CRAN Package Check Results for Maintainer ‘Christian Huber <christian.domitian.huber at gmail.com>’

Last updated on 2025-06-08 02:49:27 CEST.

Package	ERROR	NOTE
smartsnp	6	7

Package smartsnp

Current CRAN status: ERROR: 6, NOTE: 7

Version: 1.1.0
Check: Rd files
Result: NOTE checkRd: (-1) read_packedancestrymap.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:7-11: Lost braces 7 | \item{snp_data}{snp_data}{File name read from working directory. | ^ checkRd: (-1) smart_mva.Rd:100-101: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:102-103: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:106-109: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:110: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:111: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:112: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:113-114: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:115: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:116: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:117: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:118: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_mva.Rd:119: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_pca.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_pca.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_pca.Rd:64-67: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permanova.Rd:71-73: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permanova.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permanova.Rd:75-76: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permanova.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permanova.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permanova.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permdisp.Rd:78-81: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permdisp.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permdisp.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permdisp.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permdisp.Rd:85-86: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permdisp.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permdisp.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) smart_permdisp.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 1.1.0
Check: examples
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 -> <Anonymous> -> .Defunct Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.1.0
Check: examples
Result: ERROR Running examples in ‘smartsnp-Ex.R’ failed The error most likely occurred in: > ### 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 1s Scanning for invariant SNPs... Scan complete: no invariant SNPs found Time elapsed: 0h 0m 1s 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 1s Scaling values by SNP... Centering and scaling by drift dispersion... Completed scaling using drift Time elapsed: 0h 0m 1s Computing singular value decomposition using RSpectra... Completed singular value decomposition Time elapsed: 0h 0m 8s Extracting eigenvalues and eigenvectors... Eigenvalues and eigenvectors extracted Time elapsed: 0h 0m 8s Completed PCA computation Time elapsed: 0h 0m 8s 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 8s 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 -> <Anonymous> -> .Defunct Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.1.0
Check: examples
Result: ERROR Running examples in ‘smartsnp-Ex.R’ failed The error most likely occurred in: > ### 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 1s 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 1s Scaling values by SNP... Centering and scaling by drift dispersion... Completed scaling using drift Time elapsed: 0h 0m 1s Computing singular value decomposition using RSpectra... Completed singular value decomposition Time elapsed: 0h 0m 7s Extracting eigenvalues and eigenvectors... Eigenvalues and eigenvectors extracted Time elapsed: 0h 0m 7s Completed PCA computation Time elapsed: 0h 0m 7s 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 7s 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 -> <Anonymous> -> .Defunct Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.1.0
Check: examples
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 2s Extracting eigenvalues and eigenvectors... Eigenvalues and eigenvectors extracted Time elapsed: 0h 0m 2s Completed PCA computation Time elapsed: 0h 0m 2s 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 2s 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 -> <Anonymous> -> .Defunct Execution halted Flavor: r-release-linux-x86_64

Version: 1.1.0
Check: examples
Result: ERROR Running examples in 'smartsnp-Ex.R' failed The error most likely occurred in: > ### 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 -> <Anonymous> -> .Defunct Execution halted Flavor: r-release-windows-x86_64

Version: 1.1.0
Check: LazyData
Result: NOTE 'LazyData' is specified without a 'data' directory Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 1.1.0
Check: examples
Result: ERROR Running examples in 'smartsnp-Ex.R' failed The error most likely occurred in: > ### 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 2s Extracting eigenvalues and eigenvectors... Eigenvalues and eigenvectors extracted Time elapsed: 0h 0m 2s Completed PCA computation Time elapsed: 0h 0m 2s 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 2s 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 -> <Anonymous> -> .Defunct Execution halted Flavor: r-oldrel-windows-x86_64