Caitlin Page
| Snapshot Date: 2026-01-15 13:40 -0500 (Thu, 15 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/Damsel |
| git_branch: devel |
| git_last_commit: 4c35e04 |
| git_last_commit_date: 2025-10-29 11:29:38 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-16 11:11 -0500 (Fri, 16 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4849 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4628 |
| 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 516/2343 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Damsel 1.7.0 (landing page) Caitlin Page
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the Damsel package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Damsel.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. |
| Package: Damsel |
| Version: 1.7.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:Damsel.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings Damsel_1.7.0.tar.gz |
| StartedAt: 2026-01-15 22:51:34 -0500 (Thu, 15 Jan 2026) |
| EndedAt: 2026-01-15 22:57:35 -0500 (Thu, 15 Jan 2026) |
| EllapsedTime: 361.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Damsel.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:Damsel.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings Damsel_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/Damsel.Rcheck’
* using R Under development (unstable) (2025-12-22 r89219)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Damsel/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Damsel’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘Damsel’ 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
ggplot_add:
function(object, plot, ...)
ggplot_add.peak:
function(object, plot, object_name)
ggplot_add:
function(object, plot, ...)
ggplot_add.dm:
function(object, plot, object_name)
ggplot_add:
function(object, plot, ...)
ggplot_add.gatc:
function(object, plot, object_name)
ggplot_add:
function(object, plot, ...)
ggplot_add.genes_tx:
function(object, plot, object_name)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
‘[magrittr:pipe]{%>%}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotWrap 20.211 1.270 21.482
annotatePeaksGenes 15.001 0.777 15.779
plotGeneOntology 9.819 1.142 11.176
geom_genes_tx 10.303 0.473 10.777
getGatcRegions 9.378 0.469 9.848
testGeneOntology 8.254 1.234 9.493
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/Damsel.Rcheck/00check.log’
for details.
Damsel.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL Damsel ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘Damsel’ ... ** this is package ‘Damsel’ version ‘1.7.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Damsel)
Damsel.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
> # 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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(Damsel)
>
> test_check("Damsel")
default spearman's method is used
default spearman's method is used
GATC regions required
Warning: stack imbalance in '::', 97 then 99
Bias will be n_regions that are contained within the gene length
Fetching GO annotations...
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
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
For 7 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
Bias will be n_regions that are contained within the gene length
Fetching GO annotations...
For 7 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
If gene is disproportional to the plot, use gene_limits = c(y1,y2). If gene is too large, recommend setting to c(0,2) and adjusting the plot.height accordingly.
No gene data available for this region
If gene is disproportional to the plot, use gene_limits = c(y1,y2). If gene is too large, recommend setting to c(0,2) and adjusting the plot.height accordingly.
No gene data available for this region
If gene is disproportional to the plot, use gene_limits = c(y1,y2). If gene is too large, recommend setting to c(0,2) and adjusting the plot.height accordingly.
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
Constructing graphics...
Scale for y is already present.
Adding another scale for y, which will replace the existing scale.
No data available for this region
No data available for this region
No data available for this region
No data available for this region
No data available for this region
If gene is disproportional to the plot, use gene_limits = c(y1,y2). If gene is too large, recommend setting to c(0,2) and adjusting the plot.height accordingly.
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
Constructing graphics...
Scale for y is already present.
Adding another scale for y, which will replace the existing scale.
