here we would go off to the compiler to actually compile, which will op back to Rust to collect any other sources it needs.


Any reason to prefer this over Regexp.Union function?


Successfully aliased the URL <https://pakairquality-kzy505468.now.sh> to the following alias.

* https://pakairquality.now.sh


Same as above ^^^


I wasn't able to figure out a good way of passing two strings as the data payload of an op...  I could set a length property of the output code in the op and then concat the source map onto the end of the data, and the split that back out on the Rust side, but I wanted to check if I was missing something obvious about dealing with the data payloads.


This seems to block execution and so the other isolate never gets invoked.  It is currently beyond me to easily figure out how to spin these two isolates up to run concurrently.


嗯嗯嗯


@guillelle ¿Por que sacamos la verificacion? Asi se repite el mismo evento cada vez que un usuario lo agrega a una lista. ¿Por que en Evento deberiamos tener la referencia al listadoDeEventos? #


While I have spec'ed these (the ops to power the `CodeProvider` API for the runner in the runtime isolate) they aren't actually implemented anywhere yet.


hard coded to just prove the ops work


Successfully aliased the URL <https://hi-eaebhufnxw.now.sh> to the following aliases.

* https://hicto.tech
* https://www.hicto.tech


There is no differentiation between what ops are supported on what isolate, basically everything could be supported on the Rust side.  I don't think this is a big issue, but in theory, someone could fiddle around on the runtime isolate and impersonate these ops... I don't know if putting a hard barrier between what ops are supported at this stage is worth it.


最后为何要renderNull?


needs to talk to the work queue to fetch the next module (or tell the compiler to stop)...


doh! need to run this through the formatter


Much better


Yeah, I figured, thought I would let you know they exist. Also, you can use `npm version ...` to simplify it


Hi Jakub,
here we go:
```R
library(landscapemetrics)
library(raster)

mat1 <- as.matrix(augusta_nlcd)
mat2 <- as.matrix(landscape)
test <- raster("~/Downloads/lc_2008_4bit_clip.tif")
mat3 <- as.matrix(test)
n <- as.matrix(4)

res1.1 <- landscapemetrics:::rcpp_get_coocurrence_matrix(mat1, n)
res1.2 <- landscapemetrics:::rcpp_get_coocurrence_matrix(mat2, n)
res1.3 <- landscapemetrics:::rcpp_get_coocurrence_matrix(mat3, n)

res2.1 <- landscapemetrics:::rcpp_get_coocurrence_matrix2(mat1, n, ncol(mat1), nrow(mat1), unique(augusta_nlcd))
res2.2 <- landscapemetrics:::rcpp_get_coocurrence_matrix2(mat2, n, ncol(mat2), nrow(mat2), unique(landscape))
res2.3 <- landscapemetrics:::rcpp_get_coocurrence_matrix2(mat3, n, ncol(mat3), nrow(mat3), unique(test))
```
rcpp_get_coocurrence_matrix2 clearly needs a wrapper function to fit the rest of the package.

Best,
Sebastian


Code review


Created multidev environment [ilsoy#ci-166](https://dashboard.pantheon.io/sites/1b49470e-4ad3-4b49-90a2-7bb2c2f96788#ci-166).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-166-ilsoy.pantheonsite.io/)


Ah, and other neighborhoods than rooks case are currently not possible, @marcosci volunteered to fix that.


❓ ❓ ❓ Hm... whatever this does... but it looks not too bad. ❓ ❓ ❓


Po co?


The `angular.json` file should also be updated in the starters.


Push to official twrp tree, please, and write a better comment message.

With this, miui install isn't required anymore to encrypt the device, just format data with new twrp, boot rom and encrypt it.


Successfully aliased the URL <https://utch-next-vxpoyohxhr.now.sh> to the following alias.

* https://ui.utchrecords.com


This was the non-whitelisted URL. Seems like D.O. is still mostly happy to use bower 🤷♂


Masz już jedną pętle, nie lepiej było zostawić tą starą tylko zrobić, żeby była nieskończona? `while(true)` na przykład


Oops, this doesn't work in Scala 2.11. Hotfixing...


