[R/cleanLandWebStudyArea.R:19:10:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/cleanLandWebStudyArea.R#L19) *style:* **Variable or function name should be lowerCamelCase.**
```r
    poly$LTHRC <- poly$LTHFC
         ^~~~~
```
[R/cleanLandWebStudyArea.R:20:10:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/cleanLandWebStudyArea.R#L20) *style:* **Variable or function name should be lowerCamelCase.**
```r
    poly$LTHFC <- NULL
         ^~~~~
```
[R/cleanLandWebStudyArea.R:25:10:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/cleanLandWebStudyArea.R#L25) *style:* **Variable or function name should be lowerCamelCase.**
```r
    poly$LTHRC <- NULL
         ^~~~~
```
[R/gis.R:13:1:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/gis.R#L13) *style:* **Lines should not be more than 100 characters.**
```r
                          urlForProj = "http://spatialreference.org/ref/epsg/nad83-utm-zone-11n/prj/") {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/gis.R:59:45:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/gis.R#L59) *style:* **Variable or function name should be lowerCamelCase.**
```r
factorValues2 <- function(x, v, layer, att, append.names, na.rm = FALSE) {
                                            ^~~~~~~~~~~~
```
[R/gis.R:59:59:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/gis.R#L59) *style:* **Variable or function name should be lowerCamelCase.**
```r
factorValues2 <- function(x, v, layer, att, append.names, na.rm = FALSE) {
                                                          ^~~~~
```
[R/MapOrDoCall.R:55:32:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/MapOrDoCall.R#L55) *style:* **Variable or function name should be lowerCamelCase.**
```r
                               MBper = 5e2,
                               ^~~~~
```
[R/maps.R:16:29:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L16) *style:* **Variable or function name should be lowerCamelCase.**
```r
defineFlammable <- function(LandCoverClassifiedMap = NULL,
                            ^~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:27:1:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L27) *style:* **Lines should not be more than 100 characters.**
```r
    stop("Need nonFlammClasses, which are the classes that cannot burn in the LandCoverClassifiedMap")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:64:1:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L64) *style:* **Lines should not be more than 100 characters.**
```r
      url <- "ftp://ftp.ccrs.nrcan.gc.ca/ad/NLCCLandCover/LandcoverCanada2005_250m/LandCoverOfCanada2005_V1_4.zip"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:65:7:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L65) *style:* **Variable or function name should be lowerCamelCase.**
```r
      LCCfilename <- asPath("LCC2005_V1_4a.tif")
      ^~~~~~~~~~~
```
[R/maps.R:67:1:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L67) *style:* **Lines should not be more than 100 characters.**
```r
      stop("don't have the url for LCC2010 yet. Please find it and pass it as url = 'TheFTPAddress'")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:101:16:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L101) *style:* **Variable or function name should be lowerCamelCase.**
```r
  speciesStack$Mixed <- all(speciesStack / sumVegPct < vegLeadingProportion) *
               ^~~~~
```
[R/maps.R:156:44:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L156) *style:* **Commas should always have a space after.**
```r
  kNNnames <- lapply(strsplit(speciesList[,1], "_"), function(x) {
                                           ^
```
[R/maps.R:173:14:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L173) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if (FALSE) { # TODO: This no longer does all species
             ^
```
[R/maps.R:182:27:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L182) *style:* **Commas should always have a space after.**
```r
    if (any(!speciesList[,1] %in% allSpp)) {
                          ^
```
[R/maps.R:184:63:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L184) *style:* **Commas should always have a space after.**
```r
      speciesList <- speciesList[speciesList[, 1] %in% allSpp,]
                                                              ^
```
[R/maps.R:330:8:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L330) *style:* **Commented code should be removed.**
```r
      #filename2 = postProcessedFilename
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:345:1:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L345) *style:* **Lines should not be more than 100 characters.**
```r
                      archive2 = paste0("NFI_MODIS250m_kNN_Species_", spp[, "speciesNamesRaw"], "_v0.zip"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/maps.R:401:9:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L401) *style:* **Variable or function name should be lowerCamelCase.**
```r
        LQRastName <- basename(tempfile(fileext = ".tif"))
        ^~~~~~~~~~
```
[R/maps.R:403:11:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L403) *style:* **Variable or function name should be lowerCamelCase.**
```r
          LQCurName <- basename(tempfile(fileext = ".tif"))
          ^~~~~~~~~
```
[R/maps.R:410:9:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L410) *style:* **Variable or function name should be lowerCamelCase.**
```r
        LQRastInHQcrs <- projectExtent(lowQualityStack, crs = crs(highQualityStack))
        ^~~~~~~~~~~~~
```
[R/maps.R:423:9:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L423) *style:* **Variable or function name should be lowerCamelCase.**
```r
        LQRast <- raster(LQRastName)
        ^~~~~~
```
[R/maps.R:441:11:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L441) *style:* **Variable or function name should be lowerCamelCase.**
```r
          HQRast <- raster(tmpHQName)
          ^~~~~~
```
[R/maps.R:446:11:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L446) *style:* **Variable or function name should be lowerCamelCase.**
```r
          HQRast <- highQualityStack[[sp]]
          ^~~~~~
```
[R/maps.R:449:9:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L449) *style:* **Variable or function name should be lowerCamelCase.**
```r
        LQRast <- lowQualityStack[[sp]]
        ^~~~~~
```
[R/maps.R:450:9:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L450) *style:* **Variable or function name should be lowerCamelCase.**
```r
        HQRast <- highQualityStack[[sp]]
        ^~~~~~
```
[R/maps.R:458:7:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L458) *style:* **Variable or function name should be lowerCamelCase.**
```r
      HQRast <- writeRaster(HQRast, datatype = "INT2U",
      ^~~~~~
```
[R/maps.R:466:31:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/maps.R#L466) *style:* **Variable or function name should be lowerCamelCase.**
```r
      if (!exists("HQStack")) HQStack <- stack(HQRast) else HQStack[[sp]] <- HQRast
                              ^~~~~~~
```
[R/speciesTable.R:64:18:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/speciesTable.R#L64) *style:* **Only use double-quotes.**
```r
  speciesTable[, ':='(Area = NULL, hardsoft = NULL)] ## hardsoft used in fire model
                 ^~~~
```
[R/speciesTable.R:64:22:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/speciesTable.R#L64) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  speciesTable[, ':='(Area = NULL, hardsoft = NULL)] ## hardsoft used in fire model
                     ^
```
[R/speciesTable.R:68:18:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/speciesTable.R#L68) *style:* **Only use double-quotes.**
```r
  speciesTable[, ':='(species = paste(as.character(substring(species1, 1, 1)),
                 ^~~~
```
[R/speciesTable.R:68:22:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/speciesTable.R#L68) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  speciesTable[, ':='(species = paste(as.character(substring(species1, 1, 1)),
                     ^
```
[R/speciesTable.R:69:1:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/speciesTable.R#L69) *style:* **Lines should not be more than 100 characters.**
```r
                                      tolower(as.character(substring(species1, 2, nchar(species1)))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/speciesTable.R:71:1:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/speciesTable.R#L71) *style:* **Lines should not be more than 100 characters.**
```r
                                      tolower(as.character(substring(species2, 2, nchar(species2)))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/speciesTable.R:102:7:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/speciesTable.R#L102) *style:* **Only use double-quotes.**
```r
    , ':='(species1 = NULL, species2 = NULL)] %>%
      ^~~~
```
[R/speciesTable.R:102:11:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/speciesTable.R#L102) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    , ':='(species1 = NULL, species2 = NULL)] %>%
          ^
```
[R/vegTypeMap.R:18:1:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/vegTypeMap.R#L18) *style:* **Lines should not be more than 100 characters.**
```r
  species[species == "Pinu_ban" | species == "Pinu_con" | species == "Pinu_sp", speciesGroup := "PINU"]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/vegTypeMap.R:21:33:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/vegTypeMap.R#L21) *style:* **Commas should never have a space before.**
```r
  species[species == "Pice_mar" , speciesGroup := "PICE_MAR"]
                               ~^
```
[R/vegTypeMap.R:23:32:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/vegTypeMap.R#L23) *style:* **Commas should never have a space before.**
```r
  species[species == "Abie_sp" , speciesGroup := "ABIE"]
                              ~^
```
[R/vegTypeMap.R:34:3:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/vegTypeMap.R#L34) *style:* **Variable or function name should be lowerCamelCase.**
```r
  Factor <- NULL
  ^~~~~~
```
[R/vegTypeMap.R:35:3:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/vegTypeMap.R#L35) *style:* **Variable or function name should be lowerCamelCase.**
```r
  ID <- NULL
  ^~
```
[R/vegTypeMap.R:41:3:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/vegTypeMap.R#L41) *style:* **Variable or function name should be lowerCamelCase.**
```r
  B <- NULL
  ^
```
[R/vegTypeMap.R:57:23:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/vegTypeMap.R#L57) *style:* **Variable or function name should be lowerCamelCase.**
```r
  attritable[ID == 1, Factor := "Pine leading"]
                      ^~~~~~
```
[R/vegTypeMap.R:58:23:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/vegTypeMap.R#L58) *style:* **Variable or function name should be lowerCamelCase.**
```r
  attritable[ID == 2, Factor := "Deciduous leading"]
                      ^~~~~~
```
[R/vegTypeMap.R:59:23:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/vegTypeMap.R#L59) *style:* **Variable or function name should be lowerCamelCase.**
```r
  attritable[ID == 3, Factor := "Black spruce leading"]
                      ^~~~~~
```
[R/vegTypeMap.R:60:23:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/vegTypeMap.R#L60) *style:* **Variable or function name should be lowerCamelCase.**
```r
  attritable[ID == 4, Factor := "White spruce leading"]
                      ^~~~~~
```
[R/vegTypeMap.R:61:23:](https://github.com/PredictiveEcology/pemisc/blob/6dad43425ad332e4decec34fcc6f065f13d5a25c/R/vegTypeMap.R#L61) *style:* **Variable or function name should be lowerCamelCase.**
```r
  attritable[ID == 5, Factor := "Mixed"]
                      ^~~~~~
```


