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prepearing a new release
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seninp committed Jun 18, 2018
1 parent 35f0d2a commit 47d7f85
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Package: MetaComp
Version: 1.1.1
Version: 1.1.2
Title: EDGE Taxonomy Assignments Visualization
Description: Implements routines for metagenome sample taxonomy assignments collection,
aggregation, and visualization. Accepts the EDGE-formatted output from GOTTCHA/GOTTCHA2,
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4 changes: 4 additions & 0 deletions NEWS.md
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## MetaComp 1.1.2

Maintenance release. Cleaning CRAN warnings due to unspecified stringr:: imports.

## MetaComp 1.1.1

Updated package with parser for DIAMOND and PANGIA alignments.
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13 changes: 3 additions & 10 deletions cran-comments.md
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## This is resubmission
## This is new submission

Submission comments were:
* Please use tempdir() in your examples if you want to same something (like the PDF heatmap-like plots).
* We also see: New maintainer: Pavel Senin <[email protected]> Old maintainer(s): Pavel Senin <[email protected]>
Please confirm via email from the old email address.

Added examples to fix (1), and (2) I no longer have access to that email as I am no longer employed by LANL --
which shouldn't matter cause I'm the same prson, LoL.
Clearing CRAN warnings due to unspecified stringr:: imports in few tests.

## Changes

Added new functions for parsing, merging, and plotting of DIAMOND and PANGIA EDGE-like output.
Redesigned API to make to make it simple and to the point.
Used base package functionality intead of stringr:: functions.

## Test environments

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inst/site/create_table.R:19:58: style: Do not place spaces around code in parentheses or square brackets.

​  dp_selection = filter(data_df, V3 == sample(indexes, 1) ),
                                                         ^

inst/site/create_table.R:21:62: style: Do not place spaces around code in parentheses or square brackets.

​    "select * from taxonomy where V3 == ", sample(indexes, 1) )), times = 100
                                                             ^

inst/site/merge_and_plot_bwa_assignments.R:12:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_and_plot_bwa_assignments.R:13:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

inst/site/merge_and_plot_bwa_assignments.R:14:1: style: Variable or function name should be snake_case.

​taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~

inst/site/merge_and_plot_bwa_assignments.R:15:1: style: Variable or function name should be snake_case.

​plotTitleArg <- args[4]
^~~~~~~~~~~~

inst/site/merge_and_plot_bwa_assignments.R:16:1: style: Variable or function name should be snake_case.

​plotFileArg <- args[5]
^~~~~~~~~~~

inst/site/merge_and_plot_bwa_assignments.R:21:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- args[6]
  ^~~~~~~~~~~

inst/site/merge_and_plot_bwa_assignments.R:22:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_bwa_assignments.R:24:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- 60
  ^~~~~~~~~~~

inst/site/merge_and_plot_bwa_assignments.R:25:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:12:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:13:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:14:1: style: Variable or function name should be snake_case.

​taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:15:1: style: Variable or function name should be snake_case.

​plotTitleArg <- args[4]
^~~~~~~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:16:1: style: Variable or function name should be snake_case.

​plotFileArg <- args[5]
^~~~~~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:21:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- args[6]
  ^~~~~~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:22:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:24:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- 60
  ^~~~~~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:25:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:12:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_and_plot_edge_assignments.R:13:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:14:1: style: Variable or function name should be snake_case.

​taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:15:1: style: Variable or function name should be snake_case.

​plotTitleArg <- args[4]
^~~~~~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:16:1: style: Variable or function name should be snake_case.

​plotFileArg <- args[5]
^~~~~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:17:1: style: Variable or function name should be snake_case.

​assignerType <- args[6]
^~~~~~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:22:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- args[7]
  ^~~~~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:23:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- args[8]
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:25:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- 60
  ^~~~~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:26:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:12:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:13:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:14:1: style: Variable or function name should be snake_case.

​taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:15:1: style: Variable or function name should be snake_case.

​plotTitleArg <- args[4]
^~~~~~~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:16:1: style: Variable or function name should be snake_case.

​plotFileArg <- args[5]
^~~~~~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:21:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- args[6]
  ^~~~~~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:22:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:24:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- 60
  ^~~~~~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:25:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:12:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:13:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:14:1: style: Variable or function name should be snake_case.

​taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:15:1: style: Variable or function name should be snake_case.

​plotTitleArg <- args[4]
^~~~~~~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:16:1: style: Variable or function name should be snake_case.

​plotFileArg <- args[5]
^~~~~~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:21:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- args[6]
  ^~~~~~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:22:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:24:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- 60
  ^~~~~~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:25:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:12:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:13:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:14:1: style: Variable or function name should be snake_case.

​taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:15:1: style: Variable or function name should be snake_case.

​plotTitleArg <- args[4]
^~~~~~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:16:1: style: Variable or function name should be snake_case.

​plotFileArg <- args[5]
^~~~~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:21:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- args[6]
  ^~~~~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:22:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:24:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- 60
  ^~~~~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:25:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:29:69: style: Put spaces around all infix operators.

​merged <- merge_edge_assignments(load_edge_assignments(srcFile, type= "kraken"))
                                                                   ~^

inst/site/merge_and_plot_metaphlan_assignments.R:12:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_and_plot_metaphlan_assignments.R:13:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

inst/site/merge_and_plot_metaphlan_assignments.R:14:1: style: Variable or function name should be snake_case.

​taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~

inst/site/merge_and_plot_metaphlan_assignments.R:15:1: style: Variable or function name should be snake_case.

​plotTitleArg <- args[4]
^~~~~~~~~~~~

inst/site/merge_and_plot_metaphlan_assignments.R:16:1: style: Variable or function name should be snake_case.

​plotFileArg <- args[5]
^~~~~~~~~~~

inst/site/merge_and_plot_metaphlan_assignments.R:21:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- args[6]
  ^~~~~~~~~~~

inst/site/merge_and_plot_metaphlan_assignments.R:22:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_metaphlan_assignments.R:24:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- 60
  ^~~~~~~~~~~

inst/site/merge_and_plot_metaphlan_assignments.R:25:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:12:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:13:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:14:1: style: Variable or function name should be snake_case.

​taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:15:1: style: Variable or function name should be snake_case.

​plotTitleArg <- args[4]
^~~~~~~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:16:1: style: Variable or function name should be snake_case.

​plotFileArg <- args[5]
^~~~~~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:21:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- args[6]
  ^~~~~~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:22:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:24:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- 60
  ^~~~~~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:25:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~

inst/site/merge_gottcha_assignments.R:11:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_gottcha_assignments.R:14:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

R/load_edge_assignment.R:33:13: style: Variable or function name should be snake_case.

​  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
            ^~~~

R/load_edge_assignment.R:33:21: style: Variable or function name should be snake_case.

​  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
                    ^~~~~

R/load_edge_assignment.R:33:30: style: Variable or function name should be snake_case.

​  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
                             ^~~~~

R/load_edge_assignment.R:33:30: warning: local variable ‘COUNT’ assigned but may not be used

​  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
                             ^~~~~

R/load_edge_assignment.R:33:39: style: Variable or function name should be snake_case.

​  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
                                      ^~~~~~~~~

R/load_edge_assignment.R:34:3: style: Variable or function name should be snake_case.

​  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
  ^~~~~~

R/load_edge_assignment.R:34:13: style: Variable or function name should be snake_case.

​  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
            ^~~~

R/load_edge_assignment.R:34:21: style: Variable or function name should be snake_case.

​  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
                    ^~~~~~

R/load_edge_assignment.R:34:31: style: Variable or function name should be snake_case.

​  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
                              ^~~~~~~

R/load_edge_assignment.R:34:42: style: Variable or function name should be snake_case.

​  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
                                         ^~~~~~~~~~

R/load_edge_assignment.R:35:3: style: Variable or function name should be snake_case.

​  REL_ABUNDANCE <- NORM_COV <- READ_COUNT_RNR <- ASSIGNED <- NULL
  ^~~~~~~~~~~~~

R/load_edge_assignment.R:35:20: style: Variable or function name should be snake_case.

​  REL_ABUNDANCE <- NORM_COV <- READ_COUNT_RNR <- ASSIGNED <- NULL
                   ^~~~~~~~

R/load_edge_assignment.R:35:32: style: Variable or function name should be snake_case.

​  REL_ABUNDANCE <- NORM_COV <- READ_COUNT_RNR <- ASSIGNED <- NULL
                               ^~~~~~~~~~~~~~

R/load_edge_assignment.R:35:50: style: Variable or function name should be snake_case.

​  REL_ABUNDANCE <- NORM_COV <- READ_COUNT_RNR <- ASSIGNED <- NULL
                                                 ^~~~~~~~

R/load_edge_assignment.R:38:7: style: Do not place spaces around code in parentheses or square brackets.

​  if ( !file.exists(filepath) ) {
      ^

R/load_edge_assignment.R:38:30: style: Do not place spaces around code in parentheses or square brackets.

​  if ( !file.exists(filepath) ) {
                             ^

R/load_edge_assignment.R:44:7: style: Do not place spaces around code in parentheses or square brackets.

​  if ( 0 == file_info$size ) {
      ^

R/load_edge_assignment.R:44:27: style: Do not place spaces around code in parentheses or square brackets.

​  if ( 0 == file_info$size ) {
                          ^

R/load_edge_assignment.R:45:16: style: Do not place spaces around code in parentheses or square brackets.

​    data.frame( LEVEL = character(), TAXA = character(), COUNT = integer(), ABUNDANCE = double())
               ^

R/load_edge_assignment.R:54:9: style: Do not place spaces around code in parentheses or square brackets.

​    if ( 'bwa' == type ){
        ^

R/load_edge_assignment.R:54:23: style: Do not place spaces around code in parentheses or square brackets.

​    if ( 'bwa' == type ){
                      ^

R/load_edge_assignment.R:56:32: style: Do not place spaces around code in parentheses or square brackets.

​      if (0 == length(df$LEVEL) ) {
                               ^

R/load_edge_assignment.R:57:1: style: Lines should not be more than 100 characters.

​        data.frame( LEVEL = character(), TAXA = character(), COUNT = integer(), ABUNDANCE = double())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/load_edge_assignment.R:57:20: style: Do not place spaces around code in parentheses or square brackets.

​        data.frame( LEVEL = character(), TAXA = character(), COUNT = integer(), ABUNDANCE = double())
                   ^

R/load_edge_assignment.R:61:56: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​        levels <- plyr::ddply(df, "LEVEL", function(x) { sum(x$ROLLUP) })
                                                       ^

R/load_edge_assignment.R:64:12: style: Variable or function name should be snake_case.

​        df$ABUNDANCE <- df$ROLLUP / df$SUM * 100
           ^~~~~~~~~

R/load_edge_assignment.R:67:23: style: Do not place spaces around code in parentheses or square brackets.

​        as.data.frame( dplyr::select(df, LEVEL, TAXA, COUNT = ROLLUP, ABUNDANCE))
                      ^

R/load_edge_assignment.R:69:16: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'diamond' == type ){
               ^

R/load_edge_assignment.R:69:34: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'diamond' == type ){
                                 ^

R/load_edge_assignment.R:70:21: style: Do not place spaces around code in parentheses or square brackets.

​      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = ASSIGN, ABUNDANCE = REL_ABU))
                    ^

R/load_edge_assignment.R:71:16: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'gottcha2' == type ){
               ^

R/load_edge_assignment.R:71:35: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'gottcha2' == type ){
                                  ^

R/load_edge_assignment.R:72:1: style: Lines should not be more than 100 characters.

​      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = READ_COUNT, ABUNDANCE = REL_ABUNDANCE))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/load_edge_assignment.R:72:21: style: Do not place spaces around code in parentheses or square brackets.

