[R/graphs.R:239:1:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L239) *style:* **lines should not be more than 120 characters.**
```r
    if (!is.null(dataCIL) & !is.null(dataCIU)) q <- q + stat_stepribbon(aes_string(ymin = dataCIL, ymax = dataCIU), fill = "black", direction = "vh", alpha = 0.4)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:245:1:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L245) *style:* **lines should not be more than 120 characters.**
```r
    if (!is.null(dataCIL) & !is.null(dataCIU)) q <- q + geom_ribbon(aes_string(ymin = dataCIL, ymax = dataCIU), fill = "black", alpha = 0.4)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:252:1:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L252) *style:* **lines should not be more than 120 characters.**
```r
    if (includeMedium | includeHigh) q <- q + geom_point(aes_string(x = "xShifted", y = dataVal), size = 4, fill = "black", data = pd[pd$status %in% c("Medium", "High"), ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:254:1:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L254) *style:* **lines should not be more than 120 characters.**
```r
  if (includeMedium) q <- q + geom_point(aes_string(x = "xShifted", y = dataVal, colour = shQuote("L2")), size = 2, data = pd[pd$status == "Medium", ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:255:1:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L255) *style:* **lines should not be more than 120 characters.**
```r
  if (includeHigh) q <- q + geom_point(aes_string(x = "xShifted", y = dataVal, colour = shQuote("L1")), size = 2, data = pd[pd$status == "High", ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:262:5:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L262) *style:* **Commented code should be removed.**
```r
  # q <- q + scale_xcontinuous("Dato", breaks = breaksDF$xShifted,  labels = breaksDF$printLabel)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:317:1:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L317) *style:* **lines should not be more than 120 characters.**
```r
  if (includeMedium | includeHigh) q <- q + geom_point(aes_string(y = dataVal), size = 4, fill = "black", data = pd[pd$status %in% c("Medium", "High"), ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:318:1:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L318) *style:* **lines should not be more than 120 characters.**
```r
  if (includeMedium) q <- q + geom_point(aes_string(y = dataVal, colour = shQuote("L2")), size = 2, data = pd[pd$status == "Medium", ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:319:1:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L319) *style:* **lines should not be more than 120 characters.**
```r
  if (includeHigh) q <- q + geom_point(aes_string(y = dataVal, colour = shQuote("L1")), size = 2, data = pd[pd$status == "High", ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:371:1:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L371) *style:* **lines should not be more than 120 characters.**
```r
    q <- q + geom_line(aes_string(y = dataVal, colour = comparisonNames), lwd = 2, alpha = 0.8, data = pd[pd[[highlightCondition]], ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:375:1:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L375) *style:* **lines should not be more than 120 characters.**
```r
      q <- q + geom_line(aes_string(y = dataVal, colour = shQuote(newName)), lwd = 2, alpha = 0.8, data = pd[pd[[highlightCondition]] & pd[[comparisonNames]] == i, ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:404:1:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L404) *style:* **lines should not be more than 120 characters.**
```r
MakeLineExcessPlot <- function(pd, x, dataVal, dataZ, dataCIL = NULL, dataCIU = NULL, allPoints = TRUE, title = NULL, pointShift = 0, xShift = 0, weekNumbers = FALSE, step = FALSE, GetCols) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:447:7:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L447) *style:* **Commented code should be removed.**
```r
    # q <- q + stat_stepribbon(aes_string(ymin = L3, ymax = L4, fill = shQuote("L1")), direction="vh", alpha = 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:448:7:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L448) *style:* **Commented code should be removed.**
```r
    # q <- q + stat_stepribbon(aes_string(ymin = L2, ymax = L3, fill = shQuote("L2")), direction="vh", alpha = 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:449:7:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L449) *style:* **Commented code should be removed.**
