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R CMD BUILD
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* checking for file DOtools/DESCRIPTION ... OK
* preparing DOtools:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building DOtools_0.99.7.tar.gz
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BiocCheckGitClone('DOtools')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3869/c1cfe1b58a6aaa539ee443b830ccb6943d31be9a/DOtools
BiocVersion: 3.22
Package: DOtools
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3869/c1cfe1b58a6aaa539ee443b830ccb6943d31be9a/DOtools.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3869/c1cfe1b58a6aaa539ee443b830ccb6943d31be9a/DOtools
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
BiocCheck v1.45.18 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3869/c1cfe1b58a6aaa539ee443b830ccb6943d31be9a/DOtools.Rcheck
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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
* using option --no-vignettes
* checking for file DOtools/DESCRIPTION ... OK
* this is package DOtools version 0.99.7
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section Package
structure in the Writing R Extensions manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package DOtools can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See /home/pkgbuild/packagebuilder/workers/jobs/3869/c1cfe1b58a6aaa539ee443b830ccb6943d31be9a/DOtools.Rcheck/00install.out for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [12s/12s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [44s/44s] NOTE
.annoSegment: no visible global function definition for useMyCol
DO.BarplotClustert: no visible global function definition for is
DO.BarplotClustert : SEM: no visible global function definition for
var
DO.BarplotClustert: no visible global function definition for
setNames
DO.BarplotClustert: no visible binding for global variable variable
DO.BarplotClustert: no visible binding for global variable value
DO.BarplotClustert: no visible binding for global variable orig.ident
DO.BarplotClustert: no visible binding for global variable Mean
DO.BarplotWilcox: no visible global function definition for is
DO.BarplotWilcox : SEM: no visible global function definition for var
DO.BarplotWilcox: no visible global function definition for setNames
DO.BarplotWilcox: no visible binding for global variable variable
DO.BarplotWilcox: no visible binding for global variable value
DO.BarplotWilcox: no visible binding for global variable orig.ident
DO.BarplotWilcox: no visible binding for global variable Mean
DO.BoxPlot: no visible global function definition for is
DO.BoxPlot: no visible global function definition for setNames
DO.BoxPlot: no visible binding for global variable variable
DO.BoxPlot: no visible binding for global variable value
DO.BoxPlot: no visible binding for global variable all_zeros
DO.BoxPlot: no visible binding for global variable group_count
DO.BoxPlot: no visible global function definition for quantile
DO.CellComposition: no visible global function definition for is
DO.CellComposition: no visible binding for global variable variable
DO.CellComposition: no visible binding for global variable freq
DO.CellComposition: no visible binding for global variable proportion
DO.CellComposition: no visible binding for global variable p_val
DO.CellTypist: no visible global function definition for is
DO.CellTypist: no visible global function definition for as
DO.CellTypist: no visible binding for global variable cluster
DO.CellTypist: no visible binding for global variable .
DO.CellTypist: no visible binding for global variable label
DO.CellTypist: no visible binding for global variable prob
DO.CellTypist: no visible binding for global variable pct.exp
DO.Correlation: no visible global function definition for is
DO.Correlation: no visible global function definition for cor
DO.DietSCE: no visible global function definition for is
DO.DietSCE: no visible global function definition for slotNames
DO.Dotplot: no visible global function definition for is
DO.Dotplot : <anonymous>: no visible binding for global variable .
DO.Dotplot: no visible binding for global variable .
DO.Dotplot: no visible global function definition for complete.cases
DO.Dotplot: no visible binding for global variable gene
DO.Dotplot: no visible binding for global variable avg.exp
DO.Dotplot: no visible binding for global variable pct.exp
DO.Dotplot: no visible binding for global variable xaxis
DO.Dotplot: no visible binding for global variable group
DO.Dotplot: no visible global function definition for sd
DO.Dotplot: no visible binding for global variable p_val_adj
DO.Dotplot: no visible global function definition for quantile
DO.Dotplot: no visible binding for global variable stars
DO.Dotplot: no visible binding for global variable significance
DO.FullRecluster: no visible global function definition for is
DO.Heatmap: no visible global function definition for is
DO.Heatmap : <anonymous>: no visible global function definition for
heatmap
DO.Import : <anonymous> : <anonymous>: no visible global function
definition for read.csv
DO.Import: no visible binding for global variable nFeature_RNA
DO.Import: no visible binding for global variable nCount_RNA
DO.Import: no visible binding for global variable label
DO.Import: no visible global function definition for quantile
DO.Import: no visible binding for global variable UMI
DO.Import: no visible binding for global variable scDblFinder_class
DO.Integration: no visible global function definition for is
DO.MultiDGE: no visible global function definition for is
DO.MultiDGE: no visible binding for global variable p_val
DO.MultiDGE: no visible binding for global variable p_val_adj
DO.MultiDGE: no visible binding for global variable avg_log2FC
DO.MultiDGE: no visible binding for global variable gene
DO.MultiDGE: no visible binding for global variable condition
DO.MultiDGE: no visible binding for global variable p_val_PB_DESeq2
DO.MultiDGE: no visible binding for global variable
p_val_adj_PB_DESeq2
DO.MultiDGE: no visible binding for global variable
avg_log2FC_PB_DESeq2
DO.MultiDGE: no visible binding for global variable .
