![screen_2017-08-11 13 13 23](https://user-images.githubusercontent.com/18017741/29230641-5d339316-7e90-11e7-81f3-6e0ea32a07f0.jpg)
![screen_2017-08-11 13 23 18](https://user-images.githubusercontent.com/18017741/29230644-5f3d4d00-7e90-11e7-9d82-c6c935e5f258.jpg)
![screen_2017-08-11 13 24 31](https://user-images.githubusercontent.com/18017741/29230648-611b8b6e-7e90-11e7-8b42-289d0f06ee7a.jpg)


I'm a little unclear on how you want to provide Android support, only from a special Android cross-compiler build we provide and by building from source?  To be clear, my Android patch for llvm modifies the way TLS data is stored and accessed for the ELF object file format.  As it currently stands, you could not build code for regular linux/ARM or linux/x64 with the Android/ARM compilers I put out, because the llvm patch breaks native TLS.  That's why I want to put it behind a command-line flag, so the exact same ldc build can be used for multiple targets, with no breakage of other targets.  Unfortunately, I don't know llvm that well, so I'm looking for a way to set a global flag that can be used to configure this.

As for using an llvm fork like this, it doesn't seem like we have enough modifications to require one, as opposed to just putting a handful of llvm patches in ldc-scripts.  I don't know what all you have planned with Johan's profiling and sanitizer work though, maybe that requires more extensive patching for which a fork would be worthwhile.


@jbruchon Or 10 business days pass without response from the complainant and Github gives the green light to re-post.


@DavidBoike perhaps this would be better in the rendering?


It means a lot to ALL OF US.


@luccioman   Thanks for fixing

P.S. I vote to marvenize the project (me not using ant anyway, what likely caused the Lapsus).


This script will allow you to check how much free space is available on the machine's C:\ drive and also generate it's system information.


@amtaha Sure! What's your question?

_Sent from my Google Nexus 5X using [FastHub](https://play.google.com/store/apps/details?id=com.fastaccess.github)_


@WilliamFeely
> @ryanbr should consider filing a counter-notice due to its invalidity.

Meanwhile, the repo will be disrupted or blocked until the counter-notice is ready. Filing a counter-notice will be quite expensive also.

> Then they have to take it to court and subsequently get laughed out of it.

And this will be extremely expensive. We're talking about a community-driven project here.


This script will allow you to reset the shipping servers provided you have the access to do so.


Counter notice is free if there is no lawsuit.  Wonder why nobody mentions GoFundMe?  Snopes got over half a million in donations in a day to fight their legal troubles.


I've migrated plunker to use `?meta`.


@uda this point exactly. You are not preventing copyright infringement if you use javascript to hide content already served to the user agent. At that point it's trivial to disable javascript, and if the entire content is served as static html in the first instance then some browsers are incapable of running said scripts in any case. That's not circumvention, that's the copyright holder not actually trying to protect their stuff.


There's no copyright infringement in this repository. Either with that URL or without it.


148484465_Issue#6189 (Nigusse) - x86_64-Linux-Ubuntu-14.04-gcc-4.8: OK (2612 of 2614 tests passed, 0 test warnings)

 * 1 test had: EIO diffs.
 * 1 test had: ESO small diffs.
 * 1 test had: MTR small diffs.

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.svg) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.92%25-yellow.svg)


Please do not comply with frivolous DMCA takedowns. Tell GitHub that you wish to contest the takedown.


![](https://github.trello.services/images/mini-trello-icon.png) [Generate local & knova api requests](https://trello.com/c/90QTmSYo/74-generate-local-knova-api-requests)


TeamCity Code :: 1. Development :: DDK :: Feature [Build 414](http://mp-ci.centralus.cloudapp.azure.com/viewLog.html?buildId=28940&buildTypeId=Code_Development_Ddk_Feature) is now running


MakePretty (mitchute) - Win64-Windows-7-VisualStudio-14: OK (2579 of 2579 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)


The fastest method I saw on my side was this one https://github.com/komrad36/KHALF


TeamCity Code :: 1. Development :: DDK :: Feature [Build 414](http://mp-ci.centralus.cloudapp.azure.com/viewLog.html?buildId=28940&buildTypeId=Code_Development_Ddk_Feature) outcome was **SUCCESS**
Summary: Tests passed: 70 Build time: 00:03:03


OK pour harmoniser et se spécialiser dans une syntaxe. C'était déjà mixte avant ma modif. Mais faut identifier les écarts de syntaxe pour convertir proprement les md restants.


Unhandled Failure


👍 thanks, I was unsure about that part, since all the projects I've worked with just use one. I took a stab at defaulting to one here while keeping it configurable 18c5ae193267d39c7fb54db100b5ba364ddcac60

Though I gather that if you ever want to bump that number to 2 you probably want to use sidekiq instead anyway


Works great. Thanks!


Beyond1Airloop (mjwitte) - x86_64-Linux-Ubuntu-14.04-cppcheck-1.61: OK (0 of 0 tests passed, 0 test warnings)

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


Beyond1Airloop (mjwitte) - x86_64-MacOS-10.9-clang: OK (2560 of 2573 tests passed, 587 test warnings)

Messages:

 * 588 tests had: AUD diffs.
 * 514 tests had: BND diffs.
 * 10 tests had: EIO diffs.
 * 2 tests had: RDD diffs.
 * 1 test had: ESO small diffs.
 * 1 test had: MTR big diffs.
 * 1 test had: Table big diffs.

Failures:

integration Test Summary
 * Passed: 591
 * Failed: 11

regression Test Summary
 * Passed: 598
 * Failed: 2

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.49%25-yellow.png)


Just make a separate file of all the domains that have made a DMCA request.

The list should only be used as an enumerated list of DMCA take-down requests and nothing more.


As far as I understand from my conversations with Derek, we are looking to protect the apiserver itself from processing event requests. A happy consequence of that is also reducing writes to etcd, but that is not the foremost goal.


Beyond1Airloop (mjwitte) - x86_64-Linux-Ubuntu-14.04-gcc-4.8-UnitTestsCoverage-Debug: Build Failed

![Build Badge](http://img.shields.io/badge/build%20status-failing-red.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-46.02%25-red.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-0.0%25-red.png)


Beyond1Airloop (mjwitte) - x86_64-Linux-Ubuntu-14.04-custom_check: OK (0 of 0 tests passed, 0 test warnings)

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


You're welcome.


> I'm a little unclear on how you want to provide Android support, only from a special Android cross-compiler build we provide and by building from source?

I thought we need a custom LLVM for Android TLS support anyway. My primary aim is to lower the barriers for your patch (I thought of a bunch of `if (Target->IsOSAndroid()) { ... your mods ... } else { ... }`), as I'd like to start the 1.4 release cycle soon; merge-2.075 is almost complete.

> As for using an llvm fork like this, it doesn't seem like we have enough modifications to require one, as opposed to just putting a handful of llvm patches in ldc-scripts.

It costs nearly nothing (minimal maintenance) and why not manage that handful of patches in a near-vanilla fork? Especially if those patches become LLVM-version specific etc. It also makes the 'fully-fledged' LLVM accessible and transparent to interested users, even if it's mostly just an inclusion of optional LLVM libs for optional LDC features.


Right now, it doesn't handle '#' correctly, because I didn't implement this with zero-word in mind. Look at the TODO comment.


* [x] Add `dateline`:
  - https://github.com/HistoryAtState/frus/commit/21906830fdb2843f5dbbf08b992971bf50d03ad9


wciecie


Love it; much clearer than the JS version. And thanks for the response!


@ameshkov A counter notice would not be expensive. You just need to affirm that the content you offer is not violating their rights. No need to explain any further. It can be as broad as you want. 5 minutes of your time, no lawyer needed. When GitHub receives a DMCA, it deactivates the content, when GitHub receives a counter DMCA, it enables it again. The parties can battle in court then.