```r
    # q <- q + stat_stepribbon(aes_string(ymin = L1, ymax = L2, fill = shQuote("L3")), direction="vh", alpha = 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:450:1:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L450) *style:* **lines should not be more than 120 characters.**
```r
    if (!is.null(dataCIL) & !is.null(dataCIU)) q <- q + stat_stepribbon(aes_string(ymin = dataCIL, ymax = dataCIU), fill = "black", direction = "vh", alpha = 0.4)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:453:7:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L453) *style:* **Commented code should be removed.**
```r
    # q <- q + geom_ribbon(aes_string(ymin = L3, ymax = L4, fill = shQuote("L1")), alpha = 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:454:7:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L454) *style:* **Commented code should be removed.**
```r
    # q <- q + geom_ribbon(aes_string(ymin = L2, ymax = L3, fill = shQuote("L2")), alpha = 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:455:7:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L455) *style:* **Commented code should be removed.**
```r
    # q <- q + geom_ribbon(aes_string(ymin = L1, ymax = L2, fill = shQuote("L3")), alpha = 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:456:1:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L456) *style:* **lines should not be more than 120 characters.**
```r
    if (!is.null(dataCIL) & !is.null(dataCIU)) q <- q + geom_ribbon(aes_string(ymin = dataCIL, ymax = dataCIU), fill = "black", alpha = 0.4)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:463:1:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L463) *style:* **lines should not be more than 120 characters.**
```r
    if (includeMedium | includeHigh) q <- q + geom_point(aes_string(x = "xShifted", y = dataVal), size = 4, fill = "black", data = pd[pd$status %in% c("Medium", "High"), ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:465:1:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L465) *style:* **lines should not be more than 120 characters.**
```r
  if (includeMedium) q <- q + geom_point(aes_string(x = "xShifted", y = dataVal, colour = shQuote("L2")), size = 2, data = pd[pd$status == "Medium", ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:466:1:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/graphs.R#L466) *style:* **lines should not be more than 120 characters.**
```r
  if (includeHigh) q <- q + geom_point(aes_string(x = "xShifted", y = dataVal, colour = shQuote("L1")), size = 2, data = pd[pd$status == "High", ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RenderExternally.R:48:5:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/R/RenderExternally.R#L48) *style:* **Commented code should be removed.**
```r
  # file.remove(file.path(tmp_dir,tmp_name))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test.R:6:5:](https://github.com/folkehelseinstituttet/fhi/blob/dd2fb126cbdf5ceaca7557413926e45fbd147610/tests/testthat/test.R#L6) *style:* **Commented code should be removed.**
```r
  # rmarkdown::render(input=f,output_dir = tempdir())
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Successfully aliased the URL <https://timezone-butler-mbdtlbospq.now.sh> to the following alias.

* https://timezone-butler.now.sh


Will fix in https://github.com/odoo/odoo/pull/28880


I can see your point, I'll add a comment. "Better" options will have to wait because:

1. Simply adding `args[arg] = val` will work, even with other arguments besides `dest` and `source`, but doing so means that the reader knows that `--hdfs` overrides everything.
2. Proper way of handling it (and adapting to possible changes) is to move the rules about "argument A overrides argument B" into another hash (again, preferably inside pyDKB, not here) and make a single function which makes tests for arguments' interaction basing on this hash. It's possible, but let's leave that for later.


Muito triste


Chorei muito


HELLO


Tá dando seg fault aqui


Hi both, just re-cloned the repo and ran `npm install` and having a bit of an error message still @martsky-mart @jamescutts

<img width="766" alt="screen shot 2018-11-21 at 11 22 45" src="https://user-images.githubusercontent.com/29665595/48838308-e0073b80-ed7f-11e8-86e3-9872270f49d3.png">


you'll need to move into the prototype directory before running the npm commands
```
cd govuk-prototype-kit-8.3.0
npm install
npm start