DO.SplitBarGSEA : <anonymous>: no visible global function definition
for split_bar_gsea
DO.Subset: no visible global function definition for is
DO.Subset: no visible global function definition for as
DO.TransferLabel: no visible global function definition for is
DO.UMAP: no visible global function definition for is
DO.VlnPlot: no visible global function definition for is
DO.VlnPlot: no visible global function definition for setNames
DO.VlnPlot: no visible binding for global variable variable
DO.VlnPlot: no visible binding for global variable value
DO.VlnPlot: no visible binding for global variable all_zeros
DO.VlnPlot: no visible binding for global variable group_count
DO.scVI: no visible global function definition for is
DO.scVI : <anonymous>: no visible global function definition for
run_scvi
Undefined global functions or variables:
. Mean UMI all_zeros as avg.exp avg_log2FC avg_log2FC_PB_DESeq2
cluster complete.cases condition cor freq gene group group_count
heatmap is label nCount_RNA nFeature_RNA orig.ident p_val
p_val_PB_DESeq2 p_val_adj p_val_adj_PB_DESeq2 pct.exp prob proportion
quantile read.csv run_scvi scDblFinder_class sd setNames significance
slotNames split_bar_gsea stars useMyCol value var variable xaxis
Consider adding
importFrom("graphics", "stars")
importFrom("methods", "as", "is", "slotNames")
importFrom("stats", "complete.cases", "cor", "heatmap", "quantile",
"sd", "setNames", "var")
importFrom("utils", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* 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 line endings in shell scripts ... OK
* checking files in vignettes ... OK
* checking examples ... [121s/251s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DO.Integration 22.943 0.779 23.722
DO.CellComposition 8.638 4.379 8.170
DO.CellTypist 10.742 1.434 140.201
DO.SplitBarGSEA 6.631 0.137 10.420
DO.enrichR 6.476 0.265 10.281
DO.MultiDGE 6.151 0.033 6.185
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [357s/356s]
[357s/356s] ERROR
Running the tests in tests/testthat.R failed.
Last 20 lines of output:
Downloading healthy raw to /tmp/RtmpRb21Pa/dotools_test_699884db26c9b/healthy/outs/raw_feature_bc_matrix.h5
Mock download https://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_10k_protein_v3/pbmc_10k_protein_v3_raw_feature_bc_matrix.h5 -> /tmp/RtmpRb21Pa/dotools_test_699884db26c9b/healthy/outs/raw_feature_bc_matrix.h5
Downloading disease filtered to /tmp/RtmpRb21Pa/dotools_test_699884db26c9b/disease/outs/filtered_feature_bc_matrix.h5
Mock download https://cf.10xgenomics.com/samples/cell-exp/3.0.0/malt_10k_protein_v3/malt_10k_protein_v3_filtered_feature_bc_matrix.h5 -> /tmp/RtmpRb21Pa/dotools_test_699884db26c9b/disease/outs/filtered_feature_bc_matrix.h5
Downloading disease raw to /tmp/RtmpRb21Pa/dotools_test_699884db26c9b/disease/outs/raw_feature_bc_matrix.h5
Mock download https://cf.10xgenomics.com/samples/cell-exp/3.0.0/malt_10k_protein_v3/malt_10k_protein_v3_raw_feature_bc_matrix.h5 -> /tmp/RtmpRb21Pa/dotools_test_699884db26c9b/disease/outs/raw_feature_bc_matrix.h5
[ FAIL 1 | WARN 97 | SKIP 0 | PASS 414 ]
Failed tests
Error ('test-DO.CellBender.R:14:3'): .DO.BarcodeRanks returns correct names and numeric values
Error in `.barcode_ranks(assay(m, assay.type), ...)`: insufficient unique points for computing knee/inflection points
Backtrace:
1. DOtools:::.DO.BarcodeRanks(sce) at test-DO.CellBender.R:14:3
2. DropletUtils::barcodeRanks(SCE_obj)
3. DropletUtils::barcodeRanks(SCE_obj)
4. DropletUtils (local) .local(m, ...)
5. DropletUtils:::.barcode_ranks(assay(m, assay.type), ...)
[ FAIL 1 | WARN 97 | SKIP 0 | PASS 414 ]
Error: Test failures
Execution halted
* 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 ... [4s/4s] OK
* DONE
Status: 1 ERROR, 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3869/c1cfe1b58a6aaa539ee443b830ccb6943d31be9a/DOtools.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('DOtools_0.99.7.tar.gz')
===============================
Installing DOtools
Package installed successfully
DOtools session metadata
sourceDir: /tmp/Rtmpw66bqF/file69b3c7775ae3d/DOtools
BiocVersion: 3.22
Package: DOtools
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3869/c1cfe1b58a6aaa539ee443b830ccb6943d31be9a/DOtools.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /tmp/Rtmpw66bqF/file69b3c7775ae3d/DOtools
installDir: /tmp/Rtmpw66bqF/file69b3c4c2eaaef
isTarBall: TRUE
platform: unix
Running BiocCheck on DOtools
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (19%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of DOtools...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 25
functions greater than 50 lines.
The longest 5 functions are:
DO.Dotplot() (R/DO.Dotplot.R): 913 lines
...
DO.CellComposition() (R/DO.CellComposition.R): 487 lines
* Checking man page documentation...
Registered S3 method overwritten by 'zellkonverter':
method from
py_to_r.pandas.core.arrays.categorical.Categorical reticulate
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
DO.CellBender.Rd
DO.Import.Rd
DO.scVI.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 11% of man
pages use at least one of these tags.
Found in files:
DO.CellBender.Rd
DO.Import.Rd
DO.scVI.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
DO.CellBender.Rd
DO.Import.Rd
DO.scVI.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.45.18 results
0 ERRORS | 0 WARNINGS | i 4 NOTES
i See the DOtools.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.