[R/common.R:120:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L120) *style:* **Variable and function names should be all lowercase.**
```r
.toId <-
^~~~~
```
[R/common.R:131:50:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L131) *style:* **Only use double-quotes.**
```r
    return(paste("PacBio", "FileTypes", s, sep = '.'))
                                                 ^~~
```
[R/common.R:135:10:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L135) *style:* **Variable and function names should be all lowercase.**
```r
  return(.toId("task_options", s))
         ^~~~~
```
[R/common.R:139:10:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L139) *style:* **Variable and function names should be all lowercase.**
```r
  return(.toId("tasks", s))
         ^~~~~
```
[R/common.R:149:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L149) *style:* **Variable and function names should be all lowercase.**
```r
.toFileTypes <- function() {
^~~~~~~~~~~~
```
[R/common.R:151:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L151) *style:* **Variable and function names should be all lowercase.**
```r
  toF <- function(idx, baseName, fileExt, mimeType) {
  ^~~
```
[R/common.R:151:24:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L151) *style:* **Variable and function names should be all lowercase.**
```r
  toF <- function(idx, baseName, fileExt, mimeType) {
                       ^~~~~~~~
```
[R/common.R:151:34:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L151) *style:* **Variable and function names should be all lowercase.**
```r
  toF <- function(idx, baseName, fileExt, mimeType) {
                                 ^~~~~~~
```
[R/common.R:151:43:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L151) *style:* **Variable and function names should be all lowercase.**
```r
  toF <- function(idx, baseName, fileExt, mimeType) {
                                          ^~~~~~~~
```
[R/common.R:156:20:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L156) *style:* **Variable and function names should be all lowercase.**
```r
        baseName = baseName,
                   ^~~~~~~~
```
[R/common.R:158:11:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L158) *style:* **Variable and function names should be all lowercase.**
```r
          fileExt,
          ^~~~~~~
```
[R/common.R:159:20:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L159) *style:* **Variable and function names should be all lowercase.**
```r
        mimeType = mimeType
                   ^~~~~~~~
```
[R/common.R:172:10:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L172) *style:* **Variable and function names should be all lowercase.**
```r
  txt <- toF("txt", "file", "txt", "text/plain")
         ^~~
```
[R/common.R:173:12:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L173) *style:* **Variable and function names should be all lowercase.**
```r
  fasta <- toF("Fasta", "file", "fasta", "text/plain")
           ^~~
```
[R/common.R:174:12:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L174) *style:* **Variable and function names should be all lowercase.**
```r
  fastq <- toF("Fastq", "file", "fastq", "text/plain")
           ^~~
```
[R/common.R:175:10:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L175) *style:* **Variable and function names should be all lowercase.**
```r
  gff <- toF("Gff", "file", "gff", "text/plain")
         ^~~
```
[R/common.R:177:5:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L177) *style:* **Variable and function names should be all lowercase.**
```r
    toF("JsonReport", "file.report", "json", "application/json")
    ^~~
```
[R/common.R:179:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L179) *style:* **Variable and function names should be all lowercase.**
```r
  reseqCond = toF("COND_RESEQ",
  ^~~~~~~~~
```
[R/common.R:179:13:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L179) *style:* **Use <-, not =, for assignment.**
```r
  reseqCond = toF("COND_RESEQ",
            ^
```
[R/common.R:179:15:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L179) *style:* **Variable and function names should be all lowercase.**
```r
  reseqCond = toF("COND_RESEQ",
              ^~~
```
[R/common.R:190:18:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L190) *style:* **Variable and function names should be all lowercase.**
```r
    RESEQ_COND = reseqCond
                 ^~~~~~~~~
```
[R/common.R:196:14:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L196) *style:* **Variable and function names should be all lowercase.**
```r
FileTypes <- .toFileTypes()
             ^~~~~~~~~~~~
```
[R/common.R:198:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L198) *style:* **Variable and function names should be all lowercase.**
```r
.toSymbolTypes <- function() {
^~~~~~~~~~~~~~
```
[R/common.R:200:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L200) *style:* **Variable and function names should be all lowercase.**
```r
  symbolTypes <-
  ^~~~~~~~~~~
```
[R/common.R:202:10:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L202) *style:* **Variable and function names should be all lowercase.**
```r
  return(symbolTypes)
         ^~~~~~~~~~~
```
[R/common.R:209:16:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L209) *style:* **Variable and function names should be all lowercase.**
```r
SymbolTypes <- .toSymbolTypes()
               ^~~~~~~~~~~~~~
```
[R/common.R:211:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L211) *style:* **Variable and function names should be all lowercase.**
```r
.toResourceTypes <- function() {
^~~~~~~~~~~~~~~~
```
[R/common.R:212:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L212) *style:* **Variable and function names should be all lowercase.**
```r
  resourceTypes <-
  ^~~~~~~~~~~~~
```
[R/common.R:216:10:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L216) *style:* **Variable and function names should be all lowercase.**
```r
  return(resourceTypes)
         ^~~~~~~~~~~~~
```
[R/common.R:223:18:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/common.R#L223) *style:* **Variable and function names should be all lowercase.**
```r
ResourceTypes <- .toResourceTypes()
                 ^~~~~~~~~~~~~~~~
```
[R/driver.R:12:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L12) *style:* **lines should not be more than 80 characters.**
```r
  p <- argparser::add_argument(p, "mode", help = "Mode, emit-tc or run-rtc", type = "character")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/driver.R:13:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L13) *style:* **lines should not be more than 80 characters.**
```r
  p <- argparser::add_argument(p, "rtc_or_output_dir", help = "run-rtc path/to/rtc.json OR emit-tc /path/to/output-dir",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/driver.R:21:47:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L21) *style:* **Variable and function names should be all lowercase.**
