Last updated on 2023-12-02 01:51:29 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.0.1 | 22.59 | 167.69 | 190.28 | OK | |
| r-devel-linux-x86_64-debian-gcc | 3.0.1 | 19.10 | 122.49 | 141.59 | OK | |
| r-devel-linux-x86_64-fedora-clang | 3.0.1 | 246.25 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 3.0.1 | 235.77 | OK | |||
| r-devel-windows-x86_64 | 3.0.1 | 19.00 | 140.00 | 159.00 | OK | |
| r-patched-linux-x86_64 | 3.0.1 | 17.83 | 159.48 | 177.31 | OK | |
| r-release-linux-x86_64 | 3.0.1 | 14.34 | 154.49 | 168.83 | OK | |
| r-release-macos-arm64 | 3.0.1 | 70.00 | OK | |||
| r-release-macos-x86_64 | 3.0.1 | 139.00 | OK | |||
| r-release-windows-x86_64 | 3.0.1 | 27.00 | 175.00 | 202.00 | OK | |
| r-oldrel-macos-arm64 | 3.0.1 | 63.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 3.0.0 | 86.00 | OK | |||
| r-oldrel-windows-x86_64 | 3.0.1 | 26.00 | 166.00 | 192.00 | ERROR |
Version: 3.0.1
Check: examples
Result: ERROR
Running examples in ‘micromapST-Ex.R’ failed
The error most likely occurred in:
> ### Name: micromapST
> ### Title: Linked Micromap Graphics Package
> ### Aliases: micromapST micromapST.Version
>
> ### ** Examples
>
>
> ###
> #
> # micromapST - Example # 01 - map with no cumulative shading,
> # 2 columns of statistics: dot with 95% confidence interval,
> # boxplot sorted in descending order by state rates, using
> # the default border group of "USStatesBG", with default symbols.
> ###
>
> # load sample data, compute boxplot
> TDir<-"c:/projects/statnet/" # my private test PDF directory exist, don't use temp.
> if (!dir.exists(TDir)) {TDir <- paste0(tempdir(),"/") } # get a temp directory for the output
> # PDF files for the example.
> cat("TempDir:",TDir,"\n")
TempDir: /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpuvQ1T8/
>
> # replace this directory name with the location if you want to same
> # the output from the examples.
>
> utils::data(wflung00and95,wflung00and95US,wflung00cnty,envir=environment())
>
> wfboxlist = graphics::boxplot(split(wflung00cnty$rate,wflung00cnty$stabr),
+ plot=FALSE)
>
> # set up 4 column page layout
>
> panelDesc01 <- data.frame(
+ type=c("map","id","dotconf","boxplot"),
+ lab1=c("","","State Rate","County Rates"),
+ lab2=c("","","and 95% CI","(suppressed if 1-9 deaths)"),
+ lab3=c("","","Deaths per 100,000","Deaths per 100,000"),
+ col1=c(NA,NA,1,NA),col2=c(NA,NA,3,NA),col3=c(NA,NA,4,NA),
+ refVals=c(NA,NA,NA,wflung00and95US[1,1]),
+ refTexts=c(NA,NA,NA,"US Rate 2000-4"),
+ panelData= c("","","","wfboxlist")
+ )
> panelDesc <- panelDesc01
> # set up PDF output file, call package
>
> ExTitle <- c("Ex01-US White Female Lung Cancer Mortality, 2000-2004",
+ "State Rates & County Boxplots")
>
> grDevices::pdf(file=paste0(TDir,"Ex01-US-WFLung-2000-2004-St-DotCf-Co-Box.pdf"),
+ width=7.5,height=10)
>
> micromapST(wflung00and95, panelDesc01, sortVar=1, ascend=FALSE,
+ title=ExTitle
+ )
statsDFrame = wflung00and95
panelDesc = panelDesc01
End of micromapST processing.
No warnings were logged.
No stop messages were logged.