![](https://github.trello.services/images/mini-trello-icon.png) [בסיום המסלול מערכת המשתמש תציג בפני המשתמש את הניקוד שצבר לאורך המסלול.](https://trello.com/c/us8KJYdQ/81-%D7%91%D7%A1%D7%99%D7%95%D7%9D-%D7%94%D7%9E%D7%A1%D7%9C%D7%95%D7%9C-%D7%9E%D7%A2%D7%A8%D7%9B%D7%AA-%D7%94%D7%9E%D7%A9%D7%AA%D7%9E%D7%A9-%D7%AA%D7%A6%D7%99%D7%92-%D7%91%D7%A4%D7%A0%D7%99-%D7%94%D7%9E%D7%A9%D7%AA%D7%9E%D7%A9-%D7%90%D7%AA-%D7%94%D7%A0%D7%99%D7%A7%D7%95%D7%93-%D7%A9%D7%A6%D7%91%D7%A8-%D7%9C%D7%90%D7%95%D7%A8%D7%9A-%D7%94%D7%9E%D7%A1%D7%9C%D7%95%D7%9C)


> > There seems to be a bug in cmake 2.8, which reverts the order of the include list when using BEFORE.

> Why 2.8? 16.04. runs with cmake 3.5.

You are right. Seems to be an issue of 3.5 then.

> Do you have a link to reference the issue?

No, I have not. This is just the result from my debugging session, printing the cmake variables before and after adding them.


GitHub tokens


![](https://github.trello.services/images/mini-trello-icon.png) [מערכת המשתמש מציגה למשתמש את מיקומו על המפה.](https://trello.com/c/GBtckcAI/85-%D7%9E%D7%A2%D7%A8%D7%9B%D7%AA-%D7%94%D7%9E%D7%A9%D7%AA%D7%9E%D7%A9-%D7%9E%D7%A6%D7%99%D7%92%D7%94-%D7%9C%D7%9E%D7%A9%D7%AA%D7%9E%D7%A9-%D7%90%D7%AA-%D7%9E%D7%99%D7%A7%D7%95%D7%9E%D7%95-%D7%A2%D7%9C-%D7%94%D7%9E%D7%A4%D7%94)


![](https://github.trello.services/images/mini-trello-icon.png) [במהלך הניווט לנקודת ציון, מערכת המשתמש תציג למשתמש רמזים לנקודת הציון הבאה במסלול.](https://trello.com/c/KTeajzc7/105-%D7%91%D7%9E%D7%94%D7%9C%D7%9A-%D7%94%D7%A0%D7%99%D7%95%D7%95%D7%98-%D7%9C%D7%A0%D7%A7%D7%95%D7%93%D7%AA-%D7%A6%D7%99%D7%95%D7%9F-%D7%9E%D7%A2%D7%A8%D7%9B%D7%AA-%D7%94%D7%9E%D7%A9%D7%AA%D7%9E%D7%A9-%D7%AA%D7%A6%D7%99%D7%92-%D7%9C%D7%9E%D7%A9%D7%AA%D7%9E%D7%A9-%D7%A8%D7%9E%D7%96%D7%99%D7%9D-%D7%9C%D7%A0%D7%A7%D7%95%D7%93%D7%AA-%D7%94%D7%A6%D7%99%D7%95%D7%9F-%D7%94%D7%91%D7%90%D7%94-%D7%91%D7%9E%D7%A1%D7%9C%D7%95%D7%9C)


![](https://github.trello.services/images/mini-trello-icon.png) [במהלך הניווט מערכת המשתמש תספק למשתמש לפחות רמז אחד לנקודת הציון הבאה במסלול](https://trello.com/c/3etfCKqf/168-%D7%91%D7%9E%D7%94%D7%9C%D7%9A-%D7%94%D7%A0%D7%99%D7%95%D7%95%D7%98-%D7%9E%D7%A2%D7%A8%D7%9B%D7%AA-%D7%94%D7%9E%D7%A9%D7%AA%D7%9E%D7%A9-%D7%AA%D7%A1%D7%A4%D7%A7-%D7%9C%D7%9E%D7%A9%D7%AA%D7%9E%D7%A9-%D7%9C%D7%A4%D7%97%D7%95%D7%AA-%D7%A8%D7%9E%D7%96-%D7%90%D7%97%D7%93-%D7%9C%D7%A0%D7%A7%D7%95%D7%93%D7%AA-%D7%94%D7%A6%D7%99%D7%95%D7%9F-%D7%94%D7%91%D7%90%D7%94-%D7%91%D7%9E%D7%A1%D7%9C%D7%95%D7%9C)


Punt it to `Target.cppTypeMangle` like this?