![](https://github.trello.services/images/mini-trello-icon.png) [Створити класи Listener і Cheater.](https://trello.com/c/FzvwNm3z/5-%D1%81%D1%82%D0%B2%D0%BE%D1%80%D0%B8%D1%82%D0%B8-%D0%BA%D0%BB%D0%B0%D1%81%D0%B8-listener-%D1%96-cheater)


Don't Repeat Yourself


Would you please to let me know if the package updated? Thank you.


@andreyshuster  this breaks using the jenkisfile standalone (and my existing Jenkins cannot build this project any more which is part of my demo builds ...


See: https://www.drupal.org/packaging-whitelist?title=Imagesloaded


DRY


A zapytałeś się kogoś czy tak se zmieniłeś?


This key is no longer valid


te entery, żeby z 22 dodanych liń zrobić 24?


I don't believe so. `effectslots` is an array of integer IDs, which are used as an index lookup into `EffectSlotList` to say which to clear/delete.


Yeah, I already changed it in my working branch...


Now could not deploy this pull request since the "files" configuration in `now.json` lists these files or directories which do not exist:

* `.env`
* `dist`

These paths may be missing from the GitHub repository because of a `.gitignore` file.
Consider committing them to GitHub or removing them from the "files" list and generating the paths on Now instead using a [build script for a Node.js deployment](https://zeit.co/docs/deployment-types/node), or within your `Dockerfile` for a [docker deployment](https://zeit.co/docs/deployment-types/docker).

For more information on the "files" configuration in now.json, visit [https://zeit.co/docs/features/configuration#files(array)](https://zeit.co/docs/features/configuration#files(array))


Got it!  Will do.


Added jquery imports as well as a few refactoring due to syntax merge conflict


Hi, it's just now that I realized this is in a demo page, so it's perfectly fine as it serves a debugging purpose. Sorry for asking for a PR.


[R/raz_utils.R:71:3:](https://github.com/richelbilderbeek/razzo/blob/fc03afb64dae4b454873fb4cd817df4f1a74189c/R/raz_utils.R#L71) *style:* **Variable or function name should be snake_case.**
```r
  num.species <- phylo$Nnode + 1
  ^~~~~~~~~~~
```


LOL


Yes, that makes sense, the question though is how does then Rust manage it once it gets back a response?  It wouldn't want to trash the isolate, it just would either want to suspend its event loop or it would want to leave it running awaiting the response back from Rust.


`runtime_isolate`?  (And the `Runner` is part of the runtime)


@juozasg The COVALIController is updated. Please merge into your branch.


I actually did it for you :D appreciate the PR and coverage as always!

--
-Brandon


No problem! I may have been too zealous in my review.. let's keep it as is.


Hvad er egentlig pointen her?


I think so yes, please create a pr for that...


Hey just a comment, but you can add the `$likeLower` operator without modifying the source code if you look at [custom operators](https://github.com/tandg-digital/objection-filter#custom-operators).


Puzzle `9-bfa04699` discovered in   [`readme.md`](  https://github.com/nikialeksey/arspell/blob/master/readme.md)   and submitted as #13. Please, remember that the puzzle was not   necessarily added in this particular commit. Maybe it was added earlier, but   we discovered it only now.


@indutny @rvagg @shigeki Is there any reason not to upstream this to OpenSSL?


oh wow, this is fun.


Now could not deploy this pull request since the `build.env` field in the `now.json` is an array.
When using Now + GitHub, `build.env` field must be an object.

	Click here to see the contents of `now.json`

{
	"type": "docker",
	"features": {
		"cloud": "v2"
	},
	"build": {
		"env": [
			"GITHUB_USERNAME"
		]
	}
}


Esto rompe todos los contenidos de documento html subidos por documentos y adjuntado dentro de un scorm chamilo ya no se puede editar o dar formato de correciónes desde el mismo chamilo.   :expressionless:

Todos los cursos CHAPA y CHACOBU del campus chamilo fueron afectados despues de este cambio.

Adjunto captura.

![contenido_curso_chapa](https://user-images.githubusercontent.com/2940509/48800838-e8586b80-ecd8-11e8-98ad-f648283f8bb3.png)


This commit adds several SLASHEM artifacts and does a bit more balancing.