>
> x <- grDevices::dev.off()
> #
> ### End Example 01
>
> ###
> #
> # micromapST - Example # 02 - map with cumulative shading
> # from top down (mapcum), arrow and bar charts,
> # sorted in descending order by starting
> # value of arrows (1950-69 rates) using default
> # border group of "USStatesDF". This
> # example also provides custom colors for the
> # linked micromaps, highlights, etc.
> #
> ###
>
> # Load example data from package.
> utils::data(wmlung5070,wmlung5070US,envir=environment())
>
> panelDesc02 <- data.frame(
+ type=c("mapcum","id","arrow","bar"),
+ lab1=c("","","Rates in","Percent Change"),
+ lab2=c("","","1950-69 and 1970-94","1950-69 To 1970-94"),
+ lab3=c("MAPCUM","","Deaths per 100,000","Percent"),
+ col1=c(NA,NA,"RATEWM_50","PERCENT"),
+ col2=c(NA,NA,"RATEWM_70",NA)
+ )
>
> colorsRgb = matrix(c( # the basic 7 colors.
+ 213, 62, 79, #region 1: red #D53E4F - Rust Red
+ 252, 141, 89, #region 2: orange #FC8D59 - Brn/Org
+ 253, 225, 139, #region 3: green #FEE08B - Pale Brn
+ 153, 213, 148, #region 4: greenish blue #99D594 - med Green
+ 50, 136, 189, #region 5: lavendar #3288BD - Blue
+ 255, 0, 255, #region 6 #FF00FF - Magenta
+ .00, .00, .00, #region 7: black for median #000000 - Black
+ 230, 245, 152, #non-highlighted foreground #E6F598 - YellowGreen
+ 255, 174, 185, # alternate shape upper #FFAEB9 - Mauve
+ 191, 239, 255, # alternate shape lower #BFEFFF - Cyan
+ 242, 242, 242, # lightest grey for non-referenced sub-areas #F2F2F2
+ 234, 234, 234), # lighter grey for bkg - non-active sub-areas. #EAEAEA
+
+ ncol=3,byrow=TRUE)
>
> xcolors = c( grDevices::rgb(colorsRgb[,1],colorsRgb[,2],colorsRgb[,3],
+ maxColorValue=255),
+ # set solid colors
+ grDevices::rgb(colorsRgb[,1],colorsRgb[,2],colorsRgb[,3],64,
+ maxColorValue=255))
> # set translucent colors for time series.
>
> # set up reference names for color set
> names(xcolors) =c("rustred","orange","lightbrown","mediumgreen",
+ "blue","magenta", "black","yellowgreen",
+ "mauve","cyan","lightest grey","lighter grey",
+ "l_rustred","l_orange","vlightbrown","lightgreen",
+ "lightblue","l_black","l_yelgreen","l_mauve",
+ "l_cyan","l_lightest grey","l_lighter grey")
>
> ExTitle <- c("Ex02-US Change in White Male Lung Cancer Mortality Rates",
+ "from 1950-69 to 1970-94-Diff colors")
>
> grDevices::pdf(file=paste0(TDir,"Ex02-US WmLung50-70-Arrow-Bar.pdf"),width=7.5,height=10)
>
> micromapST(wmlung5070,panelDesc02,sortVar=1,ascend=FALSE,
+ title=ExTitle, colors=xcolors
+ )
statsDFrame = wmlung5070
panelDesc = panelDesc02
End of micromapST processing.
No warnings were logged.
No stop messages were logged.
>
> x <- grDevices::dev.off()
> #
> ### End Example 02
>
> ## Not run:
> ##D ###
> ##D #
> ##D # micromapST - Example # 03 - Time Series Line Plots with
> ##D # Confidence Bands maptail option highlights states from extremes
> ##D # to middle state read in time series data set example using the
> ##D # default border group of "USStatesDF".
> ##D #
> ##D ###
> ##D
> ##D # Load example data from package.