​      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = READ_COUNT, ABUNDANCE = REL_ABUNDANCE))
                    ^

R/load_edge_assignment.R:73:16: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'gottcha' == type ){
               ^

R/load_edge_assignment.R:73:34: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'gottcha' == type ){
                                 ^

R/load_edge_assignment.R:74:21: style: Do not place spaces around code in parentheses or square brackets.

​      as.data.frame( dplyr::select(df, LEVEL, TAXA, COUNT = READ_COUNT, ABUNDANCE = NORM_COV))
                    ^

R/load_edge_assignment.R:75:16: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'kraken' == type ){
               ^

R/load_edge_assignment.R:75:33: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'kraken' == type ){
                                ^

R/load_edge_assignment.R:78:10: style: Variable or function name should be snake_case.

​      df$ABUNDANCE <- df$ROLLUP / max_rollup * 100
         ^~~~~~~~~

R/load_edge_assignment.R:79:21: style: Do not place spaces around code in parentheses or square brackets.

​      as.data.frame( dplyr::select(df, LEVEL, TAXA, COUNT = ROLLUP, ABUNDANCE))
                    ^

R/load_edge_assignment.R:80:16: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'metaphlan' == type ){
               ^

R/load_edge_assignment.R:80:36: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'metaphlan' == type ){
                                   ^

R/load_edge_assignment.R:81:21: style: Do not place spaces around code in parentheses or square brackets.

​      as.data.frame( dplyr::select(df, LEVEL, TAXA, COUNT = ASSIGNED, ABUNDANCE = ROLLUP))
                    ^

R/load_edge_assignment.R:82:16: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'pangia' == type ){
               ^

R/load_edge_assignment.R:82:33: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'pangia' == type ){
                                ^

R/load_edge_assignment.R:83:10: style: Variable or function name should be snake_case.

​      df$READ_COUNT_RNR = as.integer(df$READ_COUNT_RNR)
         ^~~~~~~~~~~~~~

R/load_edge_assignment.R:83:25: style: Use <-, not =, for assignment.

​      df$READ_COUNT_RNR = as.integer(df$READ_COUNT_RNR)
                        ^

R/load_edge_assignment.R:84:1: style: Lines should not be more than 100 characters.

​      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = READ_COUNT_RNR, ABUNDANCE = REL_ABUNDANCE))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/load_edge_assignment.R:84:21: style: Do not place spaces around code in parentheses or square brackets.

​      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = READ_COUNT_RNR, ABUNDANCE = REL_ABUNDANCE))
                    ^

R/load_edge_assignment.R:86:18: style: Do not place spaces around code in parentheses or square brackets.

​      data.frame( LEVEL = character(), TAXA = character(), COUNT = integer(), ABUNDANCE = double())
                 ^

R/load_edge_assignment.R:90:1: style: Trailing blank lines are superfluous.

​
^

R/load_edge_assignment.R:91:1: style: Trailing blank lines are superfluous.

​
^

R/load_edge_assignments.R:35:7: style: Do not place spaces around code in parentheses or square brackets.

​  if ( !file.exists(filepath) ) {
      ^

R/load_edge_assignments.R:35:30: style: Do not place spaces around code in parentheses or square brackets.

​  if ( !file.exists(filepath) ) {
                             ^

R/load_edge_assignments.R:44:7: style: Use <-, not =, for assignment.

​  res = list()
      ^

R/load_edge_assignments.R:46:16: style: Use <-, not =, for assignment.

​    cur_asgnmt = load_edge_assignment(df[prj_name == df$V1, ]$V2, type)
               ^

R/load_edge_assignments.R:46:18: warning: no visible global function definition for ‘load_edge_assignment’

​    cur_asgnmt = load_edge_assignment(df[prj_name == df$V1, ]$V2, type)
                 ^~~~~~~~~~~~~~~~~~~~

R/load_edge_assignments.R:47:9: style: Use <-, not =, for assignment.

​    res = c(res, list(cur_asgnmt))
        ^

R/merge_edge_assignments.R:32:3: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- ABUNDANCE <- NULL # fix the CRAN note
  ^~~~~

R/merge_edge_assignments.R:32:12: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- ABUNDANCE <- NULL # fix the CRAN note
           ^~~~

R/merge_edge_assignments.R:32:20: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- ABUNDANCE <- NULL # fix the CRAN note
                   ^~~~~~~~~

R/merge_edge_counts.R:19:3: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- COUNT <- NULL # fix the CRAN note
  ^~~~~

R/merge_edge_counts.R:19:12: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- COUNT <- NULL # fix the CRAN note
           ^~~~

R/merge_edge_counts.R:19:20: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- COUNT <- NULL # fix the CRAN note
                   ^~~~~

R/plot_edge_assignment.R:28:3: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- ABUNDANCE <- tool <- NULL # fix the CRAN note
  ^~~~~

R/plot_edge_assignment.R:28:12: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- ABUNDANCE <- tool <- NULL # fix the CRAN note
           ^~~~

R/plot_edge_assignment.R:28:20: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- ABUNDANCE <- tool <- NULL # fix the CRAN note
                   ^~~~~~~~~

R/plot_edge_assignment.R:40:8: style: Variable or function name should be snake_case.

​  vals$ABUNDANCE <- vals$ABUNDANCE
       ^~~~~~~~~

R/plot_edge_assignment.R:43:8: style: Variable or function name should be snake_case.

​  vals$TAXA <- factor(x = vals$TAXA, levels = vals$TAXA, ordered = T)
       ^~~~

R/plot_edge_assignment.R:48:27: style: Do not place spaces around code in parentheses or square brackets.

​     p <- ggplot2::ggplot( data = vals, ggplot2::aes(y = TAXA, x = tool, fill = ABUNDANCE) ) +
                          ^

R/plot_edge_assignment.R:48:91: style: Do not place spaces around code in parentheses or square brackets.

​     p <- ggplot2::ggplot( data = vals, ggplot2::aes(y = TAXA, x = tool, fill = ABUNDANCE) ) +
                                                                                          ^

R/plot_merged_assignment.R:38:1: style: Lines should not be more than 100 characters.