Fixed #8


Thanks! My bad


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @alexandrebbruno was added to conda-forge. Welcome to conda-forge!
  Go to https://github.com/orgs/conda-forge/invitation see your invitation.

You should get push access to this feedstock and CI services.

Feel free to join the community [chat room](https://gitter.im/conda-forge/conda-forge.github.io).

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/conda-forge_gotchas.html#using-a-fork-vs-a-branch-when-updating-a-recipe)


Fixes #104
Apparently


**You nailed your code to Debian-based systems.

Ты прибил гвоздями свой код к Debian-based системам**


@gengliangwang ah, I forgot there is also a Windows .cmd version of this file. Well, I'm about to open a PR that comments out logic for 2 Scala versions, so I could update that file too and comment it out as well.


![](https://github.trello.services/images/mini-trello-icon.png) [#7 Daily Scrum](https://trello.com/c/CFFNPtmI/51-7-daily-scrum)


IBM Cloud [toolchain](https://console.bluemix.net/devops/toolchains/623ac46c-aeaa-4433-a262-223430c2e0af?env_id=ibm%3Ayp%3Aus-south "googleDictionaryAPI"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/43a8bfc9-4989-4464-8299-979f59631a9c?env_id=ibm%3Ayp%3Aus-south "googleDictionaryAPI") deployed [googleDictionaryAPI](https://github.com/meetDeveloper/googleDictionaryAPI/releases/tag/deploy-ibm-yp-eu-gb-lifeplusplus-API-s-20181120-203430 "deploy-ibm-yp-eu-gb-lifeplusplus-API-s-20181120-203430") to [API's](https://console.bluemix.net/apps/0971aef0-04d8-454a-b263-f77d06d21309?env_id=ibm:yp:eu-gb "ibm:yp:eu-gb:lifeplusplus:API's"), including this commit


This commit has been mentioned on **Discourse Meta**. There might be relevant details there:

https://meta.discourse.org/t/forcing-hostname-has-broken-support-for-onion-services/102419/1


Hi there!

Trying to use HidGuardian and I'm still not sure, have you now build this into JG or do we need to download and build HidGuardian ourself?


Er det ikke dig der har lavet det?  Men jeg tror det er for at undgå at kommandoen ikke læser alle der nogensinde har været i #diku-kanalen, som det plejede at være.


![](https://github.trello.services/images/mini-trello-icon.png) [#8 Daily Scrum](https://trello.com/c/6mM6cmRe/52-8-daily-scrum)


Try to avoid the `operator[]`, as it creates an `AllTypeVariant` and is pretty slow.
You could add a
```
#include "utils/performance_warning.hpp"
...
PerformanceWarning("operator[] used");
```
to the `ValueSegment` and the `DictionarySegment` implementation to get notified.


Are `ValueID{...}` and `static_cast<uint32_t>(...)` both necessary?
If we understood it right, `ValueID{...}` should probably be enough.


`operator[]`.
See above.


`ValueID{...}` vs `static_cast<uint32_t>(...)`.
See above.


Here you could add the `PerformanceWarning`.


`ValueID{...}` vs `static_cast<uint32_t>(...)`.
Check the rest of the file also.


Sweet way to calculate it, better than `sizeof` indeed 👍


Really nice checks 👌


`ChunkID{...}` vs `static_cast<>(...)`.


We weren't quite sure if `shared_lock` or `unique_lock` would be best in this situation.
Strictly speaking, the `Chunk` could be modified, but for now this won't be a problem.


You can use `mutable` to avoid the `const_cast`. 😉


Nicely structured private methods.


Very thorough testing 👍.


5/5 Nice!


Here, you remove dynamic contempt, but also you remove contempt !
Is this your intent ?


5/5
Total: 10/10


Houd je niet van docker toolbox?


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

* https://dialetus.now.sh


Aliasing failed with the following error:

~~~
Error! We couldn't verify the domain anton.click.
~~~


8/10

Adding student functionality?


Добавлен файл для переноса репозитория на netlify


delete


10/10
perfect!


hi akka how r u


@eldy any reason why this hidden feature would be removed?


