CRAN Package Check Results for Package ClustGeo

Last updated on 2021-09-23 22:55:49 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0 13.49 163.25 176.74 OK
r-devel-linux-x86_64-debian-gcc 2.0 13.81 124.06 137.87 OK
r-devel-linux-x86_64-fedora-clang 2.0 220.98 OK
r-devel-linux-x86_64-fedora-gcc 2.0 205.32 OK
r-devel-windows-x86_64 2.0 18.00 127.00 145.00 OK
r-devel-windows-x86_64-gcc10-UCRT 2.0 OK
r-patched-linux-x86_64 2.0 13.54 146.64 160.18 WARN
r-patched-solaris-x86 2.0 303.50 WARN
r-release-linux-x86_64 2.0 12.78 144.73 157.51 WARN
r-release-macos-arm64 2.0 OK
r-release-macos-x86_64 2.0 OK
r-release-windows-ix86+x86_64 2.0 38.00 175.00 213.00 WARN
r-oldrel-macos-x86_64 2.0 OK
r-oldrel-windows-ix86+x86_64 2.0 26.00 126.00 152.00 WARN

Check Details

Version: 2.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘intro_ClustGeo.Rmd’ using rmarkdown
    inertdiss package:ClustGeo R Documentation
    
    _<08>P_<08>s_<08>e_<08>u_<08>d_<08>o _<08>i_<08>n_<08>e_<08>r_<08>t_<08>i_<08>a _<08>o_<08>f _<08>a _<08>c_<08>l_<08>u_<08>s_<08>t_<08>e_<08>r
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     The pseudo inertia of a cluster is calculated from a dissimilarity
     matrix and not from a data matrix.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     inertdiss(D, indices = NULL, wt = NULL)
    
    _<08>A_<08>r_<08>g_<08>u_<08>m_<08>e_<08>n_<08>t_<08>s:
    
     D: an object of class "dist" with the dissimilarities between
     the n observations. The function 'as.dist' can be used to
     transform an object of class matrix to object of class
     "dist".
    
     indices: a vector with the indices of the subset of observations.
    
     wt: vector with the weights of the n observations
    
    _<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
    
     M.chavent, V. Kuentz-Simonet, A. Labenne, J. Saracco. ClustGeo:
     an R package for hierarchical clustering with spatial constraints
     arXiv:1707.03897 [stat.CO]
    
    _<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
    
     data(estuary)
     n <- nrow(estuary$dat)
     Z <- scale(estuary$dat)*sqrt(n/(n-1))
     inertdiss(dist(Z)) # pseudo inertia
     inert(Z) #equals for euclidean distance
    
     w <- estuary$map@data$POPULATION # non uniform weights
     inertdiss(dist(Z),wt=w)
    
    
    inert package:ClustGeo R Documentation
    
    _<08>I_<08>n_<08>e_<08>r_<08>t_<08>i_<08>a _<08>o_<08>f _<08>a _<08>c_<08>l_<08>u_<08>s_<08>t_<08>e_<08>r
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Computes the inertia of a cluster i.e. on a subset of rows of a
     data matrix.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     inert(Z, indices = 1:nrow(Z), wt = rep(1/nrow(Z), nrow(Z)), M = rep(1,
     ncol(Z)))
    
    _<08>A_<08>r_<08>g_<08>u_<08>m_<08>e_<08>n_<08>t_<08>s:
    
     Z: matrix data
    
     indices: vector representing the subset of rows
    
     wt: weight vector
    
     M: diagonal distance matrix
    
    _<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
    
     data(estuary)
     n <- nrow(estuary$dat)
     Z <- scale(estuary$dat)*sqrt(n/(n-1))
     inert(Z) # number of variables
    
     w <- estuary$map@data$POPULATION # non uniform weights
     inert(Z,wt=w)
    
    
    plot.choicealpha package:ClustGeo R Documentation
    
    _<08>P_<08>l_<08>o_<08>t _<08>o_<08>f _<08>t_<08>h_<08>e _<08>m_<08>i_<08>x_<08>i_<08>n_<08>g _<08>p_<08>a_<08>r_<08>a_<08>m_<08>e_<08>t_<08>e_<08>r
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Plot of the criterion Q or Qnorm obtained in output of the
     function 'choicealpha'.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     ## S3 method for class 'choicealpha'
     plot(x, norm = FALSE, lty = 1:2, pch = c(8, 16),
     type = c("b", "b"), col = 1:2, xlab = "alpha", ylab = NULL,
     legend = NULL, cex = 1, ...)
    