​#'                                        "HMP side-to-side", file.path(tempdir(), "assignment.pdf"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plot_merged_assignment.R:45:3: style: Variable or function name should be snake_case.

​  TAXA <- LEVEL <- SUM <- value <- variable <- NULL # fix the CRAN note
  ^~~~

R/plot_merged_assignment.R:45:11: style: Variable or function name should be snake_case.

​  TAXA <- LEVEL <- SUM <- value <- variable <- NULL # fix the CRAN note
          ^~~~~

R/plot_merged_assignment.R:45:20: style: Variable or function name should be snake_case.

​  TAXA <- LEVEL <- SUM <- value <- variable <- NULL # fix the CRAN note
                   ^~~

R/plot_merged_assignment.R:105:6: style: Variable or function name should be snake_case.

​  df$TAXA <- factor(x = df$TAXA, levels = unique(df$TAXA), ordered = T)
     ^~~~

R/plot_merged_assignment.R:114:71: style: Do not place spaces around code in parentheses or square brackets.

​  column_index <- c(1, project_names_order + 1, as.numeric(dim(df)[2]) )
                                                                      ^

R/plot_merged_assignment.R:116:39: style: Do not place spaces around code in parentheses or square brackets.

​  df <- dplyr::select(df, column_index )
                                      ^

R/plot_merged_assignment.R:125:24: style: Do not place spaces around code in parentheses or square brackets.

​  p <- ggplot2::ggplot( data = melted_df, ggplot2::aes(y = TAXA, x = variable, fill = value) ) +
                       ^

R/plot_merged_assignment.R:125:93: style: Do not place spaces around code in parentheses or square brackets.

​  p <- ggplot2::ggplot( data = melted_df, ggplot2::aes(y = TAXA, x = variable, fill = value) ) +
                                                                                            ^

R/plot_merged_assignment.R:164:4: style: Commented code should be removed.

​  #p1 <- suppressWarnings(gridExtra::arrangeGrob(p, top = title.grob))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plot_merged_assignment.R:171:4: style: Commented code should be removed.

​  #suppressWarnings(grid::grid.draw(p1))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plot_merged_assignment.R:180:4: style: Commented code should be removed.

​  #suppressWarnings(grid::grid.draw(p1))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test_load_bwa_assignment.R:4:1: style: Lines should not be more than 100 characters.

​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: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[1], equals(558) )
            ^

tests/testthat/test_load_bwa_assignment.R:7:38: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[1], equals(558) )
                                     ^

tests/testthat/test_load_bwa_assignment.R:10:13: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[2], equals(4) )
            ^

tests/testthat/test_load_bwa_assignment.R:10:36: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[2], equals(4) )
                                   ^

tests/testthat/test_load_bwa_assignment.R:13:35: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                  ^

tests/testthat/test_load_bwa_assignment.R:13:76: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                           ^

tests/testthat/test_load_bwa_assignment.R:13:78: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                             ^

tests/testthat/test_load_bwa_assignment.R:18:31: style: Do not place spaces around code in parentheses or square brackets.

​family_table <- dplyr::filter( dat, LEVEL == "species")
                              ^

tests/testthat/test_load_bwa_assignment.R:21:26: style: Do not place spaces around code in parentheses or square brackets.

​ent_row <- dplyr::filter( family_table, TAXA == "Moraxella catarrhalis")
                         ^

tests/testthat/test_load_bwa_assignment.R:36:40: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                       ^

tests/testthat/test_load_bwa_assignment.R:36:81: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^

tests/testthat/test_load_bwa_assignment.R:36:83: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                  ^

tests/testthat/test_load_bwa_assignment.R:37:40: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(dim(empty_df)[1], equals(0) )
                                       ^

tests/testthat/test_load_bwa_assignment.R:43:40: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                       ^

tests/testthat/test_load_bwa_assignment.R:43:81: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^

tests/testthat/test_load_bwa_assignment.R:43:83: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                  ^

tests/testthat/test_load_bwa_assignment.R:44:40: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(dim(empty_df)[1], equals(0) )
                                       ^

tests/testthat/test_load_diamond_assignment.R:8:13: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[1], equals(234) )
            ^

tests/testthat/test_load_diamond_assignment.R:8:38: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[1], equals(234) )
                                     ^

tests/testthat/test_load_diamond_assignment.R:11:13: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[2], equals(4) )
            ^

tests/testthat/test_load_diamond_assignment.R:11:36: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[2], equals(4) )
                                   ^

tests/testthat/test_load_diamond_assignment.R:14:35: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                  ^

tests/testthat/test_load_diamond_assignment.R:14:76: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                           ^

tests/testthat/test_load_diamond_assignment.R:14:78: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                             ^

tests/testthat/test_load_diamond_assignment.R:19:31: style: Do not place spaces around code in parentheses or square brackets.

​family_table <- dplyr::filter( dat, LEVEL == "family")
                              ^

tests/testthat/test_load_diamond_assignment.R:23:26: style: Do not place spaces around code in parentheses or square brackets.

​ent_row <- dplyr::filter( family_table, TAXA == "Enterobacteriaceae")
                         ^

tests/testthat/test_load_diamond_assignment.R:32:1: style: Lines should not be more than 100 characters.

​expect_that(load_edge_assignment("../test_data/nonexistentfile.txt", type = 'diamond'), throws_error())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test_load_diamond_assignment.R:38:40: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                       ^

tests/testthat/test_load_diamond_assignment.R:38:81: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^

tests/testthat/test_load_diamond_assignment.R:38:83: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                  ^

tests/testthat/test_load_diamond_assignment.R:39:40: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(dim(empty_df)[1], equals(0) )
                                       ^

tests/testthat/test_load_diamond_assignments.R:21:1: style: Lines should not be more than 100 characters.

