[ ] Breaking change (these changes would cause existing functionality to not work as expected).
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[x] Reviewer assignment: @the-mayer and @jananiravi
@the-mayer I have added a globals.R for Protein in Lineage.R As suggested. The names of most of the functions have been changed. I can update those in the issue if you'd want that.
[x] generate_fa2tre: function not found but I add .data$ to ‘tre_path’ in the updated function
[x] get_proc_medians : : no visible global function definition for ‘median’
[x] generate_msa: no visible global function definition for ‘kalign’
[ ] getJobsWithStates: not found
[x] get_proc_medians : : no visible global function definition for ‘median’
[x] IPG2Lineage updated from ipg2lin
[x] ipg2lin: no visible binding for global variable ‘Protein’
[x] ipg2lin: no visible binding for global variable ‘mergedTax’
[x] ipg2lin: no visible binding for global variable ‘gca_ipg_dt’
[x] ipg2lin: no visible binding for global variable ‘assembly_path’
[x] ipg2lin: no visible binding for global variable ‘Lineage’
[x] ipr2viz: no visible binding for global variable ‘iprscan_cols’
[x] ipr2viz: no visible binding for global variable ‘Name’
[x] ipr2viz: no visible binding for global variable ‘Lineage_short’
[x] ipr2viz: no visible binding for global variable ‘QueryName’
[x] ipr2viz: no visible binding for global variable ‘PcPositive’
[x] ipr2viz: no visible binding for global variable ‘AccNum’.
I finished these variables ipr2viz in my previous PR which were approved but even though the PR wasn't merged they have been updated.
[x] write_proc_medians_table: no visible binding for global variable ‘median_seconds’
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@the-mayer I have added a
globals.RforProteininLineage.RAs suggested. The names of most of the functions have been changed. I can update those in the issue if you'd want that.[x] generate_fa2tre: function not found but I add
.data$to ‘tre_path’ in the updated function [x] get_proc_medians : : no visible global function definition for ‘median’ [x] generate_msa: no visible global function definition for ‘kalign’ [ ] getJobsWithStates: not found [x] get_proc_medians : : no visible global function definition for ‘median’ [x] IPG2Lineage updated from ipg2lin [x] ipg2lin: no visible binding for global variable ‘Protein’ [x] ipg2lin: no visible binding for global variable ‘mergedTax’ [x] ipg2lin: no visible binding for global variable ‘gca_ipg_dt’ [x] ipg2lin: no visible binding for global variable ‘assembly_path’ [x] ipg2lin: no visible binding for global variable ‘Lineage’ [x] ipr2viz: no visible binding for global variable ‘iprscan_cols’ [x] ipr2viz: no visible binding for global variable ‘Name’ [x] ipr2viz: no visible binding for global variable ‘Lineage_short’ [x] ipr2viz: no visible binding for global variable ‘QueryName’ [x] ipr2viz: no visible binding for global variable ‘PcPositive’ [x] ipr2viz: no visible binding for global variable ‘AccNum’. I finished these variables ipr2viz in my previous PR which were approved but even though the PR wasn't merged they have been updated. [x] write_proc_medians_table: no visible binding for global variable ‘median_seconds’