[inst/cli/container_it.R:5:74:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L5) *style:* **Trailing whitespace is superfluous.**
```r
"container_it.R is a command-line interface to the R package containeRit.
                                                                         ^
```
[inst/cli/container_it.R:6:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L6) *style:* **lines should not be more than 80 characters.**
```r
It packages R sessions, scripts, workspaces and vignettes together with all dependencies to execute them in Docker containers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:9:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L9) *style:* **lines should not be more than 80 characters.**
```r
        container_it.R file [options] [--copy arg] [--cmd-render <FORMAT> | --cmd-R-file] <FILE>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:14:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L14) *style:* **lines should not be more than 80 characters.**
```r
    dir       Searches the given directory for R / Rmarkdown files and uses the first encounter for packaging
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:15:60:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L15) *style:* **Trailing whitespace is superfluous.**
```r
    file      Packages a given R script or R markdown file.
                                                           ^
```
[inst/cli/container_it.R:16:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L16) *style:* **lines should not be more than 80 characters.**
```r
              Optionally, the container can run a batch execution or rendering of the given file instead of an interactive R session.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:16:134:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L16) *style:* **Trailing whitespace is superfluous.**
```r
              Optionally, the container can run a batch execution or rendering of the given file instead of an interactive R session.
                                                                                ^
```
[inst/cli/container_it.R:17:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L17) *style:* **lines should not be more than 80 characters.**
```r
    session   Packages an empty R session in which a series of R commands may be executed (see option -e)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:18:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L18) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[inst/cli/container_it.R:20:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L20) *style:* **lines should not be more than 80 characters.**
```r
  --force -f          Force writing output even if a file of the same name already exists
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:21:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L21) *style:* **lines should not be more than 80 characters.**
```r
  --image <ARG>       Specify the Docker image that shall be used for the docker container (FROM-statement)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:22:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L22) *style:* **lines should not be more than 80 characters.**
```r
                      By default, the image is determinded from the given r_version,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:22:85:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L22) *style:* **Trailing whitespace is superfluous.**
```r
                      By default, the image is determinded from the given r_version,
                                                                                ^
```
[inst/cli/container_it.R:23:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L23) *style:* **lines should not be more than 80 characters.**
```r
                      while the version is matched with tags from the base image rocker/r-ver
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:24:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L24) *style:* **lines should not be more than 80 characters.**
```r
                      see details about the rocker/r-ver at https://hub.docker.com/r/rocker/r-ver/'
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:25:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L25) *style:* **lines should not be more than 80 characters.**
```r
  --maintainer-name -n <ARG>   Name of the dockerfile's maintainer (will be read from environment variables if not given)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:28:78:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L28) *style:* **Trailing whitespace is superfluous.**
```r
  --no-vanilla        Package a session / file without using the vanilla flag
                                                                             ^
```
[inst/cli/container_it.R:29:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L29) *style:* **lines should not be more than 80 characters.**
```r
                      (warning: site and environment files currently cannot be included in the container)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:30:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L30) *style:* **lines should not be more than 80 characters.**
```r
  --output -o FILE    Path and name of the output Dockerfile [default: ./Dockerfile]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:32:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L32) *style:* **lines should not be more than 80 characters.**
```r
  --r_version -r <ARG>  Specify an R version number that should run inside the container.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:32:90:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L32) *style:* **Trailing whitespace is superfluous.**
```r
  --r_version -r <ARG>  Specify an R version number that should run inside the container.
                                                                                ^
```
[inst/cli/container_it.R:33:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L33) *style:* **lines should not be more than 80 characters.**
```r
                      By default, the version of the currently linked R instance is used.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:34:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L34) *style:* **lines should not be more than 80 characters.**
```r
  --save -s <objects> ...    Save a list of objects from the workspace to an .RData file (overwrites --save-image)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:36:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L36) *style:* **lines should not be more than 80 characters.**
```r
  --soft              Whether to include soft dependencies among the system dependencies of R packages. [default: FALSE]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:37:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L37) *style:* **lines should not be more than 80 characters.**
```r
  --quiet -q          Run containeRit as silent as possible (print only errors and warnings) [default: FALSE]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:40:50:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L40) *style:* **Trailing whitespace is superfluous.**
```r
  --copy -c script | script_dir | <copy_file> ...
                                                 ^~~~~
```
[inst/cli/container_it.R:41:78:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L41) *style:* **Trailing whitespace is superfluous.**
```r
                      Indicates whether and how a workspace should be copied.
                                                                             ^
```
[inst/cli/container_it.R:42:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L42) *style:* **lines should not be more than 80 characters.**
```r
                      For the modes 'dir' and 'file' containeRit copies either the given input file, the complete directory
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:42:124:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L42) *style:* **Trailing whitespace is superfluous.**
```r
                      For the modes 'dir' and 'file' containeRit copies either the given input file, the complete directory
                                                                                ^
```
[inst/cli/container_it.R:43:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L43) *style:* **lines should not be more than 80 characters.**
```r
                      or a list of individual files and directories that should be located below the current directory.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:43:120:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L43) *style:* **Trailing whitespace is superfluous.**
```r
                      or a list of individual files and directories that should be located below the current directory.
                                                                                ^
```
[inst/cli/container_it.R:45:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L45) *style:* **lines should not be more than 80 characters.**
```r
  -d <DIR>            Directory to be used for packaging in mode 'dir'. Use either current dir or a folder below. [default: ./]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:46:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L46) *style:* **lines should not be more than 80 characters.**
```r
  -e <EXPR>           Expression do be executed within the R session that shall be packaged ('session' mode).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:47:32:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L47) *style:* **Trailing whitespace is superfluous.**
```r
  --cmd-render all | pdf | html
                               ^~~
```
[inst/cli/container_it.R:48:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L48) *style:* **lines should not be more than 80 characters.**
```r
                      Indicates that the given R markdown file should be rendered when running the container
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:49:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L49) *style:* **lines should not be more than 80 characters.**
```r
  --cmd-R-file        Indicates that the give R script should be executed on container startup (uses R -f example.R)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:54:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L54) *style:* **lines should not be more than 80 characters.**
```r
  # runs the first r-script / r-script file locally and prints the corresponding dockerfile
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:55:35:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L55) *style:* **Trailing whitespace is superfluous.**
```r
  container_it.R dir -p --no-write
                                  ^~
```
[inst/cli/container_it.R:56:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L56) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[inst/cli/container_it.R:58:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L58) *style:* **lines should not be more than 80 characters.**
```r
  # The Dockerfile will be written to the current directory and overwritten if it already exists
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:59:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L59) *style:* **lines should not be more than 80 characters.**
```r
  # It contains instructions to copy the script and workspace image and to execute the script on start-up
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:62:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L62) *style:* **lines should not be more than 80 characters.**
```r
  # Creates an empty R session and executes the given R commands, which later can be reproduced in the docker container
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:64:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L64) *style:* **lines should not be more than 80 characters.**
```r
  container_it.R session -p -e \"library(sp)\" -e \"demo(meuse, ask=FALSE)\" --r_version 3.3.0
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:69:9:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L69) *style:* **Variable and function names should be all lowercase.**
```r
library(containeRit)
        ^~~~~~~~~~~
```
[inst/cli/container_it.R:71:3:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L71) *style:* **Place a space before left parenthesis, except in a function call.**
```r
if(length(commandArgs(trailingOnly=TRUE))== 0){
  ^
```
[inst/cli/container_it.R:71:35:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L71) *style:* **Put spaces around all infix operators.**
```r
if(length(commandArgs(trailingOnly=TRUE))== 0){
                                 ~^~
```
[inst/cli/container_it.R:71:42:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L71) *style:* **Put spaces around all infix operators.**
```r
if(length(commandArgs(trailingOnly=TRUE))== 0){
                                        ~^
```
[inst/cli/container_it.R:73:5:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L73) *style:* **Commented code should be removed.**
```r
  # opts <- docopt::docopt(doc, "--help")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:76:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L76) *style:* **lines should not be more than 80 characters.**
```r
  opts <- docopt::docopt(doc , version = paste0("containeRit ", utils::packageVersion("containeRit"),"\n"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:76:30:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L76) *style:* **Commas should never have a space before.**
```r
  opts <- docopt::docopt(doc , version = paste0("containeRit ", utils::packageVersion("containeRit"),"\n"))
                            ~^
```
[inst/cli/container_it.R:76:102:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L76) *style:* **Commas should always have a space after.**
```r
  opts <- docopt::docopt(doc , version = paste0("containeRit ", utils::packageVersion("containeRit"),"\n"))
                                                                                ^
```
[inst/cli/container_it.R:78:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L78) *style:* **Trailing whitespace is superfluous.**
```r