​expect_that(load_edge_assignments("../test_data/nonexistentfile.txt", type = 'diamond'), throws_error())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test_load_gottcha_assignment.R:8:13: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[1], equals(65) )
            ^

tests/testthat/test_load_gottcha_assignment.R:8:37: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[1], equals(65) )
                                    ^

tests/testthat/test_load_gottcha_assignment.R:11:13: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[2], equals(4) )
            ^

tests/testthat/test_load_gottcha_assignment.R:11:36: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[2], equals(4) )

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inst/site/create_table.R:19:58: style: Do not place spaces around code in parentheses or square brackets.

​  dp_selection = filter(data_df, V3 == sample(indexes, 1) ),
                                                         ^

inst/site/create_table.R:21:62: style: Do not place spaces around code in parentheses or square brackets.

​    "select * from taxonomy where V3 == ", sample(indexes, 1) )), times = 100
                                                             ^

inst/site/merge_and_plot_bwa_assignments.R:12:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_and_plot_bwa_assignments.R:13:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

inst/site/merge_and_plot_bwa_assignments.R:14:1: style: Variable or function name should be snake_case.

​taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~

inst/site/merge_and_plot_bwa_assignments.R:15:1: style: Variable or function name should be snake_case.

​plotTitleArg <- args[4]
^~~~~~~~~~~~

inst/site/merge_and_plot_bwa_assignments.R:16:1: style: Variable or function name should be snake_case.

​plotFileArg <- args[5]
^~~~~~~~~~~

inst/site/merge_and_plot_bwa_assignments.R:21:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- args[6]
  ^~~~~~~~~~~

inst/site/merge_and_plot_bwa_assignments.R:22:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_bwa_assignments.R:24:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- 60
  ^~~~~~~~~~~

inst/site/merge_and_plot_bwa_assignments.R:25:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:12:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:13:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:14:1: style: Variable or function name should be snake_case.

​taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:15:1: style: Variable or function name should be snake_case.

​plotTitleArg <- args[4]
^~~~~~~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:16:1: style: Variable or function name should be snake_case.

​plotFileArg <- args[5]
^~~~~~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:21:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- args[6]
  ^~~~~~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:22:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:24:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- 60
  ^~~~~~~~~~~

inst/site/merge_and_plot_diamond_assignments.R:25:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:12:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_and_plot_edge_assignments.R:13:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:14:1: style: Variable or function name should be snake_case.

​taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:15:1: style: Variable or function name should be snake_case.

​plotTitleArg <- args[4]
^~~~~~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:16:1: style: Variable or function name should be snake_case.

​plotFileArg <- args[5]
^~~~~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:17:1: style: Variable or function name should be snake_case.

​assignerType <- args[6]
^~~~~~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:22:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- args[7]
  ^~~~~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:23:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- args[8]
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:25:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- 60
  ^~~~~~~~~~~

inst/site/merge_and_plot_edge_assignments.R:26:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:12:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:13:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:14:1: style: Variable or function name should be snake_case.

​taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:15:1: style: Variable or function name should be snake_case.

​plotTitleArg <- args[4]
^~~~~~~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:16:1: style: Variable or function name should be snake_case.

​plotFileArg <- args[5]
^~~~~~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:21:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- args[6]
  ^~~~~~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:22:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:24:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- 60
  ^~~~~~~~~~~

inst/site/merge_and_plot_gottcha_assignments.R:25:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:12:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:13:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:14:1: style: Variable or function name should be snake_case.

​taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:15:1: style: Variable or function name should be snake_case.

​plotTitleArg <- args[4]
^~~~~~~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:16:1: style: Variable or function name should be snake_case.

​plotFileArg <- args[5]
^~~~~~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:21:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- args[6]
  ^~~~~~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:22:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:24:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- 60
  ^~~~~~~~~~~

inst/site/merge_and_plot_gottcha2_assignments.R:25:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:12:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:13:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:14:1: style: Variable or function name should be snake_case.

​taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:15:1: style: Variable or function name should be snake_case.

​plotTitleArg <- args[4]
^~~~~~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:16:1: style: Variable or function name should be snake_case.

​plotFileArg <- args[5]
^~~~~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:21:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- args[6]
  ^~~~~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:22:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:24:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- 60
  ^~~~~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:25:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_kraken_assignments.R:29:69: style: Put spaces around all infix operators.

​merged <- merge_edge_assignments(load_edge_assignments(srcFile, type= "kraken"))
                                                                   ~^

inst/site/merge_and_plot_metaphlan_assignments.R:12:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_and_plot_metaphlan_assignments.R:13:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

inst/site/merge_and_plot_metaphlan_assignments.R:14:1: style: Variable or function name should be snake_case.

​taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~

inst/site/merge_and_plot_metaphlan_assignments.R:15:1: style: Variable or function name should be snake_case.

​plotTitleArg <- args[4]
^~~~~~~~~~~~

inst/site/merge_and_plot_metaphlan_assignments.R:16:1: style: Variable or function name should be snake_case.

​plotFileArg <- args[5]
^~~~~~~~~~~

inst/site/merge_and_plot_metaphlan_assignments.R:21:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- args[6]
  ^~~~~~~~~~~

inst/site/merge_and_plot_metaphlan_assignments.R:22:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_metaphlan_assignments.R:24:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- 60
  ^~~~~~~~~~~

inst/site/merge_and_plot_metaphlan_assignments.R:25:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:12:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:13:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:14:1: style: Variable or function name should be snake_case.

​taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:15:1: style: Variable or function name should be snake_case.

​plotTitleArg <- args[4]
^~~~~~~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:16:1: style: Variable or function name should be snake_case.

​plotFileArg <- args[5]
^~~~~~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:21:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- args[6]
  ^~~~~~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:22:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:24:3: style: Variable or function name should be snake_case.

​  rowLimitArg <- 60
  ^~~~~~~~~~~

inst/site/merge_and_plot_pangia_assignments.R:25:3: style: Variable or function name should be snake_case.

​  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~

inst/site/merge_gottcha_assignments.R:11:1: style: Variable or function name should be snake_case.

​srcFile <- args[1]
^~~~~~~

inst/site/merge_gottcha_assignments.R:14:1: style: Variable or function name should be snake_case.

