[inst/site/create_table.R:19:58:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/create_table.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  dp_selection = filter(data_df, V3 == sample(indexes, 1) ),
                                                         ^
```
[inst/site/create_table.R:21:62:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/create_table.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    "select * from taxonomy where V3 == ", sample(indexes, 1) )), times = 100
                                                             ^
```
[inst/site/merge_and_plot_bwa_assignments.R:12:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_bwa_assignments.R#L12) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_and_plot_bwa_assignments.R:13:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_bwa_assignments.R#L13) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[inst/site/merge_and_plot_bwa_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_bwa_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_bwa_assignments.R:15:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_bwa_assignments.R#L15) *style:* **Variable or function name should be snake_case.**
```r
plotTitleArg <- args[4]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_bwa_assignments.R:16:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_bwa_assignments.R#L16) *style:* **Variable or function name should be snake_case.**
```r
plotFileArg <- args[5]
^~~~~~~~~~~
```
[inst/site/merge_and_plot_bwa_assignments.R:21:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_bwa_assignments.R#L21) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- args[6]
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_bwa_assignments.R:22:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_bwa_assignments.R#L22) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_bwa_assignments.R:24:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_bwa_assignments.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- 60
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_bwa_assignments.R:25:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_bwa_assignments.R#L25) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:12:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_diamond_assignments.R#L12) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:13:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_diamond_assignments.R#L13) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_diamond_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:15:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_diamond_assignments.R#L15) *style:* **Variable or function name should be snake_case.**
```r
plotTitleArg <- args[4]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:16:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_diamond_assignments.R#L16) *style:* **Variable or function name should be snake_case.**
```r
plotFileArg <- args[5]
^~~~~~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:21:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_diamond_assignments.R#L21) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- args[6]
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:22:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_diamond_assignments.R#L22) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:24:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_diamond_assignments.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- 60
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:25:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_diamond_assignments.R#L25) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:12:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_edge_assignments.R#L12) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:13:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_edge_assignments.R#L13) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_edge_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:15:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_edge_assignments.R#L15) *style:* **Variable or function name should be snake_case.**
```r
plotTitleArg <- args[4]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:16:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_edge_assignments.R#L16) *style:* **Variable or function name should be snake_case.**
```r
plotFileArg <- args[5]
^~~~~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:17:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_edge_assignments.R#L17) *style:* **Variable or function name should be snake_case.**
```r
assignerType <- args[6]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:22:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_edge_assignments.R#L22) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- args[7]
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:23:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_edge_assignments.R#L23) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- args[8]
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:25:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_edge_assignments.R#L25) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- 60
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:26:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_edge_assignments.R#L26) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:12:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha_assignments.R#L12) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:13:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha_assignments.R#L13) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:15:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha_assignments.R#L15) *style:* **Variable or function name should be snake_case.**
```r
plotTitleArg <- args[4]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:16:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha_assignments.R#L16) *style:* **Variable or function name should be snake_case.**
```r
plotFileArg <- args[5]