^
```
[inst/cli/container_it.R:80:5:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L80) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(opts[["quiet"]])
    ^
```
[inst/cli/container_it.R:82:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L82) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[inst/cli/container_it.R:83:15:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L83) *style:* **Use <-, not =, for assignment.**
```r
  output_file =  opts[["output"]]
              ^
```
[inst/cli/container_it.R:84:5:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L84) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(file.exists(output_file) && !opts[["force"]] && !opts[["--no-write"]])
    ^
```
[inst/cli/container_it.R:85:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L85) *style:* **lines should not be more than 80 characters.**
```r
    stop("Dockerfile cannot be written because the target file already exists.\n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:86:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L86) *style:* **lines should not be more than 80 characters.**
```r
         "\t Re-run with option -f / --force in order to overwride the file or use the flag --no-write.")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:88:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L88) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[inst/cli/container_it.R:89:5:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L89) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(opts[["maintainer-name"]])){
    ^
```
[inst/cli/container_it.R:94:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L94) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[inst/cli/container_it.R:95:5:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L95) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.null(opts[["maintainer-email"]])){
    ^
```
[inst/cli/container_it.R:96:26:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L96) *style:* **Commas should always have a space after.**
```r
    slot(this_maintainer,"email") <- opts[["maintainer-email"]]
                         ^
```
[inst/cli/container_it.R:98:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L98) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[inst/cli/container_it.R:101:5:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L101) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.null(opts[["save"]])){
    ^
```
[inst/cli/container_it.R:104:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L104) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[inst/cli/container_it.R:106:5:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L106) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(opts$session == TRUE){
    ^
```
[inst/cli/container_it.R:108:7:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L108) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(!is.null(opts[["-e"]])){
      ^
```
[inst/cli/container_it.R:112:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L112) *style:* **lines should not be more than 80 characters.**
```r
    from <- clean_session(expr = expr,vanilla = !opts[["no-vanilla"]], slave = opts[["quiet"]])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:112:39:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L112) *style:* **Commas should always have a space after.**
```r
    from <- clean_session(expr = expr,vanilla = !opts[["no-vanilla"]], slave = opts[["quiet"]])
                                      ^
```
[inst/cli/container_it.R:115:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L115) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[inst/cli/container_it.R:116:7:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L116) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(opts$dir == TRUE){
      ^
```
[inst/cli/container_it.R:118:13:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L118) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    }else if(opts$file == TRUE){
            ^
```
[inst/cli/container_it.R:121:33:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L121) *style:* **Trailing whitespace is superfluous.**
```r
      stop("Invalid arguments!")
                                ^~
```
[inst/cli/container_it.R:123:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L123) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[inst/cli/container_it.R:124:7:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L124) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(!is.null(opts[["cmd-render"]]) &&
      ^
```
[inst/cli/container_it.R:127:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L127) *style:* **lines should not be more than 80 characters.**
```r
        this_cmd <- CMD_Render(from, output_format = rmarkdown::all_output_formats())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[inst/cli/container_it.R:132:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L132) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~
```
[inst/cli/container_it.R:139:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L139) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[inst/cli/container_it.R:140:39:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L140) *style:* **Trailing whitespace is superfluous.**
```r
  dockerfile_args <- list(from = from,
                                      ^
```
[inst/cli/container_it.R:141:44:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L141) *style:* **Trailing whitespace is superfluous.**
```r
                          copy = opts$copy,
                                           ^
```
[inst/cli/container_it.R:142:47:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L142) *style:* **Trailing whitespace is superfluous.**
```r
                          silent = opts$quiet,
                                              ^
```
[inst/cli/container_it.R:143:51:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L143) *style:* **Trailing whitespace is superfluous.**
```r
                          save_image = save_image,
                                                  ^
```
[inst/cli/container_it.R:144:56:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L144) *style:* **Trailing whitespace is superfluous.**
```r
                          maintainer = this_maintainer,
                                                       ^
```
[inst/cli/container_it.R:145:42:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L145) *style:* **Trailing whitespace is superfluous.**
```r
                          cmd = this_cmd,
                                         ^
```
[inst/cli/container_it.R:147:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L147) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[inst/cli/container_it.R:149:5:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L149) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.null(opts[["image"]]))
    ^
```
[inst/cli/container_it.R:151:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L151) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[inst/cli/container_it.R:152:5:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L152) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.null(opts[["r_version"]]))
    ^
```
[inst/cli/container_it.R:154:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L154) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[inst/cli/container_it.R:156:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L156) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[inst/cli/container_it.R:157:6:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L157) *style:* **Place a space before left parenthesis, except in a function call.**
```r
   if(!opts[["no-write"]]){
     ^
```
[inst/cli/container_it.R:160:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L160) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[inst/cli/container_it.R:161:5:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L161) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(opts[["print"]]){
    ^
```
[inst/cli/container_it.R:165:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/inst/cli/container_it.R#L165) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/Class-Add.R:32:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Add.R#L32) *style:* **lines should not be more than 80 characters.**
```r
            stop("The generic function docker_arguments is not implemented for class ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Cmd.R:32:3:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L32) *warning:* **no visible global function definition for ‘new’, Did you mean 'news'?**
```r
  new("Cmd",  exec = exec, params = params)
  ^~~
```
[R/Class-Cmd.R:40:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L40) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/Class-Cmd.R:50:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L50) *style:* **lines should not be more than 80 characters.**
```r
