===============================
R CMD BUILD
===============================
* checking for file ‘spectreasy/DESCRIPTION’ ... OK
* preparing ‘spectreasy’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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 ‘spectreasy_0.99.0.tar.gz’
===============================
BiocCheckGitClone('spectreasy')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4214/spectreasy_20260402101741/spectreasy
→ BiocVersion: 3.23
→ Package: spectreasy
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4214/spectreasy_20260402101741/spectreasy.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4214/spectreasy_20260402101741/spectreasy
→ 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 v1.47.20 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/4214/spectreasy_20260402101741/spectreasy.Rcheck’
* using R version 4.6.0 alpha (2026-03-30 r89742)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-02 14:18:13 UTC
* using option ‘--no-vignettes’
* checking for file ‘spectreasy/DESCRIPTION’ ... OK
* this is package ‘spectreasy’ version ‘0.99.0’
* 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 ‘spectreasy’ 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 ... 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘methods’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [6s/6s] OK
* 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 ... [3s/3s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [2s/2s]
[2s/2s] 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: 1 WARNING
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4214/spectreasy_20260402101741/spectreasy.Rcheck/00check.log’
for details.
===============================
BiocCheck('spectreasy_0.99.0.tar.gz')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
── Installing spectreasy ───────────────────────────────────────────────────────
✔ Package installed successfully
── spectreasy session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpeU129C/filee4eb437e46c23/spectreasy
→ BiocVersion: 3.23
→ Package: spectreasy
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4214/spectreasy_20260402101741/spectreasy.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /tmp/RtmpeU129C/filee4eb437e46c23/spectreasy
→ installDir: /tmp/RtmpeU129C/filee4eb41836309a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on spectreasy ─────────────────────────────────────────────
* 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 4.1.0 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...
* 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 (9%).
* 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 NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• getting_started.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of spectreasy...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/build_reference_matrix.R (line 564, column 25)
• R/report_generator.R (line 80, column 46)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• build_reference_matrix.R (line 188, column 41)
• ...
• report_generator.R (line 80, column 53)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/report_generator.R (line 58, column 30)
• ...
• print() in R/scc_check.R (line 197, column 9)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/autounmix_controls.R (line 188, column 59)
• R/build_reference_matrix.R (line 554, column 25)
• R/control_validation.R (line 196, column 53)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid '<<-' if possible (found 2 times)
• <<- in R/control_interface.R (line 490, column 31)
• <<- in R/matrix_utils.R (line 92, column 58)
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
• suppressWarnings() in R/gating_options.R (line 116, column 17)
• ...
• suppressWarnings() in R/matrix_utils.R (line 44, column 48)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 16
functions greater than 50 lines.
The longest 5 functions are:
• create_control_file() (R/control_interface.R): 634 lines
• ...
• unmix_samples() (R/unmixing.R): 228 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
• autounmix_controls.Rd
• ...
• validate_control_file_mapping.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 54% of man
pages use at least one of these tags.
Found in files:
• autounmix_controls.Rd
• ...
• validate_control_file_mapping.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• autounmix_controls.Rd
• ...
• validate_control_file_mapping.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; 434 lines (10%) are > 80 characters long.
First few lines:
• R/autounmix_controls.R#L14 #' @param control_df Optional control ma ...
• ...
• vignettes/getting_started.Rmd#L188 | `autounmix_controls()` | Build/save co
...
i NOTE: Consider multiples of 4 spaces for line indents; 83 lines (2%) are not.
First few lines:
• R/build_reference_matrix.R#L50 input_folder = "scc", ...
• ...
• vignettes/getting_started.Rmd#L168 output_dir = "spectreasy_outputs/u ...
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...
✖ ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/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 ──────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 0 WARNINGS | i 15 NOTES
i See the spectreasy.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.