^~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:21:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha_assignments.R#L21) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- args[6]
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:22:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha_assignments.R#L22) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:24:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha_assignments.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- 60
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:25:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha_assignments.R#L25) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:12:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha2_assignments.R#L12) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:13:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha2_assignments.R#L13) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha2_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:15:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha2_assignments.R#L15) *style:* **Variable or function name should be snake_case.**
```r
plotTitleArg <- args[4]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:16:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha2_assignments.R#L16) *style:* **Variable or function name should be snake_case.**
```r
plotFileArg <- args[5]
^~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:21:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha2_assignments.R#L21) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- args[6]
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:22:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha2_assignments.R#L22) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:24:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha2_assignments.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- 60
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:25:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_gottcha2_assignments.R#L25) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:12:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_kraken_assignments.R#L12) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:13:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_kraken_assignments.R#L13) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_kraken_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:15:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_kraken_assignments.R#L15) *style:* **Variable or function name should be snake_case.**
```r
plotTitleArg <- args[4]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:16:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_kraken_assignments.R#L16) *style:* **Variable or function name should be snake_case.**
```r
plotFileArg <- args[5]
^~~~~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:21:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_kraken_assignments.R#L21) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- args[6]
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:22:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_kraken_assignments.R#L22) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:24:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_kraken_assignments.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- 60
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:25:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_kraken_assignments.R#L25) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:29:69:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_kraken_assignments.R#L29) *style:* **Put spaces around all infix operators.**
```r
merged <- merge_edge_assignments(load_edge_assignments(srcFile, type= "kraken"))
                                                                   ~^
```
[inst/site/merge_and_plot_metaphlan_assignments.R:12:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_metaphlan_assignments.R#L12) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_and_plot_metaphlan_assignments.R:13:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_metaphlan_assignments.R#L13) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[inst/site/merge_and_plot_metaphlan_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_metaphlan_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_metaphlan_assignments.R:15:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_metaphlan_assignments.R#L15) *style:* **Variable or function name should be snake_case.**
```r
plotTitleArg <- args[4]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_metaphlan_assignments.R:16:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_metaphlan_assignments.R#L16) *style:* **Variable or function name should be snake_case.**
```r
plotFileArg <- args[5]
^~~~~~~~~~~
```
[inst/site/merge_and_plot_metaphlan_assignments.R:21:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_metaphlan_assignments.R#L21) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- args[6]
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_metaphlan_assignments.R:22:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_metaphlan_assignments.R#L22) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_metaphlan_assignments.R:24:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_metaphlan_assignments.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- 60
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_metaphlan_assignments.R:25:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_metaphlan_assignments.R#L25) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:12:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_pangia_assignments.R#L12) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:13:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_pangia_assignments.R#L13) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_pangia_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:15:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_pangia_assignments.R#L15) *style:* **Variable or function name should be snake_case.**
