advance/TCCIA

[giscus[bot]]

advance/TCCIA

Hiplot (ORG): cloud-based biomedical data visualization system. It is supported and maintained by the openbiox open source community.

https://hiplot.cn/advance/TCCIA

[ShixiangWang]

剑峰，app挂掉了，有空看一下哈。我查不到日志，只能查到一个5月底的日志文件。

[Miachol]

Loading required namespace: usethis
Loading required namespace: devtools
Coco running mode: dev
Coco dev database: /opt/CircleRNADb
ℹ Loading coco
Warning: replacing previous import ‘shinyWidgets::alert’ by ‘shinyjs::alert’ when loading ‘coco’
Warning: replacing previous import ‘shiny::runExample’ by ‘shinyjs::runExample’ when loading ‘coco’
You are using coco version 1.0.0
Cache path: ~/.coco_cache
Cache size: 20 GB

Listening on http://127.0.0.1:39941
Warning in gregexpr(pattern, x, ...) :
PCRE pattern compilation error
'invalid range in character class'
at '-]+)(?= |$)'
Warning: Error in gregexpr: invalid regular expression '(?<=^| ).#(?= |$)'
101: h
100: .handleSimpleError
99: gregexpr
98: match_replace
97: replace
96: FUN
95: lapply
94: match_replace
93: convert_attrs
92: move_attrs
91: markdown::mark
90: includeMarkdown
89: dots_list
88: div
87: list2
86: bootstrapPage
85: fluidPage
84: dots_list
83: div
82: tabPanel_
81: bslib::nav
80: tabPanel
79: list2
78: structure
77: navbarMenu_
76: bslib::nav_menu
75: navbarMenu
74: list2
73: dropNulls
72: buildTabset
71: navbarPage_
70: navs_bar
69: list2
68: shiny::bootstrapPage
67: as_page
66: page
65: bslib::page_navbar
64: remove_first_class
63: navbarPage
62: dots_list
61: tagList
60: ui [/app/coco/R/shiny-app.R#10]
59: ..stacktraceon..
58: force
57: withRestoreContext
56: appObj()$httpHandler
55: handler
54: handler
53: handler
52: handlers$invoke
51: withCallingHandlers
50: domain$wrapSync
49: promises::with_promise_domain
48: captureStackTraces
47: withCallingHandlers
46: withLogErrors
45: withCallingHandlers
44: force
43: withVisible
42: withCallingHandlers
41: domain$wrapSync
40: promises::with_promise_domain
39: captureStackTraces
38: doTryCatch
37: tryCatchOne
36: tryCatchList
35: tryCatch
34: do
33: hybrid_chain
32: force
31: withVisible
30: withCallingHandlers
29: domain$wrapSync
28: promises::with_promise_domain
27: captureStackTraces
26: doTryCatch
25: tryCatchOne
24: tryCatchList
23: tryCatch
22: do
21: hybrid_chain
20: handler
19: func
18: compute
17: doTryCatch
16: tryCatchOne
15: tryCatchList
14: tryCatch
13: rookCall
12:
11: execCallbacks
10: run_now
9: service
8: serviceApp
7: ..stacktracefloor..
6: withCallingHandlers
5: domain$wrapSync
4: promises::with_promise_domain
3: captureStackTraces
2: ..stacktraceoff..
1: runApp

[Miachol]

我测试下看是哪一行的问题

[Miachol]

25，29，37，57，59，67，85，99，113，143，157，171，185，187，191，203，215，227，239，255，269

[ShixiangWang]

就是标题行导致的吧？（rstudio/htmltools#380 (comment)）你看下下面的在服务器运行是否有问题。（我这边的机器都是ok的）

library(htmltools)
 
tmp_path <- tempfile(fileext = ".md")
writeLines(c(
  "## Hello Markdown {#hello}",
  "",
  "Just some regular text here."
), tmp_path)

includeMarkdown(tmp_path) |> print(browse = FALSE)

#<h2 id="hello">Hello Markdown</h2>
#<p>Just some regular text here.</p>

[Miachol]

嗯，出现相同的报错

[Miachol]

源码更新 PCRE2 至最新版本好像就可以了

[Miachol]

https://github.com/PCRE2Project/pcre2/releases/tag/pcre2-10.42

Centos 7 源码编译更新 PCRE2 10.23 => 10.42，可修复 includeMarkdown 函数的 PCRE pattern compilation error 错误

[ShixiangWang]

@Miachol 剑峰，有个事情很奇怪，https://shiny.hiplot.cn/TCCIA/ 里 repo 页面少了 4个cohort （相比 http://biotrainee.vip:18888/TCCIA/ ），比如EGAD00001008549（之前是有的），你有空的时候check下哈。