Last updated on 2025-12-20 20:49:47 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.1 | 44.86 | 369.31 | 414.17 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.2.1 | 33.73 | 272.37 | 306.10 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.1 | 78.00 | 557.00 | 635.00 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.2.1 | 72.00 | 524.62 | 596.62 | ERROR | |
| r-devel-windows-x86_64 | 0.2.1 | 44.00 | 312.00 | 356.00 | OK | |
| r-patched-linux-x86_64 | 0.2.1 | 42.69 | 370.66 | 413.35 | OK | |
| r-release-linux-x86_64 | 0.2.1 | 42.61 | 363.76 | 406.37 | OK | |
| r-release-macos-arm64 | 0.2.1 | OK | ||||
| r-release-macos-x86_64 | 0.2.1 | 27.00 | 280.00 | 307.00 | OK | |
| r-release-windows-x86_64 | 0.2.1 | 44.00 | 313.00 | 357.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.1 | OK | ||||
| r-oldrel-macos-x86_64 | 0.2.1 | 26.00 | 225.00 | 251.00 | OK | |
| r-oldrel-windows-x86_64 | 0.2.1 | 60.00 | 449.00 | 509.00 | OK |
Version: 0.2.1
Check: examples
Result: ERROR
Running examples in ‘treediff-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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 '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/treediff/extdata/Rep1-90-chr1_200000.bed' and '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/treediff/extdata/index.200000.longest18chr.abs.bed'.
Error in `[.data.table`(tabChromosomes, index == minIndex, `:=`(minStart, :
attempt access index 7/7 in VECTOR_ELT
Calls: HiC2Tree ... .fillHiCDOCDataSet -> .determineChromosomeSizes -> [ -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [22s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library("testthat")
> library("treediff")
>
> test_check("treediff")
Saving _problems/test-HiC2Tree-26.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 29 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-HiC2Tree.R:26:1'): (code run outside of `test_that()`) ─────────
Error in ``[.data.table`(tabChromosomes, index == minIndex, `:=`(minStart, round(start/width)), by = .(seqnames))`: attempt access index 7/7 in VECTOR_ELT
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:::.fillHiCDOCDataSet(object)
8. └─HiCDOC:::.determineChromosomeSizes(object)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 29 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.1
Check: examples
Result: ERROR
Running examples in ‘treediff-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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 '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/treediff/extdata/Rep1-90-chr1_200000.bed' and '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/treediff/extdata/index.200000.longest18chr.abs.bed'.
Error in `[.data.table`(tabChromosomes, index == minIndex, `:=`(minStart, :
attempt access index 7/7 in VECTOR_ELT
Calls: HiC2Tree ... .fillHiCDOCDataSet -> .determineChromosomeSizes -> [ -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [15s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library("testthat")
> library("treediff")
>
> test_check("treediff")
Saving _problems/test-HiC2Tree-26.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 29 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-HiC2Tree.R:26:1'): (code run outside of `test_that()`) ─────────
Error in ``[.data.table`(tabChromosomes, index == minIndex, `:=`(minStart, round(start/width)), by = .(seqnames))`: attempt access index 7/7 in VECTOR_ELT
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:::.fillHiCDOCDataSet(object)
8. └─HiCDOC:::.determineChromosomeSizes(object)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 29 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
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 `[.data.table`(tabChromosomes, index == minIndex, `:=`(minStart, :
attempt access index 7/7 in VECTOR_ELT
Calls: HiC2Tree ... .fillHiCDOCDataSet -> .determineChromosomeSizes -> [ -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [26s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library("testthat")
> library("treediff")
>
> test_check("treediff")
Saving _problems/test-HiC2Tree-26.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 29 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-HiC2Tree.R:26:1'): (code run outside of `test_that()`) ─────────
Error in ``[.data.table`(tabChromosomes, index == minIndex, `:=`(minStart, round(start/width)), by = .(seqnames))`: attempt access index 7/7 in VECTOR_ELT
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:::.fillHiCDOCDataSet(object)
8. └─HiCDOC:::.determineChromosomeSizes(object)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 29 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
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-devel/treediff.Rcheck/treediff/extdata/Rep1-90-chr1_200000.bed' and '/data/gannet/ripley/R/packages/tests-devel/treediff.Rcheck/treediff/extdata/index.200000.longest18chr.abs.bed'.
Error in `[.data.table`(tabChromosomes, index == minIndex, `:=`(minStart, :
attempt access index 7/7 in VECTOR_ELT
Calls: HiC2Tree ... .fillHiCDOCDataSet -> .determineChromosomeSizes -> [ -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [23s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library("testthat")
> library("treediff")
>
> test_check("treediff")
Saving _problems/test-HiC2Tree-26.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 29 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-HiC2Tree.R:26:1'): (code run outside of `test_that()`) ─────────
Error in ``[.data.table`(tabChromosomes, index == minIndex, `:=`(minStart, round(start/width)), by = .(seqnames))`: attempt access index 7/7 in VECTOR_ELT
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:::.fillHiCDOCDataSet(object)
8. └─HiCDOC:::.determineChromosomeSizes(object)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 29 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc