Last updated on 2025-12-07 07:50:44 CET.
| Package | ERROR | OK |
|---|---|---|
| nbTransmission | 1 | 12 |
Current CRAN status: ERROR: 1, OK: 12
Version: 1.2.0
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'Hmisc', 'knitr', 'rmarkdown'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.0
Check: examples
Result: ERROR
Running examples in ‘nbTransmission-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotRt
> ### Title: Creates a plot of the effective reproductive number
> ### Aliases: plotRt
>
> ### ** Examples
>
>
> ## Use the nbResults data frame included in the package which has the results
> # of the nbProbabilities() function on a TB-like outbreak.
>
> ## Getting initial estimates of the reproductive number
> # (without specifying nbResults and without confidence intervals)
> rInitial <- estimateR(nbResults, dateVar = "infectionDate",
+ indIDVar = "individualID", pVar = "pScaled",
+ timeFrame = "months")
Please choose the stable portion of the outbreak to calculate the average Rt
>
> ## Finding the stable portion of the outbreak for rangeForAvg using the plot
> plotRt(rInitial)
Error in loadNamespace(x) : there is no package called ‘Hmisc’
Calls: plotRt ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [19s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(nbTransmission)
>
> test_check("nbTransmission")
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|=================================== | 50%
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|=================================== | 50%
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|======================================================================| 100%Saving _problems/test_visualizeResults-225.R
Saving _problems/test_visualizeResults-228.R
Saving _problems/test_visualizeResults-231.R
[ FAIL 3 | WARN 2 | SKIP 1 | PASS 130 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• {Hmisc} is not installed. (1): 'test_visualizeResults.R:197:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_visualizeResults.R:224:3'): Descriptive error messages returned for plotRt ──
`plotRt(rFinal2, includeRtAvgCI = TRUE)` threw an error with unexpected message.
Expected match: "Please provide a rData list that has confidence intervals"
Actual message: "there is no package called 'Hmisc'"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test_visualizeResults.R:224:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. ├─nbTransmission::plotRt(rFinal2, includeRtAvgCI = TRUE)
7. │ └─base::gsub("s$", "", Hmisc::capitalize(rData$timeFrame))
8. │ └─base::is.factor(x)
9. └─base::loadNamespace(x)
10. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
11. └─base (local) withOneRestart(expr, restarts[[1L]])
12. └─base (local) doWithOneRestart(return(expr), restart)
── Failure ('test_visualizeResults.R:227:3'): Descriptive error messages returned for plotRt ──
`plotRt(rFinal2, includeRtCI = TRUE)` threw an error with unexpected message.
Expected match: "Please provide a rData list that has confidence intervals"
Actual message: "there is no package called 'Hmisc'"
Backtrace:
▆
1. ├─testthat::expect_error(plotRt(rFinal2, includeRtCI = TRUE), "Please provide a rData list that has confidence intervals") at test_visualizeResults.R:227:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. ├─nbTransmission::plotRt(rFinal2, includeRtCI = TRUE)
7. │ └─base::gsub("s$", "", Hmisc::capitalize(rData$timeFrame))
8. │ └─base::is.factor(x)
9. └─base::loadNamespace(x)
10. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
11. └─base (local) withOneRestart(expr, restarts[[1L]])
12. └─base (local) doWithOneRestart(return(expr), restart)
── Failure ('test_visualizeResults.R:230:3'): Descriptive error messages returned for plotRt ──
`plotRt(rFinal2, includeRtCI = TRUE, includeRtAvgCI = TRUE)` threw an error with unexpected message.
Expected match: "Please provide a rData list that has confidence intervals"
Actual message: "there is no package called 'Hmisc'"
Backtrace:
▆
1. ├─testthat::expect_error(...) at test_visualizeResults.R:230:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. ├─nbTransmission::plotRt(rFinal2, includeRtCI = TRUE, includeRtAvgCI = TRUE)
7. │ └─base::gsub("s$", "", Hmisc::capitalize(rData$timeFrame))
8. │ └─base::is.factor(x)
9. └─base::loadNamespace(x)
10. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
11. └─base (local) withOneRestart(expr, restarts[[1L]])
12. └─base (local) doWithOneRestart(return(expr), restart)
[ FAIL 3 | WARN 2 | SKIP 1 | PASS 130 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.0
Check: package vignettes
Result: NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Flavor: r-devel-linux-x86_64-debian-gcc