      return("More than one exec parameter was given: ", paste(exec, sep = ", "))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Cmd.R:51:9:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L51) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if ((length(params) > 1 && any(is.na(params))) ||
        ^
```
[R/Class-Cmd.R:53:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L53) *style:* **lines should not be more than 80 characters.**
```r
      return("If parameters are given for CMD, they cannot be empty strings or NA")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Cmd.R:54:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L54) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/Class-Cmd.R:56:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L56) *style:* **lines should not be more than 80 characters.**
```r
      "A Cmd instruction must at least have one non-empty exec-argument or one or more parameters given (i.e. as default for an entrypoint)."
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Cmd.R:61:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L61) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
.arguments.Cmd_Run <- function(obj) {
^~~~~~~~~~~~~~~~~~
```
[R/Class-Cmd.R:65:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L65) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/Class-Cmd.R:66:11:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L66) *warning:* **no visible global function definition for ‘slot’, Did you mean 'plot'?**
```r
  exec <- slot(obj, "exec")
          ^~~~
```
[R/Class-Cmd.R:67:13:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L67) *warning:* **no visible global function definition for ‘slot’, Did you mean 'plot'?**
```r
  params <- slot(obj, "params")
            ^~~~
```
[R/Class-Cmd.R:74:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L74) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/Class-Cmd.R:81:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L81) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/Class-Cmd.R:87:11:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L87) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
          .arguments.Cmd_Run)
          ^~~~~~~~~~~~~~~~~~
```
[R/Class-Cmd.R:101:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L101) *style:* **lines should not be more than 80 characters.**
```r
CMD_Rscript <- function(path, options = character(0), args = character(0), vanilla = TRUE){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Cmd.R:102:5:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L102) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(vanilla)
    ^
```
[R/Class-Cmd.R:106:3:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L106) *warning:* **no visible global function definition for ‘Cmd’, Did you mean 'C'?**
```r
  Cmd("R", params = params)
  ^~~
```
[R/Class-Cmd.R:125:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L125) *style:* **lines should not be more than 80 characters.**
```r
CMD_Render <- function(path, options = character(0), output_format = rmarkdown::html_document(), output_dir = NULL, vanilla = TRUE){
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Cmd.R:126:5:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L126) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(vanilla)
    ^
```
[R/Class-Cmd.R:129:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L129) *style:* **lines should not be more than 80 characters.**
```r
  render_call <- quote(rmarkdown::render("file", output_format = "format", output_dir = NULL))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Cmd.R:133:38:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L133) *style:* **Commas should always have a space after.**
```r
  render_call <- deparse(render_call,width.cutoff = 500)
                                     ^
```
[R/Class-Cmd.R:134:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L134) *style:* **lines should not be more than 80 characters.**
```r
  render_call <- deparse(render_call,width.cutoff = 500) #yes, twice! (command line expects R commands as strings)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Cmd.R:134:38:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L134) *style:* **Commas should always have a space after.**
```r
  render_call <- deparse(render_call,width.cutoff = 500) #yes, twice! (command line expects R commands as strings)
                                     ^
```
[R/Class-Cmd.R:135:55:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L135) *style:* **Commas should always have a space after.**
```r
  render_call <- stringr::str_replace_all(render_call,"^\\\"|\\\"$","")
                                                      ^
```
[R/Class-Cmd.R:135:69:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L135) *style:* **Commas should always have a space after.**
```r
  render_call <- stringr::str_replace_all(render_call,"^\\\"|\\\"$","")
                                                                    ^
```
[R/Class-Cmd.R:137:27:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L137) *style:* **Commas should never have a space before.**
```r
  params <- append(params , expr)
                         ~^
```
[R/Class-Cmd.R:138:3:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L138) *warning:* **no visible global function definition for ‘Cmd’, Did you mean 'C'?**
```r
  Cmd("R", params = as.character(params))
  ^~~
```
[R/Class-Cmd.R:140:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Cmd.R#L140) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/Class-Copy.R:16:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L16) *style:* **lines should not be more than 80 characters.**
```r
setClass("Copy", slots=list(src = "character", dest="character"), contains = "Instruction")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Copy.R:16:23:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L16) *style:* **Put spaces around all infix operators.**
```r
setClass("Copy", slots=list(src = "character", dest="character"), contains = "Instruction")
                     ~^~
```
[R/Class-Copy.R:16:52:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L16) *style:* **Put spaces around all infix operators.**
```r
setClass("Copy", slots=list(src = "character", dest="character"), contains = "Instruction")
                                                  ~^~
```
[R/Class-Copy.R:30:3:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L30) *warning:* **no visible global function definition for ‘new’, Did you mean 'news'?**
```r
  new("Copy",  src = src, dest=dest)
  ^~~
```
[R/Class-Copy.R:30:31:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L30) *style:* **Put spaces around all infix operators.**
```r
  new("Copy",  src = src, dest=dest)
                             ~^~
```
[R/Class-Copy.R:36:16:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L36) *style:* **Use <-, not =, for assignment.**
```r
            out=sprintf('"%s"', slot(obj, "src"))
               ^
```
[R/Class-Copy.R:36:16:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L36) *style:* **Put spaces around all infix operators.**
```r
            out=sprintf('"%s"', slot(obj, "src"))
              ~^~
```
[R/Class-Copy.R:37:16:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L37) *style:* **Use <-, not =, for assignment.**
```r
            out=append(out, sprintf('"%s"', slot(obj, "dest")))
               ^
```
[R/Class-Copy.R:37:16:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L37) *style:* **Put spaces around all infix operators.**
```r
            out=append(out, sprintf('"%s"', slot(obj, "dest")))
              ~^~
```
[R/Class-Copy.R:38:16:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L38) *style:* **Use <-, not =, for assignment.**
```r
            out=paste(out, collapse = ", ")
               ^
```
[R/Class-Copy.R:38:16:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L38) *style:* **Put spaces around all infix operators.**
```r
            out=paste(out, collapse = ", ")
              ~^~
```
[R/Class-Copy.R:39:16:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L39) *style:* **Use <-, not =, for assignment.**
```r
            out=sprintf("[%s]", out)
               ^
```
[R/Class-Copy.R:39:16:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L39) *style:* **Put spaces around all infix operators.**
```r
            out=sprintf("[%s]", out)
              ~^~
```
[R/Class-Copy.R:48:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L48) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~~~~~
```
[R/Class-Copy.R:49:17:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L49) *style:* **Place a space before left parenthesis, except in a function call.**
```r
              if(length(src) < 1){
                ^
```
[R/Class-Copy.R:50:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L50) *style:* **lines should not be more than 80 characters.**
```r
                return("Invalid RUN instruction: There must be at least one file / directory given by 'src'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Copy.R:52:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L52) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~~~~~
