Last updated on 2023-09-24 12:28:23 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 21.79 | 364.93 | 386.72 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 19.67 | 292.38 | 312.05 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 445.45 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 467.27 | NOTE | |||
| r-devel-windows-x86_64 | 1.0.0 | 26.00 | 532.00 | 558.00 | NOTE | |
| r-patched-linux-x86_64 | 1.0.0 | 17.07 | 345.04 | 362.11 | NOTE | |
| r-release-linux-x86_64 | 1.0.0 | 17.01 | 342.47 | 359.48 | NOTE | |
| r-release-macos-arm64 | 1.0.0 | 89.00 | ERROR | |||
| r-release-macos-x86_64 | 1.0.0 | 218.00 | ERROR | |||
| r-release-windows-x86_64 | 1.0.0 | 30.00 | 486.00 | 516.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.0.0 | 9.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 1.0.0 | 11.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 1.0.0 | 30.00 | 457.00 | 487.00 | ERROR |
Version: 1.0.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘ArchR’
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
Version: 1.0.0
Check: Rd \usage sections
Result: NOTE
Documented arguments not in \usage in documentation object 'simplifiedSampleTile':
‘x’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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
Version: 1.0.0
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene'
Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.0
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: 'purrr'
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.0
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene'
Flavors: r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64
Version: 1.0.0
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene',
'BSgenome.Hsapiens.UCSC.hg19', 'chromVAR'
Flavors: r-release-macos-arm64, r-release-macos-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [25s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
2. │ └─base::withVisible(...elt(i))
3. └─MOCHA::testCoAccessibilityRandom(...)
4. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
── Error ('test_testCoAccessibilityRandom.R:64:3'): testCoAccessibleLinks works on a 3 sample test dataset ──
Error in `combineSampleTileMatrix(SampleTileObj)`: Package 'chromVAR' is required for combineSampleTileMatrix. Please install 'chromVAR' to proceed.
Backtrace:
▆
1. ├─utils::capture.output(...) at test_testCoAccessibilityRandom.R:64:2
2. │ └─base::withVisible(...elt(i))
3. └─MOCHA::testCoAccessibilityRandom(...)
4. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
[ FAIL 7 | WARN 3 | SKIP 17 | PASS 21 ]
Error: Test failures
Execution halted
Flavor: r-release-macos-arm64
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [34s/66s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
2. │ └─base::withVisible(...elt(i))
3. └─MOCHA::testCoAccessibilityRandom(...)
4. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
── Error ('test_testCoAccessibilityRandom.R:64:3'): testCoAccessibleLinks works on a 3 sample test dataset ──
Error in `combineSampleTileMatrix(SampleTileObj)`: Package 'chromVAR' is required for combineSampleTileMatrix. Please install 'chromVAR' to proceed.
Backtrace:
▆
1. ├─utils::capture.output(...) at test_testCoAccessibilityRandom.R:64:2
2. │ └─base::withVisible(...elt(i))
3. └─MOCHA::testCoAccessibilityRandom(...)
4. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
[ FAIL 7 | WARN 3 | SKIP 17 | PASS 21 ]
Error: Test failures
Execution halted
Flavor: r-release-macos-x86_64
Version: 1.0.0
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene',
'BSgenome.Hsapiens.UCSC.hg19'
Flavors: r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running 'testthat.R' [359s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(MOCHA)
>
> test_check("MOCHA")
Loading required package: RaggedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
harmonizing input:
removing 1 sampleMap rows not in names(experiments)
removing 1 sampleMap rows with 'colname' not in colnames of experiments
removing 1 colData rownames not in sampleMap 'primary'
harmonizing input:
removing 3 sampleMap rows not in names(experiments)
removing 3 sampleMap rows with 'colname' not in colnames of experiments
removing 3 colData rownames not in sampleMap 'primary'
[ FAIL 9 | WARN 2 | SKIP 17 | PASS 21 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test_COVID_data_pipeline.R:1:1', 'test_MotifEnrichment.R:1:1',
'test_MotifSetEnrichmentAnalysis.R:1:1', 'test_addMotifSet.R:1:1',
'test_callOpenTiles.R:3:1', 'test_extractRegion.R:1:1',
'test_getCoAccessibleLinks.R:22:3', 'test_getCoAccessibleLinks.R:53:3',
'test_getCoverage.R:1:1', 'test_getDifferentialAccessibleTiles.R:1:1',
'test_getPopFrags.R:13:1', 'test_getSampleTileMatrix.R:18:3',
'test_subsetMOCHAObject.R:13:3', 'test_subsetMOCHAObject.R:25:3',
'test_subsetMOCHAObject.R:67:3', 'test_subsetMOCHAObject.R:97:3',
'test_subsetMOCHAObject.R:127:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_combineSampleTileMatrix.R:12:5'): combineSampleTileMatrix works on a 3-sample dataset ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. └─MOCHA::combineSampleTileMatrix(STObj) at test_combineSampleTileMatrix.R:12:4
