===============================
R CMD BUILD
===============================
* 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_0.99.1.tar.gz’
===============================
BiocCheckGitClone('DOtools')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3869/302e6d0b8a5bdeb35069c6402137467873293a37/DOtools
→ BiocVersion: 3.22
→ Package: DOtools
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3869/302e6d0b8a5bdeb35069c6402137467873293a37/DOtools.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3869/302e6d0b8a5bdeb35069c6402137467873293a37/DOtools
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• DOtools.Rproj
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* 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 v1.45.12 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3869/302e6d0b8a5bdeb35069c6402137467873293a37/DOtools.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DOtools/DESCRIPTION’ ... OK
* this is package ‘DOtools’ version ‘0.99.1’
* 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 ... OK
* 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/3869/302e6d0b8a5bdeb35069c6402137467873293a37/DOtools.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [11s/11s] 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 ... [41s/41s] 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 global function definition for ‘quantile’
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.table’
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.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: no visible binding for global variable ‘sce_obj’
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.table run_scvi scDblFinder_class sce_obj sd setNames
slotNames split_bar_gsea useMyCol value var variable xaxis
Consider adding
importFrom("methods", "as", "is", "slotNames")
importFrom("stats", "complete.cases", "cor", "heatmap", "quantile",
"sd", "setNames", "var")
importFrom("utils", "read.table")
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 ... [487s/418s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DO.scVI 396.835 2.209 202.529
DO.CellComposition 8.139 4.424 7.771
DO.CellTypist 6.693 1.442 133.438
DO.SplitBarGSEA 6.685 0.209 10.429
DO.enrichR 6.392 0.166 9.971
DO.MultiDGE 6.224 0.222 6.446
* 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: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3869/302e6d0b8a5bdeb35069c6402137467873293a37/DOtools.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('DOtools_0.99.1.tar.gz')
===============================
── Installing DOtools ──────────────────────────────────────────────────────────
✔ Package installed successfully
── DOtools session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpEr9rUe/file34b627676182a7/DOtools
→ BiocVersion: 3.22
→ Package: DOtools
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3869/302e6d0b8a5bdeb35069c6402137467873293a37/DOtools.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /tmp/RtmpEr9rUe/file34b627676182a7/DOtools
→ installDir: /tmp/RtmpEr9rUe/file34b6276ee6ed5a
→ 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...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* 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...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/plotting_functions.R (line 146, column 25)
• ...
• R/plotting_functions.R (line 2336, column 27)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• plotting_functions.R (line 136, column 15)
• ...
• plotting_functions.R (line 3144, column 17)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/plotting_functions.R (line 906, column 5)
• ...
• print() in R/utils_functions.R (line 473, column 3)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/plotting_functions.R (line 866, column 16)
• ...
• R/plotting_functions.R (line 887, column 10)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/plotting_functions.R (line 157, column 17)
• ...
• R/utils_functions.R (line 1402, column 10)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/utils_functions.R (line 141, column 15)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
• suppressWarnings() in R/utils_functions.R (line 242, column 18)
• suppressWarnings() in R/utils_functions.R (line 1170, column 23)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 18
functions greater than 50 lines.
The longest 5 functions are:
• DO.BoxPlot() (R/plotting_functions.R): 413 lines
• ...
• DO.CellComposition() (R/plotting_functions.R): 291 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/DOtools.Rd
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
i NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
Found in files:
• DO.CellBender.Rd
• DO.Import.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• DO.CellBender.Rd
• DO.Import.Rd
* Checking package NEWS...
* Checking unit tests...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 807 lines (15%) are > 80 characters long.
First few lines:
• R/plotting_functions.R#L4 #' @description Perform SEM-based graphs ...
• ...
• vignettes/DOtools.Rmd#L375 GSEA_plot <- list.files(path = base, pat ...
i NOTE: Consider multiples of 4 spaces for line indents; 2024 lines (36%) are
not.
First few lines:
• R/basilisk.R#L2 envname = "DOtools_env", ...
• ...
• vignettes/DOtools.Rmd#L359 kable_styling(bootstrap_options = c("s ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* 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 v1.45.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 15 NOTES
i See the DOtools.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.