===============================
R CMD BUILD
===============================
* checking for file ‘scafari/DESCRIPTION’ ... OK
* preparing ‘scafari’:
* 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
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘scafari/inst/extdata/clusterplot.rds’
‘scafari/inst/extdata/sce_filtered.rds’
* building ‘scafari_0.99.1.tar.gz’
===============================
BiocCheckGitClone('scafari')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3812/scafari_20250606132436/scafari
→ BiocVersion: 3.22
→ Package: scafari
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3812/scafari_20250606132436/scafari.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3812/scafari_20250606132436/scafari
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• scafari.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 v1.45.7 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/3812/scafari_20250606132436/scafari.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 ‘scafari/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scafari’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 32 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 ‘scafari’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘R.utils’
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [16s/16s] OK
* checking whether the package can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the package can be unloaded cleanly ... [15s/15s] OK
* checking whether the namespace can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the namespace can be unloaded cleanly ... [16s/16s] OK
* checking loading without being on the library search path ... [16s/16s] 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 ... [53s/53s] NOTE
annotateAmplicons: no visible binding for global variable 'id'
annotateAmplicons: no visible binding for global variable '.'
annotateAmplicons: no visible global function definition for 'head'
annotateAmplicons: no visible global function definition for
'read.delim'
annotateAmplicons: no visible binding for global variable 'Gene'
annotateAmplicons: no visible binding for global variable 'Exon'
annotateAmplicons: no visible binding for global variable 'transcript'
annotateAmplicons: no visible global function definition for 'exonsBy'
annotateAmplicons: no visible binding for global variable
'Transcript.ID'
annotateVariants: no visible binding for global variable '.'
annotateVariants: no visible global function definition for
'starts_with'
annotateVariants: no visible global function definition for 'any_of'
annotateVariants: no visible binding for global variable 'ID'
app_server: no visible global function definition for 'mtext'
app_server: no visible global function definition for 'box'
app_server: no visible binding for global variable '.'
app_server: no visible binding for global variable 'id'
app_server: no visible binding for global variable 'Protein'
app_server: no visible binding for global variable 'Gene'
app_server: no visible binding for global variable 'Chromosome'
app_server: no visible binding for global variable 'WT'
app_server: no visible binding for global variable 'Het'
app_server: no visible binding for global variable 'Hom'
app_server: no visible binding for global variable 'Missing'
app_server: no visible binding for global variable 'Total'
app_server: no visible global function definition for 'setNames'
app_server: no visible binding for global variable 'rowname'
app_server : download_with_progress: no visible global function
definition for 'download.file'
clusterVariantSelection: no visible global function definition for
'na.omit'
clusterVariantSelection: no visible global function definition for
'kmeans'
gg_color_hue: no visible global function definition for 'hcl'
logLogPlot: no visible binding for global variable '.'
logLogPlot: no visible global function definition for 'reorder'
logLogPlot: no visible binding for global variable 'barcode'
normalizeReadCounts: no visible binding for global variable 'median'
plotAmpliconDistribution: no visible binding for global variable 'id'
plotAmpliconDistribution: no visible binding for global variable '.'
plotAmpliconDistribution: no visible global function definition for
'data'
plotAmpliconDistribution: no visible binding for global variable
'ideoCyto'
plotAmpliconDistribution: no visible binding for global variable
'tooltip'
plotClusterGenotype: no visible binding for global variable 'variable'
plotClusterGenotype: no visible binding for global variable 'value'
plotClusterGenotype: no visible binding for global variable 'cluster'
plotClusterGenotype: no visible binding for global variable 'Genotype'
plotClusterVAF: no visible binding for global variable 'cluster'
plotClusterVAF: no visible binding for global variable 'value'
plotClusterVAFMap: no visible global function definition for 'all_of'
plotClusterVAFMap: no visible binding for global variable 'x'
plotClusterVAFMap: no visible binding for global variable 'y'
plotClusterVAFMap: no visible binding for global variable 'VAF'
plotClusterVAFMap: no visible binding for global variable 'cluster'
plotElbow: no visible global function definition for 'na.omit'
plotElbow: no visible binding for global variable 'kmeans'
plotGenotypequalityPerGenotype: no visible binding for global variable
'Genotype'
plotGenotypequalityPerGenotype: no visible binding for global variable
'Genotype Quality'
plotNormalizedReadCounts: no visible global function definition for
'reorder'
plotNormalizedReadCounts: no visible binding for global variable
'Amplicon'
plotNormalizedReadCounts: no visible binding for global variable
'Normalized mean read counts per amplicon'
plotPanelUniformity: no visible binding for global variable 'variable'
plotPanelUniformity: no visible binding for global variable 'value'
plotVariantHeatmap: no visible binding for global variable 'Hom'
plotVariantHeatmap: no visible binding for global variable 'Het'
plotVariantHeatmap: no visible binding for global variable 'WT'
plotVariantHeatmap: no visible binding for global variable 'Missing'
plotVariantHeatmap: no visible binding for global variable 'Total'
Undefined global functions or variables:
. Amplicon Chromosome Exon Gene Genotype Genotype Quality Het Hom ID
Missing Normalized mean read counts per amplicon Protein Total
Transcript.ID VAF WT all_of any_of barcode box cluster data
download.file exonsBy hcl head id ideoCyto kmeans median mtext
na.omit read.delim reorder rowname setNames starts_with tooltip
transcript value variable x y
Consider adding
importFrom("base", "mean")
importFrom("grDevices", "hcl")
importFrom("graphics", "box", "mtext")
importFrom("stats", "kmeans", "median", "na.omit", "reorder",
"setNames")
importFrom("utils", "data", "download.file", "head", "read.delim")
to your NAMESPACE file.