RELEASES.md


@tayyars I have pushed the latest changes. Let me know if something isn't working for you! Please bear in mind that this feature is still under development :)


This is a bit convoluted, but I suppose `real` is one of the few types we'll have to do this for (maybe the complex/imaginary reals listed above too?).


[Perfumes de equivalencia](https://www.pradyparfums.com/perfumes-prady/)


lack of time, sorry. Here are all the changes: https://github.com/globalize/globalize/compare/v5.1.0...v5.2.0


would it be possible to turn TRANSLATORS into multimap and add ability to register multiple translators for a single URN? First translator with matching predicate would be used for translation. Eg. we can have multiple GBK translations and it would be more readable to have them in separate translators, than trying to squeeze them in one impl


![](https://github.trello.services/images/mini-trello-icon.png) [Correct formatting of the results page](https://trello.com/c/Mijt7Zkk/89-correct-formatting-of-the-results-page)


![](https://github.trello.services/images/mini-trello-icon.png) [Change the left pane to show teh resulting SDG Goal](https://trello.com/c/2t7y5nDE/88-change-the-left-pane-to-show-teh-resulting-sdg-goal)


не надо внутри конкатенации делать тренарный оператор

сделай нормальный if else и там внутри два  puts


стороны могут быть не целыми


result пишется без a

выкини тренарные операторы из строк
это не читабельно вообще


сделай подсчет в одном месте puts в другом

сначала находим корни, потом выводим, не надо делать сразу 3-4 действия в одной строке


this is the point where images are succesfully being delivered from data file in single and list templates as well as home page.


Shouldn't this be false?


# v9

Util_Gam should read more like EV-0.5*lamdba*(-V_Gam_Loss)^A_GAIN
Also don't call it EV, as it's a utility function.

For your new loop trying to get the prochoice values, you don't need to use cell2mat because the data stored in the cell is in a matrix, you can just reference it as UtilDiff{GenericCount}. For cells, you can refer to the cell itself by using normal brackets i.e. UtilDiff(a) or UtilDiff{a} refers to the contents of the cell - play around with making some cells and understanding how to manipulate them. Ince you have utildiff as a matrix, just use the probchoice function as you did before, performing it elementwise.


7", screen


下記テーブル追加

m_consumption_tax
m_staff


бьт


![](https://github.trello.services/images/mini-trello-icon.png) [בסיום המסלול, מערכת המשתמש תציג למשתמש אפשרות להמשיך למסלול ארוך יותר(במידה וקיים)](https://trello.com/c/9BsL5t8U/164-%D7%91%D7%A1%D7%99%D7%95%D7%9D-%D7%94%D7%9E%D7%A1%D7%9C%D7%95%D7%9C-%D7%9E%D7%A2%D7%A8%D7%9B%D7%AA-%D7%94%D7%9E%D7%A9%D7%AA%D7%9E%D7%A9-%D7%AA%D7%A6%D7%99%D7%92-%D7%9C%D7%9E%D7%A9%D7%AA%D7%9E%D7%A9-%D7%90%D7%A4%D7%A9%D7%A8%D7%95%D7%AA-%D7%9C%D7%94%D7%9E%D7%A9%D7%99%D7%9A-%D7%9C%D7%9E%D7%A1%D7%9C%D7%95%D7%9C-%D7%90%D7%A8%D7%95%D7%9A-%D7%99%D7%95%D7%AA%D7%A8%D7%91%D7%9E%D7%99%D7%93%D7%94-%D7%95%D7%A7%D7%99%D7%99%D7%9D)


Yeah it is in the final version. I force pushed a commit which overwrites this.