​destFile <- args[2]
^~~~~~~~

R/load_edge_assignment.R:33:13: style: Variable or function name should be snake_case.

​  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
            ^~~~

R/load_edge_assignment.R:33:21: style: Variable or function name should be snake_case.

​  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
                    ^~~~~

R/load_edge_assignment.R:33:30: style: Variable or function name should be snake_case.

​  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
                             ^~~~~

R/load_edge_assignment.R:33:30: warning: local variable ‘COUNT’ assigned but may not be used

​  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
                             ^~~~~

R/load_edge_assignment.R:33:39: style: Variable or function name should be snake_case.

​  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
                                      ^~~~~~~~~

R/load_edge_assignment.R:34:3: style: Variable or function name should be snake_case.

​  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
  ^~~~~~

R/load_edge_assignment.R:34:13: style: Variable or function name should be snake_case.

​  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
            ^~~~

R/load_edge_assignment.R:34:21: style: Variable or function name should be snake_case.

​  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
                    ^~~~~~

R/load_edge_assignment.R:34:31: style: Variable or function name should be snake_case.

​  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
                              ^~~~~~~

R/load_edge_assignment.R:34:42: style: Variable or function name should be snake_case.

​  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
                                         ^~~~~~~~~~

R/load_edge_assignment.R:35:3: style: Variable or function name should be snake_case.

​  REL_ABUNDANCE <- NORM_COV <- READ_COUNT_RNR <- ASSIGNED <- NULL
  ^~~~~~~~~~~~~

R/load_edge_assignment.R:35:20: style: Variable or function name should be snake_case.

​  REL_ABUNDANCE <- NORM_COV <- READ_COUNT_RNR <- ASSIGNED <- NULL
                   ^~~~~~~~

R/load_edge_assignment.R:35:32: style: Variable or function name should be snake_case.

​  REL_ABUNDANCE <- NORM_COV <- READ_COUNT_RNR <- ASSIGNED <- NULL
                               ^~~~~~~~~~~~~~

R/load_edge_assignment.R:35:50: style: Variable or function name should be snake_case.

​  REL_ABUNDANCE <- NORM_COV <- READ_COUNT_RNR <- ASSIGNED <- NULL
                                                 ^~~~~~~~

R/load_edge_assignment.R:38:7: style: Do not place spaces around code in parentheses or square brackets.

​  if ( !file.exists(filepath) ) {
      ^

R/load_edge_assignment.R:38:30: style: Do not place spaces around code in parentheses or square brackets.

​  if ( !file.exists(filepath) ) {
                             ^

R/load_edge_assignment.R:44:7: style: Do not place spaces around code in parentheses or square brackets.

​  if ( 0 == file_info$size ) {
      ^

R/load_edge_assignment.R:44:27: style: Do not place spaces around code in parentheses or square brackets.

​  if ( 0 == file_info$size ) {
                          ^

R/load_edge_assignment.R:45:16: style: Do not place spaces around code in parentheses or square brackets.

​    data.frame( LEVEL = character(), TAXA = character(), COUNT = integer(), ABUNDANCE = double())
               ^

R/load_edge_assignment.R:54:9: style: Do not place spaces around code in parentheses or square brackets.

​    if ( 'bwa' == type ){
        ^

R/load_edge_assignment.R:54:23: style: Do not place spaces around code in parentheses or square brackets.

​    if ( 'bwa' == type ){
                      ^

R/load_edge_assignment.R:56:32: style: Do not place spaces around code in parentheses or square brackets.

​      if (0 == length(df$LEVEL) ) {
                               ^

R/load_edge_assignment.R:57:1: style: Lines should not be more than 100 characters.

​        data.frame( LEVEL = character(), TAXA = character(), COUNT = integer(), ABUNDANCE = double())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/load_edge_assignment.R:57:20: style: Do not place spaces around code in parentheses or square brackets.

​        data.frame( LEVEL = character(), TAXA = character(), COUNT = integer(), ABUNDANCE = double())
                   ^

R/load_edge_assignment.R:61:56: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​        levels <- plyr::ddply(df, "LEVEL", function(x) { sum(x$ROLLUP) })
                                                       ^

R/load_edge_assignment.R:64:12: style: Variable or function name should be snake_case.

​        df$ABUNDANCE <- df$ROLLUP / df$SUM * 100
           ^~~~~~~~~

R/load_edge_assignment.R:67:23: style: Do not place spaces around code in parentheses or square brackets.

​        as.data.frame( dplyr::select(df, LEVEL, TAXA, COUNT = ROLLUP, ABUNDANCE))
                      ^

R/load_edge_assignment.R:69:16: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'diamond' == type ){
               ^

R/load_edge_assignment.R:69:34: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'diamond' == type ){
                                 ^

R/load_edge_assignment.R:70:21: style: Do not place spaces around code in parentheses or square brackets.

​      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = ASSIGN, ABUNDANCE = REL_ABU))
                    ^

R/load_edge_assignment.R:71:16: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'gottcha2' == type ){
               ^

R/load_edge_assignment.R:71:35: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'gottcha2' == type ){
                                  ^

R/load_edge_assignment.R:72:1: style: Lines should not be more than 100 characters.

​      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = READ_COUNT, ABUNDANCE = REL_ABUNDANCE))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/load_edge_assignment.R:72:21: style: Do not place spaces around code in parentheses or square brackets.

​      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = READ_COUNT, ABUNDANCE = REL_ABUNDANCE))
                    ^

R/load_edge_assignment.R:73:16: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'gottcha' == type ){
               ^

R/load_edge_assignment.R:73:34: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'gottcha' == type ){
                                 ^

R/load_edge_assignment.R:74:21: style: Do not place spaces around code in parentheses or square brackets.

​      as.data.frame( dplyr::select(df, LEVEL, TAXA, COUNT = READ_COUNT, ABUNDANCE = NORM_COV))
                    ^

R/load_edge_assignment.R:75:16: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'kraken' == type ){
               ^

R/load_edge_assignment.R:75:33: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'kraken' == type ){
                                ^

R/load_edge_assignment.R:78:10: style: Variable or function name should be snake_case.