```r
mainRegisteryMain <- function(registry, mode, rtcOrOutputDir) {
                                              ^~~~~~~~~~~~~~
```
[R/driver.R:22:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L22) *style:* **Variable and function names should be all lowercase.**
```r
  exitCode <- -1
  ^~~~~~~~
```
[R/driver.R:25:60:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L25) *style:* **Variable and function names should be all lowercase.**
```r
    logging::loginfo(paste("attempting to load RTC from ", rtcOrOutputDir))
                                                           ^~~~~~~~~~~~~~
```
[R/driver.R:26:5:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L26) *style:* **Variable and function names should be all lowercase.**
```r
    rtcPath <- normalizePath(rtcOrOutputDir)
    ^~~~~~~
```
[R/driver.R:26:30:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L26) *style:* **Variable and function names should be all lowercase.**
```r
    rtcPath <- normalizePath(rtcOrOutputDir)
                             ^~~~~~~~~~~~~~
```
[R/driver.R:27:5:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L27) *style:* **Variable and function names should be all lowercase.**
```r
    exitCode <- registryRunner(registry, rtcPath)
    ^~~~~~~~
```
[R/driver.R:27:42:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L27) *style:* **Variable and function names should be all lowercase.**
```r
    exitCode <- registryRunner(registry, rtcPath)
                                         ^~~~~~~
```
[R/driver.R:29:5:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L29) *style:* **Variable and function names should be all lowercase.**
```r
    outputDir <- normalizePath(rtcOrOutputDir)
    ^~~~~~~~~
```
[R/driver.R:29:32:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L29) *style:* **Variable and function names should be all lowercase.**
```r
    outputDir <- normalizePath(rtcOrOutputDir)
                               ^~~~~~~~~~~~~~
```
[R/driver.R:30:63:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L30) *style:* **Variable and function names should be all lowercase.**
```r
    logging::loginfo(paste("Emitting tool contracts to dir ", outputDir))
                                                              ^~~~~~~~~
```
[R/driver.R:31:5:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L31) *style:* **Variable and function names should be all lowercase.**
```r
    exitCode <- emitRegistryToolContractsTo(registry, outputDir)
    ^~~~~~~~
```
[R/driver.R:31:55:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L31) *style:* **Variable and function names should be all lowercase.**
```r
    exitCode <- emitRegistryToolContractsTo(registry, outputDir)
                                                      ^~~~~~~~~
```
[R/driver.R:33:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L33) *style:* **lines should not be more than 80 characters.**
```r
    cat(paste("Unsupported mode ", mode, " Suppored modes 'emit-tc', and 'run-rtc'"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/driver.R:34:5:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L34) *style:* **Variable and function names should be all lowercase.**
```r
    exitCode <- 2
    ^~~~~~~~
```
[R/driver.R:38:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L38) *style:* **Variable and function names should be all lowercase.**
```r
  runTime <- 1
  ^~~~~~~
```
[R/driver.R:39:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L39) *style:* **lines should not be more than 80 characters.**
```r
  cat(paste("Exiting main with exit code ", exitCode, "in ", runTime, " secs\n"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/driver.R:39:45:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L39) *style:* **Variable and function names should be all lowercase.**
```r
  cat(paste("Exiting main with exit code ", exitCode, "in ", runTime, " secs\n"))
                                            ^~~~~~~~
```
[R/driver.R:39:62:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L39) *style:* **Variable and function names should be all lowercase.**
```r
  cat(paste("Exiting main with exit code ", exitCode, "in ", runTime, " secs\n"))
                                                             ^~~~~~~
```
[R/driver.R:40:10:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L40) *style:* **Variable and function names should be all lowercase.**
```r
  return(exitCode)
         ^~~~~~~~
```
[R/driver.R:55:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L55) *style:* **Variable and function names should be all lowercase.**
```r
  rtcOrOutputDir <- argv$rtc_or_output_dir
  ^~~~~~~~~~~~~~
```
[R/driver.R:56:44:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/driver.R#L56) *style:* **Variable and function names should be all lowercase.**
```r
  return(mainRegisteryMain(registry, mode, rtcOrOutputDir))
                                           ^~~~~~~~~~~~~~
```
[R/exampleTasks.R:7:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L7) *style:* **lines should not be more than 80 characters.**
```r
examplefilterFastaTask <- function(pathToFasta, filteredFasta, minSequenceLength) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/exampleTasks.R:7:36:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L7) *style:* **Variable and function names should be all lowercase.**
```r
examplefilterFastaTask <- function(pathToFasta, filteredFasta, minSequenceLength) {
                                   ^~~~~~~~~~~
```
[R/exampleTasks.R:7:49:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L7) *style:* **Variable and function names should be all lowercase.**
```r
examplefilterFastaTask <- function(pathToFasta, filteredFasta, minSequenceLength) {
                                                ^~~~~~~~~~~~~
```
[R/exampleTasks.R:7:64:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L7) *style:* **Variable and function names should be all lowercase.**
```r
examplefilterFastaTask <- function(pathToFasta, filteredFasta, minSequenceLength) {
                                                               ^~~~~~~~~~~~~~~~~
```
[R/exampleTasks.R:8:56:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L8) *style:* **Variable and function names should be all lowercase.**
```r
  logging::loginfo(paste("Writing filtered fasta to ", filteredFasta))
                                                       ^~~~~~~~~~~~~
```
[R/exampleTasks.R:9:40:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L9) *style:* **Variable and function names should be all lowercase.**
```r
  write(">r1\nACGT\n>r2\nACCCGGTTT\n", filteredFasta)
                                       ^~~~~~~~~~~~~
```
[R/exampleTasks.R:13:27:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L13) *style:* **Variable and function names should be all lowercase.**
```r
