CRAN Package Check Results for Package EpiSignalDetection

Last updated on 2020-04-25 01:53:01 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1.1 4.49 42.67 47.16 OK
r-devel-linux-x86_64-debian-gcc 0.1.1 3.97 33.98 37.95 OK
r-devel-linux-x86_64-fedora-clang 0.1.1 57.16 NOTE
r-devel-linux-x86_64-fedora-gcc 0.1.1 56.82 NOTE
r-devel-windows-ix86+x86_64 0.1.1 15.00 77.00 92.00 OK
r-patched-linux-x86_64 0.1.1 3.38 41.27 44.65 OK
r-patched-osx-x86_64 0.1.1 ERROR
r-patched-solaris-x86 0.1.1 82.00 ERROR
r-release-linux-x86_64 0.1.1 4.14 37.81 41.95 OK
r-release-windows-ix86+x86_64 0.1.1 12.00 73.00 85.00 OK
r-release-osx-x86_64 0.1.1 ERROR
r-oldrel-windows-ix86+x86_64 0.1.1 7.00 61.00 68.00 OK
r-oldrel-osx-x86_64 0.1.1 ERROR

Check Details

Version: 0.1.1
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘DT’ ‘ggplot2’ ‘knitr’ ‘pander’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-osx-x86_64, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.1.1
Check: examples
Result: ERROR
    Running examples in ‘EpiSignalDetection-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: runEpiSDReport
    > ### Title: Run the EpiSignalDetection report (HTML markdown)
    > ### Aliases: runEpiSDReport
    >
    > ### ** Examples
    >
    > #---> OR
    >
    > #-- First setting the parameters to run the report for
    > input <- list(
    + disease = "Salmonellosis",
    + country = "Portugal",
    + indicator = "Reported cases",
    + stratification = "Confirmed cases",
    + unit = "Month",
    + daterange = c("2011-01-01", "2016-12-31"),
    + algo = "FarringtonFlexible",
    + testingperiod = 6
    + )
    >
    > #-- Second running the report based on the EpiSignalDetection::SignalData dataset
    > #-- and store it in a temporary folder
    > runEpiSDReport(input = input)
    
    
    processing file: SignalDetectionReport.Rmd
     inline R code fragments
    
    label: Config (with options)
    List of 4
     $ echo : logi FALSE
     $ results: chr "hide"
     $ warning: logi FALSE
     $ message: logi FALSE
    
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
     ordinary text without R code
    
    label: Parameters
     ordinary text without R code
    
    label: StudyPeriod
     ordinary text without R code
    
    label: Gaps
     inline R code fragments
    
    label: GraphByReportingCountries
     inline R code fragments
    
    label: LoopByCountry (with options)
    List of 2
     $ results : chr "hide"
     $ fig.show: chr "hide"
    
     inline R code fragments
    
    label: AlarmTable (with options)
    List of 1
     $ results: chr "hide"
    
    
    
    processing file: ./subsection.Rmd
     inline R code fragments
    
    output file: SignalDetectionReport.knit.md
    
    /usr/local/bin/pandoc +RTS -K512m -RTS SignalDetectionReport.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output /var/folders/08/nc4f1s3x1jqd9ln5mnvrqzqh0000gp/T//RtmpaMEH2B/SignalDetectionReport.html --email-obfuscation none --self-contained --standalone --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --number-sections --css style.css --variable 'theme:united' --include-in-header /var/folders/08/nc4f1s3x1jqd9ln5mnvrqzqh0000gp/T//RtmpaMEH2B/rmarkdown-str1111e1d6d5806.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/rmarkdown/rmd/lua/latex-div.lua
    dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    dyld: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    Error: pandoc document conversion failed with error 6
    Execution halted
Flavor: r-patched-osx-x86_64

Version: 0.1.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘EpiSignalDetection_Vignette.Rmd’ using rmarkdown
    dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    dyld: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    Error: processing vignette 'EpiSignalDetection_Vignette.Rmd' failed with diagnostics:
    pandoc document conversion failed with error 6
    --- failed re-building ‘EpiSignalDetection_Vignette.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘EpiSignalDetection_Vignette.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-osx-x86_64

Version: 0.1.1
Check: examples
Result: ERROR
    Running examples in ‘EpiSignalDetection-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: runEpiSDReport
    > ### Title: Run the EpiSignalDetection report (HTML markdown)
    > ### Aliases: runEpiSDReport
    >
    > ### ** Examples
    >
    > #---> OR
    >
    > #-- First setting the parameters to run the report for
    > input <- list(
    + disease = "Salmonellosis",
    + country = "Portugal",
    + indicator = "Reported cases",
    + stratification = "Confirmed cases",
    + unit = "Month",
    + daterange = c("2011-01-01", "2016-12-31"),
    + algo = "FarringtonFlexible",
    + testingperiod = 6
    + )
    >
    > #-- Second running the report based on the EpiSignalDetection::SignalData dataset
    > #-- and store it in a temporary folder
    > runEpiSDReport(input = input)
    Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
    Execution halted
Flavors: r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64