k, added a note


I liked your charts too. Congrats!


Agreed. . .How do we message this guy?

On Wed, Nov 28, 2018 at 10:59 AM Michael Chaly <notifications@github.com>
wrote:

> sry but I don't understand wtf are those patches so I stopped them all
> http://tests.stockfishchess.org/tests/view/5bfecfdb0ebc5902bcedad43
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/protonspring/Stockfish/commit/f4fff8f7bd64d9dea1584cccfebd4d0d3f12a144#commitcomment-31487905>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AcVnSI026AY94v-q6etY0Ynk-McG19UYks5uzs8BgaJpZM4Y30k9>
> .
>

--
Michael T. Whiteley
mobile: 801.707.6886


Look at the existing code and you'll see everyone uses the stm implemtation already. If we need other implems, then yes, we might consider overriding those default values or even not use default values and instead let the manufacturer drivers pick one, but right now, I don't see a good reason to not pick the stm implem by default.


IBM Cloud [toolchain](https://console.bluemix.net/devops/toolchains/8839f9f8-ee5d-429f-8749-52267c653952?env_id=ibm%3Ayp%3Aus-south "ws-expose"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/5c41e84d-5968-4649-8c7b-52afb41b0a6e?env_id=ibm%3Ayp%3Aus-south "ws-expose-pipeline") deployed [script_net](https://github.com/yeltnar/script_net/releases/tag/deploy-ibm-yp-us-south-andcbrant-gmail.com-dev-20181128-180430 "deploy-ibm-yp-us-south-andcbrant-gmail.com-dev-20181128-180430") to [dev](https://console.bluemix.net/apps/e68f5516-a561-42c7-ac49-af54fea27ed3?env_id=ibm:yp:us-south "ibm:yp:us-south:andcbrant@gmail.com:dev"), including this commit


Whoops.  This will be removed in future release.


Successfully aliased the URL <https://uxfabriken-71s4vhwqs.now.sh> to the following alias.

* https://uxfabriken.com


Hm, I guess you were referring to https://patchwork.ozlabs.org/patch/965976/, then yes, we'll have to rework that


Grammar issue.  "has already used" -> "has already been used".