PR_opened/Fix_6937_RunPeriodNamesInWarnings (jmarrec) - x86_64-Linux-Ubuntu-18.04-gcc-7.3-IntegrationCoverage-Debug: OK (2422 of 2422 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-72.28%25-green.png)


Are they really unused?


[R/raz_create_bd_tree.R:70:18:](https://github.com/richelbilderbeek/razzo/blob/86dc524377eabf20affa87e18ac990e0a1f9f6bd/R/raz_create_bd_tree.R#L70) *warning:* **no visible global function definition for ‘bd_phylo_2_l_table’**
```r
  bd_l_matrix <- bd_phylo_2_l_table(bd_tree)
                 ^~~~~~~~~~~~~~~~~~
```
[R/raz_utils.R:65:10:](https://github.com/richelbilderbeek/razzo/blob/86dc524377eabf20affa87e18ac990e0a1f9f6bd/R/raz_utils.R#L65) *warning:* **no visible global function definition for ‘raz_convert_tree2brts’**
```r
  brt <- raz_convert_tree2brts(phylo)
         ^~~~~~~~~~~~~~~~~~~~~
```


IBM Cloud [toolchain](https://console.bluemix.net/devops/toolchains/623ac46c-aeaa-4433-a262-223430c2e0af?env_id=ibm%3Ayp%3Aus-south "googleDictionaryAPI"): [Delivery Pipeline](https://console.bluemix.net/devops/pipelines/43a8bfc9-4989-4464-8299-979f59631a9c?env_id=ibm%3Ayp%3Aus-south "googleDictionaryAPI") deployed [googleDictionaryAPI](https://github.com/meetDeveloper/googleDictionaryAPI/releases/tag/deploy-ibm-yp-eu-gb-lifeplusplus-API-s-20181120-204503 "deploy-ibm-yp-eu-gb-lifeplusplus-API-s-20181120-204503") to [API's](https://console.bluemix.net/apps/0971aef0-04d8-454a-b263-f77d06d21309?env_id=ibm:yp:eu-gb "ibm:yp:eu-gb:lifeplusplus:API's"), including this commit


PR_opened/Fix_6937_RunPeriodNamesInWarnings (jmarrec) - x86_64-Linux-Ubuntu-18.04-custom_check: OK (2 of 2 tests passed, 0 test warnings)

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


Runnable JAR file allowing you to paint your next masterpiece


Bro it is unused by bt stack


Paint file allowing you to paint your next masterpiece


Buuu, czemu nie WarsawJS? :)


10/10

Awesome UI! Nice!


Допустил ошибку)Надо было AssTestsAndUser.create
Невнимательность моя(


Only wcnss service is needed by bt stack


@probeadd It may take a while, because I've lost access to the PyPI account I used to upload the package. I requested an ownership transfer but I don't know how long they take to get around to those. Sorry for the inconvenience. Downloading the git repo, going into the `python` directory and doing `python setup.py install` should get you up and running.


10/10 Nice!


commenting to test.


Ims can work from vendor now bro


this is addressing #111 and #112


I'll get a PR for a fix up later as I've also regressed my fix for the selection graphical glitch in *setShowServiceMode*.


Пока работает только с Content-Type: `application/x-www-form-urlencoded` и, как видно, только в протоколе HTTP


@palmskog Sure, there is no doubt.


8/10

Adding students functionality?


Для того, чтобы работать с другими Content-Type нужно изменять код не здесь, а в `core\utils\bodyparser`


What is this commit?


Hah - falt meg ikke inn at rbkweb.com eksisterte...


Yes, they weren't currently being used / exposed at the time that they were moved. This move was just to indicate that they had not yet been updated to 0.3


PR_opened/Fix_6937_RunPeriodNamesInWarnings (jmarrec) - Win64-Windows-7-VisualStudio-14: OK (3050 of 3051 tests passed, 0 test warnings)

Failures:

regression Test Summary
 * Passed: 631
 * Failed: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.97%25-yellow.png)


Started backend


10/10

wow! the gif is so cool!


