Last updated on 2025-12-07 07:50:28 CET.
| Package | ERROR | OK |
|---|---|---|
| randPedPCA | 1 | 12 |
Current CRAN status: ERROR: 1, OK: 12
Version: 1.1.3
Check: package dependencies
Result: WARN
Cannot process vignettes
Packages suggested but not available for checking:
'knitr', 'rmarkdown', 'rgl'
VignetteBuilder package required for checking but not installed: ‘knitr’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.3
Check: examples
Result: ERROR
Running examples in ‘randPedPCA-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot3D
> ### Title: 3D plot using rgl
> ### Aliases: plot3D
>
> ### ** Examples
>
> pc <- rppca(pedLInv)
> plot3D(pc)
Error: Package "rgl" must be installed to use this function.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(randPedPCA)
Loading required package: spam
Spam version 2.11-1 (2025-01-20) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: 'spam'
The following objects are masked from 'package:base':
backsolve, forwardsolve
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:spam':
det
Loading required package: pedigreeTools
Loading required package: RSpectra
>
> test_check("randPedPCA")
'as(<dtTMatrix>, "dtCMatrix")' is deprecated.
Use 'as(., "CsparseMatrix")' instead.
See help("Deprecated") and help("Matrix-deprecated").
Downsampling to 1050 individuals.
Subsetting colours using the individual index.
Saving _problems/test_rppca-231.R
Saving _problems/test_rppca-232.R
Saving _problems/test_rppca-233.R
Saving _problems/test_rppca-234.R
Saving _problems/test_rppca-235.R
Saving _problems/test_rppca-236.R
Saving _problems/test_rppca-237.R
Saving _problems/test_rppca-238.R
Downsampling to 1050 individuals.
Subsetting colours using the individual index.
Saving _problems/test_rppca-260.R
Saving _problems/test_rppca-261.R
Saving _problems/test_rppca-262.R
Saving _problems/test_rppca-263.R
Saving _problems/test_rppca-264.R
Saving _problems/test_rppca-265.R
Saving _problems/test_rppca-266.R
Saving _problems/test_rppca-267.R
Saving _problems/test_rppca-268.R
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 80 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_rppca.R:231:3'): Plot3D ──────────────────────────────────────
Expected `plot3D(pc, col = c("yellow", "green"))` not to throw any conditions.
Actually got a <simpleError> with message:
Package "rgl" must be installed to use this function.
── Failure ('test_rppca.R:232:3'): Plot3D ──────────────────────────────────────
Expected `plot3D(pcNoV, col = c("yellow", "green"))` not to throw any conditions.
Actually got a <simpleError> with message:
Package "rgl" must be installed to use this function.
── Failure ('test_rppca.R:233:3'): Plot3D ──────────────────────────────────────
Expected `plot3D(pc, col = 2)` not to throw any conditions.
Actually got a <simpleError> with message:
Package "rgl" must be installed to use this function.
── Failure ('test_rppca.R:234:3'): Plot3D ──────────────────────────────────────
Expected `plot3D(pcNoV, col = 2)` not to throw any conditions.
Actually got a <simpleError> with message:
Package "rgl" must be installed to use this function.
── Failure ('test_rppca.R:235:3'): Plot3D ──────────────────────────────────────
Expected `plot3D(pc, col = "grey")` not to throw any conditions.
Actually got a <simpleError> with message:
Package "rgl" must be installed to use this function.
── Failure ('test_rppca.R:236:3'): Plot3D ──────────────────────────────────────
Expected `plot3D(pcNoV, col = "grey")` not to throw any conditions.
Actually got a <simpleError> with message:
Package "rgl" must be installed to use this function.
── Failure ('test_rppca.R:237:3'): Plot3D ──────────────────────────────────────
Expected `plot3D(pc, col = as.numeric(factor(pedMeta$population)))` not to throw any conditions.
Actually got a <simpleError> with message:
Package "rgl" must be installed to use this function.
── Failure ('test_rppca.R:238:3'): Plot3D ──────────────────────────────────────
Expected `plot3D(pcNoV, col = as.numeric(factor(pedMeta$population)))` not to throw any conditions.
Actually got a <simpleError> with message:
Package "rgl" must be installed to use this function.
── Failure ('test_rppca.R:260:3'): Axis labels 3D ──────────────────────────────
Expected `plot3D(pc, col = c("yellow", "green"), xlab = "123", ylab = "456")` not to throw any conditions.
Actually got a <simpleError> with message:
Package "rgl" must be installed to use this function.
── Failure ('test_rppca.R:261:3'): Axis labels 3D ──────────────────────────────
Expected `plot3D(pc, xlab = "123", ylab = "456")` not to throw any conditions.
Actually got a <simpleError> with message:
Package "rgl" must be installed to use this function.
── Failure ('test_rppca.R:262:3'): Axis labels 3D ──────────────────────────────
Expected `plot3D(pcNoV, xlab = "123", ylab = "456")` not to throw any conditions.
Actually got a <simpleError> with message:
Package "rgl" must be installed to use this function.
── Failure ('test_rppca.R:263:3'): Axis labels 3D ──────────────────────────────
Expected `plot3D(pc, col = 2, xlab = "123", ylab = "456")` not to throw any conditions.
Actually got a <simpleError> with message:
Package "rgl" must be installed to use this function.
── Failure ('test_rppca.R:264:3'): Axis labels 3D ──────────────────────────────
Expected `plot3D(pcNoV, col = 2, xlab = "123", ylab = "456")` not to throw any conditions.
Actually got a <simpleError> with message:
Package "rgl" must be installed to use this function.
── Failure ('test_rppca.R:265:3'): Axis labels 3D ──────────────────────────────
Expected `plot3D(pc, col = "grey", xlab = "123", ylab = "456")` not to throw any conditions.
Actually got a <simpleError> with message:
Package "rgl" must be installed to use this function.
── Failure ('test_rppca.R:266:3'): Axis labels 3D ──────────────────────────────
Expected `plot3D(pcNoV, col = "grey", xlab = "123", ylab = "456")` not to throw any conditions.
Actually got a <simpleError> with message:
Package "rgl" must be installed to use this function.
── Failure ('test_rppca.R:267:3'): Axis labels 3D ──────────────────────────────
Expected `plot3D(...)` not to throw any conditions.
Actually got a <simpleError> with message:
Package "rgl" must be installed to use this function.
── Failure ('test_rppca.R:268:3'): Axis labels 3D ──────────────────────────────
Expected `plot3D(...)` not to throw any conditions.
Actually got a <simpleError> with message:
Package "rgl" must be installed to use this function.
[ FAIL 17 | WARN 0 | SKIP 0 | PASS 80 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.3
Check: package vignettes
Result: NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
Flavor: r-devel-linux-x86_64-debian-gcc