```
[R/Class-Copy.R:53:17:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L53) *style:* **Place a space before left parenthesis, except in a function call.**
```r
              if(length(dest) != 1){
                ^
```
[R/Class-Copy.R:54:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Copy.R#L54) *style:* **lines should not be more than 80 characters.**
```r
                return("Invalid RUN instruction: There must be exactly one destination folder given by 'dest'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Entrypoint.R:31:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Entrypoint.R#L31) *style:* **lines should not be more than 80 characters.**
```r
            stop("The generic function docker_arguments is not implemented for class ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Env.R:33:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Env.R#L33) *style:* **lines should not be more than 80 characters.**
```r
            stop("The generic function docker_arguments is not implemented for class ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Expose.R:28:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Expose.R#L28) *style:* **lines should not be more than 80 characters.**
```r
            stop("The generic function docker_arguments is not implemented for class ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-From.R:45:12:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-From.R#L45) *warning:* **no visible global function definition for ‘new’, Did you mean 'news'?**
```r
    tag <- new("Tag", tag)
           ^~~
```
[R/Class-From.R:46:12:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-From.R#L46) *warning:* **no visible global function definition for ‘new’, Did you mean 'news'?**
```r
    return(new("From", image = image, postfix = tag))
           ^~~
```
[R/Class-From.R:60:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-From.R#L60) *style:* **Variable and function names should be all lowercase.**
```r
parseFrom <- function(string) {
^~~~~~~~~
```
[R/Class-From.R:64:12:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-From.R#L64) *warning:* **no visible global function definition for ‘From’, Did you mean 'proj'?**
```r
    return(From(image = split[1], digest = split[2]))
           ^~~~
```
[R/Class-From.R:68:12:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-From.R#L68) *warning:* **no visible global function definition for ‘From’, Did you mean 'proj'?**
```r
    return(From(image = split[1], tag = split[2]))
           ^~~~
```
[R/Class-From.R:70:12:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-From.R#L70) *warning:* **no visible global function definition for ‘From’, Did you mean 'proj'?**
```r
    return(From(string))
           ^~~~
```
[R/Class-Instruction.R:35:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Instruction.R#L35) *style:* **lines should not be more than 80 characters.**
```r
            stop("The generic function docker_arguments is not implemented for class ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Instruction.R:40:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Instruction.R#L40) *style:* **Variable and function names should be all lowercase.**
```r
.toString.Instruction <- function(x) {
^~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Instruction.R:40:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Instruction.R#L40) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
.toString.Instruction <- function(x) {
^~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Instruction.R:41:16:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Instruction.R#L41) *warning:* **no visible global function definition for ‘docker_key’**
```r
  return(paste(docker_key(x), docker_arguments(x)))
               ^~~~~~~~~~
```
[R/Class-Instruction.R:41:31:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Instruction.R#L41) *warning:* **no visible global function definition for ‘docker_arguments’**
```r
  return(paste(docker_key(x), docker_arguments(x)))
                              ^~~~~~~~~~~~~~~~
```
[R/Class-Instruction.R:47:11:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Instruction.R#L47) *style:* **Variable and function names should be all lowercase.**
```r
          .toString.Instruction)
          ^~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Instruction.R:47:11:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Instruction.R#L47) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
          .toString.Instruction)
          ^~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Instruction.R:59:11:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Instruction.R#L59) *style:* **Variable and function names should be all lowercase.**
```r
          .toString.Instruction)
          ^~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Instruction.R:59:11:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Instruction.R#L59) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
          .toString.Instruction)
          ^~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Label.R:13:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Label.R#L13) *style:* **lines should not be more than 80 characters.**
```r
setClass("Label", slots = list(data = "list", multi_line = "logical"), contains = "Instruction")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Label.R:30:3:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Label.R#L30) *warning:* **no visible global function definition for ‘new’, Did you mean 'news'?**
```r
  new("Label", data = data, multi_line = multi_line)
  ^~~
```
[R/Class-Label.R:41:40:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Label.R#L41) *style:* **Commas should always have a space after.**
```r
            values <- sprintf("\"%s\"",as.character(args))
                                       ^
```
[R/Class-Label.R:43:15:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Label.R#L43) *style:* **Place a space before left parenthesis, except in a function call.**
```r
            if(slot(obj, "multi_line"))
              ^
```
[R/Class-Maintainer.R:28:3:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Maintainer.R#L28) *warning:* **no visible global function definition for ‘new’, Did you mean 'news'?**
```r
  new("Maintainer", name = name, email = email)
  ^~~
```
[R/Class-Maintainer.R:35:56:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Maintainer.R#L35) *style:* **Put spaces around all infix operators.**
```r
setMethod("docker_arguments", signature = signature(obj="Maintainer"),
                                                      ~^~
```
[R/Class-Run.R:16:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L16) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
.arguments.Run_shell <- function(obj) {
^~~~~~~~~~~~~~~~~~~~
```
[R/Class-Run.R:20:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L20) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/Class-Run.R:21:15:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L21) *warning:* **no visible global function definition for ‘slot’, Did you mean 'plot'?**
```r
  commands <- slot(obj, "commands")
              ^~~~
```
[R/Class-Run.R:22:52:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L22) *style:* **Trailing whitespace is superfluous.**
```r
  string <- paste(commands, collapse = " \\\n && ")
                                                   ^
```
[R/Class-Run.R:28:11:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L28) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
          .arguments.Run_shell #uses the same function as Cmd for now
          ^~~~~~~~~~~~~~~~~~~~
```
[R/Class-Run.R:43:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L43) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~~~~~
```
[R/Class-Run.R:44:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L44) *style:* **lines should not be more than 80 characters.**
```r
              if(is.na(commands) || length(commands) == 0 || any(stringr::str_length(commands) == 0))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Run.R:44:17:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L44) *style:* **Place a space before left parenthesis, except in a function call.**
```r
              if(is.na(commands) || length(commands) == 0 || any(stringr::str_length(commands) == 0))
                ^
```
[R/Class-Run.R:45:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L45) *style:* **lines should not be more than 80 characters.**
```r
                return(paste("Commands must have at least one string and empty strings are not alowed. Given was: \n\t", paste(commands,collapse = "\n\t")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Run.R:45:137:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L45) *style:* **Commas should always have a space after.**
```r
                return(paste("Commands must have at least one string and empty strings are not alowed. Given was: \n\t", paste(commands,collapse = "\n\t")))