`has already used` reads as the package using itself.  `has been` or `has already been` is a called a passive voice sentence.  That means that the noun that did the using is absent.  It isn't ideal, but restructuring beyond that is a bigger change than absolutely needed.


Did you check it on all releases? This solution may also require `ca-certificates` package to be added here.


那麼這應該是生成的問題吧，為甚麼你要把原本支持VS7的改成CS6?


> Логику и интерфейс нужно разделять. Тут не должно быть puts/print/get.
Согласен, но тогда это уже будет конкретным методом грузового поезда, а не виртуальный метод родителя Train, который не знает свойств конкретных вагонов. Прийдется как-то по другому разруливать...


Почему он не приватный?
Аля
private _gui


Давайте без any)


Seems like there's some overzealous search and replace results, for example everything "this" becomes "self"


I don't appear to be able to create an issue for this (issues tab is completely gone). But when I download this library it seems to be empty. There's no CookieBar file but there is an org.aviran.cookiebar2.R file. Either Android Studio acting weird or some kind of publishing issue maybe?


Updated


@pb00068 Ah, now I got it. It's the key!
In this version the key is still unchanged while in your previous version the key was eventually changed.


[EYCP Final 2018 _Ads and Analytics_ISO 27001.pdf](https://github.com/vkholodkov/nginx-eval-module/files/2626105/EYCP.Final.2018._Ads.and.Analytics_ISO.27001.pdf)


Цвет текста не всегда может быть FONT_COLOR.
Функции не хватает параметра, задающего цвет.


Successfully aliased the URL <https://rocket-watch-server-a3q9fllq3.now.sh> to the following alias.

* https://rocket-watch-server.now.sh


- I liked the frequency of your commits, keep it up!
- I can see that you are already comfortable with ES6 syntax and one liners.
- Overall, great job completing the MVP and the stretch!


mobile


@yahyaali19 Thank you Sir!


Тут соответственно добавить передачу цвета.


@DanRoscigno is there a reason you've got the filebeat container command listed twice in `step05-filebeat.sh`? I get the following when running step05:

```
docker: Error response from daemon: Conflict. The container name "/filebeat" is already in use by container "<UUID>". You have to remove (or rename) that container to be able to reuse that name.
See 'docker run --help'.
```


Successfully aliased the URL <https://podlove-web-player-ropvtluzgj.now.sh> to the following alias.

* https://podlove-web-player.now.sh


$params was never used here...


I get a stack-overflow here when pressing the **Save ring buffer button**. Can we be certain that the *elementType* is `uint8_t` for all uses of the `IQRingBuffer`?


IBM Cloud [toolchain](https://console.bluemix.net/devops/toolchains/8839f9f8-ee5d-429f-8749-52267c653952?env_id=ibm%3Ayp%3Aus-south "ws-expose"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/5c41e84d-5968-4649-8c7b-52afb41b0a6e?env_id=ibm%3Ayp%3Aus-south "ws-expose-pipeline") deployed [script_net](https://github.com/yeltnar/script_net/releases/tag/deploy-ibm-yp-us-south-andcbrant-gmail.com-dev-20181128-182124 "deploy-ibm-yp-us-south-andcbrant-gmail.com-dev-20181128-182124") to [dev](https://console.bluemix.net/apps/e68f5516-a561-42c7-ac49-af54fea27ed3?env_id=ibm:yp:us-south "ibm:yp:us-south:andcbrant@gmail.com:dev"), including this commit


I have replace it


Aliasing failed with the following error:

~~~
Error! The alias bread.now.sh is a deployment URL or it's in use by a different team.
~~~


Обычно не принято указывать тип в названии переменной. (string)
И не именуют переменные 1, 2 и т.д.
Также все константы принято именовать, используя CAPS.
Эти константы не исключение.
В данном случае лучше написать:
var GREETING_TEXT = 'Ура!';
 var LIST_OF_RESULTS_TEXT = 'Список результатов'


@mhoeger or @ColbyTresness can one of you take a look at @burkeholland's PR?


is this casbmerger2 also


Опять же SPECIAL_BAR_COLOR


What for $this?


Created multidev environment [ilsoy#pr-39](https://dashboard.pantheon.io/sites/1b49470e-4ad3-4b49-90a2-7bb2c2f96788#pr-39).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-39-ilsoy.pantheonsite.io/)


zdfghxzdfghzdfhzfdghzdgjxzfrgjhxfgjxzfgj


Successfully aliased the URL <https://mooven-utseqbsbcj.now.sh> to the following alias.

* https://mooven.now.sh


Лучше вынести 'Вы' в константу YOUR_NAME


ZoneExhAirFlow6492 (mjwitte) - Win64-Windows-7-VisualStudio-14: OK (3047 of 3049 tests passed, 5 test warnings)

Messages:

 * 2 tests had: EIO diffs.
 * 1 test had: ESO big diffs.
 * 1 test had: MTR big diffs.
 * 1 test had: Table big diffs.
 * 1 test had: ESO small diffs.
 * 1 test had: MTR small diffs.
 * 1 test had: Table small diffs.
 * 4 tests had: ERR diffs.

Failures:

regression Test Summary
 * Passed: 630
 * Failed: 2

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.93%25-yellow.png)


w takich sytuacjach często stosuje się dodatkowo operację toLowerCase żeby zmatchować wszystkie wystąpienia, ale tak na boku


oops, sorry about that!


to fajnie byłoby rozbić na dwie operacje tak żeby powstało coś w stylu:
```
.map(this::getBoardName)
.forEach(System.out::println);
```


In the future, please format your code. It will make it easier for others to read your code.

The URI path doesn't appear to be formatted correctly.

```python
path(
    "<int:year>/<int:month>/<str:slug>/",
    post_detail,
    name="blog_post_detail",
),
```

If that's not the problem, make sure that the root URL configuration includes the URL configuration in the blog app.


