Last updated on 2025-05-03 22:50:36 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| mixKernel | 13 | ||
| NiLeDAM | 13 | ||
| RNAseqNet | 13 | ||
| SISIR | 13 | ||
| SOMbrero | 6 | 7 | |
| treediff | 1 | 12 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 6, OK: 7
Version: 1.4-2
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
superClass.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64
Version: 1.4-2
Check: for unstated dependencies in ‘demo’
Result: NOTE
'library' or 'require' call not declared from: ‘RColorBrewer’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Current CRAN status: ERROR: 1, OK: 12
Version: 0.2.1
Check: examples
Result: ERROR
Running examples in ‘treediff-Ex.R’ failed
The error most likely occurred in:
> ### Name: HiC2Tree
> ### Title: Convert Hi-C to trees
> ### Aliases: HiC2Tree
>
> ### ** Examples
>
> replicates <- 1:3
> cond <- c("90", "110")
> all_begins <- interaction(expand.grid(replicates, cond), sep = "-")
> all_begins <- as.character(all_begins)
>
> # single chromosome
> nb_chr <- 1
> chromosomes <- 1:nb_chr
> all_mat_chr <- lapply(chromosomes, function(chr) {
+ all_mat <- lapply(all_begins, function(ab) {
+ mat_file <- paste0("Rep", ab, "-chr", chr, "_200000.bed")
+ })
+ all_mat <- unlist(all_mat)
+ })
> index <- system.file("extdata", "index.200000.longest18chr.abs.bed",
+ package = "treediff")
> format <- rep("HiC-Pro", length(replicates) * length(cond) * nb_chr)
> binsize <- 200000
> files <- system.file("extdata", unlist(all_mat_chr), package = "treediff")
> replicates <- c(3, 3)
> HiC2Tree(files, format, binsize, index, chromosomes, replicates)
Parsing '/data/gannet/ripley/R/packages/tests-clang/treediff.Rcheck/treediff/extdata/Rep1-90-chr1_200000.bed' and '/data/gannet/ripley/R/packages/tests-clang/treediff.Rcheck/treediff/extdata/index.200000.longest18chr.abs.bed'.
Error in validObject(.Object) :
invalid class “HiCDOCDataSet” object: superclass "ExpData" not defined in the environment of the object's class
Calls: HiC2Tree ... .parseHiCPro -> new -> initialize -> initialize -> validObject
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [17s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library("testthat")
> library("treediff")
>
> test_check("treediff")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 29 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-HiC2Tree.R:26:1'): (code run outside of `test_that()`) ─────────
Error in `validObject(.Object)`: invalid class "HiCDOCDataSet" object: superclass "ExpData" not defined in the environment of the object's class
Backtrace:
▆
1. └─treediff::HiC2Tree(...) at test-HiC2Tree.R:26:1
2. └─treediff::HiCDOCDataSet(...)
3. └─base::sapply(...)
4. └─base::lapply(X = X, FUN = FUN, ...)
5. └─treediff (local) FUN(X[[i]], ...)
6. └─HiCDOC::HiCDOCDataSetFromHiCPro(...)
7. └─HiCDOC:::.parseHiCPro(object, replicates, conditions)
8. └─methods::new("HiCDOCDataSet", mergedinteractionSet, input = object@input)
9. ├─methods::initialize(value, ...)
10. └─methods::initialize(value, ...)
11. └─methods::validObject(.Object)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 29 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang