[tests/testthat/test_igbirth.R:30:1:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_igbirth.R#L30) *style:* **lines should not be more than 80 characters.**
```r
test_that("vectorized intergrowth birth standard centile to value conversion works", {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_igbirth.R:99:1:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_igbirth.R#L99) *style:* **lines should not be more than 80 characters.**
```r
test_that("vectorized intergrowth early birth z-score to value conversion works", {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_igbirth.R:109:1:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_igbirth.R#L109) *style:* **lines should not be more than 80 characters.**
```r
test_that("vectorized intergrowth early birth value to z-score conversion works", {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_igfet.R:27:1:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_igfet.R#L27) *style:* **lines should not be more than 80 characters.**
```r
    expect_true(igfet_value2centile(cp$ga * 7, cp$p3 / 10, var = cp$var) / 100 - 0.03 < 0.001)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_igfet.R:28:1:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_igfet.R#L28) *style:* **lines should not be more than 80 characters.**
```r
    expect_true(igfet_value2centile(cp$ga * 7, cp$p50 / 10, var = cp$var) / 100 - 0.5 < 0.001)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_igfet.R:29:1:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_igfet.R#L29) *style:* **lines should not be more than 80 characters.**
```r
    expect_true(igfet_value2centile(cp$ga * 7, cp$p97 / 10, var = cp$var) / 100 - 0.97 < 0.001)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_igfet.R:35:1:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_igfet.R#L35) *style:* **lines should not be more than 80 characters.**
```r
  expect_true(all(igfet_bpdcm2centile(cp2$ga * 7, cp2$p3 / 10) / 100 - 0.03 < 0.001))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:28:5:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_zz_ghpages.R#L28) *style:* **Commented code should be removed.**
```r
#   unlink(file.path("test_cache", paste(name, ".Rda", sep = "")))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:101:7:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_zz_ghpages.R#L101) *style:* **Commented code should be removed.**
```r
  #   print_model_json(p)
      ^~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:212:1:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_zz_ghpages.R#L212) *style:* **lines should not be more than 80 characters.**
```r
  expect_equivalent(c(cpp2_hbgd$time_vars, cpp2_hbgd$timevarying_vars), colnames(time_dt))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:214:1:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_zz_ghpages.R#L214) *style:* **lines should not be more than 80 characters.**
```r
  expect_data_frame(cpp2_hbgd$var_summ, c("variable", "label", "type", "vtype", "n_unique"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:244:5:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_zz_ghpages.R#L244) *style:* **Commented code should be removed.**
```r
  # print(str_c(standard_name, "_", type))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:251:1:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_zz_ghpages.R#L251) *style:* **lines should not be more than 80 characters.**
```r
      maybe_random_centile <- fn_to_centile(time, centile_to_fn(time, random_centile))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:259:1:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_zz_ghpages.R#L259) *style:* **lines should not be more than 80 characters.**
```r
      maybe_random_zvalue <- fn_to_zscore(time, zscore_to_fn(time, random_zvalue))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:315:1:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_zz_ghpages.R#L315) *style:* **lines should not be more than 80 characters.**
```r
      c(fn_to_centile_name, fn_to_zscore_name, centile_to_fn_name, zscore_to_fn_name),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:605:1:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_zz_ghpages.R#L605) *style:* **lines should not be more than 80 characters.**
```r
      paste("Object obtained from get_fit\\(\\) using method '", meth, "'", sep = "")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:617:1:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_zz_ghpages.R#L617) *style:* **lines should not be more than 80 characters.**
```r
  expect_fit_plot(plot(fit, x_range = c(0, 755), hover = c("agedays", "htcm"), center = TRUE))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:694:1:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_zz_ghpages.R#L694) *style:* **lines should not be more than 80 characters.**
```r
  test_vdb_conn <- trelliscope::vdbConn(name = "ghap_vdb", path = vdb_path, autoYes = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:704:5:](https://github.com/HBGDki/hbgd/blob/6f93780ab51bcf3661f8d5614a1186bdc11af561/tests/testthat/test_zz_ghpages.R#L704) *style:* **Commented code should be removed.**
```r
  # trscope_trajectories(smc_tr)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


IMHO it's time to backport your changes here and in oe-branding to the 3.4 branch.
On upstream OWIF "Theme" is now master and previous master is legacy ...

The only show-stopper is the lack of (transparent) PNGs for some boxes, because I would like to already have them in before we switch the OWIF to theme ...


Thanks this works well.  Maybe you can create a PR for this one.  Just get rid of the actual commented out block so it will be cleaner.


i use ruby 2.1.5, gem 2.2.2
I tested 3 step motor use code arduino, so 3 step motor still run.


oh I thought you owned that extension.


Can't believe it's sold to someone else :)


this is either going to work perfectly or fail catastropika-ly


interesting I never really considered css background images not having an easy way to detect load failures. Maybe there's a way but I don't know so this is fine.


+1 for remembering the license header :)


btw would be great to have an about:credits one day to display info like this and other things.


++ looks good, can't wait newtab!


dat feel


`BASH_REMATCH` doesn't work well with `zsh`. I'm on OSX


` protected void onCreate(Bundle savedInstanceState) {
        super.onCreate(savedInstanceState);
        setContentView(R.layout.activity_main);
    }
`


I might rewrite this from scratch. I don't want an angry person telling me what to do or what not to do with their code. :/


Is it viable to access the event and hide the tr element that contains the user information to achieve the same end? Instead of slicing the array.


FYI @gregvanl here are the original files.


So we're relying on list-initialization to keep the ordering guarantees? This is a nice enhancement, assuming it works, over using function parameters.


addded one testing comments


영어 해석이 잘안되는 부분입니다.


사용자의 턴에도 공격이 성공햇는지 실패햇는지 넣어보고싶습니다. 일단 그냥 state값을 넣어봤는데 컴퓨터의 공격성공여부랑 동일하게 뜹니다. 사용자도 뜨게 할라면 사용자도 따로 변수하나 만들어서 확인해야할거같습니다.


이부분은 그냥 영어루 뒀습니다.


이부분도 그냥 영어로 뒀습니다 추후에 변경하던지 놔두던지결정


여기부분 hit를 한글로 바꾸면 오류납니다. 해결방법 찾던지 그냥 둡니다.


hit와 동일


전체적으로 라인 제가 알아보기 쉽게 바꿧고요. 주석써잇는거 한글로 해석해보고
영어로 프린트되는거 한글로 수정하였습니다.
버그는 영어를 한글로 바꾸는과정에서 나올떄 생기는 버그만 발견되었습니다.


Would be nice if delete weren't needed at all.


terrible


asdgasdf


I'm not angry... I just don't want to see anyone wasting their time doing things in a totally don't way...


If you do not have any special thing in the `override` method, you can remove it.


FIles look good


Missing a space before `{`.


You can set the default value for string and bool, such as empty string (`""`). By this way, you won't need to unwrap it anymore.


Cyrus, I'm not sure why this is here as it doesn't seem to be used anywhere in the code and in fact is throwing an error in my js console.  Can you verify that we need this? Thanks!


It should be `func getFilters() -> [Filter] {`. Please be careful with the spaces.


this line is confusing, and a bad example of a cp command.. from what to where now?


It should be
```swift
if let value = filters["category_filter"] as String {
    categories = value
}
```


`var indexRow = 0` is enough.


`if filter.options[0].selected` is enough.


`} else {`.


mkdir from where? from ~/ ? from ~/.config/systemd/user/? from the git cloned directory? from where?


a=kf=wazkafad


Is this removal intentional?


Wrong indentation here.
Please re-indent your code when saving.
`cmd + A` to select whole file, then `control + I` to re-indent.