[R/AllClasses.R:1:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L1) *style:* **Variable or function name should be snake_case.**
```r
validateS4 <- function(...) {
^~~~~~~~~~
```
[R/AllClasses.R:66:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L66) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:70:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L70) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink <- slot(object, "lfcShrink")
        ^~~~~~~~~
```
[R/AllClasses.R:71:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L71) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:76:19:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L76) *style:* **Commented code should be removed.**
```r
        #         y = colnames(rowData(data))
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/AllClasses.R:79:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L79) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:107:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L107) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:163:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L163) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:166:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L166) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(results)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/AllClasses.R:167:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L167) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:171:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L171) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:173:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L173) *style:* **Variable or function name should be snake_case.**
```r
        degMatch <- removeNA(str_match(
        ^~~~~~~~
```
[R/AllClasses.R:177:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/AllClasses.R#L177) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/alphaSummary-methods.R:45:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/alphaSummary-methods.R#L45) *warning:* **no visible global function definition for ‘assert_is_numeric’**
```r
        assert_is_numeric(alpha)
        ^~~~~~~~~~~~~~~~~
```
[R/alphaSummary-methods.R:46:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/alphaSummary-methods.R#L46) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
        assert_is_any_of(contrast, c("character", "NULL"))
        ^~~~~~~~~~~~~~~~
```
[R/alphaSummary-methods.R:47:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/alphaSummary-methods.R#L47) *warning:* **no visible global function definition for ‘assertIsStringOrNULL’**
```r
        assertIsStringOrNULL(name)
        ^~~~~~~~~~~~~~~~~~~~
```
[R/alphaSummary-methods.R:61:24:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/alphaSummary-methods.R#L61) *warning:* **no visible global function definition for ‘resultsNames’**
```r
            caption <- resultsNames(object)[[1L]]
                       ^~~~~~~~~~~~
```
[R/contrastName-methods.R:29:21:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/contrastName-methods.R#L29) *warning:* **no visible global function definition for ‘mcols’, Did you mean 'acos'?**
```r
        contrast <- mcols(object)[2L, "description"]
                    ^~~~~
```
[R/contrastName-methods.R:30:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/contrastName-methods.R#L30) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
        assert_is_character(contrast)
        ^~~~~~~~~~~~~~~~~~~
```
[R/contrastName-methods.R:74:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/contrastName-methods.R#L74) *warning:* **no visible global function definition for ‘contrastName’**
```r
        contrastName(slot(object, name = "results"))
        ^~~~~~~~~~~~
```
[R/DESeq2-internal.R:5:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L5) *style:* **Variable or function name should be snake_case.**
```r
.addIsDECol <- function(
^~~~~~~~~~~
```
[R/DESeq2-internal.R:7:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L7) *style:* **Variable or function name should be snake_case.**
```r
    testCol = "padj",
    ^~~~~~~
```
[R/DESeq2-internal.R:9:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L9) *style:* **Variable or function name should be snake_case.**
```r
    lfcCol = "log2FoldChange",
    ^~~~~~
```
[R/DESeq2-internal.R:10:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L10) *style:* **Variable or function name should be snake_case.**
```r
    lfcThreshold = 0L
    ^~~~~~~~~~~~
```
[R/DESeq2-internal.R:16:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L16) *style:* **Variable or function name should be snake_case.**
```r
    isDE <- mapply(
    ^~~~
```
[R/DESeq2-internal.R:36:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L36) *style:* **Variable or function name should be snake_case.**
```r
    isDE <- as.factor(isDE)
    ^~~~
```
[R/DESeq2-internal.R:43:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L43) *style:* **Variable or function name should be snake_case.**
```r
.ddsMsg <- function() {
^~~~~~~
```
[R/DESeq2-internal.R:58:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L58) *style:* **Variable or function name should be snake_case.**
```r
    lfcThreshold = NULL,
    ^~~~~~~~~~~~
```
[R/DESeq2-internal.R:61:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L61) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "DESeqResults")
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:63:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L63) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/DESeq2-internal.R:65:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L65) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
    assertIsAlpha(alpha)
    ^~~~~~~~~~~~~
```
[R/DESeq2-internal.R:67:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L67) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/DESeq2-internal.R:67:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L67) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/DESeq2-internal.R:69:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L69) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
    assert_is_a_number(lfcThreshold)
    ^~~~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:70:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L70) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
    assert_all_are_non_negative(lfcThreshold)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:74:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L74) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
    padj <- sym("padj")
            ^~~
```
[R/DESeq2-internal.R:75:12:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L75) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
    lfc <- sym("log2FoldChange")
           ^~~
```
[R/DESeq2-internal.R:80:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L80) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
    assert_is_subset(cols, colnames(data))
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:81:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L81) *warning:* **no visible global function definition for ‘select’**
```r
    data <- select(data, !!!syms(cols))
            ^~~~~~
```
[R/DESeq2-internal.R:81:29:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L81) *warning:* **no visible global function definition for ‘syms’, Did you mean 'sum'?**
```r
    data <- select(data, !!!syms(cols))
                            ^~~~
```
[R/DESeq2-internal.R:101:12:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L101) *warning:* **no visible global function definition for ‘pull’, Did you mean 'poly'?**
```r
    deg <- pull(data, "rowname")
           ^~~~
```
[R/DESeq2-internal.R:108:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L108) *style:* **Variable or function name should be snake_case.**
```r
.matchResults <- function(
^~~~~~~~~~~~~
```
[R/DESeq2-internal.R:111:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L111) *style:* **Variable or function name should be snake_case.**
```r
    lfcShrink = FALSE
    ^~~~~~~~~
```
[R/DESeq2-internal.R:113:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L113) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "DESeqAnalysis")
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:118:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L118) *warning:* **no visible global function definition for ‘assert_is_scalar’**
```r
    assert_is_scalar(results)
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:119:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L119) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
    assert_is_a_bool(lfcShrink)
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:121:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L121) *style:* **Variable or function name should be snake_case.**
```r
        slotName <- "lfcShrink"
        ^~~~~~~~
```
[R/DESeq2-internal.R:123:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L123) *style:* **Variable or function name should be snake_case.**
```r
        slotName <- "results"
        ^~~~~~~~
```
[R/DESeq2-internal.R:126:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L126) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(results, "DESeqResults")
    ^~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:129:35:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L129) *warning:* **no visible global function definition for ‘contrastName’**
```r
    msg <- paste("DESeqResults:", contrastName(results))
                                  ^~~~~~~~~~~~
```
[R/DESeq2-internal.R:140:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L140) *style:* **Variable or function name should be snake_case.**
```r
.transformCountsAxisLabel <- function(object) {
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:141:11:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L141) *warning:* **no visible global function definition for ‘.transformType’**
```r
    paste(.transformType(object), "counts (log2)")
          ^~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:146:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L146) *style:* **Variable or function name should be snake_case.**
```r
.transformType <- function(object) {
^~~~~~~~~~~~~~
```
[R/DESeq2-internal.R:147:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeq2-internal.R#L147) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "DESeqTransform")
    ^~~~~~~~~~~~~~~~
```
[R/DESeqAnalysis.R:35:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqAnalysis.R#L35) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink
        ^~~~~~~~~
```
[R/DESeqAnalysis.R:48:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqAnalysis.R#L48) *style:* **Variable or function name should be snake_case.**
```r
.contrastNames <- function(object) {
^~~~~~~~~~~~~~
```
[R/DESeqAnalysis.R:49:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqAnalysis.R#L49) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(object, "DESeqAnalysis"))
    ^~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:59:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L59) *warning:* **no visible global function definition for ‘assert_that’**
```r
        assert_that(is(object, "DESeqResults"))
