Matteo Calgaro
| Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/benchdamic |
| git_branch: devel |
| git_last_commit: 9f9c589 |
| git_last_commit_date: 2024-11-26 03:11:57 -0400 (Tue, 26 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-19 11:47 -0400 (Wed, 19 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4742 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 160/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| benchdamic 1.13.2 (landing page) Matteo Calgaro
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the benchdamic package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/benchdamic.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: benchdamic |
| Version: 1.13.2 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings benchdamic_1.13.2.tar.gz |
| StartedAt: 2025-03-19 04:21:29 -0000 (Wed, 19 Mar 2025) |
| EndedAt: 2025-03-19 04:36:49 -0000 (Wed, 19 Mar 2025) |
| EllapsedTime: 919.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: benchdamic.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:benchdamic.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings benchdamic_1.13.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/benchdamic.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘benchdamic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘benchdamic’ version ‘1.13.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
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.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘benchdamic’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘microbiome’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) DA_Seurat.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:33-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:42-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:47-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:59-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:62-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:64-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:68-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DA_Seurat.Rd:71-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) areaCAT.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) areaCAT.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) areaCAT.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) areaCAT.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) areaCAT.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) areaCAT.Rd:24-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) areaCAT.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) areaCAT.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createConcordance.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createConcordance.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createConcordance.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createConcordance.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createConcordance.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createConcordance.Rd:36-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createEnrichment.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createEnrichment.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createEnrichment.Rd:83-84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createEnrichment.Rd:85-86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createTIEC.Rd:17-19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createTIEC.Rd:20-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createTIEC.Rd:24-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createTIEC.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) createTIEC.Rd:31-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrichmentTest.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrichmentTest.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrichmentTest.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrichmentTest.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extractDA.Rd:62-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extractDA.Rd:64-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extractDA.Rd:67-70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getDA.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getDA.Rd:60-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getDA.Rd:63-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_counts_metadata.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_counts_metadata.Rd:34-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_counts_metadata.Rd:36-37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotConcordance.Rd:21-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotConcordance.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) set_Seurat.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:29-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:31-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:43-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:64-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:68-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) set_Seurat.Rd:72: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'norm_DESeq2.Rd':
‘[DESeq2]{estimateSizeFactors}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
fitDM.Rd: MGLMreg
fitHURDLE.Rd: zlm
fitNB.Rd: glmFit
fitZIG.Rd: fitZig
fitZINB.Rd: zinbFit
norm_edgeR.Rd: calcNormFactors
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘benchdamic-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotConcordance
> ### Title: plotConcordance
> ### Aliases: plotConcordance
>
> ### ** Examples
>
> data(ps_plaque_16S)
>
> # Balanced design
> my_splits <- createSplits(
+ object = ps_plaque_16S, varName = "HMP_BODY_SUBSITE", balanced = TRUE,
+ paired = "RSID", N = 10 # N = 100 suggested
+ )
Warning in createSplits(object = ps_plaque_16S, varName = "HMP_BODY_SUBSITE", :
The variable HMP_BODY_SUBSITE is not a factor. Coercing to factor.
Working on 30 paired samples. 2 repeated measures for each RSID ID.
>
> # Make sure the subject ID variable is a factor
> phyloseq::sample_data(ps_plaque_16S)[, "RSID"] <- as.factor(
+ phyloseq::sample_data(ps_plaque_16S)[["RSID"]])
>
> # Initialize some limma based methods
> my_limma <- set_limma(design = ~ RSID + HMP_BODY_SUBSITE,
+ coef = "HMP_BODY_SUBSITESupragingival Plaque",
+ norm = c("TMM", "CSS"))
Warning in set_limma(design = ~RSID + HMP_BODY_SUBSITE, coef = "HMP_BODY_SUBSITESupragingival Plaque", :
DA_limma
One or more elements into 'norm' are not native to edgeR.
>
> # Set the normalization methods according to the DA methods
> my_norm <- setNormalizations(fun = c("norm_edgeR", "norm_CSS"),
+ method = c("TMM", "CSS"))
>
> # Run methods on split datasets
> results <- runSplits(split_list = my_splits, method_list = my_limma,
+ normalization_list = my_norm, object = ps_plaque_16S)
- Subset1
- Comparison1
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE
Differential abundance on TMM normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
- Comparison2
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE
Differential abundance on TMM normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
- Comparison3
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE
Differential abundance on TMM normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
- Comparison4
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE
Differential abundance on TMM normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
- Comparison5
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE
Differential abundance on TMM normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
- Comparison6
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE
Differential abundance on TMM normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
- Comparison7
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE
Differential abundance on TMM normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
- Comparison8
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE
Differential abundance on TMM normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
- Comparison9
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE
Differential abundance on TMM normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
- Comparison10
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE
Differential abundance on TMM normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
- Subset2
- Comparison1
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE
Differential abundance on TMM normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
- Comparison2
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE
Differential abundance on TMM normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
- Comparison3
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE
Differential abundance on TMM normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
- Comparison4
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE
Differential abundance on TMM normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
- Comparison5
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE
Differential abundance on TMM normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
- Comparison6
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE
Differential abundance on TMM normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
- Comparison7
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=TMM, weights=FALSE
Differential abundance on TMM normalized data
Estimating Differential Abundance without weighting
Extracting results for HMP_BODY_SUBSITESupragingival Plaque coefficient
- Comparison8
Splitting the samples...