> ##D utils::data(TSdata,envir=environment())
> ##D temprates <- data.frame(TSdata[,,2])
> ##D
> ##D # TSdata structure is array of size c(51,15,4),
> ##D # dimensions = 51 states, 15 years, (year label, point value, low limit,
> ##D # high limit)
> ##D
> ##D panelDesc03 <- data.frame(
> ##D type=c("maptail","id","tsconf","dot"),
> ##D lab1=c("","","Time Series","Female"),
> ##D lab2=c("","","Annual Rate per 100,000","Most Recent Rate (2010)"),
> ##D lab3=c("","","Years","Deaths per 100,000"),
> ##D lab4=c("","","Rate",""),
> ##D col1=c(NA,NA,NA,15),
> ##D panelData =c(NA,NA,"TSdata",NA)
> ##D )
> ##D ExTitle <- c("Ex03-US Time Series with Confidence bands",
> ##D "Annual Female Lung Cancer Mortality Rates, 1996-2010")
> ##D
> ##D grDevices::pdf(file=paste0(TDir,"Ex03-US Time-Series-with-Conf.pdf"),
> ##D width=7.5,height=10)
> ##D
> ##D micromapST(temprates,panelDesc03,sortVar="P15",ascend=FALSE,
> ##D title=ExTitle)
> ##D
> ##D x <- grDevices::dev.off()
> ##D #
> ##D ### End Example 03
> ## End(Not run)
>
> ###
> #
> # micromapST - Example # 03a - Time Series Line Plots with
> # Confidence Bands maptail option highlights states from extremes
> # to middle state read in time series data set example using the
> # default border group of "USStatesDF".
> #
> # Specify the x-Axis values are dates and to format them as dates.
> ###
>
> # Load example data from package.
> utils::data(TSdata,envir=environment())
> temprates <- data.frame(TSdata[,,2]) # y rate
>
> # In the original package TS data, the x data was not
> # a date value, it was the year number. To be able to demonstrate
> # the X-Axis Date format labeling, these were changed to Date values
> # by effectively substracting 1970-1-1 from the year value.
>
> ####
> #
> # Example 3a - Building TS conf array and converting years
> # into date values for the X-Axis and labels.
> #
> # example of build a TS Conf array.
> #
> # Using the old TSdata array as a starting point and source of data,
> # but build an entirely new TS array structure in a similar manner
> # that might be used to build your own time series array.
> #
>
> data(TSdata) # get old array
> TSAreas <- row.names(TSdata) # one per area (index 1)
> NewArray <- array(dim=c(51,15,4),dimnames=list(TSAreas))
> # this is for 51 states, 15 samples/observations, and 4 values per sample.
>
> for (inx in seq(1,length(TSAreas))) { # loop once per area
+
+ Samp <- TSdata[inx,,] # samples for an area
+ # each sample has 15 observations of 4 values.
+ # value 1 is the X axis data or the DATE of the observation
+ Samp[,1] <- as.Date(paste0(as.character(Samp[,1]),"-01-01"))
+ # convert simple year number to date
+ NewArray[inx,,] <- Samp
+
+ }
>
> # setting the attribute "xIsDate" on array to TRUE, signals micromapST
> # the user wants to see the x-axis values as dates.
>
> attr(NewArray,"xIsDate") <- TRUE
>
> # TSdata and NewArray structures are arrays of size c(51,15,4),
> # dimensions = 51 states, 15 years, (year label, point value, low limit, high limit)
>
> panelDesc03a <- data.frame(
+ type=c("maptail","id","tsconf","dot"),
+ lab1=c("","","Time Series (MMM-YY)","Female"),
+ # recommend adding to the column title a note about the date format used.