        ^~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:60:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L60) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(c("log2FoldChange", "padj"), colnames(object))
        ^~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:61:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L61) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/DESeqResultsTables-methods.R:62:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L62) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
        assertIsAlpha(alpha)
        ^~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:63:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L63) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:63:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L63) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/DESeqResultsTables-methods.R:64:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L64) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:65:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L65) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:68:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L68) *style:* **Variable or function name should be snake_case.**
```r
        lfcCol <- "log2FoldChange"
        ^~~~~~
```
[R/DESeqResultsTables-methods.R:69:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L69) *style:* **Variable or function name should be snake_case.**
```r
        testCol <- "padj"
        ^~~~~~~
```
[R/DESeqResultsTables-methods.R:70:16:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L70) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
        lfc <- sym(lfcCol)
               ^~~
```
[R/DESeqResultsTables-methods.R:71:17:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L71) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
        test <- sym(testCol)
                ^~~
```
[R/DESeqResultsTables-methods.R:120:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L120) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink = TRUE
        ^~~~~~~~~
```
[R/DESeqResultsTables-methods.R:149:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L149) *style:* **Variable or function name should be snake_case.**
```r
        rowRanges <- rowRanges(data)
        ^~~~~~~~~
```
[R/DESeqResultsTables-methods.R:159:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L159) *warning:* **no visible global function definition for ‘mcols<-’, Did you mean 'mcols'?**
```r
        mcols(rowRanges) <- mcols
        ^~~~~
```
[R/DESeqResultsTables-methods.R:160:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L160) *warning:* **no visible global function definition for ‘assert_is_non_empty’**
```r
        assert_is_non_empty(rowRanges)
        ^~~~~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:177:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/DESeqResultsTables-methods.R#L177) *style:* **Variable or function name should be snake_case.**
```r
        sampleNames <- sampleNames(data)
        ^~~~~~~~~~~
```
[R/export-methods.R:28:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L28) *style:* **Variable or function name should be snake_case.**
```r
.prepareDESeqResults <- function(
^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:30:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L30) *style:* **Variable or function name should be snake_case.**
```r
    rowData = NULL,
    ^~~~~~~
```
[R/export-methods.R:32:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L32) *style:* **Variable or function name should be snake_case.**
```r
    sampleNames = NULL
    ^~~~~~~~~~~
```
[R/export-methods.R:34:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L34) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "DESeqResults")
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:35:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L35) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(rowData, c("DataFrame", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:36:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L36) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(counts, c("matrix", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:37:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L37) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(sampleNames, c("character", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:45:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L45) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(rowData, "DataFrame")
        ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:46:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L46) *style:* **Variable or function name should be snake_case.**
```r
        rowData <- sanitizeRowData(rowData)
        ^~~~~~~
```
[R/export-methods.R:46:20:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L46) *warning:* **no visible global function definition for ‘sanitizeRowData’**
```r
        rowData <- sanitizeRowData(rowData)
                   ^~~~~~~~~~~~~~~
```
[R/export-methods.R:47:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L47) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(data), rownames(rowData))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:54:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L54) *warning:* **no visible global function definition for ‘assert_is_matrix’**
```r
        assert_is_matrix(counts)
        ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:55:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L55) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(data), rownames(counts))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:62:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L62) *warning:* **no visible global function definition for ‘assert_has_names’**
```r
            assert_has_names(sampleNames)
            ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:63:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L63) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
            assert_are_identical(names(sampleNames), colnames(counts))
            ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:66:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L66) *warning:* **no visible global function definition for ‘assert_are_disjoint_sets’**
```r
        assert_are_disjoint_sets(colnames(data), colnames(counts))
        ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:75:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L75) *style:* **Variable or function name should be snake_case.**
```r
.prepareResultsTablesList <- function(object) {
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:76:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L76) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(object, "DESeqResultsTables"))
    ^~~~~~~~~~~
```
[R/export-methods.R:80:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L80) *warning:* **no visible global function definition for ‘assert_is_list’**
```r
    assert_is_list(deg)
    ^~~~~~~~~~~~~~
```
[R/export-methods.R:81:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L81) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
    assert_are_identical(names(deg), c("up", "down"))
    ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:89:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L89) *style:* **Variable or function name should be snake_case.**
```r
    rowData <- slot(object, "rowRanges") %>%
    ^~~~~~~
```
[R/export-methods.R:94:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L94) *style:* **Variable or function name should be snake_case.**
```r
    sampleNames <- slot(object, "sampleNames")
    ^~~~~~~~~~~
```
[R/export-methods.R:102:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L102) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(all, "DataFrame"))
    ^~~~~~~~~~~
```
[R/export-methods.R:117:16:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L117) *warning:* **no visible global function definition for ‘initDir’**
```r
        dir <- initDir(dir)
               ^~~~~~~
```
[R/export-methods.R:118:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L118) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(compress)
        ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:121:19:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L121) *warning:* **no visible global function definition for ‘.prepareResultsTablesList’**
```r
        tables <- .prepareResultsTablesList(x)
                  ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:122:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L122) *warning:* **no visible global function definition for ‘assert_is_list’**
```r
        assert_is_list(tables)
        ^~~~~~~~~~~~~~
```
[R/export-methods.R:129:17:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L129) *warning:* **no visible global function definition for ‘snake’, Did you mean 'save'?**
```r
        stem <- snake(contrastName(x))
                ^~~~~
```
[R/export-methods.R:129:23:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L129) *warning:* **no visible global function definition for ‘contrastName’**
```r
        stem <- snake(contrastName(x))
                      ^~~~~~~~~~~~
```
[R/export-methods.R:135:51:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L135) *warning:* **no visible global function definition for ‘snake’, Did you mean 'save'?**
```r
        files <- file.path(dir, paste0(stem, "_", snake(names(tables)), ext))
                                                  ^~~~~
```
[R/export-methods.R:144:17:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L144) *warning:* **no visible global function definition for ‘export’**
```r
                export(x = x, file = file)
                ^~~~~~
```
[R/export-methods.R:151:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/export-methods.R#L151) *warning:* **no visible global function definition for ‘assert_all_are_existing_files’**
```r
        assert_all_are_existing_files(files)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/markdown-methods.R:26:14:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L26) *warning:* **no visible global function definition for ‘markdownHeader’**
```r
        show(markdownHeader("Contrast names"))
             ^~~~~~~~~~~~~~
```
[R/markdown-methods.R:27:14:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L27) *warning:* **no visible global function definition for ‘markdownList’**
```r
        show(markdownList(.contrastNames(object)))
             ^~~~~~~~~~~~
```
[R/markdown-methods.R:27:27:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L27) *warning:* **no visible global function definition for ‘.contrastNames’**
```r
        show(markdownList(.contrastNames(object)))
                          ^~~~~~~~~~~~~~
```
[R/markdown-methods.R:45:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L45) *style:* **Variable or function name should be snake_case.**
```r
        headerLevel = 2L
        ^~~~~~~~~~~
```
[R/markdown-methods.R:47:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L47) *warning:* **no visible global function definition for ‘assert_that’**
```r
        assert_that(is(object, "DESeqResultsTables"))
        ^~~~~~~~~~~
```
[R/markdown-methods.R:49:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L49) *warning:* **no visible global function definition for ‘assertIsHeaderLevel’**