                                                                                ^
```
[R/Class-Run.R:46:19:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L46) *style:* **Trailing whitespace is superfluous.**
```r
              else
                  ^~
```
[R/Class-Run.R:58:3:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L58) *warning:* **no visible global function definition for ‘new’, Did you mean 'news'?**
```r
  new("Run_shell",  commands = commands)
  ^~~
```
[R/Class-Run.R:84:3:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L84) *warning:* **no visible global function definition for ‘new’, Did you mean 'news'?**
```r
  new("Run",  exec = exec, params = params)
  ^~~
```
[R/Class-Run.R:89:11:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L89) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
          .arguments.Cmd_Run #uses the same function as Cmd for now
          ^~~~~~~~~~~~~~~~~~
```
[R/Class-Run.R:96:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L96) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~~~~~
```
[R/Class-Run.R:97:17:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L97) *style:* **Place a space before left parenthesis, except in a function call.**
```r
              if(is.na(exec) || stringr::str_length(exec) == 0)
                ^
```
[R/Class-Run.R:98:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L98) *style:* **lines should not be more than 80 characters.**
```r
                return(paste("Exec must be a non-empty string, given was: ", exec))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Run.R:103:21:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L103) *style:* **Place a space before left parenthesis, except in a function call.**
```r
                if ((length(params) > 1 && any(is.na(params))) ||
                    ^
```
[R/Class-Run.R:105:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L105) *style:* **lines should not be more than 80 characters.**
```r
                  return("If parameters are given for RUN (optional), they cannot be empty strings or NA")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Run.R:106:19:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Run.R#L106) *style:* **Trailing whitespace is superfluous.**
```r
              else
                  ^~
```
[R/Class-Volume.R:32:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Volume.R#L32) *style:* **lines should not be more than 80 characters.**
```r
            stop("The generic function docker_arguments is not implemented for class ",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/Class-Workdir.R:26:3:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/Class-Workdir.R#L26) *warning:* **no visible global function definition for ‘new’, Did you mean 'news'?**
```r
  new("Workdir", path = path)
  ^~~
```
[R/defaults.R:3:2:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/defaults.R#L3) *style:* **Commented code should be removed.**
```r
##set CRAN mirror (the rocker default MRAN is sometimes not up-to-date with current packages)
 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/defaults.R:12:10:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/defaults.R#L12) *warning:* **no visible binding for global variable ‘.default_cran_mirror’**
```r
  return(.default_cran_mirror)
         ^~~~~~~~~~~~~~~~~~~~
```
[R/defaults.R:22:3:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/defaults.R#L22) *warning:* **no visible binding for '<<-' assignment to ‘.default_cran_mirror’**
```r
  .default_cran_mirror <<- cran_url
  ^~~~~~~~~~~~~~~~~~~~
```
[R/defaults.R:34:18:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/defaults.R#L34) *style:* **Use <-, not =, for assignment.**
```r
.debian_platform = "linux-x86_64-debian-gcc"
                 ^
```
[R/defaults.R:36:18:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/defaults.R#L36) *style:* **Use <-, not =, for assignment.**
```r
.ubuntu_platform = "linux-x86_64-ubuntu-gcc"
                 ^
```
[R/defaults.R:41:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/defaults.R#L41) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/dockerfile.R:37:24:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/dockerfile.R#L37) *style:* **Variable and function names should be all lowercase.**
```r
           r_version = getRVersionTag(from),
                       ^~~~~~~~~~~~~~
```
[R/dockerfile.R:38:20:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/dockerfile.R#L38) *style:* **Variable and function names should be all lowercase.**
```r
           image = imagefromRVersion(r_version),
                   ^~~~~~~~~~~~~~~~~
```
[R/dockerfile.R:39:1:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/dockerfile.R#L39) *style:* **lines should not be more than 80 characters.**
```r
           env = list(generator = paste("containeRit", utils::packageVersion("containeRit"))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dockerfile.R:40:32:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/dockerfile.R#L40) *style:* **Trailing whitespace is superfluous.**
```r
           context = "workdir",
                               ^
```
[R/dockerfile.R:43:33:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/dockerfile.R#L43) *warning:* **Do not use absolute paths.**
```r
           container_workdir = "/payload",
                                ^~~~~~~~
```
[R/dockerfile.R:49:7:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/dockerfile.R#L49) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      {
      ^
```
[R/dockerfile.R:50:7:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/dockerfile.R#L50) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(silent){
      ^
```
[R/dockerfile.R:53:5:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/dockerfile.R#L53) *warning:* **no visible global function definition for ‘flog.debug’**
```r
    flog.debug("Creating a new Dockerfile from %s", from)
    ^~~~~~~~~~
```
[R/dockerfile.R:55:5:](https://github.com/MatthiasHinz/containerit/blob/20b1fa856cc42e6bfe0ca14bcc767c896ff0b0d5/R/dockerfile.R#L55) *style:* **Variable and function names should be all lowercase.**
```r
    .originalFrom <- class(from)
    ^~~~~~~~~~~~~
```


Good catch here as gcc 4.9 is the minimum to provide the C++11 features needed.


[R/DEploidR.R:20:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L20) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:20:38:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L20) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                     ^~~~~~~~~~~
```
[R/DEploidR.R:20:51:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L20) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                                  ^~~~~~~~~~~
```
[R/DEploidR.R:49:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L49) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:49:38:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L49) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
                                     ^~~~~~~~~~~
```
[R/DEploidR.R:49:51:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L49) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function ( vcfFileName, ADFieldIndex = 2 ){
                                                  ^~~~~~~~~~~~
```
[R/DEploidR.R:57:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L57) *style:* **Variable or function name should be snake_case.**
```r
    numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:61:13:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L61) *style:* **Variable or function name should be snake_case.**
```r
            numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:73:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L73) *style:* **Variable or function name should be snake_case.**
```r
    sampleName <- names(vcf)[10]
    ^~~~~~~~~~
```
[R/DEploidR.R:78:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L78) *style:* **Variable or function name should be snake_case.**
```r
    tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~
```
[R/DEploidR.R:79:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L79) *style:* **Variable or function name should be snake_case.**
```r
    tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~
```
[R/DEploidR.R:81:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L81) *style:* **Variable or function name should be snake_case.**
```r
    refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~
```
[R/DEploidR.R:82:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L82) *style:* **Variable or function name should be snake_case.**
```r
    altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~
```
[R/DEploidR.R:108:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L108) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function ( plafFileName ){
^~~~~~~~~~~
```
[R/DEploidR.R:108:27:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L108) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function ( plafFileName ){