Честно говоря, мне в этом файле не нравится бессистемность расставления пустых строк.
И ещё было бы неплохо как-то структурировать список методов - например, разбить их по категориям...


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

Client ID project/taskcluster/tc-github/production does not have sufficient scopes and are missing the following scopes:

```
queue:route:index.project.focus.android.preview-builds
```

You have the scopes:

```
[
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  "assume:repo:github.com/mozilla-mobile/focus-android:branch:master",
  "notify:email:*",
  "notify:irc-channel:*",
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  "queue:create-task:aws-provisioner-v1/github-worker",
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  "queue:route:garbage.*",
  "queue:route:index.garbage.*",
  "queue:route:notify.email.*",
  "queue:route:notify.irc-channel.*",
  "queue:route:notify.irc-user.*",
  "queue:scheduler-id:taskcluster-github",
  "secrets:get:garbage/*",
  "secrets:get:project/focus/firebase",
  "secrets:get:project/focus/nimbledroid",
  "secrets:get:project/focus/preview-key-store",
  "secrets:set:garbage/*"
]
```

This request requires you to satisfy this scope expression:

```
{
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    "secrets:get:project/focus/firebase",
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}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2018-11-20T20:54:12.851Z

</details>


It was a typo:
http://digikom.hu/download/geoeasy_3.1.1dev-wheezy_all.deb


Created multidev environment [next50#dev](https://dashboard.pantheon.io/sites/8e7c33cd-c6bd-4dcf-a71d-f1ade4f2e791#dev).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://dev-next50.pantheonsite.io/)


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

Client ID project/taskcluster/tc-github/production does not have sufficient scopes and are missing the following scopes:

```
queue:route:index.project.focus.android.preview-builds
```

You have the scopes:

```
[
  "assume:project:taskcluster:mozilla-github-repository",
  "assume:repo:github.com/mozilla-mobile/focus-android:branch:master",
  "notify:email:*",
  "notify:irc-channel:*",
  "notify:irc-user:*",
  "queue:create-task:aws-provisioner-v1/github-worker",
  "queue:create-task:aws-provisioner-v1/github-worker-windows",
  "queue:create-task:aws-provisioner-v1/win2012r2",
  "queue:route:garbage.*",
  "queue:route:index.garbage.*",
  "queue:route:notify.email.*",
  "queue:route:notify.irc-channel.*",
  "queue:route:notify.irc-user.*",
  "queue:scheduler-id:taskcluster-github",
  "secrets:get:garbage/*",
  "secrets:get:project/focus/firebase",
  "secrets:get:project/focus/nimbledroid",
  "secrets:get:project/focus/preview-key-store",
  "secrets:set:garbage/*"
]
```

This request requires you to satisfy this scope expression:

```
{
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    "queue:scheduler-id:taskcluster-github",
    "secrets:get:project/focus/preview-key-store",
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    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2018-11-20T20:54:34.798Z

</details>


forgotten debug logging to console?


