Package: analogue Check: differences from ‘analogue-Ex.Rout’ to ‘analogue-Ex.Rout.save’ New result: NOTE 6942d6941 < 6944a6944,6945 > -- Model Summary -- > 6950a6952,6953 > -- Eigenvalues -- > 6978d6980 < 6980a6983,6984 > -- Model Summary -- > 6987a6992,6993 > -- Eigenvalues -- > 7030d7035 < 7032a7038,7039 > -- Model Summary -- > 7037a7045,7046 > > -- Eigenvalues -- Package: betaper Check: examples New result: ERROR Running examples in ‘betaper-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: adonis_pertables > ### Title: Function to assess the efects of taxonomic uncertainty on > ### permutational multivariate analysis of variance using distance > ### matrices > ### Aliases: adonis_pertables print.adonis_pertables plot.adonis_pertables > ### Keywords: multivariate > > ### ** Examples > > > > > data(Amazonia) > data(soils) > > # Define a new index that includes the terms used in the \code{Amazonia} dataset to define > # undetermined taxa at different taxonomic levels > > index.Amazon <- c(paste("sp.", rep(1:20), sep=""), "Indet.", "indet.") > > # Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic > # uncertainty) > ## Not run: > ##D Amazonia100 <- pertables(Amazonia, index=index.Amazon, nsim=100) > ##D > ##D # Assess the effects of taxonomic uncertainty on a PERMANOVA (i.e., adonis) test: > ##D > ##D Amazonia.adonis <- adonis_pertables(Amazonia100 ~ Ca + K + Mg + Na, data=soils) > ##D > ##D Amazonia.adonis > ##D > ##D plot(Amazonia.adonis) > ## End(Not run) > # Fast example for Rcheck > > Amazonia4.p2 <- pertables.p2(Amazonia[1:50,], index=index.Amazon, nsim=4, ncl=2, iseed=4) > set.seed(2) > Amazonia.adonis <- adonis_pertables(Amazonia4.p2 ~ Ca + K + Mg + Na, data=soils) Error in adonis(formula = fmla, data = data, permutations = permutations, : 'adonis' is defunct. Use 'adonis2' instead. See help("Defunct") and help("vegan-defunct"). Calls: adonis_pertables -> adonis -> .Defunct Execution halted Package: permute Check: differences from ‘permute-Ex.Rout’ to ‘permute-Ex.Rout.save’ New result: NOTE 453c453 < detaching 'package:vegan' --- > detaching 'package:vegan', 'package:lattice' Package: SigTree Check: examples New result: ERROR Running examples in ‘SigTree-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: adonis.tree > ### Title: Function to perform adonis test of independence on p-values from > ### tests of multiple OTUs. > ### Aliases: adonis.tree > ### Keywords: tree adonis > > ### ** Examples > > ### To access the tutorial document for this package, type in R (not run here): > # vignette('SigTree') > > ### Create tree, then data frame, then use plotSigTree to plot the tree > ### Code for random tree and data frame > node.size <- 10 > seed <- 109 > # Create tree > set.seed(seed); > library(ape) > r.tree <- rtree(node.size) > # Create p-values data frame > set.seed(seed) > r.pval <- rbeta(node.size, .1, .1) > # Randomize the order of the tip labels > # (just to emphasize that labels need not be sorted) > set.seed(seed) > r.tip.label <- sample(r.tree$tip.label, size=length(r.tree$tip.label)) > r.pvalues <- data.frame(label=r.tip.label, pval=r.pval) > > # Check for dependence among p-values; lack of significance here > # indicates default test="Stouffer" would be appropriate in other > # main SigTree package functions (plotSigTree, export.figtree, > # and export.inherit); otherwise, test="Hartung" would be more > # appropriate. > adonis.tree(r.tree,r.pvalues) Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct. Use 'adonis2' instead. See help("Defunct") and help("vegan-defunct"). Calls: adonis.tree -> adonis -> .Defunct Execution halted Package: SigTree Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘SigTree.Rnw’ using Sweave Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML' Also defined by ‘S4Vectors’ Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML' Also defined by ‘S4Vectors’ Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML' Also defined by ‘S4Vectors’ Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML' Also defined by ‘S4Vectors’ Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML' Also defined by ‘S4Vectors’ Found more than one class "Annotated" in cache; using the first, from namespace 'RNeXML' Also defined by ‘S4Vectors’ Error: processing vignette 'SigTree.Rnw' failed with diagnostics: chunk 6 Error in adonis(M ~ x, permutations = perms) : 'adonis' is defunct. Use 'adonis2' instead. See help("Defunct") and help("vegan-defunct"). --- failed re-building ‘SigTree.Rnw’ SUMMARY: processing the following file failed: ‘SigTree.Rnw’ Error: Vignette re-building failed. Execution halted Package: smartsnp Check: examples New result: ERROR Running examples in ‘smartsnp-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: smart_mva > ### Title: Smart Multivariate Analyses (wrapper of PCA, PERMANOVA and > ### PERMDISP) > ### Aliases: smart_mva > > ### ** Examples > > # Path to example genotype matrix "dataSNP" > pathToGenoFile = system.file("extdata", "dataSNP", package = "smartsnp") > > # Assign 50 samples to each of two groups and colors > my_groups <- as.factor(c(rep("A", 50), rep("B", 50))); cols = c("red", "blue") > > # Run PCA, PERMANOVA and PERMDISP > mvaR <- smart_mva(snp_data = pathToGenoFile, sample_group = my_groups) Checking argument options selected... Argument options are correct... Loading data... Imported 10000 SNP by 100 sample genotype matrix Time elapsed: 0h 0m 0s Filtering data... No samples projected after PCA computation 10000 SNPs included in PCA & PERMANOVA & PERMDISP computations 1 SNPs omitted from PCA computation 100 samples included in PCA & PERMANOVA & PERMDISP computations 0 samples ommitted from PERMANOVA & PERMDISP analyses Completed data filtering Time elapsed: 0h 0m 0s Scanning for invariant SNPs... Scan complete: no invariant SNPs found Time elapsed: 0h 0m 0s Checking for missing values... 6341 SNPs contain missing values Removing SNPs with missing values... Removal completed: 6341 SNPs removed 3659 SNPs remaining Time elapsed: 0h 0m 0s Scaling values by SNP... Centering and scaling by drift dispersion... Completed scaling using drift Time elapsed: 0h 0m 0s Computing singular value decomposition using RSpectra... Completed singular value decomposition Time elapsed: 0h 0m 1s Extracting eigenvalues and eigenvectors... Eigenvalues and eigenvectors extracted Time elapsed: 0h 0m 1s Completed PCA computation Time elapsed: 0h 0m 1s Performing PERMANOVA & PERMDISP testing... Construct triangular matrix of sample by sample proximities in multidimensional space... Completed construction of triangular matrix of sample by sample proximities Time elapsed: 0h 0m 1s Computing variance partioning by PERMANOVA: global test... Error in vegan::adonis(formula = snp_eucli ~ group, permutations = permutation_n) : 'adonis' is defunct. Use 'adonis2' instead. See help("Defunct") and help("vegan-defunct"). Calls: smart_mva -> -> .Defunct Execution halted