@ppaulweber this is actually all code needed for the workspace_symbol() method defined by the lsp. There was a class missing for it and the enum class had to be defined here. But yeah I agree "LSP: updated WorkspaceSymbol implementation" would have been clearer.


![](https://github.trello.services/images/mini-trello-icon.png) [במהלך ניווט המשתמש יכול לבקש רמזים נוספים לצורך ניווט לנקודת הציון.](https://trello.com/c/vfSpQW0z/111-%D7%91%D7%9E%D7%94%D7%9C%D7%9A-%D7%A0%D7%99%D7%95%D7%95%D7%98-%D7%94%D7%9E%D7%A9%D7%AA%D7%9E%D7%A9-%D7%99%D7%9B%D7%95%D7%9C-%D7%9C%D7%91%D7%A7%D7%A9-%D7%A8%D7%9E%D7%96%D7%99%D7%9D-%D7%A0%D7%95%D7%A1%D7%A4%D7%99%D7%9D-%D7%9C%D7%A6%D7%95%D7%A8%D7%9A-%D7%A0%D7%99%D7%95%D7%95%D7%98-%D7%9C%D7%A0%D7%A7%D7%95%D7%93%D7%AA-%D7%94%D7%A6%D7%99%D7%95%D7%9F)


添加gif


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

* https://ecowasparliament.ml


@anandology hello, can we maybe get a release on pypi since now web.py supports python3.7 and a lot of bugs have been resolved by this pr? 👍 a `feature release` like `0.41` or even a `bug-fix release`? like `0.41.dev2` or something, ty in advance!


There was an issue flagged by CI: I had previously changed my filenames to snake case (to follow Ruby conventions). However the change in case had not been picked up by Git so Travis couldn't locate the correct lib files. I forced Git to update my lib filenames and tests now pass on Travis.


Ah I missed that, sorry


# improve this code of conduct
# and send to your channels for public use
Contributor Covenant Code of Conduct
Our Pledge
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Our Standards
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•	Using welcoming and inclusive language
•	Being respectful of differing viewpoints and experiences
•	Gracefully accepting constructive criticism
•	Focusing on what is best for the community
•	Showing empathy towards other community members
Examples of unacceptable behavior by participants include:
•	The use of sexualized language or imagery and unwelcome sexual attention or advances
•	Trolling, insulting/derogatory comments, and personal or political attacks
•	Public or private harassment
•	Publishing others' private information, such as a physical or electronic address, without explicit permission
•	Other conduct which could reasonably be considered inappropriate in a professional setting
Our Responsibilities
Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
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This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
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Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
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This Code of Conduct is adapted from the Contributor Covenant, version 1.4, available at http://contributor-covenant.org/version/1/4


Now could not deploy this pull request since the `now.json` file explicitly sets `dotenv` to true.
However, there's no `.env` file in the repo.

Commit a `.env` file or unset the `dotenv` flag.
For secret environment variables, check out [Now Secrets](https://zeit.co/docs/getting-started/secrets).


Je ne sais pas si il faut maintenir un organisme "Autre" ou si il faut permettre de créer des utilisateurs/observateurs sans organisme.

Car ça peut aboutir à des problèmes comme le fait qu'un utilisateur voit toutes les données des utilisateurs de l'organisme "Autre".


The last time we deleted it, we broke skyscanner :(

I _suspect_ it's safer to remove now than it used to be. We should try.


Successfully aliased the URL <https://docs-api-vhoitwrzma.now.sh> to the following alias.

* https://docs.api.nuxtjs.org


:wink:


Successfully aliased the URL <https://jade-cleric-c2k0p2aan.now.sh> to the following alias.

* https://jade-cleric.now.sh


make it bullet point uitem


Well you are right with Detection being 20 default, CallForHelp < Detection is not effective, depending on where the creatures are positioned and where the players are / also player level dependend etc...