Found the following calls to data() loading into the global environment:
File ‘scafari/R/plotAmpliconDistribution.R’:
data(ideoCyto, package = "biovizBase")
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'plotClusterGenotype.Rd':
\examples lines wider than 100 characters:
# Assume `sce` is a SingleCellExperiment object with variants in altExp() and clusterplot is the output of clusterVariantSleection().
Rd file 'plotClusterVAF.Rd':
\examples lines wider than 100 characters:
# Assume `sce` is a SingleCellExperiment object with variants in altExp() and clusterplot is the output of clusterVariantSleection().
Rd file 'plotClusterVAFMap.Rd':
\examples lines wider than 100 characters:
# Assume `sce` is a SingleCellExperiment object with variants in altExp() and clusterplot is the output of clusterVariantSleection().
These lines will be truncated in the PDF manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [87s/106s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotateAmplicons 33.732 0.975 36.146
plotVariantHeatmap 5.954 0.055 6.009
annotateVariants 1.237 0.005 18.643
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [17s/17s]
[17s/17s] OK
* 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 ... [3s/3s] OK
* DONE
Status: 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3812/scafari_20250606132436/scafari.Rcheck/00check.log’
for details.
===============================
BiocCheck('scafari_0.99.1.tar.gz')
===============================
── Installing scafari ──────────────────────────────────────────────────────────
✔ Package installed successfully
── scafari session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpxRs0nA/file136cd83bca38d/scafari
→ BiocVersion: 3.22
→ Package: scafari
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3812/scafari_20250606132436/scafari.BiocCheck
→ BiocCheckVersion: 1.45.7
→ sourceDir: /tmp/RtmpxRs0nA/file136cd83bca38d/scafari
→ installDir: /tmp/RtmpxRs0nA/file136cd850140906
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scafari ────────────────────────────────────────────────
* 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...
i NOTE: Update R version dependency from 3.5.0 to 4.5.0
* 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 (27%).
* 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...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• scafari_vignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of scafari...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• annotateAmplicons.R (line 82, column 33)
• ...
• utils.R (line 55, column 32)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/clusterVariantSelection.R (line 69, column 3)
• print() in R/utils.R (line 91, column 7)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/filterVariants.R (line 91, column 18)
• ...
• R/filterVariants.R (line 96, column 25)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/annotateVariants.R (line 138, column 19)
• ...
• R/utils.R (line 129, column 12)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/filterVariants.R (line 179, column 10)
• ...
• R/utils.R (line 129, column 18)
* 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 13
functions greater than 50 lines.
The longest 5 functions are:
• app_server() (R/app_server.R): 865 lines
• ...
• app_ui() (R/app_ui.R): 111 lines
* Checking man page documentation...
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• gg_color_hue.Rd
• ...
• theme_shiny.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
Found in files:
• launchScafariShiny.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• launchScafariShiny.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...
i NOTE: Consider shorter lines; 277 lines (8%) are > 80 characters long.
First few lines:
• R/annotateAmplicons.R#L2 #' This function takes a SingleCellExper ...
• ...
• vignettes/scafari_vignette.Rmd#L250 Further, the clusters can be analyzed re
...
i NOTE: Consider multiples of 4 spaces for line indents; 1391 lines (41%) are
not.
First few lines:
• R/annotateAmplicons.R#L16 # Check if the SCE object has metadata ...
• ...
• vignettes/scafari_vignette.Rmd#L255 gg.clust = plot$clusterpl ...
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 v1.45.7 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 14 NOTES
i See the scafari.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.