9грг


[R/AllClasses.R:1:1:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/AllClasses.R#L1) *style:* **Variable or function name should be snake_case.**
```r
validateS4 <- function(...) {
^~~~~~~~~~
```
[R/AllClasses.R:66:1:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/AllClasses.R#L66) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:70:9:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/AllClasses.R#L71) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:79:1:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/AllClasses.R#L79) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:107:1:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/AllClasses.R#L107) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:163:1:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/AllClasses.R#L163) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:166:9:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/AllClasses.R#L167) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:171:1:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/AllClasses.R#L171) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/AllClasses.R:173:9:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/AllClasses.R#L177) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/alphaSummary-methods.R:45:9:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/DESeqAnalysis.R#L35) *style:* **Variable or function name should be snake_case.**
```r
        lfcShrink
        ^~~~~~~~~
```
[R/DESeqAnalysis.R:48:1:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/DESeqResultsTables-methods.R#L187) *style:* **Variable or function name should be snake_case.**
```r
        sampleNames <- sampleNames(data)
        ^~~~~~~~~~~
```
[R/export-methods.R:41:1:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L41) *style:* **Variable or function name should be snake_case.**
```r
.prepareDESeqResults <- function(
^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:43:5:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L43) *style:* **Variable or function name should be snake_case.**
```r
    rowData = NULL,
    ^~~~~~~
```
[R/export-methods.R:45:5:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L45) *style:* **Variable or function name should be snake_case.**
```r
    sampleNames = NULL
    ^~~~~~~~~~~
```
[R/export-methods.R:47:5:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L47) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "DESeqResults")
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:48:5:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L48) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(rowData, c("DataFrame", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:49:5:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L49) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(counts, c("matrix", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:50:5:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L50) *warning:* **no visible global function definition for ‘assert_is_any_of’**
```r
    assert_is_any_of(sampleNames, c("character", "NULL"))
    ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:58:9:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L58) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
        assert_is_all_of(rowData, "DataFrame")
        ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:59:9:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L59) *style:* **Variable or function name should be snake_case.**
```r
        rowData <- sanitizeRowData(rowData)
        ^~~~~~~
```
[R/export-methods.R:59:20:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L59) *warning:* **no visible global function definition for ‘sanitizeRowData’**
```r
        rowData <- sanitizeRowData(rowData)
                   ^~~~~~~~~~~~~~~
```
[R/export-methods.R:60:9:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L60) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(data), rownames(rowData))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:67:9:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L67) *warning:* **no visible global function definition for ‘assert_is_matrix’**
```r
        assert_is_matrix(counts)
        ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:68:9:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L68) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
        assert_are_identical(rownames(data), rownames(counts))
        ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:75:13:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L75) *warning:* **no visible global function definition for ‘assert_has_names’**
```r
            assert_has_names(sampleNames)
            ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:76:13:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L76) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
            assert_are_identical(names(sampleNames), colnames(counts))
            ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:79:9:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L79) *warning:* **no visible global function definition for ‘assert_are_disjoint_sets’**
```r
        assert_are_disjoint_sets(colnames(data), colnames(counts))
        ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:93:9:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L93) *style:* **Variable or function name should be snake_case.**
```r
        rowData = NULL,
        ^~~~~~~
```
[R/export-methods.R:95:9:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L95) *style:* **Variable or function name should be snake_case.**