exampleReport <- function(outputPath) {
                          ^~~~~~~~~~
```
[R/exampleTasks.R:15:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L15) *style:* **Variable and function names should be all lowercase.**
```r
  reportUUID <- uuid::UUIDgenerate()
  ^~~~~~~~~~
```
[R/exampleTasks.R:17:14:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L17) *style:* **Use <-, not =, for assignment.**
```r
  attributes = list()
             ^
```
[R/exampleTasks.R:21:10:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L21) *style:* **Variable and function names should be all lowercase.**
```r
  uuid = reportUUID,
         ^~~~~~~~~~
```
[R/exampleTasks.R:24:16:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L24) *style:* **Variable and function names should be all lowercase.**
```r
  plotGroups = plotGroups,
               ^~~~~~~~~~
```
[R/exampleTasks.R:31:26:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L31) *style:* **Variable and function names should be all lowercase.**
```r
getPlotGroup <- function(outputPath) {
                         ^~~~~~~~~~
```
[R/exampleTasks.R:32:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L32) *style:* **Variable and function names should be all lowercase.**
```r
  plotGroupId <- "plotgroupa"
  ^~~~~~~~~~~
```
[R/exampleTasks.R:35:25:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L35) *style:* **Put spaces around all infix operators.**
```r
  fun.1 <- function(x) x^2 + x
                       ~^~
```
[R/exampleTasks.R:36:42:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L36) *warning:* **no visible binding for global variable 'x', Did you mean 'p'?**
```r
  p <- ggplot2::ggplot(data = data.frame(x = 0), mapping = ggplot2::aes(x = x))
                                         ^
```
[R/exampleTasks.R:37:62:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L37) *style:* **Commas should always have a space after.**
```r
  p + ggplot2::stat_function(fun = fun.1) + ggplot2::xlim(-5,5)
                                                             ^
```
[R/exampleTasks.R:39:19:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L39) *style:* **Variable and function names should be all lowercase.**
```r
  ggplot2::ggsave(outputPath, plot = ggplot2::last_plot())
                  ^~~~~~~~~~
```
[R/exampleTasks.R:41:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L41) *style:* **Variable and function names should be all lowercase.**
```r
  basePlotFileName <- basename(outputPath)
  ^~~~~~~~~~~~~~~~
```
[R/exampleTasks.R:41:32:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L41) *style:* **Variable and function names should be all lowercase.**
```r
  basePlotFileName <- basename(outputPath)
                               ^~~~~~~~~~
```
[R/exampleTasks.R:44:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L44) *style:* **lines should not be more than 80 characters.**
```r
  p1 <- methods::new("ReportPlot", id = "parabola_dev_example", image = basePlotFileName)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/exampleTasks.R:44:73:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L44) *style:* **Variable and function names should be all lowercase.**
```r
  p1 <- methods::new("ReportPlot", id = "parabola_dev_example", image = basePlotFileName)
                                                                        ^~~~~~~~~~~~~~~~
```
[R/exampleTasks.R:45:46:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L45) *style:* **Variable and function names should be all lowercase.**
```r
  pg <- methods::new("ReportPlotGroup", id = plotGroupId, plots = list(p1))
                                             ^~~~~~~~~~~
```
[R/exampleTasks.R:54:32:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L54) *style:* **Variable and function names should be all lowercase.**
```r
examplefastaReport <- function(pathToFasta, reportPath) {
                               ^~~~~~~~~~~
```
[R/exampleTasks.R:54:45:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L54) *style:* **Variable and function names should be all lowercase.**
```r
examplefastaReport <- function(pathToFasta, reportPath) {
                                            ^~~~~~~~~~
```
[R/exampleTasks.R:55:49:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L55) *style:* **Variable and function names should be all lowercase.**
```r
  logging::loginfo(paste("loading fasta file ", pathToFasta))
                                                ^~~~~~~~~~~
```
[R/exampleTasks.R:56:56:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L56) *style:* **Variable and function names should be all lowercase.**
```r
  logging::loginfo(paste("will be writing report to ", reportPath))
                                                       ^~~~~~~~~~
```
[R/exampleTasks.R:58:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L58) *style:* **Variable and function names should be all lowercase.**
```r
  imageName <- "report_plot.png"
  ^~~~~~~~~
```
[R/exampleTasks.R:60:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L60) *style:* **Variable and function names should be all lowercase.**
```r
  reportDir <- dirname(reportPath)
  ^~~~~~~~~
```
[R/exampleTasks.R:60:24:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L60) *style:* **Variable and function names should be all lowercase.**
```r
  reportDir <- dirname(reportPath)
                       ^~~~~~~~~~
```
[R/exampleTasks.R:61:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L61) *style:* **Variable and function names should be all lowercase.**
```r
  imagePath <- file.path(reportDir, imageName)
  ^~~~~~~~~
```
[R/exampleTasks.R:61:26:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L61) *style:* **Variable and function names should be all lowercase.**
```r
  imagePath <- file.path(reportDir, imageName)
                         ^~~~~~~~~
```
[R/exampleTasks.R:61:37:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L61) *style:* **Variable and function names should be all lowercase.**
```r
  imagePath <- file.path(reportDir, imageName)
                                    ^~~~~~~~~
```
[R/exampleTasks.R:63:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L63) *style:* **Variable and function names should be all lowercase.**
```r
  reportUUID <- uuid::UUIDgenerate()
  ^~~~~~~~~~
```
[R/exampleTasks.R:64:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L64) *style:* **Variable and function names should be all lowercase.**
```r
  reportId = "pbcommandr_dev_fasta"
  ^~~~~~~~
```
[R/exampleTasks.R:64:12:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L64) *style:* **Use <-, not =, for assignment.**
```r
  reportId = "pbcommandr_dev_fasta"
           ^
```
[R/exampleTasks.R:66:10:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L66) *style:* **Use <-, not =, for assignment.**
```r
  tables = list()
         ^
```
[R/exampleTasks.R:67:14:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L67) *style:* **Use <-, not =, for assignment.**