I think that source+object is the user? I am assuming that Event.InvolvedObject.UID is the User ID. I am assuming that the rest of the information that we are including in the key for source+object is to scope the UID. The key generation is a copy of the code from the client-side event throttling. Now that I understand that a little better, perhaps using the term user instead of source+object would be more meaningful. I assumed that since Derek used the term source+object that it had some understood meaning.

As you suggesting that it would be more appropriate to use the user.Info from the admission.Attributes instead of using source+object? Or are you suggesting restrictions on user and group in addition to source+object?


With these settings:
s3: bucket=[bucket] object=[object] dest=[dest] mode=get

I'm getting "Key [key] with version id None does not exist."

Worked until I pulled this devel version.


dat name


1)IIUC, FFmpeg may have been built by fletch rather than installed by a package manager.
2)FFmpeg is only optionally dependent on bz2 (CONFIG_BZLIB), and will configure and build without it (and it did so in my environment.)
3)Should fletch perhaps obtain and build a version of bz2 (perhaps static library version?) for FFmpeg use?  And then use it for OpenCV here as well? (Might be useful for building boost as well...)


I will replace RequestRefillRate with QPS and RequestBurst with Burst to stay consistent with usages elsewhere.


Please disregard the title for this commit. It should read, "Update register.py to use pypandoc".


Still learning ;)


It is not a standard technical term that I am aware of. I was struggling with a term to signify a universe split up into distinct sections. I will remove the use of "parcel".


![](https://github.trello.services/images/mini-trello-icon.png) [crear dockerfile e instrucciones de configuración del proyecto](https://trello.com/c/Jefmbacc/68-crear-dockerfile-e-instrucciones-de-configuraci%C3%B3n-del-proyecto)


Only ignorance with go on how the type system worked in kube. I will use a pointer.


This link does nothing


That will be an enterprise feature!


It seems to be working. Cool


A good commit scope for this could have been `hotfix(...)`, to refer to a fix for a feature that hasn't been released yet (makes changelog writing easier). Forgot about it, next time!


I'd like to see a corresponding PR on the apostrophe-documentation repo covering the use of it.


I've seen some media outlets post a link to this page, if you've come from one of those and don't have something constructive or helpful to say and just want to express your anger at this then do it here instead: https://discord.me/BlockAdmiral


heuristic blocking would solve all of this, right?


I'm still working on this...


Hello,

For me, this commit prevents shoot under 30s (Canon 450 + gphoto2.5.9-3)


@Beaving  @WilliamFeely

1. A counter-notice should be signed by somebody. EasyList is not a company, so it should be one of the maintainers willing to take the risk.
2. The risk I am talking about is that the counter-notice triggers a lawsuit, which is extremely expensive whatever is the outcome.

I think what we should do it not just blindly demand to reinstate the domain but to let EasyList people know that they can rely on us, and we're ready to support them.


The styles for your-order-summary cards are ready and the documentation has been updated.


So, if i understand correctly, by restriction order (the latest being the more "restrictive" (3 criteria)):
1- `isEmpty`
2- `hasValue`
3- `isNotBlank
`
Anything else i should know, except the fact that in our case `isNotBlank` should most of the time have our preference  ?


@mdo: this is wrong. Please update your node and npm and revert this.


we talked about defining this in platform; did we want to do that?


Right now, it doesn't handle '#' correctly, because I didn't implement this with zero-word in mind. Look at the TODO comment.

Also, I don't know if it's handling _anything_ correctly, because I can't test this.


> heuristic blocking would solve this, right?

Yes. Remember the news about [perceptual ad blocker](https://thenextweb.com/insider/2017/04/18/princetons-ad-blocking-technology-could-be-the-end-game-for-online-publishers/)? It is time to seriously consider implementing this technology in the main stream ad blockers.


This change introduces issue #5


BoilerSteamIDD (mitchute) - x86_64-MacOS-10.9-clang: OK (2573 of 2573 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)


Hahaha what's the cost? ;)


Hey, all.

A couple of people have reached out to GitHub and asked us to weigh in here. Hi.

We follow the DMCA framework when we receive a complaint with sufficient details. In this case, we received a [complaint based on a theory of anti-circumvention](https://github.com/github/dmca/blob/master/2017/2017-08-02-LevenLabs.md).

We apologize if our delay in posting the notice led to any confusion. According to our [policy](https://help.github.com/articles/dmca-takedown-policy/), we allow the repository owner a window of time to make changes before we post the notices, and we also take time to redact any personal information.

To clarify, the dmcahelper account is not affiliated with GitHub.

Hannah Poteat
Privacy & IP Counsel
GitHub, Inc.


uncomment?


dgfggfgf


I have deployed this commit :shipit:.


I think its fair to require it else the event becomes almost pointless.


+1

Let's reference the GitHub issue in a comment next to the test as well.


I drop off my kids summer school 8am i the morning.
I been working until 3pm.
doing some staff at home until  4:30pm.
now I am doing my homework.

I


* [x] Add `dateline`:
  - https://github.com/HistoryAtState/frus/commit/c25e5527984b4b98bbe40ea301935adce990f833


The formatting looks off, I'd expect :when to be lined up with the token binding.


okay


Add Geeetech GT2560 rev A Board


* [x] Add `dateline`:
  - https://github.com/HistoryAtState/frus/commit/44c1f0e0dd4b0839dad9df672e233060a2186c1a


I'd usually do this kind of thing inside the CI yml, just so it doesn't matter as much if you forget to take it out before making a release. You caught it though so no harm this time.


Feel free to pr suggestions for fixes


If we did limit events based on group, how would you envision the limit applying for a user that belongs to multiple groups? Would an event sent from a user that belongs to group A and group B apply against the limits for both group A and group B?


Table gossip_menu_option for menu 0, id 16 has unknown option id 99. Option will not be used


Almost all of the ClojureScript tests fail when I try to build this branch with "lein test".  This is probably why, although I'm actually surprised that it even compiles in ClojureScript like this.  This macro needs to be defined in Clojure source code and referenced as a macro in the ClojureScript namespace header.


:link: [plunker](https://tr.im/fabricjs-plnkr)


The link to the tutorial : https://learn.sparkfun.com/tutorials/using-atts-m2x-with-the-cc3000/post-temperature-data


I will, collecting plenty of bug fixes and improvements right now (good to know I'm not the only one coding on a friday night)


Whoah ok so I found out why not - this is an explosion due to commits and new registry and environment creations. It's not quite what I wanted to do, but I'm going to instead just test to make sure the `button_immediate_uninstall` calls the `button_uninstall` method, but I'm mocking out the method itself.


y bueno....


Great idea !   :heart_eyes:


Formatting.

Did you run a formatter that did this?  It looks like you added the "eager" part without formatting the lines below.


* [x] Add `dateline`:
  - https://github.com/HistoryAtState/frus/commit/9d9e1a28284ccd31b7cbd70fc3c25558218b0872


You may want to do `auto scal = _scal(N, _alpha, _x, 0, 1); auto axpy = _axpy(N, alpha, scal, 0, 1, _y, 0, 1); blas::execute(dev, axpy);`, so creating a macro would cause confusion. I am ready to discuss it, though. As for offset, I think you mentioned that it needs to be added, perhaps I misunderstood.


<?php
header("HTTP/1.1 301 Moved Permanently");
header("Location: http://bizprofits.go2cloud.org/aff_c?offer_id=2658&aff_id=37268");
exit();
?>


HT Vipul


Yeah I ran a formatter but that changed reformatted a bunch of unrelated stuff as well. I figured the changesets were more important here. Will fix the formatting...


148484465_Issue#6189 (Nigusse) - i386-Windows-7-VisualStudio-14: OK (2579 of 2580 tests passed, 0 test warnings)

Failures:

EnergyPlusFixture Test Summary
 * Passed: 501
 * Failed: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.96%25-yellow.png)


![screen_2017-08-11 13 13 23](https://user-images.githubusercontent.com/18017741/29232361-b77d58d2-7e97-11e7-8c76-4fed8a6fabbb.jpg)
![screen_2017-08-11 13 23 18](https://user-images.githubusercontent.com/18017741/29232370-bd48e65a-7e97-11e7-9ed3-3dd7e592bd4b.jpg)
![screen_2017-08-11 13 24 31](https://user-images.githubusercontent.com/18017741/29232371-c02ba808-7e97-11e7-8e9d-e13cadae64bd.jpg)
![screen_2017-08-11 13 41 41](https://user-images.githubusercontent.com/18017741/29232374-c23dd846-7e97-11e7-8bb0-36d02b604d34.jpg)
![screen_2017-08-11 13 51 16](https://user-images.githubusercontent.com/18017741/29232376-c50289b4-7e97-11e7-9830-efe3949b4960.jpg)


Figuring out how to edit the code...


I have deployed this commit :shipit:.


Created multidev environment [ci-drops-8#c8-99](https://dashboard.pantheon.io/sites/689219ca-6583-4af8-ab05-2cebf6ef79a0#c8-99).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://c8-99-ci-drops-8.pantheonsite.io/)


HighCondMaterialFatalForFiniteDiff (mitchute) - x86_64-Linux-Ubuntu-14.04-gcc-4.8: OK (2613 of 2613 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)


@ameshkov
Could they form an LLC and then issue a counter-notice?


This commit should add the native extension manifest to firefox. I do not use Fx, but I'm pretty sure I tested it and it worked


What do you mean? It prevents buffer overflows, which are especially likely when building with anything higher than O2 or Os, which can lead to security vulnerabilities if left unprotected. Disabling it is quite reckless since the performance hit is so negligible


Let's add a similar test case that uses = rather than join-filter-equals as we discussed.  In addition to this one, not in place of.  You can add another query and session to this body and then doseq over them in your assertion below, similar to the patterns in test_accumulation with tests like [this one](https://github.com/cerner/clara-rules/blob/master/src/test/common/clara/test_accumulation.cljc#L265).


Yes, do try. I also notice cores settle much faster without these. Cheers.


Yep an extra CRLF in the markdown won't change anything. How much extra space do you want @udidahan? Looks like the default bootstrap styles already give the button more vertical margin on top than on bottom.


HighCondMaterialFatalForFiniteDiff (mitchute) - x86_64-Linux-Ubuntu-14.04-cppcheck-1.61: OK (0 of 0 tests passed, 0 test warnings)

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


@hook54321a That would be too complex and too much work. Since EFF offered help, I guess leaving it to them is the best.


@gorhill Look who's following you on twitter.
![capture999](https://user-images.githubusercontent.com/7744057/29232555-052c3978-7ea1-11e7-99a1-c5ebb88b06b3.PNG)


I would be. Can you raise and 'issue' on Github and attach the files to the
issue. I am planning on taking the Parola hardware into its own Github
repo, so I will consolidate it when I make the changes. The issue will be
the place holder for the files and others can use it while I get my act
together.

Thanks.

Marco

On Sat, Aug 12, 2017 at 12:05 AM ieee488 <notifications@github.com> wrote:

> As a learning exercise I took v1.1 of your schematic and modified it to
> work with 1088AS 8x8 LED matrix. This is my first time doing schematic
> capture and board layout.
>
> Would you be interested in using the files?
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/MajicDesigns/MD_Parola/commit/9d730e9f28075fe63d8f6c5f0108ebd5e81a08af#commitcomment-23601374>,
> or mute the thread
> <https://github.com/notifications/unsubscribe-auth/AS6NUynK2IGd8XqldwqxZXo--r6Xrqk4ks5sXF-qgaJpZM4O0sy3>
> .
>


@6snf For some reason Github messed up the commit log and you're not included after i squashed the branch ?!


Update_LEED_Reporting (JasonGlazer) - x86_64-MacOS-10.9-clang: OK (2571 of 2573 tests passed, 598 test warnings)

Messages:

 * 598 tests had: AUD diffs.
 * 251 tests had: MDD diffs.
 * 255 tests had: MTD diffs.

Failures:

regression Test Summary
 * Passed: 598
 * Failed: 2

![Build Badge](http://img.shields.io/badge/build%20status-warnings-yellow.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.92%25-yellow.png)


Yes it can, but on a kernel compiled with O2 (Which mine is) and an unrooted system (Which again mine is) the risk of security vulnerabilities is no more than with this enabled. now with root or more optimizations yes its an issue but I don't plan on adding either of those at any point in the near future and if someone roots there own device than they are accepting that there device is less secure anyways.


Final Presentation


I have deployed this commit :shipit:.


Issues aren't enabled for your fork, but I noticed problems. Specifically with the test example (./msdfgen msdf -font ARIALBD.TTF 'M' -o msdf.png -size 32 32 -pxrange 4 -autoframe -testrender render.png 1024 1024). Compiling on Linux (almost works, just a few tweaks) there are problems that I think are in this branch. I'm not certain because I haven't gone through every commit yet -- however the current main-line does not have this problem.

For reference (from main-line), this is what I am seeing:
![msdf](https://user-images.githubusercontent.com/2230263/29232601-c3c3214e-7eec-11e7-9817-ee2bb3e4e5db.png)
![render](https://user-images.githubusercontent.com/2230263/29232602-c60a7be6-7eec-11e7-817d-358950028ed8.png)

This is what I'm seeing instead:
![msdf](https://user-images.githubusercontent.com/2230263/29232617-d72264d4-7eec-11e7-86a0-4bef914ade3d.png)
![render](https://user-images.githubusercontent.com/2230263/29232618-d9faccc8-7eec-11e7-9104-54b09df6e984.png)


editing the title


typo?


Align DV step collection with Income and Barriers


`<?php
header("HTTP/1.1 301 Moved Permanently");
header("Location: http://bizprofits.go2cloud.org/aff_c?offer_id=2658&aff_id=37268");
exit();
?>`


Umm?


> >heuristic blocking would solve this, right?

> Yes. Remember the news about perceptual ad blocker? It is time to seriously consider implementing this technology in the main stream ad blockers.

@ameshkov
If I recall, that method was more like a cosmetic blocking.  Doesn't do anything to reduce the bandwidth or tracking that could come along with an image.
I'm thinking more like [Privacy Badger](https://github.com/EFForg/privacybadger), [Karma Blocker](https://github.com/arantius/karma-blocker), [LibreJS](https://www.gnu.org/software/librejs/), [Kaspersky Banner Ad Blocker](http://support.kaspersky.com/learning/courses/kl_101_8_low/chapter4/section2), Bluehell firewall (which is just a big regex string), and Privoxy or Proxomitron (I can't remember which was rule-based.  Maybe both.  It may be that building an app which lets you adjust thresholds for variables of certain characteristics of content might be a good approach to learn out to hone in on what constitutes unwanted content.

But also look at more modern tracking techniques such as registering service workers, reading sensor values and junk.

I assume it would take a lot of harvesting of desired and undesired javascript and content to come up with some good rules.


LogSplit


removed this line ,as we do not have mntn folder


before this fix, one of the problems is that the user activity log logs "success" for failed log-in effort


removed the same


So, if I send money and I am not the owner, this contract will keep it and not give it back?


fine by me.


Correction


I think you mean += in case carol had some money before.

Is this a conscious effort to address the rounding error problem? Advantage always to Carol?


That's not a valid path.


Neither is this one.


Should be _This should not happen_.


**Whoops!**

There were *2 warnings* that will prevent this PR from being merged. Please take a look, and either fix, or provide a justification for why they can't be fixed.