```swift
return UIImage(named: selected ? "arrow_down" : "uncheck")!
```


This has the same priority as `Create Family`, it should have a different one to make the desired ordering clear.


台湾亲热


On the Mac, Java can be found in:
/Library/Java/Home

Also, you can use the following command to get java install dir:
`/System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/java_home`

both of these i found on the quota posts.


askdfjasdkfh


"Angry Person" was just a saying. Isn't the function "output" supposed to be for writing the html code of each module?


@cafeinlove, My apologies for jumping on a commit... We just installed your ModernSkylight skin. Its very nice skin. Its clean with a refreshing, unique look. Hat's off to you.


Esto tiene un nivel de isn


is that true? is that what it does?


Interesting. How do you build to get the tests built? In any case, I'll fix the tests.


This needs a replacementtypeormember


Esta lina no va, eso era para un campo imagen


Hi

When I send messagesGetMessagesViews request, the response is TLVector<Integer> or TLIntVector but it throws UnsupportedConstructorException in parsing the vector integer (Kotlogram thinks it is constructor).

So because the response was not important for me, simply I changed to not throw anything :)


IOT-Outdoor-Thermometer
This is based on Adafruit IO project, "https://learn.adafruit.com/home-automation-in-the-cloud-with-the-esp8266-and-adafruit-io" which after much Googling resulted in a few modifications.
Mod #1 "https://learn.adafruit.com/home-automation-in-the-cloud-with-the-esp8266-and-adafruit-io" this correct a change to MQTT that wasn't reflected in the original project pages.
Mod #2 "http://community.blynk.cc/t/2147483647-value-intermittend-dht11-nodemcu-and-blynk/8259" and "https://www.arduino.cc/en/Reference/Goto" This helped control random bad data from skewing feed info on Adafruit IO.


I should change the steps instead to "create the library folder outside of CommProtocol folder" rather than creating one inside CommProtocol.


[Your benchmark job](https://github.com/JuliaLang/julia/commit/c55037a0fecb608c67d7de3f4fd4325f7402e576#commitcomment-19620004) has completed - possible performance regressions were detected. A full report can be found [here](https://github.com/JuliaCI/BaseBenchmarkReports/blob/21b41a1b3283e8b04b25e84fc527f8cc101396d9/daily_2016_10_29/report.md). cc @jrevels


s/time/type ?


I'm building for Samsung Galaxy J5 at the moment.
Tried both OpenJDK 7 and 8. That is not the cause.
Test local module is built automatically.

It seems that **.thenReturn(true);** needs a workaround.
Possibly due to boolean->boolean[] changes.

Common repo here:
[https://github.com/Galaxy-J5/android_device_samsung_j5-common](url)


I have no idea what this comment is trying to say.


@babyfiv5  这个文件需要自己创建呢


Also, the libxbee3 library is needed by the CommProtoStatic library. I think if they build the CommProtoShared Library then only that library will need LibXbee3.dll.


@fichtner What about changing the core rules to a new separate file so we use the same method for registartion/generation, but not dynamically loaded?
The problem is, this stuff really needs a cleanup and all should use the same method to allow descent plugin, besides that, parts of the current filter does belong to other applications (and should go to plugins).

One other change I'm planning to push is to toggle "disabled" in stead of the optional registration, this makes auditing the rules much easier. (move` !isset($config['system']['ipv6allow']) `to "disabled" tag)


The thing is, they aren't built automatically for me, which is why I didn't notice this. That's why I'm asking how exactly you build, as in: what command do you run to invoke the build?


mka && mka bacon for me.


Ah, OK. I only run mka bacon (which is sufficient to get the zip built), that's why. I'll fix this.


I do not mean this as test (as you say it is obvious test case). I wrote this to show that every server must have get, new, update, delete functions in my implementation.


Probably correct. I said bin folder so its close


<!-- PMABOT:SPACE -->
This commit contains trailing whitespace, what is prohibited in phpMyAdmin. Please check our [Developer guidelines](https://github.com/phpmyadmin/phpmyadmin/wiki/Developer_guidelines#Indentation) for more information.

Offending files: libraries/DatabaseInterface.php


lol, it's good enough. I might fix up the commxbee stuff, but it shouldn't effect the front end API of the library.


Thank you maniac! Have a good day!


@gonetz xxHash was written against a dedicated hash function test suite designed to test for collisions of hash data among different hashes (amongst other features). I think its exactly designed for automated test scenarios.

@loganmc10 The previous hash you did was on par with FNV which is a very poor hash. Things like xxhash, Murmur and lookup3 are designed to be more thorough in how hashing is done while still being performant.


There's a type -- "time" should be "type" :)

----- Original Message -----
From: "TheFakeMateo/RedPlusPlus"
To:"TheFakeMateo/RedPlusPlus"
Cc:"Kroc Camen" , "Comment"
Sent:Fri, 28 Oct 2016 22:46:42 -0700
Subject:Re: [TheFakeMateo/RedPlusPlus] Updates to FEATURES.md and
TODO.md (bb6a57a)

	I have no idea what this comment is trying to say.

	—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub [1], or mute the
thread [2].

Links:
------
[1]
https://github.com/TheFakeMateo/RedPlusPlus/commit/bb6a57a4a828eb1fef87c60f322631f616eb606c#commitcomment-19620239
[2]
https://github.com/notifications/unsubscribe-auth/AAItOnhy_PC8bdaDrXWlwYlsDE8lZivOks5q4t3CgaJpZM4KkCKO


I was wondering the same - tracing through this method in the debugger, it seems like it's mostly misses. Also, is there a reasonable bound on the expected recursion depth?


Is there a chance these returned objects would be used by code outside of dgrid? If so, we would probably benefit from named interfaces for the return types of all these methods, rather than anonymous interfaces.


Oh, whoops. Thanks. I'll fix that up later. I'm going to sleep right now.


I know Ed already brought this up, but I don't recall the resolution of the discussion... can we avoid all these string values for configuration?


@AdSchellevis don't have to convince me. :) how about src/etc/filter.lib.inc ?


Say hello to Max.

![](http://vignette2.wikia.nocookie.net/secretlifeofpets/images/1/17/Max_dog.png/revision/latest?cb=20160801094745)


gbxml-sizing (macumber) - x86_64-Linux-Ubuntu-14.04-clang-3.5: Build Failed

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


Hm_Msgs::add("ERRConnected, but failed to authenticate**~~d~~** to the SMTP server");


I also added "?zen" to links if we're in zen mode.


Does this actually work??

Is this something worth adding to Master??

@SamCarlberg @AustinShalit


@Hobo4ssassin: I thought that you might have installed the nightly version from the PPA and wanted to test this new feature in case the PPA isn't updated yet. But as **collinss** said, a lot of thing changed in Cinnamon and/or were rewritten from scratch.