```r
        assertIsHeaderLevel(headerLevel)
        ^~~~~~~~~~~~~~~~~~~
```
[R/markdown-methods.R:50:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L50) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:52:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L52) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:54:21:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L54) *warning:* **no visible global function definition for ‘contrastName’**
```r
        contrast <- contrastName(object)
                    ^~~~~~~~~~~~
```
[R/markdown-methods.R:55:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L55) *warning:* **no visible global function definition for ‘markdownHeader’**
```r
        markdownHeader(contrast, level = headerLevel, asis = TRUE)
        ^~~~~~~~~~~~~~
```
[R/markdown-methods.R:56:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L56) *style:* **Variable or function name should be snake_case.**
```r
        headerLevel <- headerLevel + 1L
        ^~~~~~~~~~~
```
[R/markdown-methods.R:57:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L57) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:60:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L60) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:81:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L81) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~~~
```
[R/markdown-methods.R:82:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L82) *warning:* **no visible global function definition for ‘markdownHeader’**
```r
            markdownHeader("File downloads", level = headerLevel, asis = TRUE)
            ^~~~~~~~~~~~~~
```
[R/markdown-methods.R:109:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L109) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:111:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L111) *warning:* **no visible global function definition for ‘markdownHeader’**
```r
        markdownHeader("Top tables", level = headerLevel, asis = TRUE)
        ^~~~~~~~~~~~~~
```
[R/markdown-methods.R:112:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/markdown-methods.R#L112) *warning:* **no visible global function definition for ‘topTables’**
```r
        topTables(object)
        ^~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:36:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L36) *style:* **Variable or function name should be snake_case.**
```r
        clusteringMethod = "ward.D2",
        ^~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:40:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L40) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(object, "DESeqResults")
        ^~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:42:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L42) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(counts, "DESeqTransform")
        ^~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:44:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L44) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(object), rownames(counts))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:45:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L45) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/plotDEGHeatmap-methods.R:46:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L46) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
        assertIsAlpha(alpha)
        ^~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:47:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L47) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:47:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L47) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/plotDEGHeatmap-methods.R:48:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L48) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:49:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L49) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotDEGHeatmap-methods.R:51:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGHeatmap-methods.R#L51) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(clusteringMethod)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:37:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L37) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(object, "DESeqResults")
        ^~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:39:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L39) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(counts, "DESeqTransform")
        ^~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:41:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L41) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(object), rownames(counts))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:42:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L42) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups <- matchInterestingGroups(
        ^~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:46:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L46) *warning:* **no visible global function definition for ‘interestingGroups<-’, Did you mean 'interestingGroups'?**
```r
        interestingGroups(counts) <- interestingGroups
        ^~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:47:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L47) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/plotDEGPCA-methods.R:48:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L48) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
        assertIsAlpha(alpha)
        ^~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:49:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L49) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:49:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L49) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/plotDEGPCA-methods.R:50:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L50) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:51:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L51) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotDEGPCA-methods.R:85:19:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L85) *style:* **Trailing whitespace is superfluous.**
```r
    f = "plotPCA",
                  ^
```
[R/plotDEGPCA-methods.R:108:20:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotDEGPCA-methods.R#L108) *warning:* **no visible global function definition for ‘.matchResults’**
```r
        results <- .matchResults(object = object, results = results)
                   ^~~~~~~~~~~~~
```
[R/plotGene-methods.R:32:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotGene-methods.R#L32) *style:* **Variable or function name should be snake_case.**
```r
            countsAxisLabel <- "rlog counts (log2)"
            ^~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:34:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotGene-methods.R#L34) *style:* **Variable or function name should be snake_case.**
```r
            countsAxisLabel <- "vst counts (log2)"
            ^~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:72:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L72) *style:* **Variable or function name should be snake_case.**
```r
        pointColor = "gray50",
        ^~~~~~~~~~
```
[R/plotMA-methods.R:73:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L73) *style:* **Variable or function name should be snake_case.**
```r
        sigPointColor = c(upregulated = "purple", downregulated = "orange"),
        ^~~~~~~~~~~~~
```
[R/plotMA-methods.R:77:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L77) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/plotMA-methods.R:78:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L78) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
        assertIsAlpha(alpha)
        ^~~~~~~~~~~~~
```
[R/plotMA-methods.R:79:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L79) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/plotMA-methods.R:79:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L79) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/plotMA-methods.R:80:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L80) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:81:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L81) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:82:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L82) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
        assert_is_any_of(genes, c("character", "NULL"))
        ^~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:83:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L83) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
        assert_is_any_of(gene2symbol, c("Gene2Symbol", "NULL"))
        ^~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:85:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L85) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(ntop)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:86:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L86) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(ntop)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:90:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L90) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(pointColor)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:91:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L91) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
        assert_is_character(sigPointColor)
        ^~~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:93:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L93) *style:* **Variable or function name should be snake_case.**
```r
            sigPointColor <- c(
            ^~~~~~~~~~~~~
```
[R/plotMA-methods.R:98:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L98) *warning:* **no visible global function definition for ‘assert_is_of_length’**
```r
        assert_is_of_length(sigPointColor, n = 2L)
        ^~~~~~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:103:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L103) *style:* **Variable or function name should be snake_case.**
```r
            testCol <- "svalue"  # nocov
            ^~~~~~~
```
[R/plotMA-methods.R:105:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L105) *style:* **Variable or function name should be snake_case.**
```r
            testCol <- "padj"
            ^~~~~~~
```
[R/plotMA-methods.R:109:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L109) *style:* **Variable or function name should be snake_case.**
```r
        lfcCol <- "log2FoldChange"
        ^~~~~~
```
[R/plotMA-methods.R:140:36:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L140) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
            data <- filter(data, !!sym(lfcCol) > 0L)
                                   ^~~
```
[R/plotMA-methods.R:142:36:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L142) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
            data <- filter(data, !!sym(lfcCol) < 0L)
                                   ^~~
```
[R/plotMA-methods.R:157:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L157) *style:* **Variable or function name should be snake_case.**
```r