120
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.25.1
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| ||
|| filt_dam1.bam ||
|| ||
|| Paired-end : yes ||
|| Count read pairs : yes ||
|| Annotation : R data.frame ||
|| Dir for temp files : . ||
|| Threads : 2 ||
|| Level : meta-feature level ||
|| Multimapping reads : counted (fractional) ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid1412703 ... ||
|| Features : 100 ||
|| Meta-features : 100 ||
|| Chromosomes/contigs : 1 ||
|| ||
|| Process BAM file filt_dam1.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 7 ||
|| Successfully assigned alignments : 7 (100.0%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.25.1
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| ||
|| filt_sd2.BAM ||
|| ||
|| Paired-end : no ||
|| Count read pairs : no ||
|| Annotation : R data.frame ||
|| Dir for temp files : . ||
|| Threads : 2 ||
|| Level : meta-feature level ||
|| Multimapping reads : counted (fractional) ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid1412703 ... ||
|| Features : 100 ||
|| Meta-features : 100 ||
|| Chromosomes/contigs : 1 ||
|| ||
|| Process BAM file filt_sd2.BAM... ||
|| Single-end reads are included. ||
|| Total alignments : 120 ||
|| Successfully assigned alignments : 120 (100.0%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
120
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.25.1
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| ||
|| filt_dam1.bam ||
|| ||
|| Paired-end : yes ||
|| Count read pairs : yes ||
|| Annotation : R data.frame ||
|| Dir for temp files : . ||
|| Threads : 2 ||
|| Level : meta-feature level ||
|| Multimapping reads : counted (fractional) ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid1412703 ... ||
|| Features : 100 ||
|| Meta-features : 100 ||
|| Chromosomes/contigs : 1 ||
|| ||
|| Process BAM file filt_dam1.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 7 ||
|| Successfully assigned alignments : 7 (100.0%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.25.1
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| ||
|| filt_sd2.BAM ||
|| ||
|| Paired-end : no ||
|| Count read pairs : no ||
|| Annotation : R data.frame ||
|| Dir for temp files : . ||
|| Threads : 2 ||
|| Level : meta-feature level ||
|| Multimapping reads : counted (fractional) ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid1412703 ... ||
|| Features : 100 ||
|| Meta-features : 100 ||
|| Chromosomes/contigs : 1 ||
|| ||
|| Process BAM file filt_sd2.BAM... ||
|| Single-end reads are included. ||
|| Total alignments : 120 ||
|| Successfully assigned alignments : 120 (100.0%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
[ FAIL 0 | WARN 20 | SKIP 0 | PASS 104 ]
[ FAIL 0 | WARN 20 | SKIP 0 | PASS 104 ]
>
> proc.time()
user system elapsed
62.061 2.646 70.976
Damsel.Rcheck/Damsel-Ex.timings
| name | user | system | elapsed | |
| annotatePeaksGenes | 15.001 | 0.777 | 15.779 | |
| collateGenes | 1.063 | 0.023 | 1.086 | |
| countBamInGATC | 0.109 | 0.026 | 0.181 | |
| geom_dm | 1.643 | 0.048 | 1.690 | |
| geom_gatc | 0.896 | 0.000 | 0.896 | |
| geom_genes_tx | 10.303 | 0.473 | 10.777 | |
| geom_peak | 1.890 | 0.011 | 1.902 | |
| getGatcRegions | 9.378 | 0.469 | 9.848 | |
| identifyPeaks | 0.107 | 0.000 | 0.107 | |
| makeDGE | 0.351 | 0.009 | 0.360 | |
| pipe | 0.004 | 0.000 | 0.005 | |
| plotCorrHeatmap | 0.677 | 0.045 | 0.722 | |
| plotCounts | 2.445 | 0.053 | 2.498 | |
| plotCountsDistribution | 0.387 | 0.001 | 0.388 | |
| plotCountsInPeaks | 0.793 | 0.015 | 0.809 | |
| plotGeneOntology | 9.819 | 1.142 | 11.176 | |
| plotWrap | 20.211 | 1.270 | 21.482 | |
| random_counts | 0.009 | 0.000 | 0.008 | |
| random_edgeR_results | 0.008 | 0.002 | 0.011 | |
| random_regions | 0.006 | 0.000 | 0.007 | |
| testDmRegions | 0.167 | 0.005 | 0.172 | |
| testGeneOntology | 8.254 | 1.234 | 9.493 | |