+ lab2=c("","","Annual Rate per 100,000","Most Recent Rate (2010)"),
+ lab3=c("","","Years","Deaths per 100,000"),
+ lab4=c("","","Rate",""),
+ col1=c(NA,NA,NA,15),
+ panelData =c(NA,NA,"NewArray",NA)
+ )
>
> ExTitle <- c("Ex03a-US Time Series with Confidence bands with time (mmm-yy)",
+ "Annual Female Lung Cancer Mortality Rates, 1996-2010")
>
> grDevices::pdf(file=paste0(TDir,"Ex03a-US Time-Series-with-Conf wDates.pdf"),
+ width=7.5,height=10)
>
> micromapST(temprates,panelDesc03a,sortVar="P15",ascend=FALSE,
+ axisScale="s",
+ title=ExTitle)
statsDFrame = temprates
panelDesc = panelDesc03a
Error in as.Date.numeric(atRx) : 'origin' must be supplied
Calls: micromapST ... rlAreaTSConf -> DrawXAxisAndTitles -> as.Date -> as.Date.numeric
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 3.0.1
Check: examples
Result: ERROR
Running examples in 'micromapST-Ex.R' failed
The error most likely occurred in:
> ### Name: micromapST
> ### Title: Linked Micromap Graphics Package
> ### Aliases: micromapST micromapST.Version
>
> ### ** Examples
>
>
> ###
> #
> # micromapST - Example # 01 - map with no cumulative shading,
> # 2 columns of statistics: dot with 95% confidence interval,
> # boxplot sorted in descending order by state rates, using
> # the default border group of "USStatesBG", with default symbols.
> ###
>
> # load sample data, compute boxplot
> TDir<-"c:/projects/statnet/" # my private test PDF directory exist, don't use temp.
> if (!dir.exists(TDir)) {TDir <- paste0(tempdir(),"/") } # get a temp directory for the output
> # PDF files for the example.
> cat("TempDir:",TDir,"\n")
TempDir: D:\temp\Rtmpoherhy/
>
> # replace this directory name with the location if you want to same
> # the output from the examples.
>
> utils::data(wflung00and95,wflung00and95US,wflung00cnty,envir=environment())
>
> wfboxlist = graphics::boxplot(split(wflung00cnty$rate,wflung00cnty$stabr),
+ plot=FALSE)
>
> # set up 4 column page layout
>
> panelDesc01 <- data.frame(
+ type=c("map","id","dotconf","boxplot"),
+ lab1=c("","","State Rate","County Rates"),
+ lab2=c("","","and 95% CI","(suppressed if 1-9 deaths)"),
+ lab3=c("","","Deaths per 100,000","Deaths per 100,000"),
+ col1=c(NA,NA,1,NA),col2=c(NA,NA,3,NA),col3=c(NA,NA,4,NA),
+ refVals=c(NA,NA,NA,wflung00and95US[1,1]),
+ refTexts=c(NA,NA,NA,"US Rate 2000-4"),
+ panelData= c("","","","wfboxlist")
+ )
> panelDesc <- panelDesc01
> # set up PDF output file, call package
>
> ExTitle <- c("Ex01-US White Female Lung Cancer Mortality, 2000-2004",
+ "State Rates & County Boxplots")
>
> grDevices::pdf(file=paste0(TDir,"Ex01-US-WFLung-2000-2004-St-DotCf-Co-Box.pdf"),
+ width=7.5,height=10)
>
> micromapST(wflung00and95, panelDesc01, sortVar=1, ascend=FALSE,
+ title=ExTitle
+ )
statsDFrame = wflung00and95
panelDesc = panelDesc01
End of micromapST processing.
No warnings were logged.
No stop messages were logged.
>
> x <- grDevices::dev.off()
> #
> ### End Example 01
>
> ###
> #
> # micromapST - Example # 02 - map with cumulative shading
> # from top down (mapcum), arrow and bar charts,
> # sorted in descending order by starting
> # value of arrows (1950-69 rates) using default
> # border group of "USStatesDF". This
> # example also provides custom colors for the
> # linked micromaps, highlights, etc.
> #
> ###
>
> # Load example data from package.
> utils::data(wmlung5070,wmlung5070US,envir=environment())
>
> panelDesc02 <- data.frame(
+ type=c("mapcum","id","arrow","bar"),
+ lab1=c("","","Rates in","Percent Change"),
+ lab2=c("","","1950-69 and 1970-94","1950-69 To 1970-94"),
+ lab3=c("MAPCUM","","Deaths per 100,000","Percent"),
+ col1=c(NA,NA,"RATEWM_50","PERCENT"),
+ col2=c(NA,NA,"RATEWM_70",NA)
+ )
>
> colorsRgb = matrix(c( # the basic 7 colors.
