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WIP Joss debug branch #82

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commented Feb 20, 2019

Trying to debug #79

grabear added some commits Jan 24, 2019

Merge branch 'dev-master' into joss-branch
# Conflicts:
#	DESCRIPTION
#	NAMESPACE
#	NEWS.md
#	R/alpha-diversity.R
#	R/barplot.R
#	docs/CODE_OF_CONDUCT.html
#	docs/CONTRIBUTING.html
#	docs/ISSUE_TEMPLATE.html
#	docs/LICENSE-text.html
#	docs/PULL_REQUEST_TEMPLATE.html
#	docs/articles/about.html
#	docs/articles/analysis.html
#	docs/articles/analysis_files/figure-html/unnamed-chunk-7-1.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-7-2.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-7-3.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-8-1.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-8-2.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-8-3.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-9-1.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-9-2.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-9-3.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-9-4.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-9-5.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-9-6.png
#	docs/articles/color-palettes.html
#	docs/articles/data-wrangling.html
#	docs/articles/filtering.html
#	docs/articles/index.html
#	docs/articles/introduction.html
#	docs/authors.html
#	docs/index.html
#	docs/news/index.html
#	docs/reference/MicrobiomeR.html
#	docs/reference/MicrobiomeR_Formats.html
#	docs/reference/MicrobiomeR_Workflow.html
#	docs/reference/alpha_diversity_plot.html
#	docs/reference/as_MicrobiomeR_format.html
#	docs/reference/as_analyzed_format.html
#	docs/reference/as_basic_format.html
#	docs/reference/as_custom_format.html
#	docs/reference/as_phyloseq_format.html
#	docs/reference/as_raw_format.html
#	docs/reference/combination_palette.html
#	docs/reference/correlation_data.html
#	docs/reference/correlation_plot.html
#	docs/reference/correlation_plots.html
#	docs/reference/cov_filter.html
#	docs/reference/create_phyloseq.html
#	docs/reference/create_pub_table.html
#	docs/reference/get_alpha_diversity_measures.html
#	docs/reference/get_color_palette.html
#	docs/reference/heat_tree_parameters.html
#	docs/reference/heat_tree_plots.html
#	docs/reference/index.html
#	docs/reference/is_analyzed_format.html
#	docs/reference/is_basic_format.html
#	docs/reference/is_phyloseq_format.html
#	docs/reference/is_raw_format.html
#	docs/reference/metacoder_comp_func_1.html
#	docs/reference/order_metacoder_data.html
#	docs/reference/ordination_plot.html
#	docs/reference/otu_id_filter.html
#	docs/reference/otu_prevalence_filter.html
#	docs/reference/otu_proportion_filter.html
#	docs/reference/output_dir.html
#	docs/reference/parse_taxonomy_silva_128.html
#	docs/reference/permanova.html
#	docs/reference/phyloseq_silva_2.html
#	docs/reference/phyloseq_silva_3.html
#	docs/reference/pick_new_outgroup.html
#	docs/reference/pipe.html
#	docs/reference/plot_limits.html
#	docs/reference/raw_silva_2.html
#	docs/reference/raw_silva_3.html
#	docs/reference/root_by_longest_edge.html
#	docs/reference/root_phyloseq_tree.html
#	docs/reference/sample_id_filter.html
#	docs/reference/save_correlation_plots.html
#	docs/reference/save_heat_tree_plots.html
#	docs/reference/save_ordination_plots.html
#	docs/reference/save_top_coefficients_barplot.html
#	docs/reference/scico_palette.html
#	docs/reference/stacked_barplot.html
#	docs/reference/taxa_prevalence_filter.html
#	docs/reference/taxon_id_filter.html
#	docs/reference/top_coefficients_barplot.html
#	docs/reference/transformer.html
#	docs/reference/transposer.html
#	docs/reference/treatment_matrix.html
#	docs/reference/validate_MicrobiomeR_format.html
#	docs/reference/viridis_magma_palette.html
#	docs/reference/viridis_palette.html
#	docs/reference/vlookup.html
#	docs/reference/which_format.html
#	man/heat_tree_plots.Rd
#	man/ordination_plot.Rd
#	man/save_barplot.Rd
#	man/stacked_barplot.Rd
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commented Feb 21, 2019

It looks like it's going to build with what you added to travis.yml. The problem now is with it installing and/or using an updated version of dplyr based on some other package.

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commented Feb 21, 2019

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commented Feb 21, 2019

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commented Feb 21, 2019

grabear and others added some commits Feb 22, 2019

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commented Feb 22, 2019

Quitting from lines 77-78 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
invalid argument to unary operator
Execution halted
The command "R CMD build  ." failed and exited with 1 during .
Your build has been stopped.
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commented Feb 22, 2019

grabear and others added some commits Feb 22, 2019

@grabear grabear referenced this pull request Feb 26, 2019

Closed

Dependency Issues. #84

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commented Feb 26, 2019

I can fix this tonight.

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commented Feb 27, 2019

Solved by #85

@grabear grabear closed this Feb 27, 2019

@sdhutchins sdhutchins deleted the joss-debug-branch branch Mar 20, 2019

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