```r
        sampleNames = NULL
        ^~~~~~~~~~~
```
[R/export-methods.R:104:9:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L104) *warning:* **no visible global function definition for ‘export’**
```r
        export(x = x, file = file, format = format)
        ^~~~~~
```
[R/export-methods.R:120:1:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L120) *style:* **Variable or function name should be snake_case.**
```r
.prepareResultsTablesList <- function(object) {
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:121:5:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L121) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(object, "DESeqResultsTables"))
    ^~~~~~~~~~~
```
[R/export-methods.R:125:5:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L125) *warning:* **no visible global function definition for ‘assert_is_list’**
```r
    assert_is_list(deg)
    ^~~~~~~~~~~~~~
```
[R/export-methods.R:126:5:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L126) *warning:* **no visible global function definition for ‘assert_are_identical’**
```r
    assert_are_identical(names(deg), c("up", "down"))
    ^~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:134:5:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L134) *style:* **Variable or function name should be snake_case.**
```r
    rowData <- slot(object, "rowRanges") %>%
    ^~~~~~~
```
[R/export-methods.R:139:5:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L139) *style:* **Variable or function name should be snake_case.**
```r
    sampleNames <- slot(object, "sampleNames")
    ^~~~~~~~~~~
```
[R/export-methods.R:147:5:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L147) *warning:* **no visible global function definition for ‘assert_that’**
```r
    assert_that(is(all, "DataFrame"))
    ^~~~~~~~~~~
```
[R/export-methods.R:162:16:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L162) *warning:* **no visible global function definition for ‘initDir’**
```r
        dir <- initDir(dir)
               ^~~~~~~
```
[R/export-methods.R:163:9:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L163) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(compress)
        ^~~~~~~~~~~~~~~~
```
[R/export-methods.R:166:19:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L166) *warning:* **no visible global function definition for ‘.prepareResultsTablesList’**
```r
        tables <- .prepareResultsTablesList(x)
                  ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/export-methods.R:167:9:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L167) *warning:* **no visible global function definition for ‘assert_is_list’**
```r
        assert_is_list(tables)
        ^~~~~~~~~~~~~~
```
[R/export-methods.R:174:17:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L174) *warning:* **no visible global function definition for ‘snake’, Did you mean 'save'?**
```r
        stem <- snake(contrastName(x))
                ^~~~~
```
[R/export-methods.R:174:23:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L174) *warning:* **no visible global function definition for ‘contrastName’**
```r
        stem <- snake(contrastName(x))
                      ^~~~~~~~~~~~
```
[R/export-methods.R:180:51:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L180) *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:189:17:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L189) *warning:* **no visible global function definition for ‘export’**
```r
                export(x = x, file = file)
                ^~~~~~
```
[R/export-methods.R:196:9:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/export-methods.R#L196) *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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/markdown-methods.R#L50) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:52:1:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/markdown-methods.R#L52) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:54:21:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/markdown-methods.R#L57) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:60:1:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/markdown-methods.R#L60) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:81:1:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/markdown-methods.R#L81) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~~~
```
[R/markdown-methods.R:82:13:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/markdown-methods.R#L109) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/markdown-methods.R:111:9:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/plotDEGPCA-methods.R#L85) *style:* **Trailing whitespace is superfluous.**
```r
    f = "plotPCA",
                  ^
```
[R/plotDEGPCA-methods.R:108:20:](https://github.com/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/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/mjsteinbaugh/DESeqAnalysis/blob/a4900392ba527a870ecd9ef16624357577d4b2e3/R/topTables-methods.R#L126) *warning:* **no visible global function definition for ‘assertIsAnImplicitInteger’**
```r
        assertIsAnImplicitInteger(n)
        ^~~~~~~~~~~~~~~~~~~~~~~~~
```


Oh... right, you essentially already did what I just suggested. You even came up with the same file name for it. Sorry, I'm just slowly piecing together all the things that changed recently here. Makes sense then.


not good


Например, так
```
// Ctors, assignment and dtor
const_iterator(const List<Data>* list = nullptr, index_t points_to = 0);

