Bump deps

.Rbuildignore

@@ -19,3 +19,6 @@
 ^\.prettierrc.json$
 ^\.prettierignore$
 ^CONTRIBUTING\.md$
+^.eslintrc.cjs
+^PUBLISHING.md
+^tsconfig.json

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: JBrowseR
 Title: An R Interface to the JBrowse 2 Genome Browser
-Version: 0.10.1
+Version: 0.10.2
 Authors@R: 
  c(person(given = "Elliot",
  family = "Hershberg",

NEWS.md

@@ -1,3 +1,8 @@
+# JBrowseR 0.10.2
+
+- Updated to @jbrowse/react-linear-genome-view@2.10.0
+- Adds support for lzma cram
+
 # JBrowseR 0.10.1
 
 - Updated to @jbrowse/react-linear-genome-view@2.6.2

R/alignments.R

@@ -22,7 +22,7 @@
 #' @param track_data the URL to the BAM/CRAM alignments
 #' @param assembly the config string generated by \code{assembly}
 #'
-#' @return a character vector of stringified AlignmentTrack JSON configuration
+#' @return a character vector of stringified AlignmentsTrack JSON configuration
 #'
 #' @export
 #'

R/assembly.R

@@ -29,7 +29,7 @@
 #' and bgzip.
 #'
 #' For more information on creating these files, visit
-#' \url{https://jbrowse.org/jb2/docs/quickstart_cli#adding-a-genome-assembly}
+#' \url{https://jbrowse.org/jb2/docs/quickstart_web#adding-a-genome-assembly}
 #'
 #' @param assembly_data the URL to your fasta file
 #' @param bgzip whether or not your fasta is bgzip compressed

cran-comments.md

@@ -1,3 +1,27 @@
-## R CMD check results
+From Uwe:
 
-0 errors | 0 warnings | 0 notes
+```
+Thanks, we see:
+
+
+ Found the following (possibly) invalid URLs:
+ URL: https://jbrowse.org/jb2/docs/quickset_web
+ From: inst/doc/json-tutorial.html
+ Status: 404
+ Message: Not Found
+ URL: https://jbrowse.org/jb2/docs/quickset_web#adding-a-genome-assembly
+ From: man/assembly.Rd
+ Status: 404
+ Message: Not Found
+ URL: https://jbrowse.org/jb2/docs/quickset_web/
+ From: inst/doc/custom-browser-tutorial.html
+ Status: 404
+ Message: Not Found
+
+Please fix and resubmit.
+
+Best,
+
+```
+
+thanks this was an oversight, fixed!

vignettes/custom-browser-tutorial.Rmd

@@ -24,7 +24,7 @@ While all of these values are possible, the only required configuration is an as
 
 ## Preparing an assembly
 
-The steps for preparing an assembly for use in the browser can be found in the [JBrowse 2 docs](https://jbrowse.org/jb2/docs/quickstart_cli/), but we will cover them again here.
+The steps for preparing an assembly for use in the browser can be found in the [JBrowse 2 docs](https://jbrowse.org/jb2/docs/quickstart_web/), but we will cover them again here.
 In order to be used, an assembly must first be indexed.
 We will be using the Sars-CoV-2 genome for this tutorial.
 

vignettes/json-tutorial.Rmd

@@ -97,7 +97,7 @@ Here are some great resources for learning more about JBrowse 2 configuration:
 
 - [JBrowse 2 config guide](https://jbrowse.org/jb2/docs/config_guide)
 - [JBrowse 2 React component example](https://github.com/GMOD/jbrowse-components/blob/master/products/jbrowse-react-linear-genome-view/docs/example.md)
-- [JBrowse 2 CLI quickstart](https://jbrowse.org/jb2/docs/quickstart_cli)
+- [JBrowse 2 CLI quickstart](https://jbrowse.org/jb2/docs/quickstart_web)
 - [JBrowse 2 graphical config editing quickstart](https://jbrowse.org/jb2/docs/tutorials/config_gui/)
 - [JBrowse 2 test data](https://github.com/GMOD/jbrowse-components/tree/master/test_data)
 

yarn.lock

@@ -1660,78 +1660,78 @@
  resolved "https://registry.yarnpkg.com/@librpc/ee/-/ee-1.0.4.tgz#ce73a36279dc4cf93efa43f7e3564ec165947522"
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-"@mui/base@5.0.0-beta.27":
- version "5.0.0-beta.27"
- resolved "https://registry.yarnpkg.com/@mui/base/-/base-5.0.0-beta.27.tgz#21a9c7d954a5f88f6706dfee630154c651ee73af"
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+"@mui/base@5.0.0-beta.28":
+ version "5.0.0-beta.28"
+ resolved "https://registry.yarnpkg.com/@mui/base/-/base-5.0.0-beta.28.tgz#f072e55c0530f456ee5cb5cde2af788fdda3bf05"
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  dependencies:
  "@babel/runtime" "^7.23.5"
  "@floating-ui/react-dom" "^2.0.4"
  "@mui/types" "^7.2.11"
- "@mui/utils" "^5.15.0"
+ "@mui/utils" "^5.15.1"
  "@popperjs/core" "^2.11.8"
  clsx "^2.0.0"
  prop-types "^15.8.1"
 