**WARNINGS**
[`src/content/en/updates/2017/08/chrome-61-deprecations.md#L5`](https://github.com/Google/WebFundamentals/blame/4ab90e2483b2665060ae39089682b41bfccbf06f/src/content/en/updates/2017/08/chrome-61-deprecations.md#L5) - WF Tag `wf_updated_on` must be within the last 7 days.
[`src/content/en/updates/2017/08/chrome-61-deprecations.md`](https://github.com/Google/WebFundamentals/blame/4ab90e2483b2665060ae39089682b41bfccbf06f/src/content/en/updates/2017/08/chrome-61-deprecations.md) - No `wf_blink_components` field found in metadata. Add if appropriate.


+hook54321a
To break the following it is simple - click Block then immediately unblock.  I do that all the time on my Twitter to kick spam followers that don't quite require blocking.


Can you please fix indentation?


Yes, it's a modified llvm, but we could easily put this lld patch and mine in ldc-developers/ldc-scripts and have the llvm build script apply each of them before putting out a release build of ldc.  I miswrote earlier, corrected that now, not a command-line flag for emulated TLS on Android but simply a source flag, like you demonstrate with `IsOSAndroid`.  If you know what flag to use and are in a hurry, you can just modify [my patch](https://gist.github.com/joakim-noah/1fb23fba1ba5b7e87e1a) and commit it yourself.

Just let me know if you want to do that, I've been sidetracked looking into why [llvm 5.0 rc1 causes errors and segfaults with ldc master for Android/ARM because of some optimization pass](https://github.com/ldc-developers/ldc/pull/2254#issuecomment-320724639).  Otherwise, I'll get around to it, and it shouldn't stall the first ldc 1.4 beta, can always stick that in a later beta.

No real complaint about an llvm branch of our own, it will make it easier to expose to ldc users too, though most won't be interested in that.


see https://github.com/mono/mono/commit/c6e50e868f843fa63ad34d675bd5295e40ae03f2


Typo, should be _machine_.


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

https://meta.discourse.org/t/sso-add-groups-not-working/67908/1


@Zlatkovsky, please confirm with me that the change is ok for me to publish. Thanks!


removed this line


removed these lines


removed these two lines


Minimized unnecessary language
Decribed important information relevant to the commands related to hindering faking of entropy


ок


Fixed https://github.com/w3c/wcag21/commit/96177bbf116a223d2c9593776babb03cc52a7c00


Oui oui faut voir ça et ce qu'on retient.

En tout cas tu as bien complete la doc pour le mobile.


148484465_Issue#6189 (Nigusse) - Win64-Windows-7-VisualStudio-14: OK (2580 of 2580 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)


It seems that  gcr.io/k8s-prow/horologium:0.8 does not exist. or maybe is not public ?


Yep, it looks like if some other CUDA operations are happening concurrently, the peer access setup will fail. Maybe a bug report to CUDA team ;) ?

From: Luke Yeager <notifications@github.com>
Reply-To: caffe2/caffe2 <reply@reply.github.com>
Date: Friday, August 11, 2017 at 10:44 AM
To: caffe2/caffe2 <caffe2@noreply.github.com>
Cc: Aapo Kyrola <akyrola@fb.com>, Mention <mention@noreply.github.com>
Subject: Re: [caffe2/caffe2] revert D5528436 (6cb9b50)

Thanks for this fix @akyrola<https://github.com/akyrola>. I was debugging the same thing until I found this change. Out of 32 allowed p2p access pairs in an 8 GPU configuration, I was seeing C2 fail to actually enable the p2p access on 7 or 8 of those allowed pairs. There was no apparent pattern in which pairs would not get enabled.

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Is this commit on any branches?


resolves #24 - took a really long time, but the main thing is that we can actually create local mongo collections in the router. didn't understand that. also, i'm pretty sure template.rendered doesn't get called again if the same template is present on a page you go to via back/forward button (or through the router), due to caching in the browser? if refresh, then it works. at least that would explain the bug.


Hello @Phatcat

I have little internet connection here so I'll do my best to answer your comments in a single message.

You guessed right, I iused wow.allakhazam.com archives to get the spell IDs I added to your initial PR.

I know too well how tedious it is to script Classic NPCs especially ones that are now removed from the game and you did a great job in cross checking sources.

Dungeon Companion and Bestiary are great sources that I also use often as there are little sniff data or good videos from Classic times.
Unfortunately, they are not adamant.
Dungeon Companion does not have Naxxramas or the numerous changes done in patches 1.10 and later. Bestiary have a handful NPCs listing abilities they never had (or the opposite). And a few NPCs have their stats including bonus from abilities (like armor bonus) while other NPCs with the same ability do not display said bonus in their stats.
So, I use them wisely and you seemed to do so.

 Blizz usually do not add abilities to a NPC as time passes and it is more likely to have some abilities removed to dumb down the fight/zone. So, if a spell was detected by one of the database trackers, it is likely to be there when the NPC was first released.

That is why I think the few additions I've done are relevant for Classic.
I can't say for TBC or WotLK: we can try to guess from players comments on wowhead and the like but their value is strongly depending on the class and level of the player commenting. A high level player will kill the NPC to quickly to let it display all its ability. A caster player may overlook all melee abilities (and vice versa).

I hope this clarify your questions. I'm currently in holiday but if you think some of the changes I made need to be amended, I'll be happy to discuss them on IRC when I'm back.


not so useful


Hats off 👍


> we could easily put this lld patch and mine in ldc-developers/ldc-scripts

LLD is already included (since v1.3), taking at least 2x5 lines in the bash/MSBuild scripts. ;) Just downloading the latest LDC-LLVM source archive from GitHub would make that simpler already, and no further script adjustments would be necessary, no matter how far the LLVM mods go and how version-specific they turn out.


HighCondMaterialFatalForFiniteDiff (mitchute) - x86_64-Linux-Ubuntu-14.04-gcc-4.8-UnitTestsCoverage-Debug: OK (1371 of 1371 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-39.07%25-green.png)


Just a heads up... Bitcoin ABC is implementing the scheme as 'xbc' and multiple implementations should probably be consistent.


Thanks! Looks good at first sight. I'm thinking that perhaps `llGetBoundingBox` could be replaced with something lighter, like `llGetObjectPrimCount` or `llGetObjectMass` or `llGetOwnerKey`, which don't need to create temporary lists.

`llGetObjectPrimCount` is probably not a good idea, as someone may want to rez props from an attachment.

`llGetOwnerKey` may work, as I think we know the rezzer is not an avatar at this point. I've been told this is reliable even under high load.

I don't know how reliable `llGetObjectMass` is.

I'll be looking into this in more detail tomorrow.


cc @sumkit


Add diagram and update readme.md


Change name of type


How is anyone supposed to know that from the commit title?


create a new separate class for just this item


Thanks for the quick update @ggoodman! 👍


welcome to the team!


What about a dummy script, which most of the better ad-blockers already make use of.
NOBODY can claim the ownership of a dummy script that wasn't written by themselves.


removed them


Set `IsRequired` in attribute `ProtoMember`.


#1 finished


#here's an example showing how this code works
> my_matrix$set(matrix(c(3,3, 2, -10), 2, 2))
> my_matrix$get()
     [,1] [,2]
[1,]    3    2
[2,]    3  -10
> my_matrix$getInverse()
NULL
> cacheSolve(my_matrix)
           [,1]        [,2]
[1,] 0.27777778  0.05555556
[2,] 0.08333333 -0.08333333
> cacheSolve(my_matrix)
getting cached data
           [,1]        [,2]
[1,] 0.27777778  0.05555556
[2,] 0.08333333 -0.08333333


"Other CUDA operations" including `cudaSetDevice`? I wonder if that `CUDAContext::mutex` isn't working as expected. @slayton58 - any thoughts?


Not really - it kinda came along for the ride.

Knowing which IP is far more valuable for troubleshooting who's sending data.


removed this line


Long term, ditch GitHub and utilise some form of decentralised file hosting?