If you still want hover delay for hot corners for the current stable Cinnamon version (or for Cinnamon 2.8.6 (Mint 17.3)), I added this feature to my [Cinnamon Tweaks](https://cinnamon-spices.linuxmint.com/extensions/view/41) extension for Cinnamon. If you have issues with the extension, [report them in its repository](https://github.com/Odyseus/CinnamonTools), not here.


The `Dgrid.customize` object: can we just mix these methods in to the instance, rather than keeping the `customize` object and the related logic repeated in numerous methods checking the presence of implementations on the `customize` object?

Are `dom` and some vdom (`maquette`) the only renderers that would be needed, or might there be more, e.g. for Angular, React, ...? I'm in favor, if possible, of having as few renderers as possible (and One Renderer to rule them all), and providing interop with other libraries with as thin an adapter as possible, while avoiding leveraging other libraries internally (and duplicating logic).

Will dgrid always require `dojo/store`, or to be a good citizen in other worlds (Angular, React) would we have to be able to consume their stores?

We should all read and adhere to the [Dojo 2 style guide](https://github.com/dojo/meta/blob/master/STYLE.md).


gbxml-sizing (macumber) - 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-warnings-yellow.svg)


See https://github.com/sass/node-sass/issues/1766


Note to self — see if we can interpolate org name here rather than split in two.


I see ! That's clever ! Thanks a lot !


The commit is literally titled "backdoor", so I think he knows this is a security issue.


为啥要加敌方？我记得这里就是指自己的。需要在游戏中确认。可以在ui 目录下找到对应的界面文件。


@ghsr i don't know if this is the problem or not, but without this, audiorecord in 7.1 doesn't work. Haven't checked with this yet, but i think this is still needed.


BTW auto rotation fixed on my device too. It was because of selinux.
https://github.com/google-aosp/platform_system_core/commit/09dafd846b104e47430d7a93cb2e52d3c7f0300e


[tests/testthat/test_igbirth.R:30:1:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_igbirth.R#L30) *style:* **lines should not be more than 80 characters.**
```r
test_that("vectorized intergrowth birth standard centile to value conversion works", {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_igbirth.R:99:1:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_igbirth.R#L99) *style:* **lines should not be more than 80 characters.**
```r
test_that("vectorized intergrowth early birth z-score to value conversion works", {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_igbirth.R:109:1:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_igbirth.R#L109) *style:* **lines should not be more than 80 characters.**
```r
test_that("vectorized intergrowth early birth value to z-score conversion works", {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_igfet.R:27:1:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_igfet.R#L27) *style:* **lines should not be more than 80 characters.**
```r
    expect_true(igfet_value2centile(cp$ga * 7, cp$p3 / 10, var = cp$var) / 100 - 0.03 < 0.001)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_igfet.R:28:1:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_igfet.R#L28) *style:* **lines should not be more than 80 characters.**
```r
    expect_true(igfet_value2centile(cp$ga * 7, cp$p50 / 10, var = cp$var) / 100 - 0.5 < 0.001)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_igfet.R:29:1:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_igfet.R#L29) *style:* **lines should not be more than 80 characters.**
```r
    expect_true(igfet_value2centile(cp$ga * 7, cp$p97 / 10, var = cp$var) / 100 - 0.97 < 0.001)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_igfet.R:35:1:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_igfet.R#L35) *style:* **lines should not be more than 80 characters.**
```r
  expect_true(all(igfet_bpdcm2centile(cp2$ga * 7, cp2$p3 / 10) / 100 - 0.03 < 0.001))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:28:5:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_zz_ghpages.R#L28) *style:* **Commented code should be removed.**
```r
#   unlink(file.path("test_cache", paste(name, ".Rda", sep = "")))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:101:7:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_zz_ghpages.R#L101) *style:* **Commented code should be removed.**
```r
  #   print_model_json(p)
      ^~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:212:1:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_zz_ghpages.R#L212) *style:* **lines should not be more than 80 characters.**
```r
  expect_equivalent(c(cpp2_hbgd$time_vars, cpp2_hbgd$timevarying_vars), colnames(time_dt))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:214:1:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_zz_ghpages.R#L214) *style:* **lines should not be more than 80 characters.**
```r
  expect_data_frame(cpp2_hbgd$var_summ, c("variable", "label", "type", "vtype", "n_unique"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:244:5:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_zz_ghpages.R#L244) *style:* **Commented code should be removed.**
```r
  # print(str_c(standard_name, "_", type))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:251:1:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_zz_ghpages.R#L251) *style:* **lines should not be more than 80 characters.**
```r
      maybe_random_centile <- fn_to_centile(time, centile_to_fn(time, random_centile))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:259:1:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_zz_ghpages.R#L259) *style:* **lines should not be more than 80 characters.**
```r
      maybe_random_zvalue <- fn_to_zscore(time, zscore_to_fn(time, random_zvalue))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:315:1:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_zz_ghpages.R#L315) *style:* **lines should not be more than 80 characters.**
```r
      c(fn_to_centile_name, fn_to_zscore_name, centile_to_fn_name, zscore_to_fn_name),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:605:1:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_zz_ghpages.R#L605) *style:* **lines should not be more than 80 characters.**
```r
      paste("Object obtained from get_fit\\(\\) using method '", meth, "'", sep = "")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:617:1:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_zz_ghpages.R#L617) *style:* **lines should not be more than 80 characters.**
```r
  expect_fit_plot(plot(fit, x_range = c(0, 755), hover = c("agedays", "htcm"), center = TRUE))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:694:1:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_zz_ghpages.R#L694) *style:* **lines should not be more than 80 characters.**
```r
  test_vdb_conn <- trelliscope::vdbConn(name = "ghap_vdb", path = vdb_path, autoYes = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_zz_ghpages.R:704:5:](https://github.com/HBGDki/hbgd/blob/57eec7923d5bcdbd71351640b16ca9efe8c8cf38/tests/testthat/test_zz_ghpages.R#L704) *style:* **Commented code should be removed.**
```r
  # trscope_trajectories(smc_tr)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Hi @pliard-chromium ,