2. └─BSgenome::getBSgenome(genome)
3. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
4. └─BSgenome:::.stopOnAvailablePkg(genome)
── Error ('test_combineSampleTileMatrix.R:30:5'): combineSampleTileMatrix works on a 1-sample dataset ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. └─MOCHA::combineSampleTileMatrix(STObj) at test_combineSampleTileMatrix.R:30:4
2. └─BSgenome::getBSgenome(genome)
3. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
4. └─BSgenome:::.stopOnAvailablePkg(genome)
── Error ('test_dimensionalityReduction.R:31:5'): bulkDimReduction works on a 3 sample test dataset ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. ├─utils::capture.output(...) at test_dimensionalityReduction.R:31:4
2. │ └─base::withVisible(...elt(i))
3. └─MOCHA::bulkDimReduction(SampleTileMatrix, cellType = "all", componentNumber = 2)
4. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
5. └─BSgenome::getBSgenome(genome)
6. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
7. └─BSgenome:::.stopOnAvailablePkg(genome)
── Error ('test_dimensionalityReduction.R:51:5'): bulkDimReduction errors NA columns ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. ├─testthat::expect_error(...) at test_dimensionalityReduction.R:51:4
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─MOCHA::bulkDimReduction(SampleTileMatrix, cellType = "all", componentNumber = 2)
8. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
9. └─BSgenome::getBSgenome(genome)
10. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
11. └─BSgenome:::.stopOnAvailablePkg(genome)
── Error ('test_testCoAccessibilityChromVar.R:23:3'): testCoAccessibleLinks works on a 1 sample test dataset ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:23:2
2. │ └─base::withVisible(...elt(i))
3. └─MOCHA::testCoAccessibilityChromVar(...)
4. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
5. └─BSgenome::getBSgenome(genome)
6. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
7. └─BSgenome:::.stopOnAvailablePkg(genome)
── Error ('test_testCoAccessibilityChromVar.R:65:3'): testCoAccessibleLinks works on a 3 sample test dataset ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:65:2
2. │ └─base::withVisible(...elt(i))
3. └─MOCHA::testCoAccessibilityChromVar(...)
4. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
5. └─BSgenome::getBSgenome(genome)
6. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
7. └─BSgenome:::.stopOnAvailablePkg(genome)
── Error ('test_testCoAccessibilityChromVar.R:107:3'): testCoAccessibleLinks works on a 3 sample test dataset with highMem=TRUE ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:107:2
2. │ └─base::withVisible(...elt(i))
3. └─MOCHA::testCoAccessibilityChromVar(...)
4. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
5. └─BSgenome::getBSgenome(genome)
6. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
7. └─BSgenome:::.stopOnAvailablePkg(genome)
── Error ('test_testCoAccessibilityRandom.R:23:3'): testCoAccessibleLinks works on a 1 sample test dataset ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. ├─utils::capture.output(...) at test_testCoAccessibilityRandom.R:23:2
2. │ └─base::withVisible(...elt(i))
3. └─MOCHA::testCoAccessibilityRandom(...)
4. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
5. └─BSgenome::getBSgenome(genome)
6. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
7. └─BSgenome:::.stopOnAvailablePkg(genome)
── Error ('test_testCoAccessibilityRandom.R:64:3'): testCoAccessibleLinks works on a 3 sample test dataset ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. ├─utils::capture.output(...) at test_testCoAccessibilityRandom.R:64:2
2. │ └─base::withVisible(...elt(i))
3. └─MOCHA::testCoAccessibilityRandom(...)
4. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
5. └─BSgenome::getBSgenome(genome)
6. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
7. └─BSgenome:::.stopOnAvailablePkg(genome)
[ FAIL 9 | WARN 2 | SKIP 17 | PASS 21 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 1.0.0
Check: package dependencies
Result: ERROR
Packages required but not available:
'plyranges', 'RaggedExperiment', 'MultiAssayExperiment', 'ggbio',
'OrganismDbi'
Packages suggested but not available for checking:
'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene',
'BSgenome.Hsapiens.UCSC.hg19', 'chromVAR'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-arm64
Version: 1.0.0
Check: package dependencies
Result: ERROR
Packages required but not available: 'RaggedExperiment', 'ggbio'
Packages suggested but not available for checking:
'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene',
'BSgenome.Hsapiens.UCSC.hg19'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-oldrel-macos-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running 'testthat.R' [340s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(MOCHA)
>
> test_check("MOCHA")
Loading required package: RaggedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
harmonizing input:
removing 1 sampleMap rows not in names(experiments)
removing 1 sampleMap rows with 'colname' not in colnames of experiments
removing 1 colData rownames not in sampleMap 'primary'
harmonizing input:
removing 3 sampleMap rows not in names(experiments)