    _<08>A_<08>r_<08>g_<08>u_<08>m_<08>e_<08>n_<08>t_<08>s:
    
     x: an object of class 'choicealpha'.
    
     norm: if TRUE, the criterion Qnorm is plotted. Otherwise, it is Q.
    
     lty: a vector of size 2 with the line types of the two curves. See
     par
    
     pch: a vector of size 2 specifying the symbol for the points of
     the two curves. See par
    
     type: a vector of size 2 specifying the type of lines of the two
     curves. See par
    
     col: a vector of size 2 specifying the colors the two curves. See
     par
    
     xlab: the title fot the x axis.
    
     ylab: the title fot the y axis.
    
     legend: a vector of size two the the text for the legend of the two
     curves.
    
     cex: text size in the legend.
    
     ...: further arguments passed to or from other methods.
    
    _<08>S_<08>e_<08>e _<08>A_<08>l_<08>s_<08>o:
    
     'choicealpha'
    
    _<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
    
     data(estuary)
     D0 <- dist(estuary$dat)
     D1 <- as.dist(estuary$D.geo) # the geographic distances between the cities
     range.alpha <- seq(0,1,0.1)
     K <- 5
     cr <- choicealpha(D0,D1,range.alpha,K,graph=FALSE)
     plot(cr,cex=0.8,norm=FALSE,cex.lab=0.8,ylab="pev",
     col=3:4,legend=c("socio-demo","geo"), xlab="mixing parameter")
     plot(cr,cex=0.8,norm=TRUE,cex.lab=0.8,ylab="pev",
     col=5:6,pch=5:6,legend=c("socio-demo","geo"), xlab="mixing parameter")
    
    
    Quitting from lines 234-242 (intro_ClustGeo.Rmd)
    Error: processing vignette 'intro_ClustGeo.Rmd' failed with diagnostics:
    package rgeos required for finding out which hole belongs to which exterior ring
    --- failed re-building ‘intro_ClustGeo.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘intro_ClustGeo.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64

Version: 2.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘intro_ClustGeo.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
    inertdiss package:ClustGeo R Documentation
    
    _<08>P_<08>s_<08>e_<08>u_<08>d_<08>o _<08>i_<08>n_<08>e_<08>r_<08>t_<08>i_<08>a _<08>o_<08>f _<08>a _<08>c_<08>l_<08>u_<08>s_<08>t_<08>e_<08>r
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     The pseudo inertia of a cluster is calculated from a dissimilarity
     matrix and not from a data matrix.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     inertdiss(D, indices = NULL, wt = NULL)
    
    _<08>A_<08>r_<08>g_<08>u_<08>m_<08>e_<08>n_<08>t_<08>s:
    
     D: an object of class "dist" with the dissimilarities between
     the n observations. The function 'as.dist' can be used to
     transform an object of class matrix to object of class
     "dist".
    
     indices: a vector with the indices of the subset of observations.
    
     wt: vector with the weights of the n observations
    
    _<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
    
     M.chavent, V. Kuentz-Simonet, A. Labenne, J. Saracco. ClustGeo:
     an R package for hierarchical clustering with spatial constraints
     arXiv:1707.03897 [stat.CO]
    
    _<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
    
     data(estuary)
     n <- nrow(estuary$dat)
     Z <- scale(estuary$dat)*sqrt(n/(n-1))
     inertdiss(dist(Z)) # pseudo inertia
     inert(Z) #equals for euclidean distance
    
     w <- estuary$map@data$POPULATION # non uniform weights
     inertdiss(dist(Z),wt=w)
    
    
    inert package:ClustGeo R Documentation
    
    _<08>I_<08>n_<08>e_<08>r_<08>t_<08>i_<08>a _<08>o_<08>f _<08>a _<08>c_<08>l_<08>u_<08>s_<08>t_<08>e_<08>r
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Computes the inertia of a cluster i.e. on a subset of rows of a
     data matrix.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     inert(Z, indices = 1:nrow(Z), wt = rep(1/nrow(Z), nrow(Z)), M = rep(1,
     ncol(Z)))
    