I have the same thought that as you ! Between 1.0.0-rc4 and 1.0.0 release, FCB locks have been changed and the scope of them are more "big" and lock during Oplock. I tried to look on documentation if oplock should be locking or not but I found nothing 😢

I think we should review again the lock FCB and only use it when updating values and reading variables that can change during life time of FCB.


-25mV undervolt on IO voltage.


@whyrusleeping see this and this:
https://botbot.me/freenode/ipfs/2016-10-29/?msg=75666310&page=1


For me audio recording works without this commit. You've got crashes during the record?

Maybe it requires additional selinux updates in the kernel.


Added 100MHz Frequency to GPU.


So now items can not have meta 0?


What about the video recording on android-7.1, it works?


Try a later version of ruby:
```
sudo apt-get remove ruby* --purge
gpg --keyserver hkp://keys.gnupg.net --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3
curl -L https://get.rvm.io | bash -s stable --ruby
```
Maybe try these?
```
gem install bundler
bundle install
```
I don't remember them being necessary though. It's been a while since I've tried testing with this simulator.


![](https://github.trello.services/images/mini-trello-icon.png) [Блокирование производства определенного вида оружия в мастерской доспехов](https://trello.com/c/158t5Ykf/15--)


sgs_ex.lua里CreateViewHasSkill那段忘了relate_to_place的设置。


好好的协作开发工具被用来写日志，浪费浪费


this is by myself to test the pullrequest.


It's most likely the ruby version, needs to be 2.2 or greater.

You can also try these to test the firmware:
```
  git clone https://github.com/FarmBot/farmbot-serial.git
  cd farmbot-serial
  ruby console.rb

```

From there, you can type commands, such as:

```
move_relative x: 100
```


Actually phone gets freezed when i take log with recording. Even logcat stucked. So no idea if it's crashing due to this.
And video recording is totally broken for me. Also camera focus.


@leiradel C89 backwards compatibility has been broken here -

cheevos.c: In function 'cheevos_eval_md5':
cheevos.c:1828:51: error: pointer of type 'void *' used in arithmetic [-Werror=pointer-arith]
       MD5_Update(ctx, (void*)(uint8_t*)info->data + offset, max_size);
                                                   ^
cheevos.c: In function 'cheevos_find_game_id_nes':
cheevos.c:2024:28: warning: overflow in implicit constant conversion [-Woverflow]
    cheevos_fill_md5(count, 0xff, &ctx);
                            ^~~~


I do not understand the benefits of personal frame, if the oUF player's frame so close.


Kwangjin


Lulz, dat ol' merge conflict.


Well It could come useful if you wanted to track certain ones to pay attention to. Just a thought.


Sorry about that. This is a mock file used for our automated tests. It was generated at a time where you were a backer. Apologies. I've just filed a PR for this: https://github.com/OpenCollective/opencollective-website/pull/527


@NikoKrause

> It is hard for me to track your changes. Could you first create an initial commit, which doesn't has keynavigation for contextMenu, and then do your changes in a second commit. That would make it much easier to read the code.

I didn't thought of that. I think that it would be better if I added the keyboard navigation code to a fork of the original applet instead of my own fork. It would be much more simple for you.


@fichtner sounds good! I will refactor it later this weekend


@Creeperface01 idk, but it maybe just makes those items no matter have what meta can be cooked. Sorry for my bad English.


本番で動かす想定はカードの方です


Great, thank you for this refactoring! I have some feedback for the next time:

1. When renaming identifiers, be careful not to change upper and lower case. I have found a few occurrences of `taskInstance` modified to `TaskSession`
2. Also it is a good idea to check that you have renamed all occurrences. Useful command: ` git grep --ignore-case "task_instance"`. You have missed one `TASK_INSTANCE`.
3. After modifying Python code, always run tests to check that nothing has broken - but the above mentioned issues were all in visualization code, so it is also useful to do a quick check that the visualization work (go to the visualization folder, `npm run start` and see if there are some errors reported in terminal or development console). Unfortunately, we still do not have tests for visualization.

I have already fixed these small issues by 192b1a77446834cc2cd4ee567981d4825f1b323f.


バーコードリーダーは据え置きということですね


kiva (nealkruis) - x86_64-MacOS-10.9-clang: OK (1771 of 1771 tests passed, 0 test warnings)

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


その通りです


@Too-Naive 当然不是，然而也就几十K的文件，再慢也慢不到哪里去啊


very positive and kind person


amazing \w/


Can't remove these lines. Gives compiler error because doesn't know what "self" refers to anymore.


