===============================
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
* building ‘scafari_0.99.10.tar.gz’
===============================
BiocCheckGitClone('scafari')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3812/3f8b37232d5cded9864e1e470e1d361f49d2512e/scafari
→ BiocVersion: 3.22
→ Package: scafari
→ PackageVersion: 0.99.10
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3812/3f8b37232d5cded9864e1e470e1d361f49d2512e/scafari.BiocCheck
→ BiocCheckVersion: 1.45.11
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3812/3f8b37232d5cded9864e1e470e1d361f49d2512e/scafari
→ 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 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 v1.45.11 results ──────────────────────────────────────────────────
✖ 0 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/3812/3f8b37232d5cded9864e1e470e1d361f49d2512e/scafari.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 ‘scafari/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scafari’ version ‘0.99.10’
* 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 ... INFO
installed size is 5.9Mb
sub-directories of 1Mb or more:
extdata 5.7Mb
* 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 ... [21s/21s] OK
* checking whether the package can be loaded with stated dependencies ... [18s/18s] OK
* checking whether the package can be unloaded cleanly ... [18s/18s] OK
* checking whether the namespace can be loaded with stated dependencies ... [18s/18s] OK
* checking whether the namespace can be unloaded cleanly ... [19s/19s] OK
* checking loading without being on the library search path ... [19s/19s] 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 ... [60s/60s] NOTE
annotateAmplicons: no visible binding for global variable 'id'
annotateAmplicons: no visible binding for global variable '.'
annotateAmplicons: no visible global function definition for 'seqlen'
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 'any_of'
annotateVariants: no visible binding for global variable 'ID'
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 binding for global variable 'rowname'
logLogPlot: no visible binding for global variable '.'
logLogPlot: no visible binding for global variable 'barcode'
plotAmpliconDistribution: no visible binding for global variable 'id'
plotAmpliconDistribution: no visible binding for global variable '.'
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'
plotGenotypequalityPerGenotype: no visible binding for global variable
'Genotype'
plotGenotypequalityPerGenotype: no visible binding for global variable
'Genotype Quality'
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 cluster exonsBy id
ideoCyto rowname seqlen tooltip transcript value variable x y
* 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 files in ‘vignettes’ ... OK
* checking examples ... [108s/125s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotateAmplicons 45.803 1.154 48.397
plotVariantHeatmap 6.283 0.029 6.313
annotateVariants 1.060 0.006 17.199
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [24s/41s]
[25s/41s] 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 ... [4s/4s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3812/3f8b37232d5cded9864e1e470e1d361f49d2512e/scafari.Rcheck/00check.log’
for details.
===============================
BiocCheck('scafari_0.99.10.tar.gz')
===============================
── Installing scafari ──────────────────────────────────────────────────────────
✔ Package installed successfully
── scafari session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpCqIzmM/file194874400645c/scafari
→ BiocVersion: 3.22
→ Package: scafari
→ PackageVersion: 0.99.10
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3812/3f8b37232d5cded9864e1e470e1d361f49d2512e/scafari.BiocCheck
→ BiocCheckVersion: 1.45.11
→ sourceDir: /tmp/RtmpCqIzmM/file194874400645c/scafari
→ installDir: /tmp/RtmpCqIzmM/file194874f4f8e69
→ 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...
* 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...
* 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...
* 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 9
functions greater than 50 lines.
The longest 5 functions are:
• app_server() (R/app_server.R): 1024 lines
• ...
• plotGenotypequalityPerGenotype() (R/plotGenoqualityPerGenotype.R): 121 lines
* Checking man page documentation...
* 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 v1.45.11 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 2 NOTES
i See the scafari.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.