                          ^~~~~~~~~~~~
```
[R/DEploidR.R:139:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L139) *style:* **Variable or function name should be snake_case.**
```r
plotProportions <- function (proportions, title = "Components",
^~~~~~~~~~~~~~~
```
[R/DEploidR.R:140:24:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L140) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                       ^~~~~~~
```
[R/DEploidR.R:140:37:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L140) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                    ^~~~~~~~
```
[R/DEploidR.R:140:51:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L140) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                                  ^~~~~~~~
```
[R/DEploidR.R:141:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L141) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[R/DEploidR.R:183:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L183) *style:* **Variable or function name should be snake_case.**
```r
plotAltVsRef <- function ( ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~
```
[R/DEploidR.R:184:21:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L184) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~
```
[R/DEploidR.R:184:40:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L184) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~
```
[R/DEploidR.R:185:21:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L185) *style:* **Variable or function name should be snake_case.**
```r
                    cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                    ^~~~~~~
```
[R/DEploidR.R:185:34:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L185) *style:* **Variable or function name should be snake_case.**
```r
                    cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                 ^~~~~~~~
```
[R/DEploidR.R:185:48:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L185) *style:* **Variable or function name should be snake_case.**
```r
                    cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                               ^~~~~~~~
```
[R/DEploidR.R:189:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L189) *style:* **Variable or function name should be snake_case.**
```r
    tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~
```
[R/DEploidR.R:243:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L243) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function ( obsWSAF, exclusive = TRUE,
^~~~~~~~
```
[R/DEploidR.R:243:24:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L243) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function ( obsWSAF, exclusive = TRUE,
                       ^~~~~~~
```
[R/DEploidR.R:245:17:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L245) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                ^~~~~~~
```
[R/DEploidR.R:245:30:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L245) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                             ^~~~~~~~
```
[R/DEploidR.R:245:44:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L245) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                           ^~~~~~~~
```
[R/DEploidR.R:246:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L246) *style:* **Variable or function name should be snake_case.**
```r
    tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~
```
[R/DEploidR.R:248:9:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L248) *style:* **Variable or function name should be snake_case.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0) ) == 1)
        ^~~~~~~~~~~~
```
[R/DEploidR.R:295:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L295) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~
```
[R/DEploidR.R:295:36:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L295) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
                                   ^~~~~~~
```
[R/DEploidR.R:295:45:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L295) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function ( plaf, obsWSAF, expWSAF = c(),
                                            ^~~~~~~
```
[R/DEploidR.R:297:23:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L297) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                      ^~~~~~~
```
[R/DEploidR.R:297:36:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L297) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                   ^~~~~~~~
```
[R/DEploidR.R:297:50:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L297) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                                 ^~~~~~~~
```
[R/DEploidR.R:336:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L336) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function (obsWSAF, expWSAF,
^~~~~~~~~~~~~~
```
[R/DEploidR.R:336:29:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L336) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function (obsWSAF, expWSAF,
                            ^~~~~~~
```
[R/DEploidR.R:336:38:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L336) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function (obsWSAF, expWSAF,
                                     ^~~~~~~
```
[R/DEploidR.R:338:23:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L338) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                      ^~~~~~~
```
[R/DEploidR.R:338:36:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L338) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                   ^~~~~~~~
```
[R/DEploidR.R:338:50:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L338) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1 ){
                                                 ^~~~~~~~
```
[R/DEploidR.R:374:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L374) *style:* **Variable or function name should be snake_case.**
```r
computeObsWSAF <- function (alt, ref) {
^~~~~~~~~~~~~~
```
[R/DEploidR.R:391:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L391) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function (posteriorProbabilities, title = "", labelScaling){
^~~~~~~~~~~~~~~~
```
[R/DEploidR.R:391:31:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L391) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function (posteriorProbabilities, title = "", labelScaling){
                              ^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:391:67:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L391) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function (posteriorProbabilities, title = "", labelScaling){
                                                                  ^~~~~~~~~~~~
```
[R/DEploidR.R:392:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/R/DEploidR.R#L392) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L3) *style:* **Variable or function name should be snake_case.**
```r
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:5:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:7:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L7) *style:* **Variable or function name should be snake_case.**
```r
panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:9:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L9) *style:* **Variable or function name should be snake_case.**
```r
refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:10:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L10) *style:* **Variable or function name should be snake_case.**
```r
altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:12:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L12) *style:* **Variable or function name should be snake_case.**
```r
PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:15:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L15) *style:* **Variable or function name should be snake_case.**
```r
PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:18:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L18) *style:* **Variable or function name should be snake_case.**
```r
expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:21:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L21) *style:* **Variable or function name should be snake_case.**
```r
    PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:44:5:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-DEploid_tools.R#L44) *style:* **Variable or function name should be snake_case.**
```r
    obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~
```
[tests/testthat/test-dEploid.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-dEploid.R#L3) *style:* **Variable or function name should be snake_case.**
```r
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~
```
[tests/testthat/test-dEploid.R:5:1:](https://github.com/mcveanlab/DEploid-r/blob/be1f6f4ec2e294ba378d7e6286b6c1074dfa8317/tests/testthat/test-dEploid.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```