[R/dEploidTools.R:1:22:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L1) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
fun.parse <- function( args ){
                     ^
```
[R/dEploidTools.R:1:28:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L1) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
fun.parse <- function( args ){
                           ^
```
[R/dEploidTools.R:2:5:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L2) *style:* **Variable and function names should be all lowercase.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:2:5:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L2) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:2:48:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L2) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    fun.local.checkAndIncreaseArgI <- function ( ){
                                               ^
```
[R/dEploidTools.R:3:15:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L3) *style:* **Use <-, not =, for assignment.**
```r
        arg_i = arg_i+1
              ^
```
[R/dEploidTools.R:3:22:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L3) *style:* **Put spaces around all infix operators.**
```r
        arg_i = arg_i+1
                    ~^~
```
[R/dEploidTools.R:6:5:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L6) *style:* **Variable and function names should be all lowercase.**
```r
    outPrefix = "dataExplore"
    ^~~~~~~~~
```
[R/dEploidTools.R:6:15:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L6) *style:* **Use <-, not =, for assignment.**
```r
    outPrefix = "dataExplore"
              ^
```
[R/dEploidTools.R:7:5:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L7) *style:* **Variable and function names should be all lowercase.**
```r
    vcfFileName = ""
    ^~~~~~~~~~~
```
[R/dEploidTools.R:7:17:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L7) *style:* **Use <-, not =, for assignment.**
```r
    vcfFileName = ""
                ^
```
[R/dEploidTools.R:8:5:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L8) *style:* **Variable and function names should be all lowercase.**
```r
    refFileName = ""
    ^~~~~~~~~~~
```
[R/dEploidTools.R:8:17:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L8) *style:* **Use <-, not =, for assignment.**
```r
    refFileName = ""
                ^
```
[R/dEploidTools.R:9:5:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L9) *style:* **Variable and function names should be all lowercase.**
```r
    altFileName = ""
    ^~~~~~~~~~~
```
[R/dEploidTools.R:9:17:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L9) *style:* **Use <-, not =, for assignment.**
```r
    altFileName = ""
                ^
```
[R/dEploidTools.R:10:5:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L10) *style:* **Variable and function names should be all lowercase.**
```r
    plafFileName = ""
    ^~~~~~~~~~~~
```
[R/dEploidTools.R:10:18:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L10) *style:* **Use <-, not =, for assignment.**
```r
    plafFileName = ""
                 ^
```
[R/dEploidTools.R:11:5:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L11) *style:* **Variable and function names should be all lowercase.**
```r
    excludeFileName = ""
    ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:11:21:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L11) *style:* **Use <-, not =, for assignment.**
```r
    excludeFileName = ""
                    ^
```
[R/dEploidTools.R:12:5:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L12) *style:* **Variable and function names should be all lowercase.**
```r
    dEploidPrefix = ""
    ^~~~~~~~~~~~~
```
[R/dEploidTools.R:12:19:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L12) *style:* **Use <-, not =, for assignment.**
```r
    dEploidPrefix = ""
                  ^
```
[R/dEploidTools.R:13:5:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L13) *style:* **Variable and function names should be all lowercase.**
```r
    excludeBool = FALSE
    ^~~~~~~~~~~
```
[R/dEploidTools.R:13:17:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L13) *style:* **Use <-, not =, for assignment.**
```r
    excludeBool = FALSE
                ^
```
[R/dEploidTools.R:15:11:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L15) *style:* **Use <-, not =, for assignment.**
```r
    arg_i = 1
          ^
```
[R/dEploidTools.R:16:11:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    while ( arg_i < length(args) ){
          ^
```
[R/dEploidTools.R:16:33:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    while ( arg_i < length(args) ){
                                ^
```
[R/dEploidTools.R:17:14:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L17) *style:* **Use <-, not =, for assignment.**
```r
        argv = args[arg_i]
             ^
```
[R/dEploidTools.R:18:12:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( argv == "-vcf" ){
           ^
```
[R/dEploidTools.R:18:28:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        if ( argv == "-vcf" ){
                           ^
```
[R/dEploidTools.R:19:19:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L19) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:19:21:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L19) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:19:21:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L19) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:19:52:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:20:13:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L20) *style:* **Variable and function names should be all lowercase.**
```r
            vcfFileName = args[arg_i]
            ^~~~~~~~~~~
```
[R/dEploidTools.R:20:25:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L20) *style:* **Use <-, not =, for assignment.**
```r
            vcfFileName = args[arg_i]
                        ^
```
[R/dEploidTools.R:21:19:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-plaf" ){
                  ^
```
[R/dEploidTools.R:21:36:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-plaf" ){
                                   ^
```
[R/dEploidTools.R:22:19:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L22) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:22:21:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L22) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:22:21:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L22) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:22:52:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L22) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:23:13:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L23) *style:* **Variable and function names should be all lowercase.**
```r
            plafFileName = args[arg_i]
            ^~~~~~~~~~~~
```
[R/dEploidTools.R:23:26:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L23) *style:* **Use <-, not =, for assignment.**
```r
            plafFileName = args[arg_i]
                         ^
```
[R/dEploidTools.R:24:19:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L24) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-ref" ){
                  ^
```
[R/dEploidTools.R:24:35:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L24) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-ref" ){
                                  ^
```
[R/dEploidTools.R:25:19:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L25) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:25:21:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L25) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:25:21:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L25) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:25:52:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L25) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:26:13:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L26) *style:* **Variable and function names should be all lowercase.**
```r
            refFileName = args[arg_i]
            ^~~~~~~~~~~
```
[R/dEploidTools.R:26:25:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L26) *style:* **Use <-, not =, for assignment.**
```r
            refFileName = args[arg_i]
                        ^
```
[R/dEploidTools.R:27:19:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-alt" ){
                  ^
```
[R/dEploidTools.R:27:35:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L27) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-alt" ){
                                  ^
```
[R/dEploidTools.R:28:19:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L28) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:28:21:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L28) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:28:21:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L28) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:28:52:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L28) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:29:13:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L29) *style:* **Variable and function names should be all lowercase.**
```r
            altFileName = args[arg_i]
            ^~~~~~~~~~~
```
[R/dEploidTools.R:29:25:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L29) *style:* **Use <-, not =, for assignment.**
```r
            altFileName = args[arg_i]
                        ^
```
[R/dEploidTools.R:30:19:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-exclude" ){
                  ^
```
[R/dEploidTools.R:30:39:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-exclude" ){
                                      ^
```
[R/dEploidTools.R:31:19:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L31) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:31:21:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L31) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:31:21:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L31) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:31:52:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L31) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:32:13:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L32) *style:* **Variable and function names should be all lowercase.**
```r
            excludeFileName = args[arg_i]
            ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:32:29:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L32) *style:* **Use <-, not =, for assignment.**
```r
            excludeFileName = args[arg_i]
                            ^
```
[R/dEploidTools.R:33:13:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L33) *style:* **Variable and function names should be all lowercase.**
```r
            excludeBool = TRUE
            ^~~~~~~~~~~
```
[R/dEploidTools.R:33:25:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L33) *style:* **Use <-, not =, for assignment.**
```r