removing 3 sampleMap rows with 'colname' not in colnames of experiments
removing 3 colData rownames not in sampleMap 'primary'
[ FAIL 9 | WARN 2 | SKIP 17 | PASS 21 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test_COVID_data_pipeline.R:1:1', 'test_MotifEnrichment.R:1:1',
'test_MotifSetEnrichmentAnalysis.R:1:1', 'test_addMotifSet.R:1:1',
'test_callOpenTiles.R:3:1', 'test_extractRegion.R:1:1',
'test_getCoAccessibleLinks.R:22:3', 'test_getCoAccessibleLinks.R:53:3',
'test_getCoverage.R:1:1', 'test_getDifferentialAccessibleTiles.R:1:1',
'test_getPopFrags.R:13:1', 'test_getSampleTileMatrix.R:18:3',
'test_subsetMOCHAObject.R:13:3', 'test_subsetMOCHAObject.R:25:3',
'test_subsetMOCHAObject.R:67:3', 'test_subsetMOCHAObject.R:97:3',
'test_subsetMOCHAObject.R:127:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_combineSampleTileMatrix.R:12:5'): combineSampleTileMatrix works on a 3-sample dataset ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. └─MOCHA::combineSampleTileMatrix(STObj) at test_combineSampleTileMatrix.R:12:4
2. └─BSgenome::getBSgenome(genome)
3. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
4. └─BSgenome:::.stopOnAvailablePkg(genome)
── Error ('test_combineSampleTileMatrix.R:30:5'): combineSampleTileMatrix works on a 1-sample dataset ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. └─MOCHA::combineSampleTileMatrix(STObj) at test_combineSampleTileMatrix.R:30:4
2. └─BSgenome::getBSgenome(genome)
3. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
4. └─BSgenome:::.stopOnAvailablePkg(genome)
── Error ('test_dimensionalityReduction.R:31:5'): bulkDimReduction works on a 3 sample test dataset ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. ├─utils::capture.output(...) at test_dimensionalityReduction.R:31:4
2. │ └─base::withVisible(...elt(i))
3. └─MOCHA::bulkDimReduction(SampleTileMatrix, cellType = "all", componentNumber = 2)
4. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
5. └─BSgenome::getBSgenome(genome)
6. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
7. └─BSgenome:::.stopOnAvailablePkg(genome)
── Error ('test_dimensionalityReduction.R:51:5'): bulkDimReduction errors NA columns ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. ├─testthat::expect_error(...) at test_dimensionalityReduction.R:51:4
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─MOCHA::bulkDimReduction(SampleTileMatrix, cellType = "all", componentNumber = 2)
8. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
9. └─BSgenome::getBSgenome(genome)
10. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
11. └─BSgenome:::.stopOnAvailablePkg(genome)
── Error ('test_testCoAccessibilityChromVar.R:23:3'): testCoAccessibleLinks works on a 1 sample test dataset ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:23:2
2. │ └─base::withVisible(...elt(i))
3. └─MOCHA::testCoAccessibilityChromVar(...)
4. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
5. └─BSgenome::getBSgenome(genome)
6. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
7. └─BSgenome:::.stopOnAvailablePkg(genome)
── Error ('test_testCoAccessibilityChromVar.R:65:3'): testCoAccessibleLinks works on a 3 sample test dataset ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:65:2
2. │ └─base::withVisible(...elt(i))
3. └─MOCHA::testCoAccessibilityChromVar(...)
4. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
5. └─BSgenome::getBSgenome(genome)
6. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
7. └─BSgenome:::.stopOnAvailablePkg(genome)
── Error ('test_testCoAccessibilityChromVar.R:107:3'): testCoAccessibleLinks works on a 3 sample test dataset with highMem=TRUE ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:107:2
2. │ └─base::withVisible(...elt(i))
3. └─MOCHA::testCoAccessibilityChromVar(...)
4. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
5. └─BSgenome::getBSgenome(genome)
6. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
7. └─BSgenome:::.stopOnAvailablePkg(genome)
── Error ('test_testCoAccessibilityRandom.R:23:3'): testCoAccessibleLinks works on a 1 sample test dataset ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. ├─utils::capture.output(...) at test_testCoAccessibilityRandom.R:23:2
2. │ └─base::withVisible(...elt(i))
3. └─MOCHA::testCoAccessibilityRandom(...)
4. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
5. └─BSgenome::getBSgenome(genome)
6. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
7. └─BSgenome:::.stopOnAvailablePkg(genome)
── Error ('test_testCoAccessibilityRandom.R:64:3'): testCoAccessibleLinks works on a 3 sample test dataset ──
Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
You first need to install it, which you can do with:
library(BiocManager)
install("BSgenome.Hsapiens.UCSC.hg19")
Backtrace:
▆
1. ├─utils::capture.output(...) at test_testCoAccessibilityRandom.R:64:2
2. │ └─base::withVisible(...elt(i))
3. └─MOCHA::testCoAccessibilityRandom(...)
4. └─MOCHA::combineSampleTileMatrix(SampleTileObj)
5. └─BSgenome::getBSgenome(genome)
6. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
7. └─BSgenome:::.stopOnAvailablePkg(genome)
[ FAIL 9 | WARN 2 | SKIP 17 | PASS 21 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64