+ 213, 62, 79, #region 1: red #D53E4F - Rust Red
+ 252, 141, 89, #region 2: orange #FC8D59 - Brn/Org
+ 253, 225, 139, #region 3: green #FEE08B - Pale Brn
+ 153, 213, 148, #region 4: greenish blue #99D594 - med Green
+ 50, 136, 189, #region 5: lavendar #3288BD - Blue
+ 255, 0, 255, #region 6 #FF00FF - Magenta
+ .00, .00, .00, #region 7: black for median #000000 - Black
+ 230, 245, 152, #non-highlighted foreground #E6F598 - YellowGreen
+ 255, 174, 185, # alternate shape upper #FFAEB9 - Mauve
+ 191, 239, 255, # alternate shape lower #BFEFFF - Cyan
+ 242, 242, 242, # lightest grey for non-referenced sub-areas #F2F2F2
+ 234, 234, 234), # lighter grey for bkg - non-active sub-areas. #EAEAEA
+
+ ncol=3,byrow=TRUE)
>
> xcolors = c( grDevices::rgb(colorsRgb[,1],colorsRgb[,2],colorsRgb[,3],
+ maxColorValue=255),
+ # set solid colors
+ grDevices::rgb(colorsRgb[,1],colorsRgb[,2],colorsRgb[,3],64,
+ maxColorValue=255))
> # set translucent colors for time series.
>
> # set up reference names for color set
> names(xcolors) =c("rustred","orange","lightbrown","mediumgreen",
+ "blue","magenta", "black","yellowgreen",
+ "mauve","cyan","lightest grey","lighter grey",
+ "l_rustred","l_orange","vlightbrown","lightgreen",
+ "lightblue","l_black","l_yelgreen","l_mauve",
+ "l_cyan","l_lightest grey","l_lighter grey")
>
> ExTitle <- c("Ex02-US Change in White Male Lung Cancer Mortality Rates",
+ "from 1950-69 to 1970-94-Diff colors")
>
> grDevices::pdf(file=paste0(TDir,"Ex02-US WmLung50-70-Arrow-Bar.pdf"),width=7.5,height=10)
>
> micromapST(wmlung5070,panelDesc02,sortVar=1,ascend=FALSE,
+ title=ExTitle, colors=xcolors
+ )
statsDFrame = wmlung5070
panelDesc = panelDesc02
End of micromapST processing.
No warnings were logged.
No stop messages were logged.
>
> x <- grDevices::dev.off()
> #
> ### End Example 02
>
> ## Not run:
> ##D ###
> ##D #
> ##D # micromapST - Example # 03 - Time Series Line Plots with
> ##D # Confidence Bands maptail option highlights states from extremes
> ##D # to middle state read in time series data set example using the
> ##D # default border group of "USStatesDF".
> ##D #
> ##D ###
> ##D
> ##D # Load example data from package.
> ##D utils::data(TSdata,envir=environment())
> ##D temprates <- data.frame(TSdata[,,2])
> ##D
> ##D # TSdata structure is array of size c(51,15,4),
> ##D # dimensions = 51 states, 15 years, (year label, point value, low limit,
> ##D # high limit)
> ##D
> ##D panelDesc03 <- data.frame(
> ##D type=c("maptail","id","tsconf","dot"),
> ##D lab1=c("","","Time Series","Female"),
> ##D lab2=c("","","Annual Rate per 100,000","Most Recent Rate (2010)"),
> ##D lab3=c("","","Years","Deaths per 100,000"),
> ##D lab4=c("","","Rate",""),
> ##D col1=c(NA,NA,NA,15),
> ##D panelData =c(NA,NA,"TSdata",NA)
> ##D )
> ##D ExTitle <- c("Ex03-US Time Series with Confidence bands",
> ##D "Annual Female Lung Cancer Mortality Rates, 1996-2010")
> ##D
> ##D grDevices::pdf(file=paste0(TDir,"Ex03-US Time-Series-with-Conf.pdf"),
> ##D width=7.5,height=10)
> ##D
> ##D micromapST(temprates,panelDesc03,sortVar="P15",ascend=FALSE,
> ##D title=ExTitle)
> ##D
> ##D x <- grDevices::dev.off()
> ##D #
> ##D ### End Example 03
> ## End(Not run)
>
> ###
> #
> # micromapST - Example # 03a - Time Series Line Plots with
> # Confidence Bands maptail option highlights states from extremes
> # to middle state read in time series data set example using the
> # default border group of "USStatesDF".