            excludeBool = TRUE
                        ^
```
[R/dEploidTools.R:34:19:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-o" ){
                  ^
```
[R/dEploidTools.R:34:33:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-o" ){
                                ^
```
[R/dEploidTools.R:35:19:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L35) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:35:21:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L35) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:35:21:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L35) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:35:52:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:36:13:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L36) *style:* **Variable and function names should be all lowercase.**
```r
            outPrefix = args[arg_i]
            ^~~~~~~~~
```
[R/dEploidTools.R:36:23:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L36) *style:* **Use <-, not =, for assignment.**
```r
            outPrefix = args[arg_i]
                      ^
```
[R/dEploidTools.R:37:19:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-dEprefix" ){
                  ^
```
[R/dEploidTools.R:37:40:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        } else if ( argv == "-dEprefix" ){
                                       ^
```
[R/dEploidTools.R:38:19:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L38) *style:* **Use <-, not =, for assignment.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                  ^
```
[R/dEploidTools.R:38:21:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L38) *style:* **Variable and function names should be all lowercase.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:38:21:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L38) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:38:52:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
            arg_i = fun.local.checkAndIncreaseArgI ( )
                                                   ^
```
[R/dEploidTools.R:39:13:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L39) *style:* **Variable and function names should be all lowercase.**
```r
            dEploidPrefix = args[arg_i]
            ^~~~~~~~~~~~~
```
[R/dEploidTools.R:39:27:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L39) *style:* **Use <-, not =, for assignment.**
```r
            dEploidPrefix = args[arg_i]
                          ^
```
[R/dEploidTools.R:44:15:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L44) *style:* **Use <-, not =, for assignment.**
```r
        arg_i = arg_i + 1
              ^
```
[R/dEploidTools.R:51:8:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( plafFileName == "" ){
       ^
```
[R/dEploidTools.R:51:10:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L51) *style:* **Variable and function names should be all lowercase.**
```r
    if ( plafFileName == "" ){
         ^~~~~~~~~~~~
```
[R/dEploidTools.R:51:28:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L51) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( plafFileName == "" ){
                           ^
```
[R/dEploidTools.R:58:12:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( list ( vcfFileName = vcfFileName,
           ^
```
[R/dEploidTools.R:58:19:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L58) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return ( list ( vcfFileName = vcfFileName,
                  ^
```
[R/dEploidTools.R:58:35:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L58) *style:* **Variable and function names should be all lowercase.**
```r
    return ( list ( vcfFileName = vcfFileName,
                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:59:35:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L59) *style:* **Variable and function names should be all lowercase.**
```r
                    refFileName = refFileName,
                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:60:35:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L60) *style:* **Variable and function names should be all lowercase.**
```r
                    altFileName = altFileName,
                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:61:36:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L61) *style:* **Variable and function names should be all lowercase.**
```r
                    plafFileName = plafFileName,
                                   ^~~~~~~~~~~~
```
[R/dEploidTools.R:62:33:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L62) *style:* **Variable and function names should be all lowercase.**
```r
                    outPrefix = outPrefix,
                                ^~~~~~~~~
```
[R/dEploidTools.R:63:37:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L63) *style:* **Variable and function names should be all lowercase.**
```r
                    dEploidPrefix = dEploidPrefix,
                                    ^~~~~~~~~~~~~
```
[R/dEploidTools.R:64:39:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L64) *style:* **Variable and function names should be all lowercase.**
```r
                    excludeFileName = excludeFileName,
                                      ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:65:35:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L65) *style:* **Variable and function names should be all lowercase.**
```r
                    excludeBool = excludeBool) )
                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:65:47:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L65) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                    excludeBool = excludeBool) )
                                              ^
```
[R/dEploidTools.R:69:1:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L69) *style:* **Variable and function names should be all lowercase.**
```r
fun.dEploidPrefix <- function ( prefix ){
^~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:81:1:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L81) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.extract.coverage <- function ( inputs ){
^~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:82:17:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L82) *style:* **Variable and function names should be all lowercase.**
```r
    if ( inputs$vcfFileName != "" ){
                ^~~~~~~~~~~
```
[R/dEploidTools.R:83:17:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:83:17:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L83) *warning:* **no visible global function definition for ‘extractCoverageFromVcf’**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:83:48:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L83) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromVcf (inputs$vcfFileName))
                                               ^~~~~~~~~~~
```
[R/dEploidTools.R:85:17:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:85:17:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L85) *warning:* **no visible global function definition for ‘extractCoverageFromTxt’**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                ^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:85:48:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                               ^~~~~~~~~~~
```
[R/dEploidTools.R:85:68:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
        return (extractCoverageFromTxt (inputs$refFileName, inputs$altFileName))
                                                                   ^~~~~~~~~~~
```
[R/dEploidTools.R:109:1:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:109:38:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                     ^~~~~~~~~~~
```
[R/dEploidTools.R:109:51:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L109) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromTxt <- function ( refFileName, altFileName ){
                                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:110:9:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L110) *style:* **Use <-, not =, for assignment.**
```r
    ref = read.table(refFileName, header = TRUE, comment.char = "")
        ^
```
[R/dEploidTools.R:110:22:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L110) *style:* **Variable and function names should be all lowercase.**
```r
    ref = read.table(refFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~
```
[R/dEploidTools.R:111:9:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L111) *style:* **Use <-, not =, for assignment.**
```r
    alt = read.table(altFileName, header = TRUE, comment.char = "")
        ^
```
[R/dEploidTools.R:111:22:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L111) *style:* **Variable and function names should be all lowercase.**
```r
    alt = read.table(altFileName, header = TRUE, comment.char = "")
                     ^~~~~~~~~~~
```
[R/dEploidTools.R:112:39:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L112) *style:* **Commas should always have a space after.**
```r
    return ( data.frame( CHROM = ref[,1],
                                      ^
```
[R/dEploidTools.R:113:37:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L113) *style:* **Commas should always have a space after.**
```r
                         POS = ref[,2],
                                    ^
```
[R/dEploidTools.R:114:42:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L114) *style:* **Commas should always have a space after.**
```r
                         refCount = ref[,3],
                                         ^
```
[R/dEploidTools.R:115:42:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L115) *style:* **Commas should always have a space after.**
```r
                         altCount = alt[,3] )
                                         ^
```
[R/dEploidTools.R:120:1:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L120) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
^~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:120:34:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L120) *style:* **Variable and function names should be all lowercase.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
                                 ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:120:51:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L120) *style:* **Variable and function names should be all lowercase.**
```r
fun.extract.exclude <- function (excludeFileName, excludeBool){
                                                  ^~~~~~~~~~~
```
[R/dEploidTools.R:121:10:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L121) *style:* **Variable and function names should be all lowercase.**
```r
    if ( excludeBool ) {
         ^~~~~~~~~~~
```
[R/dEploidTools.R:122:39:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L122) *style:* **Variable and function names should be all lowercase.**
```r