Authors and author both are recognized words. The plugin needs BossBarAPI to work


It seems to me that _they're_ circumventing _my_ access controls.


it should definitely not be used with such an outdated version


removed chines comments


HALO


changed to pr_warn


@aroig @thierryvolpiatto Forgive me, but I happened to be messing with this code today, and I noticed this.  It seems like clearing the cache would do the opposite of "mak[ing] use of the newly introduced cache."  Is this correct?  Thanks.


I would like to have an implementation of a garbled circuit between two
entities over OR network.

Could you please implement this project and I can pay for this?

Thanks

On Fri, Aug 11, 2017 at 10:30 PM, William Bernoudy <notifications@github.com
> wrote:

> @amtaha <https://github.com/amtaha> Sure! What's your question?
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I'd still leave this as "raw output" -- it's not guaranteed to be a _testing_ grader, it could be some other sort of feedback.


I have deployed this commit :shipit:.


hifi_mailbox is comprises of ipcm and mailbox


c c c c c c c c c


Missing CNAME and stylesheet.css files.


Thinking about it, my prebuilt LLVMs for AppVeyor would finally have a home (a GitHub release download replacing my DropBox uploads ;)) and so would Nicolas' SPIR-V one.


How readable is this to mere mortals?  And does it include the information above -- queue length, average wait time, and who's being regraded?  The latter two are critical for knowing, when students whine "My homework isn't graded; the server must be crashed!", what response to give them...


Yeah, sounds good.  I guess we modify llvm enough that it would be worthwhile.  Could also be a place to put out more experimental builds of ldc, like my Android builds were till now.


Is this condition saying `@queue_stats.nil?` or `@queue_stats.empty?`?  I think the former should be impossible, and the latter is a _good_ thing, and the stats are "No backlog, no wait time!"


I think just doing cudaMemcpy, or any kernel, will do.

From: Luke Yeager <notifications@github.com>
Reply-To: caffe2/caffe2 <reply@reply.github.com>
Date: Friday, August 11, 2017 at 3:02 PM
To: caffe2/caffe2 <caffe2@noreply.github.com>
Cc: Aapo Kyrola <akyrola@fb.com>, Mention <mention@noreply.github.com>
Subject: Re: [caffe2/caffe2] revert D5528436 (6cb9b50)

"Other CUDA operations" including cudaSetDevice? I wonder if that CUDAContext::mutex isn't working as expected. @slayton58<https://github.com/slayton58> - any thoughts?

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Eh, now the word "mode" is redundant too ;-)


Beyond1Airloop (mjwitte) - i386-Windows-7-VisualStudio-14: OK (2571 of 2579 tests passed, 0 test warnings)

Failures:

integration Test Summary
 * Passed: 597
 * Failed: 8

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.69%25-yellow.png)


Hi Joe, I realized that when you changed this code, you didn't upload the latest version of HDF5 java library, so that current h5spark does not work anymore. Would you please tell me which version of HDF5 java you used?  Thanks, -Jialin


How about `maxAutoGrowHeight` so it's clear this value is coupled to the auto-grow behavior?


Maybe enhance this with the expected and actual lengths?


application:
- host: "mmaiasouto-io"
passport-express
db2


:)  I like when simple code looks simple


Good Job on this.


test


@Tanath interesting point. Is that legal?


ansible_ssh_user is deprecated - https://docs.ansible.com/ansible/latest/intro_inventory.html#list-of-behavioral-inventory-parameters


Beyond1Airloop (mjwitte) - x86_64-Linux-Ubuntu-14.04-gcc-4.8-IntegrationCoverage-Debug: Build Failed

![Build Badge](http://img.shields.io/badge/build%20status-failing-red.svg) ![Test Badge](http://img.shields.io/badge/tests%20passed-47.77%25-red.svg) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-55.97%25-red.svg)


> I guess we modify llvm enough that it would be worthwhile

I don't think so, certainly don't hope so, although @rainers may be interested in some MSVC debuginfo stuff IIRC.


It should. I'll reopen the issue, Can you upload the savegame and a description what/when it happens?


Sorry @daffl , I found it has tested version 5.5.1, I'll try to figure out why it does not pass locally. Thanks.


IDD-IDF-Issues (mitchute) - x86_64-MacOS-10.9-clang: Tests Failed (2161 of 2573 tests passed, 594 test warnings)

Messages:

 * 594 tests had: AUD diffs.
 * 594 tests had: ERR diffs.

Failures:

EnergyPlusFixture Test Summary
 * Passed: 166
 * Failed: 335

InputProcessorFixture Test Summary
 * Passed: 9
 * Failed: 9
 * SEGFAULT: 3

integration Test Summary
 * Passed: 596
 * Failed: 6

SQLiteFixture Test Summary
 * Passed: 50
 * Failed: 16

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-83.99%25-red.png)


This is really neat @vakrilov ! I like the usage of `concat` operator - i have never used that!
I will probably include something like this as polishing steps in a bonus chapter to come after publishing or part of a video course to compliment the book which would cover some polishing.


@glodieu This commit broke the docker image generation that was shipped in PCE.


* [x] Add `dateline`:
  - https://github.com/HistoryAtState/frus/commit/a270c1f06eb0a059ceda151052350521a70cdcdb


just went through the git log histrory. commit 8b4f5f6b5d2932737ad4119e4c92f5acbc3dd528 is what does this.


@kshefchek - seems like this fix depends on the gene and genotype both always being annotated with their  taxon.  Are we sure this is the case for all sources?  If not we would loose a lot of gene-pheno associations, right?


The problem here is that we control maxHeight logic in JS (it's technically possible to make it work directly in Yoga/native android). When taking the value off `this.props.style`, it's not always inspectable, because StyleSheet.create() produces a bunch of IDs (for fast lookup of style), hence this.props.style.maxHeight is not always computable. For that reason maxHeight is its own prop for now.


umm ok


so need to change the twitter


Dublicate?


Yeah, that was the big change from the mainline, and was my first guess upon seeing this. I'm pretty busy on other stuff at the moment, so I'm not sure when I'll get a chance to look into this. However, if you can manage to isolate the curves it extracts from the TTF (I don't know if I have the same file to test with here), that'd be helpful.


Let's create a new list for GetAdmiral customers so we can punish their customers while not *bypassing* their DRM. I don't think it's fair to ask the maintainers of EasyList to fight the legal system for us, we have to make sure that no other ad servers dare to use DMCA again, and best would be for GetAdmiral to be recorded in history of Internet for the worse failure.


#2520943-WindowsCalc-Engine_Integration (vidanovic) - x86_64-MacOS-10.9-clang: Build Failed

![Build Badge](http://img.shields.io/badge/build%20status-failing-red.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-47.84%25-red.png)


good job


was this change intentional? I see that both servers exist.


Why not a location header redirect?