~const_iterator() = default;

const_iterator(const_iterator&&) = default;
const_iterator(const const_iterator&) = default;

const_iterator& operator=(const_iterator&&) = default;
const_iterator& operator=(const const_iterator&) = default;

// Swap
friend void swap(const_iterator&, const_iterator&);

// Equality
bool operator==(const const_iterator&) const;
bool operator!=(const const_iterator&) const;

// Access
const Data& operator*();
const Data* operator->();

// Iteration
const_iterator& operator++();
const_iterator operator++(int);
const_iterator& operator--();
const_iterator  operator--(int);
```


Overall, looks good. My comments would be

1. Test cases missing, could you add some into mysql_client_test

2.Can if you investigate, if following is feasible / easy to implement?

Not to collect all ranges into insert_ids array, and bind id to THD, and write the result set when the whole bulk is finished.
Instead, maybe you could write result set rows somewhere inside execute_bulk_loop() (and result set metadata before this function). You only need to write a row when sequence "breaks", and/or at the very end of the loop.
(You might also need change thd->get_stmt_da() so that status is DA_EOF rather than DA_OK_BULK in case of generated ID resultset, so that proper EOF is returned when BULK-with-generated-ids finishes)

I believe that may bring some benefits - less memory usage, less pollution of the THD, code would be more localized in prepared statement code rather than THD.

3.Very minor - I think insert_id_desc::sequence  would be better called "count" or "len", because "sequence" is more suggestive of container name, e.g array or list , but not number.


la makhdmatch lik chi haja hatha hna f commentair


i would say something more strongly.  Like, this will only return 'null' in the event of a parameter symbol with yadda yadda yadda.

The above only implies that you can get null from a parameter.  not that it's only possible to get null only if you were working with a parameter.


In fact, yes, line 436 `self.time_focus = None` shouldn't touch time_focus. If there's service selected or no events on the service, then it's not possible to what time the user wants, so best left alone.


Thanks for this very clear and synthetic explanation, Rob. Much more clear now. And the article helps a lot too.


this will not work because of the wrong syntax
check this article https://idg.net.ua/blog/uchebnik-css/ispolzovanie-css/transform/translate

here is reference spec https://developer.mozilla.org/en-US/docs/Web/CSS/transform-function/translate


I thought that we score the normal contempt on line https://github.com/official-stockfish/Stockfish/blob/4b88bea4fcd5c4cb931610f97460615dd71ff35b/src/search.cpp#L345


Yes. I am aware of this keyword change. Problem is that the truffle metacoin box we are using as a template for the projects has most Solidity contracts in 0.4.19. And more importantly, at some point in previous lessons, we installed  Truffle version v4.0.7 (core: 4.0.7) and this version goes together with Solidity v0.4.19 (solc-js). I guess I should update truffle so that I can run the last solidity version with my projects. What's the command to update Truffle?


Perfectly understood. All clear. Many thanks for the complete explanation.


Much better!

I'm surprised though that you're using `centos7-s2i-nodejs` instead of the `-webapp` version?


The "old function" in the commit message refers to `plot_frame_with_text`.


Very useful explanation, Rob. Many thanks. I see I have to change my code a lot and that the token idea makes no sense at all.

Actually, the way the Project2 assignment is written is very misleading because it says that two passwords are produced, and it is said in more than one occasion (in the bullet points and in the text), when actually there is only one password.

From the steps you describe, there is something I need to ask about. When you say "So, we'll start by thinking of the inputs for the hash function. This is the puzzle.". What about the password/secret that Alice created and hashed at the beginning? Are there two hashing functions, one for the password and one for the puzzle, or the puzzle is hashed with the password? In the next sentence you say "Alice will compute the hash with these inputs ..." this makes me think that the password hash is hashed together with the puzzle. Is that correct? So, two hashing functions.


Hi! Is this something you think I should backport? Thanks!


Very well understood.


*.txp file removed from all instalation package


10/10
cooool!


PR_opened/Fix_6937_RunPeriodNamesInWarnings (jmarrec) - x86_64-Linux-Ubuntu-18.04-gcc-7.3-UnitTestsCoverage-Debug: OK (1785 of 1785 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-41.51%25-green.png)


Ты слышал о header-guard-ах?


I am confused about this pattern, in English we do not need count and `one` `other` split is a very English thing. Is this hiding some transifex quirk ? @gerhard


I see your point here. Thanks for making it so clear. However, from Rob's clarification above on how the puzzle and password(s) are produced I see that there is only one password and not two as described in Project's 2 assignment. Therefore no need for that check in this case but very useful to know for future projects.


Got it. Thanks for explaining it to me.


Thanks for your clarification.


Wait, are we talking about line 117-129?

I'm confused about the
> I just tested that last master and this has broken the special building iteraction that I just pushed this
> morning...?

This was there for a while? Or is this about the GridAnimation?


The line that gives a compilation error is the following:
` remittanceBoxes[owner] = NewRemittance(recipient1, recipient2, amount, 30, passHash1, passHash2);`
I declared ` remittanceBoxes` in the mapping:
` mapping (bytes32 => NewRemittance) public remittanceBoxes;`
The error message points at ` [owner]` and does not refer to an ` uint` but to ` bytes32`. It reads as follows: "Type error: Type address is not implicitly convertible to expected type bytes32". I do not understand why the compiler checks for convertibility of ` owner` into ` bytes32`.


These endpoints could also be under `/api/v1/teams/:team/volumes` where a `POST` can create a specific type of volume for the artifacts, and return the created handle. There could be other methods on individual volumes to`GET` the contents of the volume, and query parameters to find specific user artifacts.

What do you think?

We'll also want a separate interface which decouples this volume management behaviour from the internals of the `worker` and even the specifics of volumes and the pool of workers overall (per our meatspace conversation about the API handlers doing this directly). [The K8s RFC](https://github.com/concourse/rfcs/pull/2) kind of covers some of the details for that, and could maybe be changed to a generic "runtime interface" RFC.


PR_opened/Fix_6937_RunPeriodNamesInWarnings (jmarrec) - x86_64-Linux-Ubuntu-18.04-custom_check: OK (2 of 2 tests passed, 0 test warnings)

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