```r
plotTitleArg <- args[4]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:16:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_pangia_assignments.R#L16) *style:* **Variable or function name should be snake_case.**
```r
plotFileArg <- args[5]
^~~~~~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:21:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_pangia_assignments.R#L21) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- args[6]
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:22:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_pangia_assignments.R#L22) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:24:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_pangia_assignments.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- 60
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:25:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_and_plot_pangia_assignments.R#L25) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_gottcha_assignments.R:11:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_gottcha_assignments.R#L11) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_gottcha_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/inst/site/merge_gottcha_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[R/load_edge_assignment.R:33:13:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L33) *style:* **Variable or function name should be snake_case.**
```r
  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
            ^~~~
```
[R/load_edge_assignment.R:33:21:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L33) *style:* **Variable or function name should be snake_case.**
```r
  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
                    ^~~~~
```
[R/load_edge_assignment.R:33:30:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L33) *style:* **Variable or function name should be snake_case.**
```r
  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
                             ^~~~~
```
[R/load_edge_assignment.R:33:30:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L33) *warning:* **local variable ‘COUNT’ assigned but may not be used**
```r
  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
                             ^~~~~
```
[R/load_edge_assignment.R:33:39:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L33) *style:* **Variable or function name should be snake_case.**
```r
  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
                                      ^~~~~~~~~
```
[R/load_edge_assignment.R:34:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L34) *style:* **Variable or function name should be snake_case.**
```r
  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
  ^~~~~~
```
[R/load_edge_assignment.R:34:13:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L34) *style:* **Variable or function name should be snake_case.**
```r
  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
            ^~~~
```
[R/load_edge_assignment.R:34:21:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L34) *style:* **Variable or function name should be snake_case.**
```r
  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
                    ^~~~~~
```
[R/load_edge_assignment.R:34:31:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L34) *style:* **Variable or function name should be snake_case.**
```r
  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
                              ^~~~~~~
```
[R/load_edge_assignment.R:34:42:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L34) *style:* **Variable or function name should be snake_case.**
```r
  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
                                         ^~~~~~~~~~
```
[R/load_edge_assignment.R:35:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L35) *style:* **Variable or function name should be snake_case.**
```r
  REL_ABUNDANCE <- NORM_COV <- READ_COUNT_RNR <- ASSIGNED <- NULL
  ^~~~~~~~~~~~~
```
[R/load_edge_assignment.R:35:20:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L35) *style:* **Variable or function name should be snake_case.**
```r
  REL_ABUNDANCE <- NORM_COV <- READ_COUNT_RNR <- ASSIGNED <- NULL
                   ^~~~~~~~
```
[R/load_edge_assignment.R:35:32:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L35) *style:* **Variable or function name should be snake_case.**
```r
  REL_ABUNDANCE <- NORM_COV <- READ_COUNT_RNR <- ASSIGNED <- NULL
                               ^~~~~~~~~~~~~~
```
[R/load_edge_assignment.R:35:50:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L35) *style:* **Variable or function name should be snake_case.**
```r
  REL_ABUNDANCE <- NORM_COV <- READ_COUNT_RNR <- ASSIGNED <- NULL
                                                 ^~~~~~~~
```
[R/load_edge_assignment.R:38:7:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !file.exists(filepath) ) {
      ^
```
[R/load_edge_assignment.R:38:30:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !file.exists(filepath) ) {
                             ^
```
[R/load_edge_assignment.R:44:7:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L44) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( 0 == file_info$size ) {
      ^
```
[R/load_edge_assignment.R:44:27:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L44) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( 0 == file_info$size ) {
                          ^
```
[R/load_edge_assignment.R:45:16:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L45) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    data.frame( LEVEL = character(), TAXA = character(), COUNT = integer(), ABUNDANCE = double())
               ^
```
[R/load_edge_assignment.R:54:9:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L54) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( 'bwa' == type ){
        ^
```
[R/load_edge_assignment.R:54:23:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L54) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( 'bwa' == type ){
                      ^
```