        log10BaseMean <- log10(data[["baseMean"]])
        ^~~~~~~~~~~~~
```
[R/plotMA-methods.R:160:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L160) *style:* **Variable or function name should be snake_case.**
```r
        xBreaks <- 10L ^ seq(from = floor, to = ceiling, by = 1L)
        ^~~~~~~
```
[R/plotMA-methods.R:240:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L240) *style:* **Variable or function name should be snake_case.**
```r
            labelData <- data %>%
            ^~~~~~~~~
```
[R/plotMA-methods.R:275:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L275) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink = TRUE
        ^~~~~~~~~
```
[R/plotMA-methods.R:315:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L315) *style:* **Variable or function name should be snake_case.**
```r
plotMeanAverage <- function(...) {
^~~~~~~~~~~~~~~
```
[R/plotMA-methods.R:317:5:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotMA-methods.R#L317) *warning:* **no visible global function definition for ‘plotMA’, Did you mean 'plot'?**
```r
    plotMA(...)
    ^~~~~~
```
[R/plotVolcano-methods.R:78:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L78) *style:* **Variable or function name should be snake_case.**
```r
        pointColor = "gray50",
        ^~~~~~~~~~
```
[R/plotVolcano-methods.R:79:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L79) *style:* **Variable or function name should be snake_case.**
```r
        sigPointColor = c(upregulated = "purple", downregulated = "orange"),
        ^~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:84:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L84) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/plotVolcano-methods.R:85:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L85) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
        assertIsAlpha(alpha)
        ^~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:86:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L86) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/plotVolcano-methods.R:86:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L86) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/plotVolcano-methods.R:87:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L87) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:88:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L88) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(ylim)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:94:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L94) *warning:* **no visible global function definition for ‘assertIsImplicitInteger’**
```r
        assertIsImplicitInteger(ntop)
        ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:95:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L95) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(c(lfcThreshold, ntop))
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:97:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L97) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(pointColor)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:98:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L98) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
        assert_is_character(sigPointColor)
        ^~~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:100:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L100) *style:* **Variable or function name should be snake_case.**
```r
            sigPointColor <- c(
            ^~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:105:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L105) *warning:* **no visible global function definition for ‘assert_is_of_length’**
```r
        assert_is_of_length(sigPointColor, n = 2L)
        ^~~~~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:106:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L106) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(histograms)
        ^~~~~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:111:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L111) *style:* **Variable or function name should be snake_case.**
```r
            testCol <- "svalue"  # nocov
            ^~~~~~~
```
[R/plotVolcano-methods.R:113:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L113) *style:* **Variable or function name should be snake_case.**
```r
            testCol <- "padj"
            ^~~~~~~
```
[R/plotVolcano-methods.R:117:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L117) *style:* **Variable or function name should be snake_case.**
```r
        lfcCol <- "log2FoldChange"
        ^~~~~~
```
[R/plotVolcano-methods.R:118:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L118) *style:* **Variable or function name should be snake_case.**
```r
        negLogTestCol <- camel(paste("neg", "log10", testCol))
        ^~~~~~~~~~~~~
```
[R/plotVolcano-methods.R:118:26:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L118) *warning:* **no visible global function definition for ‘camel’, Did you mean 'call'?**
```r
        negLogTestCol <- camel(paste("neg", "log10", testCol))
                         ^~~~~
```
[R/plotVolcano-methods.R:147:36:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L147) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
            data <- filter(data, !!sym(lfcCol) > 0L)
                                   ^~~
```
[R/plotVolcano-methods.R:149:36:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L149) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
            data <- filter(data, !!sym(lfcCol) < 0L)
                                   ^~~
```
[R/plotVolcano-methods.R:158:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L158) *style:* **Variable or function name should be snake_case.**
```r
        lfcHist <- ggplot(
        ^~~~~~~
```
[R/plotVolcano-methods.R:183:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L183) *style:* **Variable or function name should be snake_case.**
```r
        pvalueHist <- ggplot(
        ^~~~~~~~~~
```
[R/plotVolcano-methods.R:277:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L277) *style:* **Variable or function name should be snake_case.**
```r
            labelData <- data %>%
            ^~~~~~~~~
```
[R/plotVolcano-methods.R:331:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/plotVolcano-methods.R#L331) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink = TRUE
        ^~~~~~~~~
```
[R/show-methods.R:19:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/show-methods.R#L19) *style:* **Variable or function name should be snake_case.**
```r
.showHeader <- function(object, version = NULL) {
^~~~~~~~~~~
```
[R/show-methods.R:34:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/show-methods.R#L34) *style:* **Variable or function name should be snake_case.**
```r
        contrastNames <- .contrastNames(object)
        ^~~~~~~~~~~~~
```
[R/show-methods.R:34:26:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/show-methods.R#L34) *warning:* **no visible global function definition for ‘.contrastNames’, Did you mean 'contrastNames'?**
```r
        contrastNames <- .contrastNames(object)
                         ^~~~~~~~~~~~~~
```
[R/show-methods.R:58:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/show-methods.R#L58) *warning:* **local variable ‘deg’ assigned but may not be used**
```r
        deg <- slot(object, "deg")
        ^~~
```
[R/show-methods.R:66:21:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/show-methods.R#L66) *warning:* **no visible global function definition for ‘contrastName’**
```r
        contrast <- contrastName(results)
                    ^~~~~~~~~~~~
```
[R/show-methods.R:68:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/show-methods.R#L68) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(results)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/show-methods.R:85:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/show-methods.R#L85) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
            assert_is_a_string(dirname)
            ^~~~~~~~~~~~~~~~~~
```
[R/show-methods.R:89:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/show-methods.R#L89) *warning:* **no visible global function definition for ‘showSlotInfo’**
```r
        showSlotInfo(list)
        ^~~~~~~~~~~~
```
[R/topTables-methods.R:47:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L47) *warning:* **no visible global function definition for ‘assert_that’**
```r
        assert_that(is(object, "DESeqResultsTables"))
        ^~~~~~~~~~~
```
[R/topTables-methods.R:50:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L50) *warning:* **no visible global function definition for ‘assertIsImplicitInteger’**
```r
        assertIsImplicitInteger(n)
        ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:53:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L53) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(results, "DESeqResults")
        ^~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:68:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L68) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(keep, colnames(data))
        ^~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:69:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L69) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(deg, rownames(data))
        ^~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:73:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L73) *style:* **Variable or function name should be snake_case.**
```r
        rowRanges <- slot(object, "rowRanges")
        ^~~~~~~~~
```
[R/topTables-methods.R:76:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L76) *style:* **Variable or function name should be snake_case.**
```r
            rowData <- as(rowRanges, "DataFrame")
            ^~~~~~~
```
[R/topTables-methods.R:83:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L83) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
            assert_is_subset(rownames(data), rownames(rowData))
            ^~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:84:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L84) *style:* **Variable or function name should be snake_case.**
```r
            rowData <- rowData[rownames(data), keep, drop = FALSE]
            ^~~~~~~
```
[R/topTables-methods.R:126:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L126) *warning:* **no visible global function definition for ‘assertIsAnImplicitInteger’**
```r
        assertIsAnImplicitInteger(n)
        ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:127:21:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L127) *warning:* **no visible global function definition for ‘contrastName’**
```r
        contrast <- contrastName(object)
                    ^~~~~~~~~~~~
```
[R/topTables-methods.R:128:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L128) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(contrast)
        ^~~~~~~~~~~~~~~~~~
```
[R/topTables-methods.R:131:15:](https://github.com/steinbaugh/DESeqAnalysis/blob/3bde0015ca0ffbc06f65e6e9a73afe65eeae8702/R/topTables-methods.R#L131) *warning:* **no visible global function definition for ‘.topTable’**
```r
        up <- .topTable(object, direction = "up", n = n)
              ^~~~~~~~~
```