```r
  attributes = list()
             ^
```
[R/exampleTasks.R:68:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L68) *style:* **Variable and function names should be all lowercase.**
```r
  plotGroups <- list(getPlotGroup(imagePath))
  ^~~~~~~~~~
```
[R/exampleTasks.R:68:35:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L68) *style:* **Variable and function names should be all lowercase.**
```r
  plotGroups <- list(getPlotGroup(imagePath))
                                  ^~~~~~~~~
```
[R/exampleTasks.R:72:10:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L72) *style:* **Variable and function names should be all lowercase.**
```r
  uuid = reportUUID,
         ^~~~~~~~~~
```
[R/exampleTasks.R:74:8:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L74) *style:* **Variable and function names should be all lowercase.**
```r
  id = reportId,
       ^~~~~~~~
```
[R/exampleTasks.R:75:16:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L75) *style:* **Variable and function names should be all lowercase.**
```r
  plotGroups = plotGroups,
               ^~~~~~~~~~
```
[R/exampleTasks.R:79:23:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L79) *style:* **Variable and function names should be all lowercase.**
```r
  writeReport(report, reportPath)
                      ^~~~~~~~~~
```
[R/exampleTasks.R:80:46:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L80) *style:* **Variable and function names should be all lowercase.**
```r
  logging::loginfo(paste("Wrote report to ", reportPath))
                                             ^~~~~~~~~~
```
[R/exampleTasks.R:89:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L89) *style:* **Variable and function names should be all lowercase.**
```r
  minLength <- 25
  ^~~~~~~~~
```
[R/exampleTasks.R:91:5:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L91) *style:* **Variable and function names should be all lowercase.**
```r
    minLength))
    ^~~~~~~~~
```
[R/exampleTasks.R:99:27:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L99) *style:* **Variable and function names should be all lowercase.**
```r
runHelloWorld <- function(inputTxt, outputTxt) {
                          ^~~~~~~~
```
[R/exampleTasks.R:99:37:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L99) *style:* **Variable and function names should be all lowercase.**
```r
runHelloWorld <- function(inputTxt, outputTxt) {
                                    ^~~~~~~~~
```
[R/exampleTasks.R:100:44:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L100) *style:* **Variable and function names should be all lowercase.**
```r
  msg <- paste("Hello World. Input File ", inputTxt)
                                           ^~~~~~~~
```
[R/exampleTasks.R:101:19:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L101) *style:* **Variable and function names should be all lowercase.**
```r
  cat(msg, file = outputTxt)
                  ^~~~~~~~~
```
[R/exampleTasks.R:113:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L113) *style:* **lines should not be more than 80 characters.**
```r
  # The driver is what pbsmrtpipe will call with the path to resolved tool contract
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/exampleTasks.R:114:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L114) *style:* **lines should not be more than 80 characters.**
```r
  # JSON file FIXME. Not sure how to package exes with R to create a 'console entry
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/exampleTasks.R:116:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L116) *style:* **lines should not be more than 80 characters.**
```r
  # FIXME. There's an extra shell layer to get packrat loaded so the exampleHelloWorld.R
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/exampleTasks.R:119:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L119) *style:* **lines should not be more than 80 characters.**
```r
  # could be more clever and use partial application for registry, but this is fine
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/exampleTasks.R:120:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L120) *style:* **lines should not be more than 80 characters.**
```r
  registerTool(r, "filterFasta", "0.1.0", c(FileTypes$FASTA), c(FileTypes$FASTA),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/exampleTasks.R:122:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/exampleTasks.R#L122) *style:* **lines should not be more than 80 characters.**
```r
  registerTool(r, "fastaReport", "0.1.0", c(FileTypes$FASTA), c(FileTypes$REPORT),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:23:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L23) *style:* **lines should not be more than 80 characters.**
```r
  return(methods::new("InputFileType", title = d$title, id=d$title, fileTypeId=d$file_type_id, description = d$description))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:23:59:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L23) *style:* **Put spaces around all infix operators.**
```r
  return(methods::new("InputFileType", title = d$title, id=d$title, fileTypeId=d$file_type_id, description = d$description))
                                                         ~^~
```
[R/io.R:23:79:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L23) *style:* **Put spaces around all infix operators.**
```r
  return(methods::new("InputFileType", title = d$title, id=d$title, fileTypeId=d$file_type_id, description = d$description))
                                                                             ~^~
```
[R/io.R:28:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L28) *style:* **lines should not be more than 80 characters.**
```r
  return(methods::new("OutputFileType", title = d$title, id=d$title, fileTypeId=d$file_type_id, description = d$description, baseName=d$default_name))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:28:60:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L28) *style:* **Put spaces around all infix operators.**
```r
  return(methods::new("OutputFileType", title = d$title, id=d$title, fileTypeId=d$file_type_id, description = d$description, baseName=d$default_name))
                                                          ~^~
```
[R/io.R:28:80:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L28) *style:* **Put spaces around all infix operators.**
```r
  return(methods::new("OutputFileType", title = d$title, id=d$title, fileTypeId=d$file_type_id, description = d$description, baseName=d$default_name))
                                                                              ~^~
```
[R/io.R:28:134:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L28) *style:* **Put spaces around all infix operators.**
```r
  return(methods::new("OutputFileType", title = d$title, id=d$title, fileTypeId=d$file_type_id, description = d$description, baseName=d$default_name))
