Last updated on 2025-09-10 23:49:48 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.1 | 16.73 | 141.49 | 158.22 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.3.1 | 10.87 | 96.52 | 107.39 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.3.1 | 245.10 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.3.1 | 226.74 | OK | |||
| r-devel-windows-x86_64 | 1.3.1 | 24.00 | 154.00 | 178.00 | OK | |
| r-patched-linux-x86_64 | 1.3.1 | 16.22 | 133.39 | 149.61 | ERROR | |
| r-release-linux-x86_64 | 1.3.1 | 14.92 | 132.28 | 147.20 | ERROR | |
| r-release-macos-arm64 | 1.3.1 | 62.00 | OK | |||
| r-release-macos-x86_64 | 1.3.1 | 107.00 | OK | |||
| r-release-windows-x86_64 | 1.3.1 | 16.00 | 132.00 | 148.00 | OK | |
| r-oldrel-macos-arm64 | 1.3.1 | 75.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.3.1 | 94.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.3.1 | 23.00 | 185.00 | 208.00 | OK |
Version: 1.3.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [21s/24s]
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(ggplot2)
> library(OmicFlow)
Loading required package: R6
Loading required package: data.table
Loading required package: Matrix
> library(patchwork)
> set.seed(100)
> test_check("OmicFlow")
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
i Processing ... column: CONTRAST_sex
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
processing file: report.Rmd
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
[ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (9): 'test-alpha_diversity.R:15:3', 'test-composition.R:15:3',
'test-dfe.R:18:3', 'test-hill.R:12:3', 'test-metagenomics.R:15:3',
'test-ordination.R:17:3', 'test-subsetting.R:10:3',
'test-transformations.R:10:3', 'test-utils.R:15:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-autoflow.R:9:5'): Tests autoFlow report creation ───────────────
Error in `file(con, "w")`: cannot open the connection
Backtrace:
▆
1. ├─base::suppressWarnings(taxa$autoFlow(filename = output_file)) at test-autoflow.R:9:5
2. │ └─base::withCallingHandlers(...)
3. └─taxa$autoFlow(filename = output_file)
4. └─rmarkdown::render(...)
5. └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
6. └─xfun::write_utf8(res, output)
7. └─base::writeLines(enc2utf8(text), con, ..., useBytes = TRUE)
8. └─base::file(con, "w")
[ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.3.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/17s]
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(ggplot2)
> library(OmicFlow)
Loading required package: R6
Loading required package: data.table
Loading required package: Matrix
> library(patchwork)
> set.seed(100)
> test_check("OmicFlow")
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
i Processing ... column: CONTRAST_sex
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
processing file: report.Rmd
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
[ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (9): 'test-alpha_diversity.R:15:3', 'test-composition.R:15:3',
'test-dfe.R:18:3', 'test-hill.R:12:3', 'test-metagenomics.R:15:3',
'test-ordination.R:17:3', 'test-subsetting.R:10:3',
'test-transformations.R:10:3', 'test-utils.R:15:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-autoflow.R:9:5'): Tests autoFlow report creation ───────────────
Error in `file(con, "w")`: cannot open the connection
Backtrace:
▆
1. ├─base::suppressWarnings(taxa$autoFlow(filename = output_file)) at test-autoflow.R:9:5
2. │ └─base::withCallingHandlers(...)
3. └─taxa$autoFlow(filename = output_file)
4. └─rmarkdown::render(...)
5. └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
6. └─xfun::write_utf8(res, output)
7. └─base::writeLines(enc2utf8(text), con, ..., useBytes = TRUE)
8. └─base::file(con, "w")
[ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.3.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [20s/27s]
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(ggplot2)
> library(OmicFlow)
Loading required package: R6
Loading required package: data.table
Loading required package: Matrix
> library(patchwork)
> set.seed(100)
> test_check("OmicFlow")
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
i Processing ... column: CONTRAST_sex
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
processing file: report.Rmd
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
[ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (9): 'test-alpha_diversity.R:15:3', 'test-composition.R:15:3',
'test-dfe.R:18:3', 'test-hill.R:12:3', 'test-metagenomics.R:15:3',
'test-ordination.R:17:3', 'test-subsetting.R:10:3',
'test-transformations.R:10:3', 'test-utils.R:15:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-autoflow.R:9:5'): Tests autoFlow report creation ───────────────
Error in `file(con, "w")`: cannot open the connection
Backtrace:
▆
1. ├─base::suppressWarnings(taxa$autoFlow(filename = output_file)) at test-autoflow.R:9:5
2. │ └─base::withCallingHandlers(...)
3. └─taxa$autoFlow(filename = output_file)
4. └─rmarkdown::render(...)
5. └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
6. └─xfun::write_utf8(res, output)
7. └─base::writeLines(enc2utf8(text), con, ..., useBytes = TRUE)
8. └─base::file(con, "w")
[ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.3.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [19s/23s]
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(ggplot2)
> library(OmicFlow)
Loading required package: R6
Loading required package: data.table
Loading required package: Matrix
> library(patchwork)
> set.seed(100)
> test_check("OmicFlow")
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
i Processing ... column: CONTRAST_sex
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
processing file: report.Rmd
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
v Metadata template passed the JSON validation.
i Checking for duplicated identifiers ..
v featureData is loaded.
v countData is loaded.
v treeData is loaded.
i Final steps .. cleaning & creating back-up
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
## metagenomics-class object
## countData: [ 4 Samples and 242 Features ]
## metaData: [ 9 Variables and 4 Samples ]
## taxData: [ 7 Ranks and 242 Taxa ]
## treeData: [ 242 Tips and 241 Nodes ]
[ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (9): 'test-alpha_diversity.R:15:3', 'test-composition.R:15:3',
'test-dfe.R:18:3', 'test-hill.R:12:3', 'test-metagenomics.R:15:3',
'test-ordination.R:17:3', 'test-subsetting.R:10:3',
'test-transformations.R:10:3', 'test-utils.R:15:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-autoflow.R:9:5'): Tests autoFlow report creation ───────────────
Error in `file(con, "w")`: cannot open the connection
Backtrace:
▆
1. ├─base::suppressWarnings(taxa$autoFlow(filename = output_file)) at test-autoflow.R:9:5
2. │ └─base::withCallingHandlers(...)
3. └─taxa$autoFlow(filename = output_file)
4. └─rmarkdown::render(...)
5. └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
6. └─xfun::write_utf8(res, output)
7. └─base::writeLines(enc2utf8(text), con, ..., useBytes = TRUE)
8. └─base::file(con, "w")
[ FAIL 1 | WARN 0 | SKIP 9 | PASS 2 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
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