So it just boils down to what the scripted callforhelp radius should be (it is not generic, they have unique emote for that)


[R/AllClasses.R:1:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/AllClasses.R#L66) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:70:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/AllClasses.R#L71) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:76:19:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/AllClasses.R#L79) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:107:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/AllClasses.R#L107) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:163:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/AllClasses.R#L163) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:166:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/AllClasses.R#L167) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:171:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/AllClasses.R#L171) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:173:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/AllClasses.R#L177) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/alphaSummary-methods.R:45:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqAnalysis.R#L49) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(object, "DESeqAnalysis"))
    ^~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:69:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L69) *warning:* **no visible global function definition for ‘assert_that’**
```r
        assert_that(is(object, "DESeqResults"))
        ^~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:70:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L70) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(c("log2FoldChange", "padj"), colnames(object))
        ^~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:71:18:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L71) *warning:* **no visible global function definition for ‘metadata’**
```r
        alpha <- metadata(object)[["alpha"]]
                 ^~~~~~~~
```
[R/DESeqResultsTables-methods.R:72:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L72) *warning:* **no visible global function definition for ‘assertIsAlpha’**
```r
        assertIsAlpha(alpha)
        ^~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:73:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L73) *style:* **Variable or function name should be snake_case.**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
        ^~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:73:25:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L73) *warning:* **no visible global function definition for ‘metadata’**
```r
        lfcThreshold <- metadata(object)[["lfcThreshold"]]
                        ^~~~~~~~
```
[R/DESeqResultsTables-methods.R:74:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L74) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:75:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L75) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(lfcThreshold)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:78:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L78) *style:* **Variable or function name should be snake_case.**
```r
        lfcCol <- "log2FoldChange"
        ^~~~~~
```
[R/DESeqResultsTables-methods.R:79:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L79) *style:* **Variable or function name should be snake_case.**
```r
        testCol <- "padj"
        ^~~~~~~
```
[R/DESeqResultsTables-methods.R:80:16:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L80) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
        lfc <- sym(lfcCol)
               ^~~
```
[R/DESeqResultsTables-methods.R:81:17:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L81) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
        test <- sym(testCol)
                ^~~
```
[R/DESeqResultsTables-methods.R:130:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L130) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink = TRUE
        ^~~~~~~~~
```
[R/DESeqResultsTables-methods.R:159:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L159) *style:* **Variable or function name should be snake_case.**
```r
        rowRanges <- rowRanges(data)
        ^~~~~~~~~
```
[R/DESeqResultsTables-methods.R:169:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L169) *warning:* **no visible global function definition for ‘mcols<-’, Did you mean 'mcols'?**
```r
        mcols(rowRanges) <- mcols
        ^~~~~
```
[R/DESeqResultsTables-methods.R:170:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L170) *warning:* **no visible global function definition for ‘assert_is_non_empty’**
```r
        assert_is_non_empty(rowRanges)
        ^~~~~~~~~~~~~~~~~~~
```
[R/DESeqResultsTables-methods.R:187:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/DESeqResultsTables-methods.R#L187) *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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/markdown-methods.R#L50) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:52:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/markdown-methods.R#L52) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:54:21:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/markdown-methods.R#L57) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:60:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/markdown-methods.R#L60) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:81:1:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/markdown-methods.R#L81) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~~~
```
[R/markdown-methods.R:82:13:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/markdown-methods.R#L109) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:111:9:](https://github.com/steinbaugh/DESeqAnalysis/blob/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/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/4e42ec007d29a4e78d8ef224f1b3f44b4fdc181c/R/topTables-methods.R#L131) *warning:* **no visible global function definition for ‘.topTable’**
```r
        up <- .topTable(object, direction = "up", n = n)
              ^~~~~~~~~
```


Good spot, thanks.


Je me demande si dans certains cas, ces 3 applications ne peuvent pas contenir des majuscules, genre GeoNature, TaxHub, UsersHub... ?
Dans ce cas, je ne sais pas si le ``ilike`` est sensible à la casse ou non.


This commit added some invalid CSS, like `<table style="cellspacing:0 callpadding: 0">`. In CSS, these properties have no direct inline equivalent. But they shouldn't be necessary anyway - we set them to 0 by default in main.css.