​      df$ABUNDANCE <- df$ROLLUP / max_rollup * 100
         ^~~~~~~~~

R/load_edge_assignment.R:79:21: style: Do not place spaces around code in parentheses or square brackets.

​      as.data.frame( dplyr::select(df, LEVEL, TAXA, COUNT = ROLLUP, ABUNDANCE))
                    ^

R/load_edge_assignment.R:80:16: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'metaphlan' == type ){
               ^

R/load_edge_assignment.R:80:36: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'metaphlan' == type ){
                                   ^

R/load_edge_assignment.R:81:21: style: Do not place spaces around code in parentheses or square brackets.

​      as.data.frame( dplyr::select(df, LEVEL, TAXA, COUNT = ASSIGNED, ABUNDANCE = ROLLUP))
                    ^

R/load_edge_assignment.R:82:16: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'pangia' == type ){
               ^

R/load_edge_assignment.R:82:33: style: Do not place spaces around code in parentheses or square brackets.

​    } else if ( 'pangia' == type ){
                                ^

R/load_edge_assignment.R:83:10: style: Variable or function name should be snake_case.

​      df$READ_COUNT_RNR = as.integer(df$READ_COUNT_RNR)
         ^~~~~~~~~~~~~~

R/load_edge_assignment.R:83:25: style: Use <-, not =, for assignment.

​      df$READ_COUNT_RNR = as.integer(df$READ_COUNT_RNR)
                        ^

R/load_edge_assignment.R:84:1: style: Lines should not be more than 100 characters.

​      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = READ_COUNT_RNR, ABUNDANCE = REL_ABUNDANCE))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/load_edge_assignment.R:84:21: style: Do not place spaces around code in parentheses or square brackets.

​      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = READ_COUNT_RNR, ABUNDANCE = REL_ABUNDANCE))
                    ^

R/load_edge_assignment.R:86:18: style: Do not place spaces around code in parentheses or square brackets.

​      data.frame( LEVEL = character(), TAXA = character(), COUNT = integer(), ABUNDANCE = double())
                 ^

R/load_edge_assignment.R:90:1: style: Trailing blank lines are superfluous.

​
^

R/load_edge_assignment.R:91:1: style: Trailing blank lines are superfluous.

​
^

R/load_edge_assignments.R:35:7: style: Do not place spaces around code in parentheses or square brackets.

​  if ( !file.exists(filepath) ) {
      ^

R/load_edge_assignments.R:35:30: style: Do not place spaces around code in parentheses or square brackets.

​  if ( !file.exists(filepath) ) {
                             ^

R/load_edge_assignments.R:44:7: style: Use <-, not =, for assignment.

​  res = list()
      ^

R/load_edge_assignments.R:46:16: style: Use <-, not =, for assignment.

​    cur_asgnmt = load_edge_assignment(df[prj_name == df$V1, ]$V2, type)
               ^

R/load_edge_assignments.R:46:18: warning: no visible global function definition for ‘load_edge_assignment’

​    cur_asgnmt = load_edge_assignment(df[prj_name == df$V1, ]$V2, type)
                 ^~~~~~~~~~~~~~~~~~~~

R/load_edge_assignments.R:47:9: style: Use <-, not =, for assignment.

​    res = c(res, list(cur_asgnmt))
        ^

R/merge_edge_assignments.R:32:3: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- ABUNDANCE <- NULL # fix the CRAN note
  ^~~~~

R/merge_edge_assignments.R:32:12: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- ABUNDANCE <- NULL # fix the CRAN note
           ^~~~

R/merge_edge_assignments.R:32:20: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- ABUNDANCE <- NULL # fix the CRAN note
                   ^~~~~~~~~

R/merge_edge_counts.R:19:3: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- COUNT <- NULL # fix the CRAN note
  ^~~~~

R/merge_edge_counts.R:19:12: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- COUNT <- NULL # fix the CRAN note
           ^~~~

R/merge_edge_counts.R:19:20: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- COUNT <- NULL # fix the CRAN note
                   ^~~~~

R/plot_edge_assignment.R:28:3: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- ABUNDANCE <- tool <- NULL # fix the CRAN note
  ^~~~~

R/plot_edge_assignment.R:28:12: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- ABUNDANCE <- tool <- NULL # fix the CRAN note
           ^~~~

R/plot_edge_assignment.R:28:20: style: Variable or function name should be snake_case.

​  LEVEL <- TAXA <- ABUNDANCE <- tool <- NULL # fix the CRAN note
                   ^~~~~~~~~

R/plot_edge_assignment.R:40:8: style: Variable or function name should be snake_case.

​  vals$ABUNDANCE <- vals$ABUNDANCE
       ^~~~~~~~~

R/plot_edge_assignment.R:43:8: style: Variable or function name should be snake_case.

​  vals$TAXA <- factor(x = vals$TAXA, levels = vals$TAXA, ordered = T)
       ^~~~

R/plot_edge_assignment.R:48:27: style: Do not place spaces around code in parentheses or square brackets.

​     p <- ggplot2::ggplot( data = vals, ggplot2::aes(y = TAXA, x = tool, fill = ABUNDANCE) ) +
                          ^

R/plot_edge_assignment.R:48:91: style: Do not place spaces around code in parentheses or square brackets.

​     p <- ggplot2::ggplot( data = vals, ggplot2::aes(y = TAXA, x = tool, fill = ABUNDANCE) ) +
                                                                                          ^

R/plot_merged_assignment.R:38:1: style: Lines should not be more than 100 characters.

​#'                                        "HMP side-to-side", file.path(tempdir(), "assignment.pdf"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plot_merged_assignment.R:45:3: style: Variable or function name should be snake_case.

​  TAXA <- LEVEL <- SUM <- value <- variable <- NULL # fix the CRAN note
  ^~~~

R/plot_merged_assignment.R:45:11: style: Variable or function name should be snake_case.

