Last updated on 2024-05-03 08:42:30 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.5 | 5.26 | 59.05 | 64.31 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.3.5 | 79.51 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 0.3.5 | 100.70 | NOTE | |||
| r-devel-windows-x86_64 | 0.3.5 | 6.00 | 81.00 | 87.00 | NOTE | |
| r-patched-linux-x86_64 | 0.3.5 | 4.84 | 56.82 | 61.66 | NOTE | |
| r-release-linux-x86_64 | 0.3.5 | 4.58 | 56.22 | 60.80 | NOTE | |
| r-release-macos-arm64 | 0.3.5 | 34.00 | NOTE | |||
| r-release-windows-x86_64 | 0.3.5 | 5.00 | 76.00 | 81.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.3.5 | 38.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.3.5 | 48.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 0.3.5 | 7.00 | 83.00 | 90.00 | NOTE |
Version: 0.3.5
Check: Rd files
Result: NOTE
checkRd: (-1) parse.extra.Rd:5: Lost braces
5 | \title{Parse the configuration {{var}} format, and replace it by extra.list values}
| ^
checkRd: (-1) parse.extra.Rd:40: Lost braces
40 | Parse the configuration {{var}} format, and replace it by extra.list values
| ^
checkRd: (-1) parse.extra.Rd:21: Lost braces
21 | \item{extra.list}{A list that can replace the configuration file '{{debug}}' by list(debug = TRUE), and {{debug}} will be setted to TRUE}
| ^
checkRd: (-1) parse.extra.Rd:21: Lost braces
21 | \item{extra.list}{A list that can replace the configuration file '{{debug}}' by list(debug = TRUE), and {{debug}} will be setted to TRUE}
| ^
checkRd: (-1) parse.extra.Rd:23: Lost braces
23 | \item{other.config}{Path of another configuration file that can replace the configuration file '{{key:value}}'}
| ^
checkRd: (-1) parse.extra.Rd:29: Lost braces
29 | \item{glue.parse}{Logical wheather parse '!!glue{1:5}' in config to ['1','2','3','4','5'];
| ^
checkRd: (-1) read.config.Rd:25: Lost braces
25 | \item{extra.list}{A list that can replace the configuration file '{{debug}}' by list(debug = 'TRUE'),
| ^
checkRd: (-1) read.config.Rd:26: Lost braces
26 | and {{debug}} will be setted to 'TRUE'}
| ^
checkRd: (-1) read.config.Rd:28: Lost braces
28 | \item{other.config}{Path of another configuration file that can replace the configuration file '{{key:value}}'}
| ^
checkRd: (-1) read.config.Rd:34: Lost braces
34 | \item{glue.parse}{Logical wheather parse '!!glue{1:5}' in config to ['1','2','3','4','5'];
| ^
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-windows-x86_64
Version: 0.3.5
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.3.5
Check: examples
Result: ERROR
Running examples in 'configr-Ex.R' failed
The error most likely occurred in:
> ### Name: fetch.config
> ### Title: Fetch configuration file and generate a merged list
> ### Aliases: fetch.config
>
> ### ** Examples
>
> links <- c(paste0('https://raw.githubusercontent.com/JhuangLab',
+ '/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'),
+ paste0('https://raw.githubusercontent.com/JhuangLab/BioInstaller',
+ '/master/inst/extdata/config/db/db_main.toml'),
+ system.file('extdata', 'config.toml', package = 'configr'))
> x <- fetch.config(links)
trying URL 'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'
Warning in download.file(link, config.download.tmp) :
URL 'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml': status was 'SSL connect error'
Error in download.file(link, config.download.tmp) :
cannot open URL 'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'
Calls: fetch.config -> download.file
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.3.5
Check: tests
Result: ERROR
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(configr)
> library(stringr)
>
>
> test_check("configr")
trying URL 'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 284 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_m_fetch.R:5:3'): fetch.config ──────────────────────────────────
Error in `download.file(link, config.download.tmp)`: cannot open URL 'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'
Backtrace:
▆
1. └─configr::fetch.config(links) at test_m_fetch.R:5:3
2. └─utils::download.file(link, config.download.tmp)
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 284 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.3.5
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'configr.Rmd' using rmarkdown
trying URL 'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'
Quitting from lines at lines 96-101 [unnamed-chunk-8] (configr.Rmd)
Error: processing vignette 'configr.Rmd' failed with diagnostics:
cannot open URL 'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'
--- failed re-building 'configr.Rmd'
--- re-building 'filetypes.Rmd' using rmarkdown
--- finished re-building 'filetypes.Rmd'
SUMMARY: processing the following file failed:
'configr.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-windows-x86_64