CRAN Package Check Results for Package MOCHA

Last updated on 2024-06-12 19:54:28 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.0 22.40 312.17 334.57 NOTE
r-devel-linux-x86_64-debian-gcc 1.1.0 0.49 1.92 2.41 ERROR
r-devel-linux-x86_64-fedora-clang 1.1.0 449.96 NOTE
r-devel-linux-x86_64-fedora-gcc 1.1.0 382.44 NOTE
r-devel-windows-x86_64 1.1.0 23.00 420.00 443.00 NOTE
r-patched-linux-x86_64 1.1.0 17.88 290.94 308.82 NOTE
r-release-linux-x86_64 1.1.0 20.85 291.06 311.91 NOTE
r-release-macos-arm64 1.1.0 5.00 ERROR
r-release-macos-x86_64 1.1.0 343.00 ERROR
r-release-windows-x86_64 1.1.0 24.00 409.00 433.00 NOTE
r-oldrel-macos-arm64 1.1.0 138.00 ERROR
r-oldrel-macos-x86_64 1.1.0 285.00 ERROR
r-oldrel-windows-x86_64 1.1.0 29.00 599.00 628.00 NOTE

Additional issues

noSuggests

Check Details

Version: 1.1.0
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-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.1.0
Check: package dependencies
Result: ERROR Packages required but not available: 'plyranges', 'dplyr', 'MultiAssayExperiment', 'stringr', 'ggbio', 'AnnotationDbi', 'GenomicFeatures', 'ensembldb', 'ggplot2', 'ggrepel', 'qvalue', 'tidyr', 'ggridges', 'tidyselect' Packages suggested but not available for checking: 'ArchR', 'RMariaDB', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'org.Hs.eg.db', 'chromVAR', 'testthat', 'glmmTMB', 'waldo', 'purrr', 'lmerTest', 'lme4', 'cowplot', 'mixtools' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.1.0
Check: package dependencies
Result: NOTE Package suggested but not available for checking: ‘ArchR’ Imports includes 31 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: 1.1.0
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene' Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 1.1.0
Check: package dependencies
Result: ERROR Package required but not available: ‘ggbio’ Packages suggested but not available for checking: 'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'BSgenome.Hsapiens.UCSC.hg19' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavor: r-release-macos-arm64

Version: 1.1.0
Check: package dependencies
Result: NOTE Packages suggested but not available for checking: 'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'BSgenome.Hsapiens.UCSC.hg19' Flavor: r-release-macos-x86_64

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [80s/157s] Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ── Error ('test_exportOpenTiles.R:13:3'): exportDifferentials 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. └─MOCHA::exportOpenTiles(...) at test_exportOpenTiles.R:13:3 2. └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome) 3. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked) 4. └─BSgenome:::.stopOnAvailablePkg(genome) [ FAIL 2 | WARN 13 | SKIP 23 | PASS 21 ] Error: Test failures Execution halted Flavor: r-release-macos-x86_64

Version: 1.1.0
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-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [45s/54s] Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ── Error ('test_exportOpenTiles.R:13:3'): exportDifferentials 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. └─MOCHA::exportOpenTiles(...) at test_exportOpenTiles.R:13:3 2. └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome) 3. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked) 4. └─BSgenome:::.stopOnAvailablePkg(genome) [ FAIL 2 | WARN 13 | SKIP 23 | PASS 21 ] Error: Test failures Execution halted Flavor: r-oldrel-macos-arm64

Version: 1.1.0
Check: running R code from vignettes
Result: WARN Errors in running code in vignettes: when running code in ‘COVID-walkthrough.Rmd’ ... > knitr::opts_chunk$set(collapse = TRUE, comment = "#>", + eval = FALSE) > library(MOCHA) > library(ArchR) When sourcing ‘COVID-walkthrough.R’: Error: there is no package called ‘ArchR’ Execution halted when running code in ‘ImportingFromOtherSources.Rmd’ ... The following objects are masked from ‘package:base’: intersect, t > library(SeuratDisk) When sourcing ‘ImportingFromOtherSources.R’: Error: there is no package called ‘SeuratDisk’ Execution halted ‘COVID-walkthrough.Rmd’ using ‘UTF-8’... failed ‘ImportingFromOtherSources.Rmd’ using ‘UTF-8’... failed Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 1.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [72s/124s] Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ── Error ('test_exportOpenTiles.R:13:3'): exportDifferentials 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. └─MOCHA::exportOpenTiles(...) at test_exportOpenTiles.R:13:3 2. └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome) 3. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked) 4. └─BSgenome:::.stopOnAvailablePkg(genome) [ FAIL 2 | WARN 13 | SKIP 23 | PASS 21 ] Error: Test failures Execution halted Flavor: r-oldrel-macos-x86_64