[R/load_edge_assignment.R:56:32:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L56) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      if (0 == length(df$LEVEL) ) {
                               ^
```
[R/load_edge_assignment.R:57:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L57) *style:* **Lines should not be more than 100 characters.**
```r
        data.frame( LEVEL = character(), TAXA = character(), COUNT = integer(), ABUNDANCE = double())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/load_edge_assignment.R:57:20:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L57) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        data.frame( LEVEL = character(), TAXA = character(), COUNT = integer(), ABUNDANCE = double())
                   ^
```
[R/load_edge_assignment.R:61:56:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L61) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
        levels <- plyr::ddply(df, "LEVEL", function(x) { sum(x$ROLLUP) })
                                                       ^
```
[R/load_edge_assignment.R:64:12:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L64) *style:* **Variable or function name should be snake_case.**
```r
        df$ABUNDANCE <- df$ROLLUP / df$SUM * 100
           ^~~~~~~~~
```
[R/load_edge_assignment.R:67:23:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L67) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        as.data.frame( dplyr::select(df, LEVEL, TAXA, COUNT = ROLLUP, ABUNDANCE))
                      ^
```
[R/load_edge_assignment.R:69:16:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L69) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'diamond' == type ){
               ^
```
[R/load_edge_assignment.R:69:34:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L69) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'diamond' == type ){
                                 ^
```
[R/load_edge_assignment.R:70:21:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L70) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = ASSIGN, ABUNDANCE = REL_ABU))
                    ^
```
[R/load_edge_assignment.R:71:16:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L71) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'gottcha2' == type ){
               ^
```
[R/load_edge_assignment.R:71:35:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L71) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'gottcha2' == type ){
                                  ^
```
[R/load_edge_assignment.R:72:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L72) *style:* **Lines should not be more than 100 characters.**
```r
      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = READ_COUNT, ABUNDANCE = REL_ABUNDANCE))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/load_edge_assignment.R:72:21:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L72) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = READ_COUNT, ABUNDANCE = REL_ABUNDANCE))
                    ^
```
[R/load_edge_assignment.R:73:16:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L73) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'gottcha' == type ){
               ^
```
[R/load_edge_assignment.R:73:34:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L73) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'gottcha' == type ){
                                 ^
```
[R/load_edge_assignment.R:74:21:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L74) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      as.data.frame( dplyr::select(df, LEVEL, TAXA, COUNT = READ_COUNT, ABUNDANCE = NORM_COV))
                    ^
```
[R/load_edge_assignment.R:75:16:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L75) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'kraken' == type ){
               ^
```
[R/load_edge_assignment.R:75:33:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L75) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'kraken' == type ){
                                ^
```
[R/load_edge_assignment.R:78:10:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L78) *style:* **Variable or function name should be snake_case.**
```r
      df$ABUNDANCE <- df$ROLLUP / max_rollup * 100
         ^~~~~~~~~
```
[R/load_edge_assignment.R:79:21:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L79) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      as.data.frame( dplyr::select(df, LEVEL, TAXA, COUNT = ROLLUP, ABUNDANCE))
                    ^
```
[R/load_edge_assignment.R:80:16:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L80) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'metaphlan' == type ){
               ^
```
[R/load_edge_assignment.R:80:36:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L80) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'metaphlan' == type ){
                                   ^
```
[R/load_edge_assignment.R:81:21:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L81) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      as.data.frame( dplyr::select(df, LEVEL, TAXA, COUNT = ASSIGNED, ABUNDANCE = ROLLUP))
                    ^
```
[R/load_edge_assignment.R:82:16:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L82) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'pangia' == type ){
               ^
```
[R/load_edge_assignment.R:82:33:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L82) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'pangia' == type ){
                                ^
```
[R/load_edge_assignment.R:83:10:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L83) *style:* **Variable or function name should be snake_case.**
```r
      df$READ_COUNT_RNR = as.integer(df$READ_COUNT_RNR)
         ^~~~~~~~~~~~~~
```
[R/load_edge_assignment.R:83:25:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L83) *style:* **Use <-, not =, for assignment.**
```r
      df$READ_COUNT_RNR = as.integer(df$READ_COUNT_RNR)
                        ^
```