<div class="row">


the class is set to: `class="dirty fa fa-circle"` as expected.


Fixed https://github.com/dart-lang/sdk/commit/0d785a7f414637ea5aab28ba321841df092c06d4


`<div class="row">`


-define('API_URL', 'https://api.telegram.org/bot'.BOT_TOKEN.'/');


use col-md-* as it will scale at the same size as the sidebar


@gtmanfred is there an open issue I can take a look at?


Validate that an nfs volume can't be mounted from inside container. The command below should fail

docker run -ti --net=routed --privileged --ip=192.168.2.2 debian /bin/sh -c 'mount -t nfs --read-write 10.1.1.233:/data foo -o async'


это лучше сделать даже ссылкой. Потому-что вполне возможно, что там может быть переход на отдельную страницу с формой.


I believe what was happening was that with the defer in place a tool from the initial set had started its loadedCorpus handling, got destroyed by replacePanel, and then tried to handle callbacks related to the loadedCorpus handling, e.g. initializing stores that no longer existed.


почему ссылка-то пустая?


To keep with the material theme, use the {%block actions%} so the button will be in the bottom right corner. See floating buttons on https://mdbootstrap.com/mdb3/components/buttons/


I kinda figured this entire page will be changing, hence why i didn't put too much thought into this


Sorry, I thought I linked it https://github.com/saltstack/salt/issues/39995
On Fri, Mar 17, 2017 at 4:13 PM Ivan Babrou <notifications@github.com>
wrote:

> @gtmanfred <https://github.com/gtmanfred> is there an open issue I can
> take a look at?
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <https://github.com/saltstack/salt/commit/9a34fbeba9aa526079a80a14eda29aa790d0dd6a#commitcomment-21380580>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AAssoQLDyKnaplugARkITdGvalQCj31Hks5rmwVfgaJpZM4MhIyH>
> .
>


HI my name is Milan and i just started to mess with Kinect in unity. I have found an interesting issue - when i try to run the Dressing room i get the error that the UnityInterface.dll is not found and the error is reported on line 508 in Nite.cs which is referencing to OpenNI.xml (which is also present). after that initial report DressingRoom.cs starts an infinite loop of trying to get GUI components. I was wondering if you could help me with this issue since i can't seem to be able to find a solution to any similar issue online.
Thance in advance :D


State returns mState so it basically doesn't matter.


again, this page is not going to stay like this, i just needed a way to get to the page that wasn't typing in a URL haha


Кнопка "отправить" в попапе не должна прыгать


We need to discuss what is going on this page in the future


how very pass of you lol


кнопка закрыть в попапе теперь пропало чет


Several people (and me too) struck into this previously. This could be simply fixed, but requires simultaneous fix to `gym`. I can prepare a PR if you are interested.


Is the "life-ring" commonly used for "help" ... seems strange for me. I'd expect: "fa-question-circle"


Any suggestions on how to resolve that problem while still supporting the panels param?


оптимизация с картой конечно хороша
но сделай её по людски.
http://prntscr.com/elaf17
а то не красиво смотрится
её нужно или в контейрен ставить, или просто центровать
или растягивать bgc-size : cover;


и спрайта(корзины) не видно терь


@a-frobot docs-v0.5.0


Good file! I like how it works


предварительные комменты.
завтра ещё гляну код


Fixes #353


After digging into how to remove these warnings (passing function as children), I'm now seeing that the warnings are temporarily removed.

It's not clear to me how passing a function with the components children would affect the `appliedStyle`. Could you provide an example of how to override the default style without using the style prop?


One thing to note here - you can only perform 500 mutations in a single call (or in one transaction).
We *don't* perform the batching for you transparently, because there are too many different ways you can handle it.

If you import the MoreLinq NuGet package, you can use:

```csharp
// Removed currying function - don't think it was adding much
var reportEntityBatches = summary.Reports.Select(report => BuildReportEntity(report, reportKeyFactory)).Batch(500);
foreach (var batch in reportEntityBatches)
{
    DatastoreDb.Insert(batch);
}
```


oops, thought it was covered by bin in the bin key


It's issue #6 from antergos-repo-priority


Just had a thought, can this end up in `CloseReceived` or `CloseSent` when the connection dispose? Does it matter if it is not in `Closed`?


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


Good Stuff!


You might be, did you checkout latest on v0.7 and npm install?


Looks like a white-space issue here with the `^M` character rather than a proper tab.


[DateRangeInput] Add selectAllOnFocus prop (#858)

Preview: docs
Coverage: core | datetime


I'm new to Spock and this seems like a smell, is there a more Spock idiomatic way of doing this sort of thing?


Strange, what do you see?


Also, line breaks are weird.


How did you dig this up :) I have no memory of this.
Anyway, what I meant is something like: https://gist.github.com/yang-g/6889905ccce930787b3f693c575ffa1b


Yeah it's a bit old-school but it is. We'll try the question mark though


Yep, good call.


line 656 should not have a comma at the end I think?


wait how the hell did you commit as me?


You used git-duet....


I will take a look tommorow


I didn't. it's git commit --amend --author.


I see the circle. but it's black, no margin-left and too big. :/ ... I'll try to rebuild all.


Hey Jack,

you have any news on what's happening? You can either mail me at d3gigi@gmail.com or answer here publicly.

gigi


yeah this update broke localplayer


From pull request, Ana: "Just made a few small tweaks to the style of the current stories tab, i.e. placed the add button inside the input field and made it scrollable for longer story title inputs and adjusted the width of the tab."


Bluemix [toolchain](https://console.ng.bluemix.net/devops/toolchains/b1724b57-4629-4513-b04f-ae11bb974e1d "gaiotto test 1 (Java + Watson)"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/50d667dc-1fc2-4d2a-936c-4566e1da2131 "gaiotto test 1 (Java + Watson)") deployed this commit to [dev](https://console.ng.bluemix.net/apps/cbedb480-d49b-4fc7-ad58-643fe81fe870 "ibm:yp:us-south:rgaiotto@br.ibm.com:dev")


@alexmaloteaux Did https://github.com/henkaku/henkaku/pull/47 fix your issue?


Why don't you use `git pull --rebase` instead of just `git pull`? Would avoid this merge commit thingy.


main.de.robotricker.transportpipes should be de.robotricker.transportpipes


este calendario ficou top!


![](https://github.trello.services/images/mini-trello-icon.png) [presentation de l entreprise](https://trello.com/c/mgSKuIHZ/1-presentation-de-l-entreprise)


Cool


LMAO Thanks bruh :D


first commit


Awesome! That's one (or two) more completed task(s) you can cross out at https://github.com/cmangos/issues/issues/53


Got it from David K

On Fri, Mar 17, 2017 at 3:09 PM, PivotalSarge <notifications@github.com>
wrote:

> Good catch here as gcc 4.9 is the minimum to provide the C++11 features
> needed.
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/apache/geode-native/commit/6eb93f686ebc031b063128268df867f1c8d93e5d#commitcomment-21380545>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AMh6OZypoA36hBo_rbKMkR9MRfh9Mgepks5rmwS2gaJpZM4MhJ8V>
> .
>


Totallly using this in my server. Sleep time!


Thanks Egan!


My understanding is that the only proper way to "Dispose" the connection is to call Close. Otherwise bizarre things can happen - the router might think the connection is closed and ignore its messages, but the connection is still open.


To Get a script that perform that exact functions you can
at a cheaper rate of N25,000 only you can reach me
you can call or message me through watsapp through
this details:
+234 07067797338
odeymartin070@yahoo.com

or

You can also make payment to my bitcoin wallet account
12jC4ZKhmFN1czagZWwBTbhSwzyfJamDKi


Instead of only running pep8, we're running the whole test suite via tox.


No longer used.


Yay! Badges!


:)

On Fri, Mar 17, 2017 at 3:49 PM, passanpm <notifications@github.com> wrote:

> Thanks Egan!
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <https://github.com/egandunning/learn-crypto/commit/82a3faf264e80ead70fd1f52a086f7dba274a56c#commitcomment-21381029>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AKzMviYoAvqGhpy3619WbtgPwvzQYui9ks5rmw3cgaJpZM4MhFiJ>
> .
>


I have halaa patch coming up as well. Whenever I have time to export it and someone has time to merge it.


Since we have `requirements_test.txt` now, I figured that would be a better place to require `pep8`.