​  TAXA <- LEVEL <- SUM <- value <- variable <- NULL # fix the CRAN note
          ^~~~~

R/plot_merged_assignment.R:45:20: style: Variable or function name should be snake_case.

​  TAXA <- LEVEL <- SUM <- value <- variable <- NULL # fix the CRAN note
                   ^~~

R/plot_merged_assignment.R:105:6: style: Variable or function name should be snake_case.

​  df$TAXA <- factor(x = df$TAXA, levels = unique(df$TAXA), ordered = T)
     ^~~~

R/plot_merged_assignment.R:114:71: style: Do not place spaces around code in parentheses or square brackets.

​  column_index <- c(1, project_names_order + 1, as.numeric(dim(df)[2]) )
                                                                      ^

R/plot_merged_assignment.R:116:39: style: Do not place spaces around code in parentheses or square brackets.

​  df <- dplyr::select(df, column_index )
                                      ^

R/plot_merged_assignment.R:125:24: style: Do not place spaces around code in parentheses or square brackets.

​  p <- ggplot2::ggplot( data = melted_df, ggplot2::aes(y = TAXA, x = variable, fill = value) ) +
                       ^

R/plot_merged_assignment.R:125:93: style: Do not place spaces around code in parentheses or square brackets.

​  p <- ggplot2::ggplot( data = melted_df, ggplot2::aes(y = TAXA, x = variable, fill = value) ) +
                                                                                            ^

R/plot_merged_assignment.R:164:4: style: Commented code should be removed.

​  #p1 <- suppressWarnings(gridExtra::arrangeGrob(p, top = title.grob))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plot_merged_assignment.R:171:4: style: Commented code should be removed.

​  #suppressWarnings(grid::grid.draw(p1))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plot_merged_assignment.R:180:4: style: Commented code should be removed.

​  #suppressWarnings(grid::grid.draw(p1))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test_load_bwa_assignment.R:4:1: style: Lines should not be more than 100 characters.

​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: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[1], equals(558) )
            ^

tests/testthat/test_load_bwa_assignment.R:7:38: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[1], equals(558) )
                                     ^

tests/testthat/test_load_bwa_assignment.R:10:13: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[2], equals(4) )
            ^

tests/testthat/test_load_bwa_assignment.R:10:36: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[2], equals(4) )
                                   ^

tests/testthat/test_load_bwa_assignment.R:13:35: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                  ^

tests/testthat/test_load_bwa_assignment.R:13:76: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                           ^

tests/testthat/test_load_bwa_assignment.R:13:78: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                             ^

tests/testthat/test_load_bwa_assignment.R:18:31: style: Do not place spaces around code in parentheses or square brackets.

​family_table <- dplyr::filter( dat, LEVEL == "species")
                              ^

tests/testthat/test_load_bwa_assignment.R:21:26: style: Do not place spaces around code in parentheses or square brackets.

​ent_row <- dplyr::filter( family_table, TAXA == "Moraxella catarrhalis")
                         ^

tests/testthat/test_load_bwa_assignment.R:36:40: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                       ^

tests/testthat/test_load_bwa_assignment.R:36:81: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^

tests/testthat/test_load_bwa_assignment.R:36:83: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                  ^

tests/testthat/test_load_bwa_assignment.R:37:40: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(dim(empty_df)[1], equals(0) )
                                       ^

tests/testthat/test_load_bwa_assignment.R:43:40: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                       ^

tests/testthat/test_load_bwa_assignment.R:43:81: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^

tests/testthat/test_load_bwa_assignment.R:43:83: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                  ^

tests/testthat/test_load_bwa_assignment.R:44:40: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(dim(empty_df)[1], equals(0) )
                                       ^

tests/testthat/test_load_diamond_assignment.R:8:13: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[1], equals(234) )
            ^

tests/testthat/test_load_diamond_assignment.R:8:38: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[1], equals(234) )
                                     ^

tests/testthat/test_load_diamond_assignment.R:11:13: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[2], equals(4) )
            ^

tests/testthat/test_load_diamond_assignment.R:11:36: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[2], equals(4) )
                                   ^

tests/testthat/test_load_diamond_assignment.R:14:35: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                  ^

tests/testthat/test_load_diamond_assignment.R:14:76: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                           ^

tests/testthat/test_load_diamond_assignment.R:14:78: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                             ^

tests/testthat/test_load_diamond_assignment.R:19:31: style: Do not place spaces around code in parentheses or square brackets.

​family_table <- dplyr::filter( dat, LEVEL == "family")
                              ^

tests/testthat/test_load_diamond_assignment.R:23:26: style: Do not place spaces around code in parentheses or square brackets.

​ent_row <- dplyr::filter( family_table, TAXA == "Enterobacteriaceae")
                         ^

tests/testthat/test_load_diamond_assignment.R:32:1: style: Lines should not be more than 100 characters.

​expect_that(load_edge_assignment("../test_data/nonexistentfile.txt", type = 'diamond'), throws_error())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test_load_diamond_assignment.R:38:40: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                       ^

tests/testthat/test_load_diamond_assignment.R:38:81: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^

tests/testthat/test_load_diamond_assignment.R:38:83: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                  ^

tests/testthat/test_load_diamond_assignment.R:39:40: style: Do not place spaces around code in parentheses or square brackets.

​expect_that(dim(empty_df)[1], equals(0) )
                                       ^

tests/testthat/test_load_diamond_assignments.R:21:1: style: Lines should not be more than 100 characters.

​expect_that(load_edge_assignments("../test_data/nonexistentfile.txt", type = 'diamond'), throws_error())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test_load_gottcha_assignment.R:8:13: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[1], equals(65) )
            ^

tests/testthat/test_load_gottcha_assignment.R:8:37: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[1], equals(65) )
                                    ^

tests/testthat/test_load_gottcha_assignment.R:11:13: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[2], equals(4) )
            ^

tests/testthat/test_load_gottcha_assignment.R:11:36: style: Do not place spaces around code in parentheses or square brackets.

​expect_that( dim(dat)[2], equals(4) )

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