[R/load_edge_assignment.R:84:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L84) *style:* **Lines should not be more than 100 characters.**
```r
      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = READ_COUNT_RNR, ABUNDANCE = REL_ABUNDANCE))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/load_edge_assignment.R:84:21:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L84) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = READ_COUNT_RNR, ABUNDANCE = REL_ABUNDANCE))
                    ^
```
[R/load_edge_assignment.R:86:18:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L86) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      data.frame( LEVEL = character(), TAXA = character(), COUNT = integer(), ABUNDANCE = double())
                 ^
```
[R/load_edge_assignment.R:90:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L90) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/load_edge_assignment.R:91:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignment.R#L91) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/load_edge_assignments.R:35:7:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignments.R#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !file.exists(filepath) ) {
      ^
```
[R/load_edge_assignments.R:35:30:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignments.R#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !file.exists(filepath) ) {
                             ^
```
[R/load_edge_assignments.R:44:7:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignments.R#L44) *style:* **Use <-, not =, for assignment.**
```r
  res = list()
      ^
```
[R/load_edge_assignments.R:46:16:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignments.R#L46) *style:* **Use <-, not =, for assignment.**
```r
    cur_asgnmt = load_edge_assignment(df[prj_name == df$V1, ]$V2, type)
               ^
```
[R/load_edge_assignments.R:46:18:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignments.R#L46) *warning:* **no visible global function definition for ‘load_edge_assignment’**
```r
    cur_asgnmt = load_edge_assignment(df[prj_name == df$V1, ]$V2, type)
                 ^~~~~~~~~~~~~~~~~~~~
```
[R/load_edge_assignments.R:47:9:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/load_edge_assignments.R#L47) *style:* **Use <-, not =, for assignment.**
```r
    res = c(res, list(cur_asgnmt))
        ^
```
[R/merge_edge_assignments.R:32:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/merge_edge_assignments.R#L32) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- ABUNDANCE <- NULL # fix the CRAN note
  ^~~~~
```
[R/merge_edge_assignments.R:32:12:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/merge_edge_assignments.R#L32) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- ABUNDANCE <- NULL # fix the CRAN note
           ^~~~
```
[R/merge_edge_assignments.R:32:20:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/merge_edge_assignments.R#L32) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- ABUNDANCE <- NULL # fix the CRAN note
                   ^~~~~~~~~
```
[R/merge_edge_counts.R:19:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/merge_edge_counts.R#L19) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- COUNT <- NULL # fix the CRAN note
  ^~~~~
```
[R/merge_edge_counts.R:19:12:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/merge_edge_counts.R#L19) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- COUNT <- NULL # fix the CRAN note
           ^~~~
```
[R/merge_edge_counts.R:19:20:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/merge_edge_counts.R#L19) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- COUNT <- NULL # fix the CRAN note
                   ^~~~~
```
[R/plot_edge_assignment.R:28:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_edge_assignment.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- ABUNDANCE <- tool <- NULL # fix the CRAN note
  ^~~~~
```
[R/plot_edge_assignment.R:28:12:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_edge_assignment.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- ABUNDANCE <- tool <- NULL # fix the CRAN note
           ^~~~
```
[R/plot_edge_assignment.R:28:20:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_edge_assignment.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- ABUNDANCE <- tool <- NULL # fix the CRAN note
                   ^~~~~~~~~
```
[R/plot_edge_assignment.R:40:8:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_edge_assignment.R#L40) *style:* **Variable or function name should be snake_case.**
```r
  vals$ABUNDANCE <- vals$ABUNDANCE
       ^~~~~~~~~
```
[R/plot_edge_assignment.R:43:8:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_edge_assignment.R#L43) *style:* **Variable or function name should be snake_case.**
```r
  vals$TAXA <- factor(x = vals$TAXA, levels = vals$TAXA, ordered = T)
       ^~~~
```
[R/plot_edge_assignment.R:48:27:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_edge_assignment.R#L48) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
     p <- ggplot2::ggplot( data = vals, ggplot2::aes(y = TAXA, x = tool, fill = ABUNDANCE) ) +
                          ^
```
[R/plot_edge_assignment.R:48:91:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_edge_assignment.R#L48) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
     p <- ggplot2::ggplot( data = vals, ggplot2::aes(y = TAXA, x = tool, fill = ABUNDANCE) ) +
                                                                                ^
```
[R/plot_merged_assignment.R:38:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_merged_assignment.R#L38) *style:* **Lines should not be more than 100 characters.**
```r
#'                                        "HMP side-to-side", file.path(tempdir(), "assignment.pdf"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_merged_assignment.R:45:3:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_merged_assignment.R#L45) *style:* **Variable or function name should be snake_case.**
```r
  TAXA <- LEVEL <- SUM <- value <- variable <- NULL # fix the CRAN note
  ^~~~
```
