make_df_iprscan_domains: no visible binding for global variable ‘id_domain’

Hi fellow outreachy interns. These set of functions have been worked on.

[Klangina]

Can I work on #4 (comment)

generate_fa2tre: no visible binding for global variable ‘tre_path’
generate_fa2tre: no visible binding for global variable ‘prot’
generate_fa2tre: no visible global function definition for ‘midpoint’

post the changes in #108 ?

The warning in devtools::check post the changes are as follows:

createFA2Tree: no visible global function definition for ‘midpoint’
createFA2Tree: no visible binding for global variable ‘fit_optimized2’

@the-mayer @jananiravi