Keeping taxa with more than 0 counts in more than 0 samples.
Computing normalizations...
+ Running now:norm_edgeR
Parameters:method=TMM
NF.TMM column has been added.
+ Running now:norm_CSS
Parameters:method=CSS
Default value being used.
NF.CSS column has been added.
Differential abundance:
* Running now:DA_limma
Parameters:assay_name=counts, pseudo_count=FALSE, design=~RSID + HMP_BODY_SUBSITE, coef=HMP_BODY_SUBSITESupragingival Plaque, norm=CSS, weights=FALSE
Warning in DA_limma(object = new("phyloseq", otu_table = new("otu_table", :
DA_limma
CSS normalization is not a native edgeR normalization. Make sure you know what you are doing, otherwise choose between 'TMM', 'TMMwsp', 'RLE', 'upperquartile', 'posupperquartile', or 'none'.
Automatically converting NF.CSS scaling/size factors to normalization factors.
Differential abundance on CSS normalized data
Estimating Differential Abundance without weighting
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
createConcordance 7.368 0.018 8.515
areaCAT 6.283 0.055 7.755
DA_ALDEx2 5.480 0.220 5.715
DA_DESeq2 5.437 0.068 5.519
createTIEC 4.041 0.021 6.023
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’/home/biocbuild/R/R/bin/BATCH: line 60: 118085 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(benchdamic)
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/benchdamic.Rcheck/00check.log’
for details.
benchdamic.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL benchdamic ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘benchdamic’ ... ** this is package ‘benchdamic’ version ‘1.13.2’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics' Also defined by ‘spam’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics' Also defined by ‘spam’ ** testing if installed package can be loaded from final location Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics' Also defined by ‘spam’ ** testing if installed package keeps a record of temporary installation path * DONE (benchdamic)
benchdamic.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(benchdamic)
benchdamic.Rcheck/benchdamic-Ex.timings
| name | user | system | elapsed | |
| CAT | 0.006 | 0.000 | 0.006 | |
| DA_ALDEx2 | 5.480 | 0.220 | 5.715 | |
| DA_ANCOM | 1.196 | 0.044 | 1.242 | |
| DA_DESeq2 | 5.437 | 0.068 | 5.519 | |
| DA_MAST | 1.878 | 0.044 | 1.925 | |
| DA_Maaslin2 | 0.316 | 0.012 | 0.338 | |
| DA_NOISeq | 1.737 | 0.027 | 1.772 | |
| DA_Seurat | 2.368 | 0.084 | 2.459 | |
| DA_ZicoSeq | 1.041 | 0.008 | 1.053 | |
| DA_basic | 0.042 | 0.000 | 0.043 | |
| DA_corncob | 1.301 | 0.044 | 1.378 | |
| DA_dearseq | 0.074 | 0.000 | 0.075 | |
| DA_edgeR | 0.248 | 0.000 | 0.251 | |
| DA_limma | 0.099 | 0.000 | 0.100 | |
| DA_linda | 0.073 | 0.000 | 0.073 | |
| DA_metagenomeSeq | 0.36 | 0.00 | 0.37 | |
| DA_mixMC | 0.956 | 0.000 | 1.051 | |
| RMSE | 0.001 | 0.000 | 0.001 | |
| addKnowledge | 0.232 | 0.000 | 0.233 | |
| areaCAT | 6.283 | 0.055 | 7.755 | |
| checkNormalization | 0 | 0 | 0 | |
| createColors | 0.007 | 0.000 | 0.007 | |
| createConcordance | 7.368 | 0.018 | 8.515 | |
| createEnrichment | 0.363 | 0.000 | 0.363 | |
| createMocks | 0.003 | 0.001 | 0.003 | |
| createPositives | 1.390 | 0.014 | 2.659 | |
| createSplits | 0.049 | 0.008 | 0.113 | |
| createTIEC | 4.041 | 0.021 | 6.023 | |
| enrichmentTest | 0.191 | 0.000 | 0.381 | |
| extractDA | 0.284 | 0.000 | 0.570 | |
| extractStatistics | 0.279 | 0.004 | 0.581 | |
| fitDM | 0.050 | 0.000 | 0.111 | |
| fitHURDLE | 1.079 | 0.004 | 1.276 | |
| fitModels | 3.474 | 0.036 | 4.052 | |
| fitNB | 0.06 | 0.00 | 0.06 | |
| fitZIG | 0.070 | 0.000 | 0.071 | |
| fitZINB | 0.642 | 0.000 | 0.663 | |
| getDA | 0.157 | 0.000 | 0.166 | |
| getPositives | 0.114 | 0.000 | 0.115 | |
| getStatistics | 0.099 | 0.000 | 0.099 | |
| get_counts_metadata | 0.158 | 0.004 | 0.193 | |
| iterative_ordering | 0.014 | 0.000 | 0.018 | |
| meanDifferences | 0.002 | 0.000 | 0.002 | |
| norm_CSS | 0.099 | 0.000 | 0.100 | |
| norm_DESeq2 | 0.664 | 0.000 | 0.982 | |
| norm_TSS | 0.052 | 0.000 | 0.104 | |
| norm_edgeR | 0.059 | 0.000 | 0.120 | |