        return ( list ( excludeBool = excludeBool,
                                      ^~~~~~~~~~~
```
[R/dEploidTools.R:123:1:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L123) *style:* **lines should not be more than 80 characters.**
```r
                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:123:51:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L123) *style:* **Variable and function names should be all lowercase.**
```r
                        excludeTable = read.table(excludeFileName, header = TRUE, comment.char = "")))
                                                  ^~~~~~~~~~~~~~~
```
[R/dEploidTools.R:125:39:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L125) *style:* **Variable and function names should be all lowercase.**
```r
        return ( list ( excludeBool = excludeBool ))
                                      ^~~~~~~~~~~
```
[R/dEploidTools.R:147:1:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
^~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:147:38:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                     ^~~~~~~
```
[R/dEploidTools.R:147:47:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L147) *style:* **Variable and function names should be all lowercase.**
```r
extractCoverageFromVcf <- function ( vcfName, ADFieldIndex = 2 ){
                                              ^~~~~~~~~~~~
```
[R/dEploidTools.R:150:12:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L150) *style:* **Place a space before left parenthesis, except in a function call.**
```r
         if( any( grepl( "gzfile connection", w) ) )
           ^
```
[R/dEploidTools.R:154:9:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L154) *style:* **Use <-, not =, for assignment.**
```r
    gzf = gzfile(vcfFile, open = "rb")
        ^
```
[R/dEploidTools.R:154:18:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L154) *style:* **Variable and function names should be all lowercase.**
```r
    gzf = gzfile(vcfFile, open = "rb")
                 ^~~~~~~
```
[R/dEploidTools.R:154:18:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L154) *warning:* **no visible binding for global variable ‘vcfFile’**
```r
    gzf = gzfile(vcfFile, open = "rb")
                 ^~~~~~~
```
[R/dEploidTools.R:155:5:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L155) *style:* **Variable and function names should be all lowercase.**
```r
    skipNum = 0
    ^~~~~~~
```
[R/dEploidTools.R:155:13:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L155) *style:* **Use <-, not =, for assignment.**
```r
    skipNum = 0
            ^
```
[R/dEploidTools.R:156:10:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L156) *style:* **Use <-, not =, for assignment.**
```r
    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
         ^
```
[R/dEploidTools.R:156:49:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L156) *style:* **Put spaces around all infix operators.**
```r
    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                               ~^~
```
[R/dEploidTools.R:156:61:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L156) *style:* **Put spaces around all infix operators.**
```r
    line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                           ~^~
```
[R/dEploidTools.R:158:21:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L158) *style:* **Commented code should be removed.**
```r
        if (grepl("##", line )){
                    ^~~~~~~~~~~~
```
[R/dEploidTools.R:159:13:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L159) *style:* **Variable and function names should be all lowercase.**
```r
            skipNum = skipNum+1
            ^~~~~~~
```
[R/dEploidTools.R:159:21:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L159) *style:* **Use <-, not =, for assignment.**
```r
            skipNum = skipNum+1
                    ^
```
[R/dEploidTools.R:159:23:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L159) *style:* **Variable and function names should be all lowercase.**
```r
            skipNum = skipNum+1
                      ^~~~~~~
```
[R/dEploidTools.R:159:30:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L159) *style:* **Put spaces around all infix operators.**
```r
            skipNum = skipNum+1
                            ~^~
```
[R/dEploidTools.R:163:14:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L163) *style:* **Use <-, not =, for assignment.**
```r
        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
             ^
```
[R/dEploidTools.R:163:53:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L163) *style:* **Put spaces around all infix operators.**
```r
        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                   ~^~
```
[R/dEploidTools.R:163:65:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L163) *style:* **Put spaces around all infix operators.**
```r
        line = withCallingHandlers( readLines(gzf, n=1), warning=h)
                                                               ~^~
```
[R/dEploidTools.R:167:1:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L167) *style:* **lines should not be more than 80 characters.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:167:10:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L167) *style:* **Use <-, not =, for assignment.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
         ^
```
[R/dEploidTools.R:167:31:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L167) *style:* **Variable and function names should be all lowercase.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                              ^~~~~~~
```
[R/dEploidTools.R:167:45:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L167) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                           ~^~
```
[R/dEploidTools.R:167:46:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L167) *style:* **Variable and function names should be all lowercase.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                             ^~~~~~~
```
[R/dEploidTools.R:167:61:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L167) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                           ~^~
```
[R/dEploidTools.R:167:77:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L167) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                           ~^~
```
[R/dEploidTools.R:167:119:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L167) *style:* **Put spaces around all infix operators.**
```r
    vcf  = read.table( gzfile(vcfName), skip=skipNum, header=T, comment.char="", stringsAsFactors = FALSE, check.names=FALSE)
                                                                                ~^~
```
[R/dEploidTools.R:169:5:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L169) *style:* **Variable and function names should be all lowercase.**
```r
    sampleName = names(vcf)[10]
    ^~~~~~~~~~
```
[R/dEploidTools.R:169:16:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L169) *style:* **Use <-, not =, for assignment.**
```r
    sampleName = names(vcf)[10]
               ^
```
[R/dEploidTools.R:171:9:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L171) *style:* **Use <-, not =, for assignment.**
```r
    tmp = vcf[[sampleName]]
        ^
```
[R/dEploidTools.R:171:16:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L171) *style:* **Variable and function names should be all lowercase.**
```r
    tmp = vcf[[sampleName]]
               ^~~~~~~~~~
```
[R/dEploidTools.R:172:11:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L172) *style:* **Use <-, not =, for assignment.**
```r
    field = strsplit(as.character(tmp),":")
          ^
```
[R/dEploidTools.R:172:40:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L172) *style:* **Commas should always have a space after.**
```r
    field = strsplit(as.character(tmp),":")
                                       ^
```
[R/dEploidTools.R:174:5:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L174) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~
```
[R/dEploidTools.R:174:15:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L174) *style:* **Use <-, not =, for assignment.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
              ^
```
[R/dEploidTools.R:174:44:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L174) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCovStr = unlist(lapply(field, `[[`, ADFieldIndex))
                                           ^~~~~~~~~~~~
```
[R/dEploidTools.R:175:5:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L175) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
    ^~~~~~
```
[R/dEploidTools.R:175:12:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L175) *style:* **Use <-, not =, for assignment.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
           ^
```
[R/dEploidTools.R:175:36:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L175) *style:* **Variable and function names should be all lowercase.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
                                   ^~~~~~~~~
```
[R/dEploidTools.R:175:47:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L175) *style:* **Commas should always have a space after.**
```r
    tmpCov = strsplit(as.character(tmpCovStr),",")
                                              ^
```
[R/dEploidTools.R:177:5:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L177) *style:* **Variable and function names should be all lowercase.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~
```
[R/dEploidTools.R:177:14:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L177) *style:* **Use <-, not =, for assignment.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
             ^
```
[R/dEploidTools.R:177:41:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L177) *style:* **Variable and function names should be all lowercase.**
```r
    refCount = as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
                                        ^~~~~~
```
[R/dEploidTools.R:178:5:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L178) *style:* **Variable and function names should be all lowercase.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~
```
[R/dEploidTools.R:178:14:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L178) *style:* **Use <-, not =, for assignment.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
             ^
```
[R/dEploidTools.R:178:41:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L178) *style:* **Variable and function names should be all lowercase.**
```r
    altCount = as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
                                        ^~~~~~
```
[R/dEploidTools.R:180:39:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L180) *style:* **Commas should always have a space after.**
```r
    return ( data.frame( CHROM = vcf[,1],
                                      ^
```