-"@mui/core-downloads-tracker@^5.15.0":
- version "5.15.0"
- resolved "https://registry.yarnpkg.com/@mui/core-downloads-tracker/-/core-downloads-tracker-5.15.0.tgz#6b45d5bff38f305402d24d3bf86075b56c578909"
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+"@mui/core-downloads-tracker@^5.15.1":
+ version "5.15.1"
+ resolved "https://registry.yarnpkg.com/@mui/core-downloads-tracker/-/core-downloads-tracker-5.15.1.tgz#8aad47e2b198640244f05f6486a927ce362e814e"
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- resolved "https://registry.yarnpkg.com/@mui/icons-material/-/icons-material-5.15.0.tgz#fdc93611ca77ce3b79128be02fb6c1ae79b972b8"
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+ version "5.15.1"
+ resolved "https://registry.yarnpkg.com/@mui/icons-material/-/icons-material-5.15.1.tgz#38f51a88d224a107e753313b4d9815247caa5398"
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  dependencies:
  "@babel/runtime" "^7.23.5"
 
 "@mui/material@^5.0.0", "@mui/material@^5.10.17":
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- resolved "https://registry.yarnpkg.com/@mui/material/-/material-5.15.0.tgz#f801cf56d505cc52dca225438360ab9c62057285"
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+ version "5.15.1"
+ resolved "https://registry.yarnpkg.com/@mui/material/-/material-5.15.1.tgz#5fc15c6eb9efe4b62b0c30b13bf5fa042bda71a1"
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  dependencies:
  "@babel/runtime" "^7.23.5"
- "@mui/base" "5.0.0-beta.27"
- "@mui/core-downloads-tracker" "^5.15.0"
- "@mui/system" "^5.15.0"
+ "@mui/base" "5.0.0-beta.28"
+ "@mui/core-downloads-tracker" "^5.15.1"
+ "@mui/system" "^5.15.1"
  "@mui/types" "^7.2.11"
- "@mui/utils" "^5.15.0"
- "@types/react-transition-group" "^4.4.9"
+ "@mui/utils" "^5.15.1"
+ "@types/react-transition-group" "^4.4.10"
  clsx "^2.0.0"
  csstype "^3.1.2"
  prop-types "^15.8.1"
  react-is "^18.2.0"
  react-transition-group "^4.4.5"
 
-"@mui/private-theming@^5.15.0":
- version "5.15.0"
- resolved "https://registry.yarnpkg.com/@mui/private-theming/-/private-theming-5.15.0.tgz#96de66ce097ba417e1b6b769cd67cbf516bd8876"
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+"@mui/private-theming@^5.15.1":
+ version "5.15.1"
+ resolved "https://registry.yarnpkg.com/@mui/private-theming/-/private-theming-5.15.1.tgz#58fd8da48295e105067fa7361734ee0b166d9cca"
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  dependencies:
  "@babel/runtime" "^7.23.5"
- "@mui/utils" "^5.15.0"
+ "@mui/utils" "^5.15.1"
  prop-types "^15.8.1"
 
-"@mui/styled-engine@^5.15.0":
- version "5.15.0"
- resolved "https://registry.yarnpkg.com/@mui/styled-engine/-/styled-engine-5.15.0.tgz#44e068dbb855699053b9e6e4e6d3ed5efe98b7d9"
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+"@mui/styled-engine@^5.15.1":
+ version "5.15.1"
+ resolved "https://registry.yarnpkg.com/@mui/styled-engine/-/styled-engine-5.15.1.tgz#00f179e51afe252022bf356f72354968f9c5bf25"
+ integrity sha512-7WDZTJLqGexWDjqE9oAgjU8ak6hEtUw2yQU7SIYID5kLVO2Nj/Wi/KicbLsXnTsJNvSqePIlUIWTBSXwWJCPZw==
  dependencies:
  "@babel/runtime" "^7.23.5"
  "@emotion/cache" "^11.11.0"
  csstype "^3.1.2"
  prop-types "^15.8.1"
 
-"@mui/system@^5.15.0":
- version "5.15.0"
- resolved "https://registry.yarnpkg.com/@mui/system/-/system-5.15.0.tgz#d4f6fd65ad8e404d4d7c7b56d755d2a63b0edddb"
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+"@mui/system@^5.15.1":
+ version "5.15.1"
+ resolved "https://registry.yarnpkg.com/@mui/system/-/system-5.15.1.tgz#e2a79b5e188ca89a3e58aa4d27e3484edf9e24b0"
+ integrity sha512-LAnP0ls69rqW9eBgI29phIx/lppv+WDGI7b3EJN7VZIqw0RezA0GD7NRpV12BgEYJABEii6z5Q9B5tg7dsX0Iw==
  dependencies:
  "@babel/runtime" "^7.23.5"
- "@mui/private-theming" "^5.15.0"
- "@mui/styled-engine" "^5.15.0"
+ "@mui/private-theming" "^5.15.1"
+ "@mui/styled-engine" "^5.15.1"
  "@mui/types" "^7.2.11"
- "@mui/utils" "^5.15.0"
+ "@mui/utils" "^5.15.1"
  clsx "^2.0.0"
  csstype "^3.1.2"
  prop-types "^15.8.1"
@@ -1741,10 +1741,10 @@
  resolved "https://registry.yarnpkg.com/@mui/types/-/types-7.2.11.tgz#36b99a88f8010dc716128e568dc05681a69dc7ae"
  integrity sha512-KWe/QTEsFFlFSH+qRYf3zoFEj3z67s+qAuSnMMg+gFwbxG7P96Hm6g300inQL1Wy///gSRb8juX7Wafvp93m3w==
 