[R/plot_merged_assignment.R:45:11:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_merged_assignment.R#L45) *style:* **Variable or function name should be snake_case.**
```r
  TAXA <- LEVEL <- SUM <- value <- variable <- NULL # fix the CRAN note
          ^~~~~
```
[R/plot_merged_assignment.R:45:20:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_merged_assignment.R#L45) *style:* **Variable or function name should be snake_case.**
```r
  TAXA <- LEVEL <- SUM <- value <- variable <- NULL # fix the CRAN note
                   ^~~
```
[R/plot_merged_assignment.R:105:6:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_merged_assignment.R#L105) *style:* **Variable or function name should be snake_case.**
```r
  df$TAXA <- factor(x = df$TAXA, levels = unique(df$TAXA), ordered = T)
     ^~~~
```
[R/plot_merged_assignment.R:114:71:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_merged_assignment.R#L114) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  column_index <- c(1, project_names_order + 1, as.numeric(dim(df)[2]) )
                                                                      ^
```
[R/plot_merged_assignment.R:116:39:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_merged_assignment.R#L116) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  df <- dplyr::select(df, column_index )
                                      ^
```
[R/plot_merged_assignment.R:125:24:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_merged_assignment.R#L125) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  p <- ggplot2::ggplot( data = melted_df, ggplot2::aes(y = TAXA, x = variable, fill = value) ) +
                       ^
```
[R/plot_merged_assignment.R:125:93:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_merged_assignment.R#L125) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  p <- ggplot2::ggplot( data = melted_df, ggplot2::aes(y = TAXA, x = variable, fill = value) ) +
                                                                                ^
```
[R/plot_merged_assignment.R:164:4:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_merged_assignment.R#L164) *style:* **Commented code should be removed.**
```r
  #p1 <- suppressWarnings(gridExtra::arrangeGrob(p, top = title.grob))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_merged_assignment.R:171:4:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_merged_assignment.R#L171) *style:* **Commented code should be removed.**
```r
  #suppressWarnings(grid::grid.draw(p1))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_merged_assignment.R:180:4:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/R/plot_merged_assignment.R#L180) *style:* **Commented code should be removed.**
```r
  #suppressWarnings(grid::grid.draw(p1))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_load_bwa_assignment.R:4:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L4) *style:* **Lines should not be more than 100 characters.**
```r
dat <- data.frame(load_edge_assignment("../test_data/SSputum-no-RAB/bwa/allReads-bwa.list.txt", type = 'bwa'))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_load_bwa_assignment.R:7:13:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L7) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[1], equals(558) )
            ^
```
[tests/testthat/test_load_bwa_assignment.R:7:38:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L7) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[1], equals(558) )
                                     ^
```
[tests/testthat/test_load_bwa_assignment.R:10:13:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L10) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[2], equals(4) )
            ^
```
[tests/testthat/test_load_bwa_assignment.R:10:36:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L10) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[2], equals(4) )
                                   ^
```
[tests/testthat/test_load_bwa_assignment.R:13:35:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L13) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                  ^
```
[tests/testthat/test_load_bwa_assignment.R:13:76:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L13) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                           ^
```
[tests/testthat/test_load_bwa_assignment.R:13:78:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L13) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                             ^
```
[tests/testthat/test_load_bwa_assignment.R:18:31:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
family_table <- dplyr::filter( dat, LEVEL == "species")
                              ^
```
[tests/testthat/test_load_bwa_assignment.R:21:26:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
ent_row <- dplyr::filter( family_table, TAXA == "Moraxella catarrhalis")
                         ^
```
[tests/testthat/test_load_bwa_assignment.R:36:40:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                       ^
```
[tests/testthat/test_load_bwa_assignment.R:36:81:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^
```
[tests/testthat/test_load_bwa_assignment.R:36:83:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^
```
[tests/testthat/test_load_bwa_assignment.R:37:40:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(dim(empty_df)[1], equals(0) )
                                       ^
```
[tests/testthat/test_load_bwa_assignment.R:43:40:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L43) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                       ^
```
[tests/testthat/test_load_bwa_assignment.R:43:81:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L43) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^
```
[tests/testthat/test_load_bwa_assignment.R:43:83:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L43) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^
```
[tests/testthat/test_load_bwa_assignment.R:44:40:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_bwa_assignment.R#L44) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(dim(empty_df)[1], equals(0) )