> #
> # Specify the x-Axis values are dates and to format them as dates.
> ###
>
> # Load example data from package.
> utils::data(TSdata,envir=environment())
> temprates <- data.frame(TSdata[,,2]) # y rate
>
> # In the original package TS data, the x data was not
> # a date value, it was the year number. To be able to demonstrate
> # the X-Axis Date format labeling, these were changed to Date values
> # by effectively substracting 1970-1-1 from the year value.
>
> ####
> #
> # Example 3a - Building TS conf array and converting years
> # into date values for the X-Axis and labels.
> #
> # example of build a TS Conf array.
> #
> # Using the old TSdata array as a starting point and source of data,
> # but build an entirely new TS array structure in a similar manner
> # that might be used to build your own time series array.
> #
>
> data(TSdata) # get old array
> TSAreas <- row.names(TSdata) # one per area (index 1)
> NewArray <- array(dim=c(51,15,4),dimnames=list(TSAreas))
> # this is for 51 states, 15 samples/observations, and 4 values per sample.
>
> for (inx in seq(1,length(TSAreas))) { # loop once per area
+
+ Samp <- TSdata[inx,,] # samples for an area
+ # each sample has 15 observations of 4 values.
+ # value 1 is the X axis data or the DATE of the observation
+ Samp[,1] <- as.Date(paste0(as.character(Samp[,1]),"-01-01"))
+ # convert simple year number to date
+ NewArray[inx,,] <- Samp
+
+ }
>
> # setting the attribute "xIsDate" on array to TRUE, signals micromapST
> # the user wants to see the x-axis values as dates.
>
> attr(NewArray,"xIsDate") <- TRUE
>
> # TSdata and NewArray structures are arrays of size c(51,15,4),
> # dimensions = 51 states, 15 years, (year label, point value, low limit, high limit)
>
> panelDesc03a <- data.frame(
+ type=c("maptail","id","tsconf","dot"),
+ lab1=c("","","Time Series (MMM-YY)","Female"),
+ # recommend adding to the column title a note about the date format used.
+ lab2=c("","","Annual Rate per 100,000","Most Recent Rate (2010)"),
+ lab3=c("","","Years","Deaths per 100,000"),
+ lab4=c("","","Rate",""),
+ col1=c(NA,NA,NA,15),
+ panelData =c(NA,NA,"NewArray",NA)
+ )
>
> ExTitle <- c("Ex03a-US Time Series with Confidence bands with time (mmm-yy)",
+ "Annual Female Lung Cancer Mortality Rates, 1996-2010")
>
> grDevices::pdf(file=paste0(TDir,"Ex03a-US Time-Series-with-Conf wDates.pdf"),
+ width=7.5,height=10)
>
> micromapST(temprates,panelDesc03a,sortVar="P15",ascend=FALSE,
+ axisScale="s",
+ title=ExTitle)
statsDFrame = temprates
panelDesc = panelDesc03a
Error in as.Date.numeric(atRx) : 'origin' must be supplied
Calls: micromapST ... rlAreaTSConf -> DrawXAxisAndTitles -> as.Date -> as.Date.numeric
Execution halted
Flavor: r-oldrel-windows-x86_64