Last updated on 2025-06-06 09:50:34 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.0 | 21.24 | 51.59 | 72.83 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.1.0 | 13.89 | 38.02 | 51.91 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.1.0 | 127.30 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.0 | 93.21 | ERROR | |||
| r-devel-windows-x86_64 | 1.1.0 | 32.00 | 88.00 | 120.00 | NOTE | |
| r-patched-linux-x86_64 | 1.1.0 | 17.85 | 46.51 | 64.36 | NOTE | |
| r-release-linux-x86_64 | 1.1.0 | 19.90 | 47.12 | 67.02 | NOTE | |
| r-release-macos-arm64 | 1.1.0 | 37.00 | NOTE | |||
| r-release-macos-x86_64 | 1.1.0 | 72.00 | NOTE | |||
| r-release-windows-x86_64 | 1.1.0 | 31.00 | 91.00 | 122.00 | NOTE | |
| r-oldrel-macos-arm64 | 1.1.0 | 36.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.1.0 | 58.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.1.0 | 37.00 | 110.00 | 147.00 | NOTE |
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:
> ### 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 6s
Extracting eigenvalues and eigenvectors...
Eigenvalues and eigenvectors extracted
Time elapsed: 0h 0m 6s
Completed PCA computation
Time elapsed: 0h 0m 6s
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 6s
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: 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