===============================
R CMD BUILD
===============================
* checking for file Seqtometry/DESCRIPTION ... OK
* preparing Seqtometry:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building Seqtometry_0.99.2.tar.gz
===============================
BiocCheckGitClone('Seqtometry')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4068/b37b0f47bfb669df3cda8bfc59e183fbaa51d518/Seqtometry
BiocVersion: 3.23
Package: Seqtometry
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4068/b37b0f47bfb669df3cda8bfc59e183fbaa51d518/Seqtometry.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4068/b37b0f47bfb669df3cda8bfc59e183fbaa51d518/Seqtometry
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...
* Checking that provided CITATION file is correctly formatted...
BiocCheck v1.47.20 results
0 ERRORS | 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/4068/b37b0f47bfb669df3cda8bfc59e183fbaa51d518/Seqtometry.Rcheck
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-15 01:04:00 UTC
* using option --no-vignettes
* checking for file Seqtometry/DESCRIPTION ... OK
* this is package Seqtometry version 0.99.2
* 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 Seqtometry can be installed ... OK
* used C++ compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* 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 ... [5s/5s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the package can be unloaded cleanly ... [5s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [5s/5s] OK
* checking loading without being on the library search path ... [5s/5s] 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 ... [18s/18s] NOTE
score: warning in assert_list(signatures, type = "character"): partial
argument match of 'type' to 'types'
* 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 C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
-Werror=format-security
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in vignettes ... OK
* checking examples ... [189s/190s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
impute 87.439 4.941 92.810
score 84.153 4.843 89.414
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [6s/6s]
[6s/6s] 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: 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/4068/b37b0f47bfb669df3cda8bfc59e183fbaa51d518/Seqtometry.Rcheck/00check.log
for details.
===============================
BiocCheck('Seqtometry_0.99.2.tar.gz')
===============================
Installing Seqtometry
Package installed successfully
Seqtometry session metadata
sourceDir: /tmp/RtmpgzHk7P/file3eac63305948d/Seqtometry
BiocVersion: 3.23
Package: Seqtometry
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4068/b37b0f47bfb669df3cda8bfc59e183fbaa51d518/Seqtometry.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /tmp/RtmpgzHk7P/file3eac63305948d/Seqtometry
installDir: /tmp/RtmpgzHk7P/file3eac6356cecce8
isTarBall: TRUE
platform: unix
Running BiocCheck on Seqtometry
* 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 4.5.0 to 4.6.0
* 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...
i NOTE: Consider adding these automatically suggested biocViews: FlowCytometry
i Search 'biocViews' at https://contributions.bioconductor.org
* 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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (18%).
* 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 Seqtometry...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* 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...
i NOTE: Consider shorter lines; 38 lines (6%) are > 80 characters long.
First few lines:
R/impute.R#L3 #' Calculates a graph diffusion operator ...
...
vignettes/Seqtometry.Rmd#L170 Additional characterization of cells can ...
i NOTE: Consider multiples of 4 spaces for line indents; 128 lines (21%) are
not.
First few lines:
R/impute.R#L88 .check_params(environment()) ...
...
vignettes/Seqtometry.Rmd#L162 Seqtometry::score(gated_imputed_gex, 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 v1.47.20 results
0 ERRORS | 0 WARNINGS | i 5 NOTES
i See the Seqtometry.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.