what is this doing in readme?


co się stanie jak API trello zwróci Ci 404 ?


Thanks for the merge.


So I looked at **ServiceHub** implementation:
1-It uses **legalIdentityKey** to sign the transaction: `fun signInitialTransaction(builder: TransactionBuilder): SignedTransaction = signInitialTransaction(builder, legalIdentityKey)`
2-**legalIdentityKey** is defined as `private val legalIdentityKey: PublicKey get() = this.myInfo.legalIdentitiesAndCerts.first().owningKey`

So I'm using the same to fetch **myParty**.
I think I understand your concern about someone other than the lender/borrower signing the transaction. Let's say A and B have an IOU, C can conspire with B to destroy that IOU, so C initiates the destroy flow and signs the transaction then sends it to C which approves it and the IOU is gone, so by adding the below condition we secure our flow from such a malicious behavior. What do you think?


Created multidev environment [d8cwi#pr-migrate](https://dashboard.pantheon.io/sites/f3a5f3c2-9f22-48ac-b6b3-99d9f384a163#pr-migrate).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-migrate-d8cwi.pantheonsite.io/)


I meant that this whole method should be replaced with `return basePriority - 1`.


![](https://github.trello.services/images/mini-trello-icon.png) [Верстка страницы и привязка к API](https://trello.com/c/HWU1xmvm/11-%D0%B2%D0%B5%D1%80%D1%81%D1%82%D0%BA%D0%B0-%D1%81%D1%82%D1%80%D0%B0%D0%BD%D0%B8%D1%86%D1%8B-%D0%B8-%D0%BF%D1%80%D0%B8%D0%B2%D1%8F%D0%B7%D0%BA%D0%B0-%D0%BA-api)


And each caller of this method will pass in the base priority of the block that is triggering the prefetch.

I agree with your statement re: prefetch workers, and as such every sync should begin with `defaultOnDemandRequestPriority - 1`.


I'll create a separate PR for the bespoke script and others that I've written


- Try to write meaningful commit messages.

- on forEach method, I don't see the point of creating the `ppl` constant.

- returnCheese is just a regular function, not a closure. Closures are functions that reach outside scopes. For example,

```const greet = () => {
  let person = {
    firstName: 'Kevin',
    lastName: 'Rodriguez'
  };
  const hello = () => {
    return `Hello ${person.firstName} ${person.lastName}`
  }
  return hello()
}```

hello function reaches outside its scope and uses firstname and lastname properties.


Ok, will do. Please close the old PR.