[R/dEploidTools.R:181:37:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L181) *style:* **Commas should always have a space after.**
```r
                         POS = vcf[,2],
                                    ^
```
[R/dEploidTools.R:182:37:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L182) *style:* **Variable and function names should be all lowercase.**
```r
                         refCount = refCount,
                                    ^~~~~~~~
```
[R/dEploidTools.R:183:37:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L183) *style:* **Variable and function names should be all lowercase.**
```r
                         altCount = altCount )
                                    ^~~~~~~~
```
[R/dEploidTools.R:204:1:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L204) *style:* **Variable and function names should be all lowercase.**
```r
extractPLAF<- function ( plafName ){
^~~~~~~~~~~
```
[R/dEploidTools.R:204:12:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L204) *style:* **Put spaces around all infix operators.**
```r
extractPLAF<- function ( plafName ){
          ~^
```
[R/dEploidTools.R:204:26:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L204) *style:* **Variable and function names should be all lowercase.**
```r
extractPLAF<- function ( plafName ){
                         ^~~~~~~~
```
[R/dEploidTools.R:205:25:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L205) *style:* **Variable and function names should be all lowercase.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                        ^~~~~~~~
```
[R/dEploidTools.R:205:41:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L205) *style:* **Put spaces around all infix operators.**
```r
    return ( read.table(plafName, header=T)$PLAF )
                                       ~^~
```
[R/dEploidTools.R:210:11:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
         ~^~~
```
[R/dEploidTools.R:210:19:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                 ~^~
```
[R/dEploidTools.R:210:23:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                     ~^~
```
[R/dEploidTools.R:210:24:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L210) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                       ^
```
[R/dEploidTools.R:210:26:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                        ~^~
```
[R/dEploidTools.R:210:28:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L210) *style:* **Put spaces around all infix operators.**
```r
    f.samp<-f.samp+err*(1-2*f.samp);
                          ~^~
```
[R/dEploidTools.R:211:1:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L211) *style:* **lines should not be more than 80 characters.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:211:8:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
      ~^~~
```
[R/dEploidTools.R:211:23:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                     ~^~
```
[R/dEploidTools.R:211:30:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                            ~^~
```
[R/dEploidTools.R:211:43:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                         ~^~
```
[R/dEploidTools.R:211:44:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L211) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                           ^
```
[R/dEploidTools.R:211:46:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                            ~^~
```
[R/dEploidTools.R:211:54:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                    ~^~
```
[R/dEploidTools.R:211:59:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                         ~^~
```
[R/dEploidTools.R:211:72:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                      ~^~
```
[R/dEploidTools.R:211:77:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L211) *style:* **Commas should always have a space after.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                            ^
```
[R/dEploidTools.R:211:77:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L211) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                            ^
```
[R/dEploidTools.R:211:79:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                             ~^~
```
[R/dEploidTools.R:211:87:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L211) *style:* **Put spaces around all infix operators.**
```r
    llk<-lbeta(cov.alt+f.samp*fac, cov.ref+(1-f.samp)*fac)-lbeta(f.samp*fac,(1-f.samp)*fac);
                                                                                ~^~
```
[R/dEploidTools.R:212:1:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L212) *style:* **lines should not be more than 80 characters.**
```r
    #  llk<-lgamma(fac*f.samp+cov.alt)+lgamma(fac*(1-f.samp)+cov.ref)-lgamma(fac*f.samp)-lgamma(fac*(1-f.samp));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:212:8:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L212) *style:* **Commented code should be removed.**
```r
    #  llk<-lgamma(fac*f.samp+cov.alt)+lgamma(fac*(1-f.samp)+cov.ref)-lgamma(fac*f.samp)-lgamma(fac*(1-f.samp));
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:213:25:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L213) *style:* **Put spaces around all infix operators.**
```r
    if (sum(is.nan(llk))>1){
                       ~^~
```
[R/dEploidTools.R:220:1:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L220) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.dic.by.llk.var <- function ( tmpllk ){
^~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:221:1:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L221) *style:* **lines should not be more than 80 characters.**
```r
     return (  mean(-2*tmpllk) + var(-2*tmpllk)/2 )# D_bar + 1/2 var (D_theta), where D_theta = -2*tmpllk, and D_bar = mean(D_theta)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:221:23:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L221) *style:* **Put spaces around all infix operators.**
```r
     return (  mean(-2*tmpllk) + var(-2*tmpllk)/2 )# D_bar + 1/2 var (D_theta), where D_theta = -2*tmpllk, and D_bar = mean(D_theta)
                     ~^~
```
[R/dEploidTools.R:221:40:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L221) *style:* **Put spaces around all infix operators.**
```r
     return (  mean(-2*tmpllk) + var(-2*tmpllk)/2 )# D_bar + 1/2 var (D_theta), where D_theta = -2*tmpllk, and D_bar = mean(D_theta)
                                      ~^~
```
[R/dEploidTools.R:221:48:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L221) *style:* **Put spaces around all infix operators.**
```r
     return (  mean(-2*tmpllk) + var(-2*tmpllk)/2 )# D_bar + 1/2 var (D_theta), where D_theta = -2*tmpllk, and D_bar = mean(D_theta)
                                              ~^~
```
[R/dEploidTools.R:225:1:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L225) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
fun.dic.by.theta <- function ( tmpllk, thetallk ){
^~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:226:5:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L226) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    DIC.WSAF.bar = -2 * sum(thetallk)
    ^~~~~~~~~~~~
```
[R/dEploidTools.R:226:18:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L226) *style:* **Use <-, not =, for assignment.**
```r
    DIC.WSAF.bar = -2 * sum(thetallk)
                 ^
```
[R/dEploidTools.R:227:1:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L227) *style:* **lines should not be more than 80 characters.**
```r
    return (  mean(-2*tmpllk) + (mean(-2*tmpllk) - DIC.WSAF.bar) ) # D_bar + pD, where pD = D_bar - D_theta, and D_bar = mean(D_theta)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/dEploidTools.R:227:22:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L227) *style:* **Put spaces around all infix operators.**
```r
    return (  mean(-2*tmpllk) + (mean(-2*tmpllk) - DIC.WSAF.bar) ) # D_bar + pD, where pD = D_bar - D_theta, and D_bar = mean(D_theta)
                    ~^~
```
[R/dEploidTools.R:227:41:](https://github.com/mcveanlab/DEploid-r/blob/021ff2984e616e9ee7fcd8db111c60f42f2bbbb1/R/dEploidTools.R#L227) *style:* **Put spaces around all infix operators.**
```r
    return (  mean(-2*tmpllk) + (mean(-2*tmpllk) - DIC.WSAF.bar) ) # D_bar + pD, where pD = D_bar - D_theta, and D_bar = mean(D_theta)
                                       ~^~
```


Sorry for breaking the package, but as I wrote, I didn't have time for some tests. Maybe there is a way to let AJAXRenderer.generateBootsFacesAJAXAndJavaScript(context, (ClientBehaviorHolder) navlink, rw); run only the javascript part without the ajax part? The main question still remains, if the response for a "ajax = false" attributed tag is a partial response (which is wrong) or a complete html page (as expected). I'm too busy to solve that bug, maybe it would be better to have one of the main developers to look into that.


Ohh no no not the code, the empty lines between the lines of code. Like line 15, 17, 19


Thanks


@MSF-Jarvis revert it. We dont need it. we already have smooth animation.


@hbashton


→_→噢 是吗.jpg 你不能体会到我pull的感受


Anyone


Oop :)


Salut
Tu vas avoir un soucis par rapport au langue. La plupart des users laissent tout par défaut à l'installation du serveur et ils ont un debian en anglais ^^ Et pareil si c'est un brésilien :D le fr.lang on oublie, du coup ça va planter vu qu'il n'y a pas de L310 sur les autres.

Ce que je te conseille, vu que je ne peux plus avoir les trad dans toute les langues, c'est de mettre le message en anglais par défaut sur tous les autres fichiers .lang pour ton 310 là.

En anglais de bazar google-trad ça nous donne:
Taper le numéro, \n1) pour plex, \n2) pour emby, \n3) pour **ne** rien installer :
Type the number, \n1) for plex, \n2) for emby, \n3) not to install anything :
Ex.


Yep. Initial plan was to make it work first on linux before a port to all OS. However we never managed to spot the issue... It would be also nice to port the core to use C++11 thread construct instead of pthread but it is less important.


Yep. But that method is triggered by the entry script.


kiva (nealkruis) - x86_64-Linux-Ubuntu-14.04-gcc-4.8: OK (1791 of 1791 tests passed, 0 test warnings)

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


Nope, we're sticking with it unless someone has concrete evidence this sucks


This breaks the web interface. Without this call, the content-type is not set properly (xml vs json), which totally messes up the js running in the web pages.


kiva (nealkruis) - 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)


I'm actually redesigning the memory model to get rid of these `Delete`s, everything in the engine will be freed automatically.


pull


Si vous avez des erreurs à la compilation (donc pas exactement la même distribution de latex) je vous envois mes fichiers .cls


i update old install scrip