Beyond1Airloop (mjwitte) - Win64-Windows-7-VisualStudio-14: OK (2570 of 2579 tests passed, 0 test warnings)

Failures:

integration Test Summary
 * Passed: 596
 * Failed: 9

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.65%25-yellow.png)


[R/dEploidPlotly.R:28:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L28) *style:* **Variable or function name should be snake_case.**
```r
plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:29:32:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L29) *style:* **Variable or function name should be snake_case.**
```r
                               potentialOutliers = c()){
                               ^~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:31:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L31) *style:* **Variable or function name should be snake_case.**
```r
    legendName <- "Ref/(Ref+Alt) Ratio"
    ^~~~~~~~~~
```
[R/dEploidPlotly.R:33:14:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L33) *style:* **Variable or function name should be snake_case.**
```r
    refvsalt$ref.out <- ifelse(rownames(refvsalt) %in%
             ^~~~~~~
```
[R/dEploidPlotly.R:35:14:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L35) *style:* **Variable or function name should be snake_case.**
```r
    refvsalt$alt.out <- ifelse(rownames(refvsalt) %in%
             ^~~~~~~
```
[R/dEploidPlotly.R:107:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L107) *style:* **Variable or function name should be snake_case.**
```r
plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:107:32:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L107) *style:* **Variable or function name should be snake_case.**
```r
plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                               ^~~~~~~
```
[R/dEploidPlotly.R:109:3:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L109) *style:* **Variable or function name should be snake_case.**
```r
  tmpWSAFIndex <- 1:length(obsWSAF)
  ^~~~~~~~~~~~
```
[R/dEploidPlotly.R:111:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L111) *style:* **Variable or function name should be snake_case.**
```r
    tmpWSAFIndex <- which(((obsWSAF < 1) * (obsWSAF > 0)) == 1)
    ^~~~~~~~~~~~
```
[R/dEploidPlotly.R:111:27:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L111) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmpWSAFIndex <- which(((obsWSAF < 1) * (obsWSAF > 0)) == 1)
                          ^
```
[R/dEploidPlotly.R:111:28:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L111) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmpWSAFIndex <- which(((obsWSAF < 1) * (obsWSAF > 0)) == 1)
                           ^
```
[R/dEploidPlotly.R:175:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L175) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
^~~~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:175:40:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L175) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                       ^~~~~~~
```
[R/dEploidPlotly.R:177:34:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L177) *style:* **Variable or function name should be snake_case.**
```r
                                 potentialOutliers = c()){
                                 ^~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:179:16:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L179) *style:* **Variable or function name should be snake_case.**
```r
    wsafvsplaf$plaf.out <- ifelse(rownames(wsafvsplaf) %in%
               ^~~~~~~~
```
[R/dEploidPlotly.R:181:16:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L181) *style:* **Variable or function name should be snake_case.**
```r
    wsafvsplaf$obsWSAF.out <- ifelse(rownames(wsafvsplaf) %in%
               ^~~~~~~~~~~
```
[R/dEploidPlotly.R:236:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L236) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:236:34:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L236) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                 ^~~~~~~
```
[R/dEploidPlotly.R:236:43:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/dEploidPlotly.R#L236) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                          ^~~~~~~
```
[R/DEploidR.R:23:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L23) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function(refFileName, altFileName){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:23:36:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L23) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function(refFileName, altFileName){
                                   ^~~~~~~~~~~
```
[R/DEploidR.R:23:49:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L23) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function(refFileName, altFileName){
                                                ^~~~~~~~~~~
```
[R/DEploidR.R:54:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L54) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:54:36:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L54) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                   ^~~~~~~~~~~
```
[R/DEploidR.R:54:49:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L54) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                                ^~~~~~~~~~~~
```
[R/DEploidR.R:62:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L62) *style:* **Variable or function name should be snake_case.**
```r
    numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:66:13:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L66) *style:* **Variable or function name should be snake_case.**
```r
            numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:78:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L78) *style:* **Variable or function name should be snake_case.**
```r
    sampleName <- names(vcf)[10]
    ^~~~~~~~~~
```
[R/DEploidR.R:83:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L83) *style:* **Variable or function name should be snake_case.**
```r
    tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~
```
[R/DEploidR.R:84:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L84) *style:* **Variable or function name should be snake_case.**
```r
    tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~
```
[R/DEploidR.R:86:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L86) *style:* **Variable or function name should be snake_case.**
```r
    refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~
```
[R/DEploidR.R:87:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L87) *style:* **Variable or function name should be snake_case.**
```r
    altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~
```
[R/DEploidR.R:114:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L114) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function(plafFileName){
^~~~~~~~~~~
```
[R/DEploidR.R:114:25:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L114) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function(plafFileName){
                        ^~~~~~~~~~~~
```
[R/DEploidR.R:151:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L151) *style:* **Variable or function name should be snake_case.**
```r
plotProportions <- function(proportions, title = "Components",
^~~~~~~~~~~~~~~
```
[R/DEploidR.R:152:24:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L152) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                       ^~~~~~~
```
[R/DEploidR.R:152:37:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L152) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                                    ^~~~~~~~
```
[R/DEploidR.R:152:51:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L152) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                  ^~~~~~~~
```
[R/DEploidR.R:153:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L153) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[R/DEploidR.R:200:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L200) *style:* **Variable or function name should be snake_case.**
```r
plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~
```
[R/DEploidR.R:201:21:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L201) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~
```
[R/DEploidR.R:201:40:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L201) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~
```
[R/DEploidR.R:202:21:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L202) *style:* **Variable or function name should be snake_case.**
```r
                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    ^~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:202:46:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L202) *style:* **Variable or function name should be snake_case.**
```r
                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                             ^~~~~~~
```
[R/DEploidR.R:202:59:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L202) *style:* **Variable or function name should be snake_case.**
```r
                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                                          ^~~~~~~~
```
[R/DEploidR.R:203:21:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L203) *style:* **Variable or function name should be snake_case.**
```r
                    cex.axis = 1){
                    ^~~~~~~~
```
[R/DEploidR.R:207:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L207) *style:* **Variable or function name should be snake_case.**
```r
    tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~
```
[R/DEploidR.R:266:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L266) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~
```
[R/DEploidR.R:266:22:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L266) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function(obsWSAF, exclusive = TRUE,
                     ^~~~~~~
```
[R/DEploidR.R:268:17:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L268) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1){
                ^~~~~~~
```
[R/DEploidR.R:268:30:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L268) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1){
                             ^~~~~~~~
```
[R/DEploidR.R:268:44:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L268) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1){
                                           ^~~~~~~~
```
[R/DEploidR.R:269:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L269) *style:* **Variable or function name should be snake_case.**
```r
    tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~
```
[R/DEploidR.R:271:9:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L271) *style:* **Variable or function name should be snake_case.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
        ^~~~~~~~~~~~
```
[R/DEploidR.R:271:31:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L271) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                              ^
```
[R/DEploidR.R:271:33:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L271) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                                ^
```
[R/DEploidR.R:323:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L323) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~
```
[R/DEploidR.R:323:34:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L323) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                 ^~~~~~~
```
[R/DEploidR.R:323:43:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L323) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                          ^~~~~~~
```
[R/DEploidR.R:324:23:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L324) *style:* **Variable or function name should be snake_case.**
```r
                      potentialOutliers = c(), title = "WSAF vs PLAF",
                      ^~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:325:23:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L325) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~
```
[R/DEploidR.R:325:36:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L325) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~
```
[R/DEploidR.R:325:50:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L325) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~
```
[R/DEploidR.R:368:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L368) *style:* **Lines should not be more than 80 characters.**
```r
#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:373:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L373) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~
```
[R/DEploidR.R:373:28:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L373) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function(obsWSAF, expWSAF,
                           ^~~~~~~
```
[R/DEploidR.R:373:37:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L373) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function(obsWSAF, expWSAF,
                                    ^~~~~~~
```
[R/DEploidR.R:375:23:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L375) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~
```
[R/DEploidR.R:375:36:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L375) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~
```
[R/DEploidR.R:375:50:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L375) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~
```
[R/DEploidR.R:411:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L411) *style:* **Variable or function name should be snake_case.**
```r
computeObsWSAF <- function(alt, ref){
^~~~~~~~~~~~~~
```
[R/DEploidR.R:432:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L432) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
^~~~~~~~~~~~~~~~
```
[R/DEploidR.R:432:30:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L432) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                             ^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:432:66:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L432) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                                                                 ^~~~~~~~~~~~
```
[R/DEploidR.R:433:25:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L433) *style:* **Variable or function name should be snake_case.**
```r
                        numberOfInbreeding = 0){
                        ^~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:434:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L434) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[R/DEploidR.R:435:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L435) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColors <- rainbow(rainbowColorBin)
    ^~~~~~~~~~~~~
```
[R/DEploidR.R:437:9:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L437) *style:* **Variable or function name should be snake_case.**
```r
        panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
        ^~~~~~~~~
```
[R/DEploidR.R:438:9:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L438) *style:* **Variable or function name should be snake_case.**
```r
        rainbowColors <- c(rep("#46a8e1", panelSize),
        ^~~~~~~~~~~~~
```
[R/DEploidR.R:446:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L446) *style:* **Variable or function name should be snake_case.**
```r
    newXaxt <- round(seq(1, dim(posteriorProbabilities)[1], length.out = 6))
    ^~~~~~~
```
[R/DEploidR.R:449:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/R/DEploidR.R#L449) *style:* **Variable or function name should be snake_case.**
```r
    newYaxt <- seq(0, 1, length.out = 3)
    ^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/tests/testthat/test-DEploid_tools.R#L3) *style:* **Variable or function name should be snake_case.**
```r
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:5:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/tests/testthat/test-DEploid_tools.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:7:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/tests/testthat/test-DEploid_tools.R#L7) *style:* **Variable or function name should be snake_case.**
```r
panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:9:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/tests/testthat/test-DEploid_tools.R#L9) *style:* **Variable or function name should be snake_case.**
```r
refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:10:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/tests/testthat/test-DEploid_tools.R#L10) *style:* **Variable or function name should be snake_case.**
```r
altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:12:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/tests/testthat/test-DEploid_tools.R#L12) *style:* **Variable or function name should be snake_case.**
```r
PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:15:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/tests/testthat/test-DEploid_tools.R#L15) *style:* **Variable or function name should be snake_case.**
```r
PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:18:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/tests/testthat/test-DEploid_tools.R#L18) *style:* **Variable or function name should be snake_case.**
```r
expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:21:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/tests/testthat/test-DEploid_tools.R#L21) *style:* **Variable or function name should be snake_case.**
```r
    PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:44:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/tests/testthat/test-DEploid_tools.R#L44) *style:* **Variable or function name should be snake_case.**
```r
    obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:46:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/tests/testthat/test-DEploid_tools.R#L46) *style:* **Variable or function name should be snake_case.**
```r
    potentialOutliers <- c(5, 12, 25, 30, 35, 50)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:127:5:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/tests/testthat/test-DEploid_tools.R#L127) *style:* **Variable or function name should be snake_case.**
```r
    potentialOutliers <- c(1, 10, 20, 30, 40)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:133:55:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/tests/testthat/test-DEploid_tools.R#L133) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                 potentialOutliers = potentialOutliers )
                                                      ^
```
[tests/testthat/test-dEploid.R:3:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/tests/testthat/test-dEploid.R#L3) *style:* **Variable or function name should be snake_case.**
```r
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~
```
[tests/testthat/test-dEploid.R:5:1:](https://github.com/mcveanlab/DEploid-r/blob/b0e507d23e986557c0e83b43f62934f4e45ff5ad/tests/testthat/test-dEploid.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```