                                       ^
```
[tests/testthat/test_load_diamond_assignment.R:8:13:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_diamond_assignment.R#L8) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[1], equals(234) )
            ^
```
[tests/testthat/test_load_diamond_assignment.R:8:38:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_diamond_assignment.R#L8) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[1], equals(234) )
                                     ^
```
[tests/testthat/test_load_diamond_assignment.R:11:13:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_diamond_assignment.R#L11) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[2], equals(4) )
            ^
```
[tests/testthat/test_load_diamond_assignment.R:11:36:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_diamond_assignment.R#L11) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[2], equals(4) )
                                   ^
```
[tests/testthat/test_load_diamond_assignment.R:14:35:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_diamond_assignment.R#L14) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                  ^
```
[tests/testthat/test_load_diamond_assignment.R:14:76:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_diamond_assignment.R#L14) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                           ^
```
[tests/testthat/test_load_diamond_assignment.R:14:78:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_diamond_assignment.R#L14) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                             ^
```
[tests/testthat/test_load_diamond_assignment.R:19:31:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_diamond_assignment.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
family_table <- dplyr::filter( dat, LEVEL == "family")
                              ^
```
[tests/testthat/test_load_diamond_assignment.R:23:26:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_diamond_assignment.R#L23) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
ent_row <- dplyr::filter( family_table, TAXA == "Enterobacteriaceae")
                         ^
```
[tests/testthat/test_load_diamond_assignment.R:32:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_diamond_assignment.R#L32) *style:* **Lines should not be more than 100 characters.**
```r
expect_that(load_edge_assignment("../test_data/nonexistentfile.txt", type = 'diamond'), throws_error())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_load_diamond_assignment.R:38:40:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_diamond_assignment.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                       ^
```
[tests/testthat/test_load_diamond_assignment.R:38:81:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_diamond_assignment.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^
```
[tests/testthat/test_load_diamond_assignment.R:38:83:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_diamond_assignment.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^
```
[tests/testthat/test_load_diamond_assignment.R:39:40:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_diamond_assignment.R#L39) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(dim(empty_df)[1], equals(0) )
                                       ^
```
[tests/testthat/test_load_diamond_assignments.R:21:1:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_diamond_assignments.R#L21) *style:* **Lines should not be more than 100 characters.**
```r
expect_that(load_edge_assignments("../test_data/nonexistentfile.txt", type = 'diamond'), throws_error())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_load_gottcha_assignment.R:8:13:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_gottcha_assignment.R#L8) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[1], equals(65) )
            ^
```
[tests/testthat/test_load_gottcha_assignment.R:8:37:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_gottcha_assignment.R#L8) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[1], equals(65) )
                                    ^
```
[tests/testthat/test_load_gottcha_assignment.R:11:13:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_gottcha_assignment.R#L11) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[2], equals(4) )
            ^
```
[tests/testthat/test_load_gottcha_assignment.R:11:36:](https://github.com/seninp-bioinfo/MetaComp/blob/47d7f8536b89d8a465781b6a661c27b9633f1851/tests/testthat/test_load_gottcha_assignment.R#L11) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[2], equals(4) )


You don't need this. Look at like 11.
Plus, you are leaving this promise chain hanging alone. So you lost control on what happens when.


ยากทำไหดีทุกทุกยาง


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Created multidev environment [ci-30](https://dashboard.pantheon.io/sites/87c029d1-419a-4431-86a2-376625d9be3f#ci-30) for den-pantheon-ci-project.


🔥 [Jenkins job](http://xamarin-jenkins.guest.corp.microsoft.com:8080/job/macios/job/xcode10/20/display/redirect) (on internal Jenkins) failed in stage 'Test run' 🔥 : hudson.AbortException: script returned exit code 2

✅ [Build succeeded](http://xamarin-jenkins.guest.corp.microsoft.com:8080/job/macios/job/xcode10/20//console)
✅ [API Diff (from stable)](http://xamarin-storage/jenkins/xamarin-macios/xcode10/345ccdec9c118abb66209be00018a1288bf2e7eb/20/jenkins-results/api-diff/index.html)
✅ [API Diff (from PR only)](http://xamarin-storage/jenkins/xamarin-macios/xcode10/345ccdec9c118abb66209be00018a1288bf2e7eb/20/jenkins-results/apicomparison/index.html) (please review changes)
✅ [Generator Diff](http://xamarin-storage/jenkins/xamarin-macios/xcode10/345ccdec9c118abb66209be00018a1288bf2e7eb/20/jenkins-results/generator-diff/index.html) (only version changes)
🔥 [Test run failed](http://xamarin-storage/jenkins/xamarin-macios/xcode10/345ccdec9c118abb66209be00018a1288bf2e7eb/20/jenkins-results/tests/index.html) 🔥

# Test results

1 tests failed, 160 tests passed.