                                                                                ~^~
```
[R/io.R:34:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L34) *style:* **Variable and function names should be all lowercase.**
```r
  taskId <- tc$tool_contract_id
  ^~~~~~
```
[R/io.R:35:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L35) *style:* **Variable and function names should be all lowercase.**
```r
  inputFiles <- Map(dToInputType, tc$input_types)
  ^~~~~~~~~~
```
[R/io.R:36:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L36) *style:* **Variable and function names should be all lowercase.**
```r
  outputFiles <- Map(dToOutputType, tc$output_types)
  ^~~~~~~~~~~
```
[R/io.R:38:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L38) *style:* **lines should not be more than 80 characters.**
```r
  toolContractTask <- methods::new("ToolContractTask", name = tc$name, description = tc$description,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:38:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L38) *style:* **Variable and function names should be all lowercase.**
```r
  toolContractTask <- methods::new("ToolContractTask", name = tc$name, description = tc$description,
  ^~~~~~~~~~~~~~~~
```
[R/io.R:39:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L39) *style:* **lines should not be more than 80 characters.**
```r
    taskId = taskId, inputTypes = inputFiles, outputTypes = outputFiles, nproc = nproc)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:39:14:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L39) *style:* **Variable and function names should be all lowercase.**
```r
    taskId = taskId, inputTypes = inputFiles, outputTypes = outputFiles, nproc = nproc)
             ^~~~~~
```
[R/io.R:39:35:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L39) *style:* **Variable and function names should be all lowercase.**
```r
    taskId = taskId, inputTypes = inputFiles, outputTypes = outputFiles, nproc = nproc)
                                  ^~~~~~~~~~
```
[R/io.R:39:61:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L39) *style:* **Variable and function names should be all lowercase.**
```r
    taskId = taskId, inputTypes = inputFiles, outputTypes = outputFiles, nproc = nproc)
                                                            ^~~~~~~~~~~
```
[R/io.R:41:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L41) *style:* **lines should not be more than 80 characters.**
```r
  toolContract <- methods::new("ToolContract", task = toolContractTask, driver = driver)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:41:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L41) *style:* **Variable and function names should be all lowercase.**
```r
  toolContract <- methods::new("ToolContract", task = toolContractTask, driver = driver)
  ^~~~~~~~~~~~
```
[R/io.R:41:55:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L41) *style:* **Variable and function names should be all lowercase.**
```r
  toolContract <- methods::new("ToolContract", task = toolContractTask, driver = driver)
                                                      ^~~~~~~~~~~~~~~~
```
[R/io.R:42:10:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L42) *style:* **Variable and function names should be all lowercase.**
```r
  return(toolContract)
         ^~~~~~~~~~~~
```
[R/io.R:54:31:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L54) *style:* **Variable and function names should be all lowercase.**
```r
writeToolContract <- function(toolContract, jsonPath) {
                              ^~~~~~~~~~~~
```
[R/io.R:54:45:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L54) *style:* **Variable and function names should be all lowercase.**
```r
writeToolContract <- function(toolContract, jsonPath) {
                                            ^~~~~~~~
```
[R/io.R:57:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L57) *style:* **lines should not be more than 80 characters.**
```r
  logging::logdebug(paste("Writing tool contract", toolContract@task@taskId, "to", jsonPath))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:57:52:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L57) *style:* **Variable and function names should be all lowercase.**
```r
  logging::logdebug(paste("Writing tool contract", toolContract@task@taskId, "to", jsonPath))
                                                   ^~~~~~~~~~~~
```
[R/io.R:57:84:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L57) *style:* **Variable and function names should be all lowercase.**
```r
  logging::logdebug(paste("Writing tool contract", toolContract@task@taskId, "to", jsonPath))
                                                                                ^~~~~~~~
```
[R/io.R:59:40:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L59) *style:* **Variable and function names should be all lowercase.**
```r
  desc <- paste("Tool Contract from ", toolContract@task@taskId)
                                       ^~~~~~~~~~~~
```
[R/io.R:60:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L60) *style:* **lines should not be more than 80 characters.**
```r
  authorComment <- paste("Created from pbcommandR version ", PB_COMMANDR_VERSION)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:60:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L60) *style:* **Variable and function names should be all lowercase.**
```r
  authorComment <- paste("Created from pbcommandR version ", PB_COMMANDR_VERSION)
  ^~~~~~~~~~~~~
```
[R/io.R:61:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L61) *style:* **Variable and function names should be all lowercase.**
```r
  isDistributed <- FALSE
  ^~~~~~~~~~~~~
```
[R/io.R:62:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L62) *style:* **Variable and function names should be all lowercase.**
```r
  schemaOptions <- list()
  ^~~~~~~~~~~~~
```
[R/io.R:64:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L64) *style:* **lines should not be more than 80 characters.**
```r
  # The 'id' needs to be fixed. ft@fileTypeId_{index} this isn't really used in the
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:66:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L66) *style:* **Variable and function names should be all lowercase.**
```r
  toInputType <- function(ft, i) {
  ^~~~~~~~~~~
```
[R/io.R:67:18:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L67) *style:* **Use <-, not =, for assignment.**
```r
    file_type_id = ft@fileTypeId
                 ^
```
[R/io.R:70:5:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L70) *style:* **Variable and function names should be all lowercase.**
```r
    splitID = strsplit(ft@fileTypeId, "\\.")[[1]]
    ^~~~~~~
```
[R/io.R:70:13:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L70) *style:* **Use <-, not =, for assignment.**