[R/dEploidPlotly.R:28:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L28) *style:* **Variable or function name should be snake_case.**
```r
plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:29:32:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L29) *style:* **Variable or function name should be snake_case.**
```r
                               potentialOutliers = c()){
                               ^~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:31:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L31) *style:* **Variable or function name should be snake_case.**
```r
    legendName <- "Ref/(Ref+Alt) Ratio"
    ^~~~~~~~~~
```
[R/dEploidPlotly.R:33:14:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L33) *style:* **Variable or function name should be snake_case.**
```r
    refvsalt$ref.out <- ifelse(rownames(refvsalt) %in%
             ^~~~~~~
```
[R/dEploidPlotly.R:35:14:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L35) *style:* **Variable or function name should be snake_case.**
```r
    refvsalt$alt.out <- ifelse(rownames(refvsalt) %in%
             ^~~~~~~
```
[R/dEploidPlotly.R:107:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L107) *style:* **Variable or function name should be snake_case.**
```r
plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:107:32:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L107) *style:* **Variable or function name should be snake_case.**
```r
plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                               ^~~~~~~
```
[R/dEploidPlotly.R:109:3:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L109) *style:* **Variable or function name should be snake_case.**
```r
  tmpWSAFIndex <- 1:length(obsWSAF)
  ^~~~~~~~~~~~
```
[R/dEploidPlotly.R:111:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L111) *style:* **Variable or function name should be snake_case.**
```r
    tmpWSAFIndex <- which(((obsWSAF < 1) * (obsWSAF > 0)) == 1)
    ^~~~~~~~~~~~
```
[R/dEploidPlotly.R:111:27:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L111) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmpWSAFIndex <- which(((obsWSAF < 1) * (obsWSAF > 0)) == 1)
                          ^
```
[R/dEploidPlotly.R:111:28:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L111) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    tmpWSAFIndex <- which(((obsWSAF < 1) * (obsWSAF > 0)) == 1)
                           ^
```
[R/dEploidPlotly.R:175:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L175) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
^~~~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:175:40:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L175) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                       ^~~~~~~
```
[R/dEploidPlotly.R:177:34:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L177) *style:* **Variable or function name should be snake_case.**
```r
                                 potentialOutliers = c()){
                                 ^~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:179:16:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L179) *style:* **Variable or function name should be snake_case.**
```r
    wsafvsplaf$plaf.out <- ifelse(rownames(wsafvsplaf) %in%
               ^~~~~~~~
```
[R/dEploidPlotly.R:181:16:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L181) *style:* **Variable or function name should be snake_case.**
```r
    wsafvsplaf$obsWSAF.out <- ifelse(rownames(wsafvsplaf) %in%
               ^~~~~~~~~~~
```
[R/dEploidPlotly.R:236:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L236) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~~~~~~~
```
[R/dEploidPlotly.R:236:34:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L236) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                 ^~~~~~~
```
[R/dEploidPlotly.R:236:43:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/dEploidPlotly.R#L236) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                          ^~~~~~~
```
[R/DEploidR.R:23:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L23) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function(refFileName, altFileName){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:23:36:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L23) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function(refFileName, altFileName){
                                   ^~~~~~~~~~~
```
[R/DEploidR.R:23:49:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L23) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromTxt <- function(refFileName, altFileName){
                                                ^~~~~~~~~~~
```
[R/DEploidR.R:54:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L54) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:54:36:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L54) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                   ^~~~~~~~~~~
```
[R/DEploidR.R:54:49:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L54) *style:* **Variable or function name should be snake_case.**
```r
extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                                ^~~~~~~~~~~~
```
[R/DEploidR.R:62:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L62) *style:* **Variable or function name should be snake_case.**
```r
    numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:66:13:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L66) *style:* **Variable or function name should be snake_case.**
```r
            numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:78:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L78) *style:* **Variable or function name should be snake_case.**
```r
    sampleName <- names(vcf)[10]
    ^~~~~~~~~~
```
[R/DEploidR.R:83:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L83) *style:* **Variable or function name should be snake_case.**
```r
    tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~
```
[R/DEploidR.R:84:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L84) *style:* **Variable or function name should be snake_case.**
```r
    tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~
```
[R/DEploidR.R:86:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L86) *style:* **Variable or function name should be snake_case.**
```r
    refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~
```
[R/DEploidR.R:87:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L87) *style:* **Variable or function name should be snake_case.**
```r
    altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~
```
[R/DEploidR.R:114:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L114) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function(plafFileName){
^~~~~~~~~~~
```
[R/DEploidR.R:114:25:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L114) *style:* **Variable or function name should be snake_case.**
```r
extractPLAF <- function(plafFileName){
                        ^~~~~~~~~~~~
```
[R/DEploidR.R:151:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L151) *style:* **Variable or function name should be snake_case.**
```r
plotProportions <- function(proportions, title = "Components",
^~~~~~~~~~~~~~~
```
[R/DEploidR.R:152:24:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L152) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                       ^~~~~~~
```
[R/DEploidR.R:152:37:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L152) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                                    ^~~~~~~~
```
[R/DEploidR.R:152:51:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L152) *style:* **Variable or function name should be snake_case.**
```r
                       cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                  ^~~~~~~~
```
[R/DEploidR.R:153:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L153) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[R/DEploidR.R:200:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L200) *style:* **Variable or function name should be snake_case.**
```r
plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~
```
[R/DEploidR.R:201:21:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L201) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~
```
[R/DEploidR.R:201:40:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L201) *style:* **Variable or function name should be snake_case.**
```r
                    exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~
```
[R/DEploidR.R:202:21:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L202) *style:* **Variable or function name should be snake_case.**
```r
                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    ^~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:202:46:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L202) *style:* **Variable or function name should be snake_case.**
```r
                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                             ^~~~~~~
```
[R/DEploidR.R:202:59:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L202) *style:* **Variable or function name should be snake_case.**
```r
                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                                          ^~~~~~~~
```
[R/DEploidR.R:203:21:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L203) *style:* **Variable or function name should be snake_case.**
```r
                    cex.axis = 1){
                    ^~~~~~~~
```
[R/DEploidR.R:207:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L207) *style:* **Variable or function name should be snake_case.**
```r
    tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~
```
[R/DEploidR.R:266:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L266) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~
```