    _<08>A_<08>r_<08>g_<08>u_<08>m_<08>e_<08>n_<08>t_<08>s:
    
     Z: matrix data
    
     indices: vector representing the subset of rows
    
     wt: weight vector
    
     M: diagonal distance matrix
    
    _<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
    
     data(estuary)
     n <- nrow(estuary$dat)
     Z <- scale(estuary$dat)*sqrt(n/(n-1))
     inert(Z) # number of variables
    
     w <- estuary$map@data$POPULATION # non uniform weights
     inert(Z,wt=w)
    
    
    plot.choicealpha package:ClustGeo R Documentation
    
    _<08>P_<08>l_<08>o_<08>t _<08>o_<08>f _<08>t_<08>h_<08>e _<08>m_<08>i_<08>x_<08>i_<08>n_<08>g _<08>p_<08>a_<08>r_<08>a_<08>m_<08>e_<08>t_<08>e_<08>r
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Plot of the criterion Q or Qnorm obtained in output of the
     function 'choicealpha'.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     ## S3 method for class 'choicealpha'
     plot(x, norm = FALSE, lty = 1:2, pch = c(8, 16),
     type = c("b", "b"), col = 1:2, xlab = "alpha", ylab = NULL,
     legend = NULL, cex = 1, ...)
    
    _<08>A_<08>r_<08>g_<08>u_<08>m_<08>e_<08>n_<08>t_<08>s:
    
     x: an object of class 'choicealpha'.
    
     norm: if TRUE, the criterion Qnorm is plotted. Otherwise, it is Q.
    
     lty: a vector of size 2 with the line types of the two curves. See
     par
    
     pch: a vector of size 2 specifying the symbol for the points of
     the two curves. See par
    
     type: a vector of size 2 specifying the type of lines of the two
     curves. See par
    
     col: a vector of size 2 specifying the colors the two curves. See
     par
    
     xlab: the title fot the x axis.
    
     ylab: the title fot the y axis.
    
     legend: a vector of size two the the text for the legend of the two
     curves.
    
     cex: text size in the legend.
    
     ...: further arguments passed to or from other methods.
    
    _<08>S_<08>e_<08>e _<08>A_<08>l_<08>s_<08>o:
    
     'choicealpha'
    
    _<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
    
     data(estuary)
     D0 <- dist(estuary$dat)
     D1 <- as.dist(estuary$D.geo) # the geographic distances between the cities
     range.alpha <- seq(0,1,0.1)
     K <- 5
     cr <- choicealpha(D0,D1,range.alpha,K,graph=FALSE)
     plot(cr,cex=0.8,norm=FALSE,cex.lab=0.8,ylab="pev",
     col=3:4,legend=c("socio-demo","geo"), xlab="mixing parameter")
     plot(cr,cex=0.8,norm=TRUE,cex.lab=0.8,ylab="pev",
     col=5:6,pch=5:6,legend=c("socio-demo","geo"), xlab="mixing parameter")
    
    
    Quitting from lines 234-242 (intro_ClustGeo.Rmd)
    Error: processing vignette 'intro_ClustGeo.Rmd' failed with diagnostics:
    package rgeos required for finding out which hole belongs to which exterior ring
    --- failed re-building ‘intro_ClustGeo.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘intro_ClustGeo.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 2.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'intro_ClustGeo.Rmd' using rmarkdown
    Quitting from lines 234-242 (intro_ClustGeo.Rmd)
    Error: processing vignette 'intro_ClustGeo.Rmd' failed with diagnostics:
    package rgeos required for finding out which hole belongs to which exterior ring
    --- failed re-building 'intro_ClustGeo.Rmd'
    
    SUMMARY: processing the following file failed:
     'intro_ClustGeo.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64