## Failed tests

 * System/iOS Unified 64-bits - simulator/Debug: Failed


read this. https://review.lineageos.org/#/c/LineageOS/android_device_htc_msm8974-common/+/205256/


хотя конечно последний варинат несколько путанныый получается... надо тогда как-то правильно переименовать методы... типа:
```ruby
  train = find_train(choose_train_index)
```
или как-то еще... ну или остановиться на предыдущем варианте ))


`.then(function(txObj) {`. Take this opportunity to confirm the event.


Avoid using the `deployed` instance because that creates a dependency from one `it` to the next.
Instead, use a `beforeEach` to create a new instance.
Testing the deployed instance is a valid proposition, but only in the context of asserting it was deployed according to specs.


Convert `.toString(10)` as a matter of fact and you will avoid painful debugging sessions. Javascript damages numbers.


Kiva saada Kitupiikki myös maceille.

Olen siirtämässä Kitupiikin Windows-käännökset Linuxissa ristiinkäännettäväksi (tätä on kokeilu mxe-haarassa), jolloin popplerin include saa myös Windowsissa muodon `#include <poppler/qt/poppler-qt5.h>`.
Toimisikohan tämä muoto myös macOSissa, jos .pro-tiedostoon lisäisi
`INCLUDEPATH +=  /usr/local/opt/poppler/include`

(Muuten, myös mxe vaati tuon std::roundin muuttamisen qRound:iksi)


Have you confirmed that this test runs equally well on Ganache and on Geth?


Not needed if keymaster is provided as blob. This helps only if you build it from source.


Can be useful for example when we are observing multiple agents, in turn, interacting with the environment


I remembered this flags removed on los15.1 but still check again.


thanks, will merge


thanks will merge. I enabled globe mode default but good to go with an option.


I'm getting this when I try to run it: `Uncaught TypeError: Cannot set property 'Your' of null
    at Object.save (contactCollection.js:33)
    at HTMLButtonElement.contactForm (contactForm.js:16)`


Wrong formula...
Use String color = pi.getRed(pixel)*8 + ", " + pi.getGreen(pixel)*4 + ", " + pi.getBlue(pixel)*8;


This is a bit of an odd ordering when reading the code. I suggest moving the class definition to L87 with assigning to the prototype following immediately after.


I suggest moving the class definition to above L119.


"instantiation" applies to classes. I do not believe that `reorderArguments` is a class. I would change this benchmark namespace to avoid confusion.


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-31-den-pantheon-ci-project.pantheonsite.io/)

Created multidev environment [ci-31](https://dashboard.pantheon.io/sites/87c029d1-419a-4431-86a2-376625d9be3f#ci-31) for den-pantheon-ci-project.


Modulo is a relatively expensive operation and you are repeating two different modulo operations twice.


158368465-Improve-error-#6375 (lgu1234) - i386-Windows-7-VisualStudio-14: OK (2929 of 2929 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png)


cache_allocator.cpp and .h should ideally by hexagon_cache_allocator or some such target specific name because cache_allocator hints at a generic interface.


Created multidev environment [dgreat#pr-dblock](https://dashboard.pantheon.io/sites/41cad7fe-472d-43a9-a470-d391b9622376#pr-dblock).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-dblock-dgreat.pantheonsite.io/)


The following doc(s) have been deployed to the [dnsuncolla](https://dnsuncolla-static-docs.pantheonsite.io/docs) Multidev environment:
- [/docs/dns](https://dnsuncolla-static-docs.pantheonsite.io/docs/dns)


I am not ensure sure you need to do all this. Just swap the same two indices back and forth over the course of the benchmark. This would involve, at most, one modulo operation, if you just repeatedly swapped, say, indices `2` and `1` back and forth.