```r
    splitID = strsplit(ft@fileTypeId, "\\.")[[1]]
            ^
```
[R/io.R:71:9:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L71) *style:* **Use <-, not =, for assignment.**
```r
    ext = splitID[length(splitID)]
        ^
```
[R/io.R:71:11:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L71) *style:* **Variable and function names should be all lowercase.**
```r
    ext = splitID[length(splitID)]
          ^~~~~~~
```
[R/io.R:71:26:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L71) *style:* **Variable and function names should be all lowercase.**
```r
    ext = splitID[length(splitID)]
                         ^~~~~~~
```
[R/io.R:74:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L74) *style:* **lines should not be more than 80 characters.**
```r
      sep = "_"), title = paste("Display name ", file_type_id), description = paste("File type ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:75:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L75) *style:* **lines should not be more than 80 characters.**
```r
                                                                                file_type_id)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:79:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L79) *style:* **Variable and function names should be all lowercase.**
```r
  toOutputType <- function(ft) {
  ^~~~~~~~~~~~
```
[R/io.R:80:9:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L80) *style:* **Use <-, not =, for assignment.**
```r
    tmp = toInputType(ft)
        ^
```
[R/io.R:80:11:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L80) *style:* **Variable and function names should be all lowercase.**
```r
    tmp = toInputType(ft)
          ^~~~~~~~~~~
```
[R/io.R:85:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
  inputTypes <- Map(toInputType, toolContract@task@inputTypes)
  ^~~~~~~~~~
```
[R/io.R:85:21:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
  inputTypes <- Map(toInputType, toolContract@task@inputTypes)
                    ^~~~~~~~~~~
```
[R/io.R:85:34:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
  inputTypes <- Map(toInputType, toolContract@task@inputTypes)
                                 ^~~~~~~~~~~~
```
[R/io.R:86:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L86) *style:* **Variable and function names should be all lowercase.**
```r
  outputTypes <- Map(toOutputType, toolContract@task@outputTypes)
  ^~~~~~~~~~~
```
[R/io.R:86:22:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L86) *style:* **Variable and function names should be all lowercase.**
```r
  outputTypes <- Map(toOutputType, toolContract@task@outputTypes)
                     ^~~~~~~~~~~~
```
[R/io.R:86:36:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L86) *style:* **Variable and function names should be all lowercase.**
```r
  outputTypes <- Map(toOutputType, toolContract@task@outputTypes)
                                   ^~~~~~~~~~~~
```
[R/io.R:88:49:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L88) *style:* **Variable and function names should be all lowercase.**
```r
  jdriver <- list(serialization = "json", exe = toolContract@driver@exe)
                                                ^~~~~~~~~~~~
```
[R/io.R:90:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L90) *style:* **lines should not be more than 80 characters.**
```r
  jt <- list(task_type = "pbsmrtpipe.task_types.standard", resource_types = list(),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:91:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L91) *style:* **lines should not be more than 80 characters.**
```r
    description = desc, name = toolContract@task@name, nproc = toolContract@task@nproc,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:91:32:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L91) *style:* **Variable and function names should be all lowercase.**
```r
    description = desc, name = toolContract@task@name, nproc = toolContract@task@nproc,
                               ^~~~~~~~~~~~
```
[R/io.R:91:64:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L91) *style:* **Variable and function names should be all lowercase.**
```r
    description = desc, name = toolContract@task@name, nproc = toolContract@task@nproc,
                                                               ^~~~~~~~~~~~
```
[R/io.R:92:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L92) *style:* **lines should not be more than 80 characters.**
```r
    is_distributed = isDistributed, schema_options = schemaOptions, tool_contract_id = toolContract@task@taskId,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:92:22:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L92) *style:* **Variable and function names should be all lowercase.**
```r
    is_distributed = isDistributed, schema_options = schemaOptions, tool_contract_id = toolContract@task@taskId,
                     ^~~~~~~~~~~~~
```
[R/io.R:92:54:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L92) *style:* **Variable and function names should be all lowercase.**
```r
    is_distributed = isDistributed, schema_options = schemaOptions, tool_contract_id = toolContract@task@taskId,
                                                     ^~~~~~~~~~~~~
```
[R/io.R:92:88:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L92) *style:* **Variable and function names should be all lowercase.**
```r
    is_distributed = isDistributed, schema_options = schemaOptions, tool_contract_id = toolContract@task@taskId,
                                                                                ^~~~~~~~~~~~
```
[R/io.R:93:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L93) *style:* **lines should not be more than 80 characters.**
```r
    input_types = inputTypes, output_types = outputTypes, comment = authorComment)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:93:19:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L93) *style:* **Variable and function names should be all lowercase.**
```r
    input_types = inputTypes, output_types = outputTypes, comment = authorComment)
                  ^~~~~~~~~~
```
[R/io.R:93:46:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L93) *style:* **Variable and function names should be all lowercase.**
```r
    input_types = inputTypes, output_types = outputTypes, comment = authorComment)
                                             ^~~~~~~~~~~
```
[R/io.R:93:69:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L93) *style:* **Variable and function names should be all lowercase.**
```r
    input_types = inputTypes, output_types = outputTypes, comment = authorComment)
                                                                    ^~~~~~~~~~~~~
```
[R/io.R:95:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L95) *style:* **lines should not be more than 80 characters.**
```r