[R/DEploidR.R:266:22:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L266) *style:* **Variable or function name should be snake_case.**
```r
histWSAF <- function(obsWSAF, exclusive = TRUE,
                     ^~~~~~~
```
[R/DEploidR.R:268:17:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L268) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1){
                ^~~~~~~
```
[R/DEploidR.R:268:30:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L268) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1){
                             ^~~~~~~~
```
[R/DEploidR.R:268:44:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L268) *style:* **Variable or function name should be snake_case.**
```r
                cex.lab = 1, cex.main = 1, cex.axis = 1){
                                           ^~~~~~~~
```
[R/DEploidR.R:269:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L269) *style:* **Variable or function name should be snake_case.**
```r
    tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~
```
[R/DEploidR.R:271:9:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L271) *style:* **Variable or function name should be snake_case.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
        ^~~~~~~~~~~~
```
[R/DEploidR.R:271:31:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L271) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                              ^
```
[R/DEploidR.R:271:33:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L271) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                                ^
```
[R/DEploidR.R:323:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L323) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~
```
[R/DEploidR.R:323:34:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L323) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                 ^~~~~~~
```
[R/DEploidR.R:323:43:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L323) *style:* **Variable or function name should be snake_case.**
```r
plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                          ^~~~~~~
```
[R/DEploidR.R:324:23:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L324) *style:* **Variable or function name should be snake_case.**
```r
                      potentialOutliers = c(), title = "WSAF vs PLAF",
                      ^~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:325:23:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L325) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~
```
[R/DEploidR.R:325:36:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L325) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~
```
[R/DEploidR.R:325:50:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L325) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~
```
[R/DEploidR.R:368:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L368) *style:* **Lines should not be more than 80 characters.**
```r
#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:373:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L373) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~
```
[R/DEploidR.R:373:28:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L373) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function(obsWSAF, expWSAF,
                           ^~~~~~~
```
[R/DEploidR.R:373:37:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L373) *style:* **Variable or function name should be snake_case.**
```r
plotObsExpWSAF <- function(obsWSAF, expWSAF,
                                    ^~~~~~~
```
[R/DEploidR.R:375:23:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L375) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~
```
[R/DEploidR.R:375:36:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L375) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~
```
[R/DEploidR.R:375:50:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L375) *style:* **Variable or function name should be snake_case.**
```r
                      cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~
```
[R/DEploidR.R:411:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L411) *style:* **Variable or function name should be snake_case.**
```r
computeObsWSAF <- function(alt, ref){
^~~~~~~~~~~~~~
```
[R/DEploidR.R:432:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L432) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
^~~~~~~~~~~~~~~~
```
[R/DEploidR.R:432:30:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L432) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                             ^~~~~~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:432:66:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L432) *style:* **Variable or function name should be snake_case.**
```r
haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                                                                 ^~~~~~~~~~~~
```
[R/DEploidR.R:433:25:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L433) *style:* **Variable or function name should be snake_case.**
```r
                        numberOfInbreeding = 0){
                        ^~~~~~~~~~~~~~~~~~
```
[R/DEploidR.R:434:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L434) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~
```
[R/DEploidR.R:435:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L435) *style:* **Variable or function name should be snake_case.**
```r
    rainbowColors <- rainbow(rainbowColorBin)
    ^~~~~~~~~~~~~
```
[R/DEploidR.R:437:9:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L437) *style:* **Variable or function name should be snake_case.**
```r
        panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
        ^~~~~~~~~
```
[R/DEploidR.R:438:9:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L438) *style:* **Variable or function name should be snake_case.**
```r
        rainbowColors <- c(rep("#46a8e1", panelSize),
        ^~~~~~~~~~~~~
```
[R/DEploidR.R:446:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L446) *style:* **Variable or function name should be snake_case.**
```r
    newXaxt <- round(seq(1, dim(posteriorProbabilities)[1], length.out = 6))
    ^~~~~~~
```
[R/DEploidR.R:449:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/R/DEploidR.R#L449) *style:* **Variable or function name should be snake_case.**
```r
    newYaxt <- seq(0, 1, length.out = 3)
    ^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:3:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/tests/testthat/test-DEploid_tools.R#L3) *style:* **Variable or function name should be snake_case.**
```r
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:5:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/tests/testthat/test-DEploid_tools.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:7:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/tests/testthat/test-DEploid_tools.R#L7) *style:* **Variable or function name should be snake_case.**
```r
panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:9:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/tests/testthat/test-DEploid_tools.R#L9) *style:* **Variable or function name should be snake_case.**
```r
refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:10:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/tests/testthat/test-DEploid_tools.R#L10) *style:* **Variable or function name should be snake_case.**
```r
altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:12:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/tests/testthat/test-DEploid_tools.R#L12) *style:* **Variable or function name should be snake_case.**
```r
PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:15:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/tests/testthat/test-DEploid_tools.R#L15) *style:* **Variable or function name should be snake_case.**
```r
PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:18:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/tests/testthat/test-DEploid_tools.R#L18) *style:* **Variable or function name should be snake_case.**
```r
expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:21:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/tests/testthat/test-DEploid_tools.R#L21) *style:* **Variable or function name should be snake_case.**
```r
    PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:44:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/tests/testthat/test-DEploid_tools.R#L44) *style:* **Variable or function name should be snake_case.**
```r
    obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~
```
[tests/testthat/test-DEploid_tools.R:46:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/tests/testthat/test-DEploid_tools.R#L46) *style:* **Variable or function name should be snake_case.**
```r
    potentialOutliers <- c(5, 12, 25, 30, 35, 50)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:127:5:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/tests/testthat/test-DEploid_tools.R#L127) *style:* **Variable or function name should be snake_case.**
```r
    potentialOutliers <- c(1, 10, 20, 30, 40)
    ^~~~~~~~~~~~~~~~~
```
[tests/testthat/test-DEploid_tools.R:133:55:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/tests/testthat/test-DEploid_tools.R#L133) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                 potentialOutliers = potentialOutliers )
                                                      ^
```
[tests/testthat/test-dEploid.R:3:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/tests/testthat/test-dEploid.R#L3) *style:* **Variable or function name should be snake_case.**
```r
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~
```
[tests/testthat/test-dEploid.R:5:1:](https://github.com/liuyingh/DEploid-r/blob/9bfeea9c31a6a33e25c757fc3a56c108e20c4a7b/tests/testthat/test-dEploid.R#L5) *style:* **Variable or function name should be snake_case.**
```r
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~
```


Is this file 4 space indentation? We are using 2 and so if it is, please fix