-"@mui/utils@^5.14.16", "@mui/utils@^5.15.0":
- version "5.15.0"
- resolved "https://registry.yarnpkg.com/@mui/utils/-/utils-5.15.0.tgz#87b4db92dd2ddf3e2676377427f50662124013b4"
- integrity sha512-XSmTKStpKYamewxyJ256+srwEnsT3/6eNo6G7+WC1tj2Iq9GfUJ/6yUoB7YXjOD2jTZ3XobToZm4pVz1LBt6GA==
+"@mui/utils@^5.14.16", "@mui/utils@^5.15.1":
+ version "5.15.1"
+ resolved "https://registry.yarnpkg.com/@mui/utils/-/utils-5.15.1.tgz#71d69dc8c0f13a1fd6aca20b53ec496636e6b854"
+ integrity sha512-V1/d0E3Bju5YdB59HJf2G0tnHrFEvWLN+f8hAXp9+JSNy/LC2zKyqUfPPahflR6qsI681P8G9r4mEZte/SrrYA==
  dependencies:
  "@babel/runtime" "^7.23.5"
  "@types/prop-types" "^15.7.11"
@@ -1802,9 +1802,9 @@
  "@types/estree" "*"
 
 "@types/eslint@*":
- version "8.44.9"
- resolved "https://registry.yarnpkg.com/@types/eslint/-/eslint-8.44.9.tgz#5799663009645637bd1c45b2e1a7c8f4caf89534"
- integrity sha512-6yBxcvwnnYoYT1Uk2d+jvIfsuP4mb2EdIxFnrPABj5a/838qe5bGkNLFOiipX4ULQ7XVQvTxOh7jO+BTAiqsEw==
+ version "8.56.0"
+ resolved "https://registry.yarnpkg.com/@types/eslint/-/eslint-8.56.0.tgz#e28d045b8e530a33c9cbcfbf02332df0d1380a2c"
+ integrity sha512-FlsN0p4FhuYRjIxpbdXovvHQhtlG05O1GG/RNWvdAxTboR438IOTwmrY/vLA+Xfgg06BTkP045M3vpFwTMv1dg==
  dependencies:
  "@types/estree" "*"
  "@types/json-schema" "*"
@@ -1851,7 +1851,7 @@
  resolved "https://registry.yarnpkg.com/@types/prop-types/-/prop-types-15.7.11.tgz#2596fb352ee96a1379c657734d4b913a613ad563"
  integrity sha512-ga8y9v9uyeiLdpKddhxYQkxNDrfvuPrlFb0N1qnZZByvcElJaXthF1UhvCh9TLWJBEHeNtdnbysW7Y6Uq8CVng==
 
-"@types/react-transition-group@^4.4.9":
+"@types/react-transition-group@^4.4.10":
  version "4.4.10"
  resolved "https://registry.yarnpkg.com/@types/react-transition-group/-/react-transition-group-4.4.10.tgz#6ee71127bdab1f18f11ad8fb3322c6da27c327ac"
  integrity sha512-hT/+s0VQs2ojCX823m60m5f0sL5idt9SO6Tj6Dg+rdphGPIeJbJ6CxvBYkgkGKrYeDjvIpKTR38UzmtHJOGW3Q==
@@ -2933,9 +2933,9 @@ dompurify@^3.0.0:
  integrity sha512-ilkD8YEnnGh1zJ240uJsW7AzE+2qpbOUYjacomn3AvJ6J4JhKGSZ2nh4wUIXPZrEPppaCLx5jFe8T89Rk8tQ7w==
 
 electron-to-chromium@^1.4.601:
- version "1.4.614"
- resolved "https://registry.yarnpkg.com/electron-to-chromium/-/electron-to-chromium-1.4.614.tgz#2fe789d61fa09cb875569f37c309d0c2701f91c0"
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+ version "1.4.615"
+ resolved "https://registry.yarnpkg.com/electron-to-chromium/-/electron-to-chromium-1.4.615.tgz#b1c41839962d2e4e63dca05519da9040e34848c2"
+ integrity sha512-/bKPPcgZVUziECqDc+0HkT87+0zhaWSZHNXqF8FLd2lQcptpmUFwoCSWjCdOng9Gdq+afKArPdEg/0ZW461Eng==
 
 elliptic@^6.5.3, elliptic@^6.5.4:
  version "6.5.4"