  j <- list(version = PB_COMMANDR_VERSION, driver = jdriver, tool_contract_id = toolContract@task@taskId,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:95:81:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L95) *style:* **Variable and function names should be all lowercase.**
```r
  j <- list(version = PB_COMMANDR_VERSION, driver = jdriver, tool_contract_id = toolContract@task@taskId,
                                                                                ^~~~~~~~~~~~
```
[R/io.R:98:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L98) *style:* **Variable and function names should be all lowercase.**
```r
  jsonToolContract <- jsonlite::toJSON(j, pretty = TRUE, auto_unbox = TRUE)
  ^~~~~~~~~~~~~~~~
```
[R/io.R:99:7:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L99) *style:* **Variable and function names should be all lowercase.**
```r
  cat(jsonToolContract, file = jsonPath)
      ^~~~~~~~~~~~~~~~
```
[R/io.R:99:32:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L99) *style:* **Variable and function names should be all lowercase.**
```r
  cat(jsonToolContract, file = jsonPath)
                               ^~~~~~~~
```
[R/io.R:100:10:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L100) *style:* **Variable and function names should be all lowercase.**
```r
  return(jsonToolContract)
         ^~~~~~~~~~~~~~~~
```
[R/io.R:107:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L107) *style:* **Variable and function names should be all lowercase.**
```r
  taskId <- t$tool_contract_id
  ^~~~~~
```
[R/io.R:110:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L110) *style:* **Variable and function names should be all lowercase.**
```r
  inputFiles <- t$input_files
  ^~~~~~~~~~
```
[R/io.R:112:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L112) *style:* **Variable and function names should be all lowercase.**
```r
  outputFiles <- t$output_files
  ^~~~~~~~~~~
```
[R/io.R:116:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L116) *style:* **Variable and function names should be all lowercase.**
```r
  taskType <- "NA"
  ^~~~~~~~
```
[R/io.R:117:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L117) *style:* **Variable and function names should be all lowercase.**
```r
  taskOptions <- list()
  ^~~~~~~~~~~
```
[R/io.R:120:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L120) *style:* **lines should not be more than 80 characters.**
```r
  resolvedToolContractTask <- methods::new("ResolvedToolContractTask", taskId = taskId,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:120:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L120) *style:* **Variable and function names should be all lowercase.**
```r
  resolvedToolContractTask <- methods::new("ResolvedToolContractTask", taskId = taskId,
  ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:120:81:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L120) *style:* **Variable and function names should be all lowercase.**
```r
  resolvedToolContractTask <- methods::new("ResolvedToolContractTask", taskId = taskId,
                                                                                ^~~~~~
```
[R/io.R:121:16:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L121) *style:* **Variable and function names should be all lowercase.**
```r
    taskType = taskType, inputFiles = inputFiles, outputFiles = outputFiles,
               ^~~~~~~~
```
[R/io.R:121:39:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L121) *style:* **Variable and function names should be all lowercase.**
```r
    taskType = taskType, inputFiles = inputFiles, outputFiles = outputFiles,
                                      ^~~~~~~~~~
```
[R/io.R:121:65:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L121) *style:* **Variable and function names should be all lowercase.**
```r
    taskType = taskType, inputFiles = inputFiles, outputFiles = outputFiles,
                                                                ^~~~~~~~~~~
```
[R/io.R:122:19:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L122) *style:* **Variable and function names should be all lowercase.**
```r
    taskOptions = taskOptions, nproc = nproc, resources = resources)
                  ^~~~~~~~~~~
```
[R/io.R:124:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L124) *style:* **lines should not be more than 80 characters.**
```r
  methods::new("ResolvedToolContract", task = resolvedToolContractTask, driver = driver)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:124:47:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L124) *style:* **Variable and function names should be all lowercase.**
```r
  methods::new("ResolvedToolContract", task = resolvedToolContractTask, driver = driver)
                                              ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/io.R:136:34:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L136) *style:* **Variable and function names should be all lowercase.**
```r
                      condId = d$condId,
                                 ^~~~~~
```
[R/io.R:144:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L144) *style:* **Variable and function names should be all lowercase.**
```r
  pipelineId <- d$pipelineId
  ^~~~~~~~~~
```
[R/io.R:144:19:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L144) *style:* **Variable and function names should be all lowercase.**
```r
  pipelineId <- d$pipelineId
                  ^~~~~~~~~~
```
[R/io.R:147:36:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/io.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
                      pipelineId = pipelineId,
                                   ^~~~~~~~~~
```
[R/pbreportsModel.R:19:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L19) *style:* **lines should not be more than 80 characters.**
```r
setClass("ReportAttribute", representation(value = "numeric", id = "character", name = "character"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pbreportsModel.R:22:1:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L22) *style:* **lines should not be more than 80 characters.**
```r
setClass("Report", representation(id = "character", version = "character", uuid = "character", attributes = "list", plotGroups = "list",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pbreportsModel.R:27:28:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L27) *style:* **Variable and function names should be all lowercase.**
```r
writeReport <- function(r, outputPath) {
                           ^~~~~~~~~~
```
[R/pbreportsModel.R:30:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L30) *style:* **Variable and function names should be all lowercase.**
```r
  toI <- function(i) {
  ^~~
```
[R/pbreportsModel.R:31:30:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L31) *style:* **Put spaces around all infix operators.**
```r
    return(paste(r@id, i, sep="."))