NewErrorWhenHoursShownInFirstColumnOfTable (JasonGlazer) - x86_64-Linux-Ubuntu-14.04-gcc-4.8-IntegrationCoverage-Debug: OK (1889 of 1889 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-71.49%25-green.png)


Doesn't work. :/


NewErrorWhenHoursShownInFirstColumnOfTable (JasonGlazer) - x86_64-Linux-Ubuntu-14.04-custom_check: OK (0 of 0 tests passed, 0 test warnings)

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


Love it.


Didn't actually fix the URLs...


Ctrl+C & Ctrl+V is horrible evil... this should be bc_module_core_pll_disable();


I'm not sure what you have in mind. Is there still a bug?


`install_requires` in `setup.py` can't handle all same formats as `pip` (like this GitHub repo). Since we're populating `install_requires` by reading `requirements.txt`, I had to move the `git+sideboard` line into a separate file, `requirements_test.txt`.


Bluemix [toolchain](https://console.ng.bluemix.net/devops/toolchains/b1724b57-4629-4513-b04f-ae11bb974e1d "gaiotto test 1 (Java + Watson)"): [Delivery Pipeline](https://console.ng.bluemix.net/devops/pipelines/50d667dc-1fc2-4d2a-936c-4566e1da2131 "gaiotto test 1 (Java + Watson)") deployed this commit to [dev](https://console.ng.bluemix.net/apps/cbedb480-d49b-4fc7-ad58-643fe81fe870 "ibm:yp:us-south:rgaiotto@br.ibm.com:dev")


this nigger is crazy


Shouldn't this be `if ($this->type == 'yii\caching\ApcCache' && !function_exists('apc_add') && !function_exists('apcu_add')) {` ?


@flavioamieiro feito!


NewErrorWhenHoursShownInFirstColumnOfTable (JasonGlazer) - x86_64-MacOS-10.9-clang: OK (2483 of 2483 tests passed, 0 test warnings)

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


Keep the same group of includes together ... you have bc + bc + stm + bc ... Thanks !


It's not a big deal.  Leave it there just in case we move anything else around ;)


On a fresh FreeBSD 12-head (r315463) with this patch, I've got on the console error message "Route message contains errors(1500), SKIPPING." and routes are not synced.


PS: Ignore the link towards "#4" in the title, it's incorrect.


This is completely unclear comment + please avoid "..." convention with TODO comments. Just follow it with uppercase imperative style (like with commit messages). Thanks :-)


> On the other hand, JS tests are currently broken anyways due to ceylon/ceylon#6984.

Wait, nevermind, I forgot I changed the implementation of `serialize` before even committing the old version. (It used to read `` !attribute.declaringType.supertypeOf(`Basic`) ``, but then it turned out that wasn’t enough to exclude e. g. `string` on types that redefine it, so I changed it to the current implementation of `` !`Object`.getAttribute(attribute.declaration.name) exists ``.)


Well, function name is `getScreenRGB`, but it returns `BGRX` (reverted order + extra byte), so technically speaking yeah, there is still a bug.


NOTES:
https://trac.transmissionbt.com/ticket/3959#comment:12
https://trac.transmissionbt.com/changeset/11800


If we do it 6 times in the same file we can better make a helper function.


Comments should be concise across source codes and this should be only "Enable PLL"


@shajra sorry, didn't see your response.

``` nix
haskellPackages.override {
  overrides = self: super: {
    mkDerivation = drv: super.mkDerivation.override {
      hscolour = ghc.hscolour;
    } (drv // {
    });
  };
}
```

`super.mkDerivation.override` doesn't exist.


![bitmoji](https://render.bitstrips.com/v2/cpanel/10216707-133377979_27-s1-v1.png?transparent=1&palette=1&width=246)

@mxiao26


if I run "npm run watch" I get:

```
[23:55:51] Plumber found unhandled error:
 Error in plugin 'gulp-less'
Message:
    './components/editor-header.less' wasn't found. Tried - /home/mario/git/beaker/app/stylesheets/builtin-pages/components/editor-header.less,components/editor-header.less in file /home/mario/git/beaker/app/stylesheets/builtin-pages/editor.less line no. 11
Details:
    type: File
    filename: /home/mario/git/beaker/app/stylesheets/builtin-pages/editor.less
    index: 302
    line: 11
    callLine: NaN
    callExtract: undefined
    column: 0
    extract: @import "./components/editor-options.less";,@import "./components/editor-header.less";,@import "./components/protip.less";
    lineNumber: 11
    fileName: /home/mario/git/beaker/app/stylesheets/builtin-pages/editor.less
```


This is not robust against integer underflow...


pitäsko olla vaan :dev ja :test?


Sounds good


Please use while ((RCC->CR & RCC_CR_PLLRDY) != 0) instead


Please use while ((RCC->CR & RCC_CR_HSIRDY) != 0) instead


You completely deleted label, which caused Null Pointer Exception.


Moved the `__table_args__` back to the proper place in the `Attendee` class.


Question, are there any limits to the number of calls per hour/IP that are known?
If not what rates have been used successfully?
Thanks.


Long strings preserve whitespace iirc


Another label changed. Deleted fx:id caused another Null Pointer Exception.


A nitpick: this formatting kinda looks as if next line is an unrelated separated statement, might be confusing.


This can probably be better, but `c.TEST_DB_FILE` will only exists if `test-defaults.ini` was loaded.


What is this for? It might potentially break assumptions as ESM are always strict by default.


Nice


thanks!


Initially it had more functions, clearly separating "mark kind" and "pressing states" into separate enums.

See : https://github.com/Virtual-TreeView/Virtual-TreeView/issues/620

Personalyl i find it rather useful in the legacy code i woork with, where there were lot of CASE operators that like

```
CASE xxx of
 csCheckedNormal, csCheckedPressed: .....
 csUnCheckedNormal, csUnCheckedPressed: .....
END
```

obviously lacking new MIXED modes that were introduced in last 10 years :-D

so, i can now update them to clearly branch over the aspect they need


Renaming the function will break things, so I'll just document it clearly.


Just accidentally saw this. Not introduced by this change but could this be a bug? The file has two versions of expression battery_low ? "OK" : "LOW". If the condition is correct then the battery_low name is a bug ;-).


here we test only if package is present and have log file. it doesn't test configuration which by default is almost inexistent in many distributions

few guides on top of my head
https://linux-audit.com/configuring-and-auditing-linux-systems-with-audit-daemon/
https://access.redhat.com/documentation/en-US/Red_Hat_Enterprise_Linux/6/html/Security_Guide/chap-system_auditing.html
(french 6.7.3) https://www.ssi.gouv.fr/guide/recommandations-de-securite-relatives-a-un-systeme-gnulinux/

also discover recently that it's conflicting if osquery present with file integrity monitoring configured
https://osquery.readthedocs.io/en/stable/deployment/process-auditing/


develop (EnergyArchmage) - x86_64-Linux-Ubuntu-14.04-gcc-4.8: OK (1905 of 1905 tests passed, 0 test warnings)

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