                            ~^~
```
[R/pbreportsModel.R:34:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L34) *style:* **Variable and function names should be all lowercase.**
```r
  attributeToD <- function(a) {
  ^~~~~~~~~~~~
```
[R/pbreportsModel.R:35:22:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L35) *style:* **Variable and function names should be all lowercase.**
```r
    return(list(id = toI(a@id), value = a@value, name = a@name))
                     ^~~
```
[R/pbreportsModel.R:38:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L38) *style:* **Variable and function names should be all lowercase.**
```r
  plotToD <- function(p) {
  ^~~~~~~
```
[R/pbreportsModel.R:39:53:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L39) *style:* **Variable and function names should be all lowercase.**
```r
    return(list(caption = NA, image = p@image, id = toI(p@id)))
                                                    ^~~
```
[R/pbreportsModel.R:42:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L42) *style:* **Variable and function names should be all lowercase.**
```r
  plotGroupToD <- function(p) {
  ^~~~~~~~~~~~
```
[R/pbreportsModel.R:43:18:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L43) *style:* **Variable and function names should be all lowercase.**
```r
    plots <- Map(plotToD, p@plots)
                 ^~~~~~~
```
[R/pbreportsModel.R:44:7:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L44) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(length(p@plots) == 0) {
      ^
```
[R/pbreportsModel.R:51:12:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L51) *style:* **Variable and function names should be all lowercase.**
```r
      id = toI(p@id),
           ^~~
```
[R/pbreportsModel.R:58:21:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L58) *style:* **Variable and function names should be all lowercase.**
```r
  attributes <- Map(attributeToD, r@attributes)
                    ^~~~~~~~~~~~
```
[R/pbreportsModel.R:59:3:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L59) *style:* **Variable and function names should be all lowercase.**
```r
  plotGroups <- Map(plotGroupToD, r@plotGroups)
  ^~~~~~~~~~
```
[R/pbreportsModel.R:59:21:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L59) *style:* **Variable and function names should be all lowercase.**
```r
  plotGroups <- Map(plotGroupToD, r@plotGroups)
                    ^~~~~~~~~~~~
```
[R/pbreportsModel.R:67:18:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L67) *style:* **Variable and function names should be all lowercase.**
```r
    plotGroups = plotGroups,
                 ^~~~~~~~~~
```
[R/pbreportsModel.R:71:20:](https://github.com/PacificBiosciences/pbcommandR/blob/eac75e88a31e9a92d611515acc2a972c6c5f16df/R/pbreportsModel.R#L71) *style:* **Variable and function names should be all lowercase.**
```r
  write(sx, file = outputPath)
                   ^~~~~~~~~~
```


this fix need a kernel fix too.

https://github.com/visi0nary/android_kernel_elephone_p8000/commit/35dbbf8f37cdd74a83a0c9fb954c6ad83641c8a6


Use textit


No one likes this new icon, please bring back the old one
https://m.reddit.com/r/cyanogenmod/comments/4i1f96/eleven_music_player_new_icon/?ref=readnext


Full stop


Which $S$


No meu está aparecendo a seguinte mensagem:

> Transação inválida. Sempre inicie transações a partir de sites confiáveis.

Sabe como posso resolver?


Given that CompositeOutputDevice is created with already-constructed devices, IMHO it's just as easy to do
```python
mydevice = CompositeOutputDevice(subdevice1=foo, subdevice2=bar, _order=('subdevice1', 'subdevice2'))
mydevice.value = (True, False)
```
as it is to do
```python
mydevice = CompositeOutputDevice(subdevice1=foo, subdevice2=bar, _order=('subdevice1', 'subdevice2'), initial_value=(True, False))
```
especially as the latter would effectively do the same as the former anyway. IYSWIM!

And of course if the `initial_value` really **is** important, you'd need to specify it when constructing the subdevices themselves.