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BiocCheckGitClone('CycleMix')
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── Running Git clone checks on CycleMix ────────────────────────────────────────
* Checking valid files...
* Checking for inst/doc folders...
* Checking DESCRIPTION readability...
* Checking for valid use of maintainer fields...
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R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4252/CycleMix_20261027133936/CycleMix.Rcheck’
* using R version 4.6.1 (2026-06-24)
* 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 24.04.5 LTS
* using session charset: UTF-8
* current time: 2026-10-27 17:42:55 UTC
* using option ‘--no-vignettes’
* checking for file ‘CycleMix/DESCRIPTION’ ... OK
* this is package ‘CycleMix’ version ‘0.99.51’
* 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 ‘CycleMix’ can be installed ... OK
* checking installed package size ... INFO
installed size is 5.9Mb
sub-directories of 1Mb or more:
data 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 ... [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 ... [37s/36s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'AssignPhase.Rd':
\usage lines wider than 90 characters:
classifyCells(obj, CC_table, expr_name="logcounts", do.scale=FALSE, symbol_column=NULL, allow.multi=FALSE)
\examples lines wider than 100 characters:
expr_mat <- prepData(esc_Smartseq_example, symbol_column="feature_symbol") # esc_Smartseq_example = SingleCellesc_Smartseq_exam ... [TRUNCATED]
classification <- classifyCells(esc_Smartseq_example, MGeneSets$Cyclone, do.scale=TRUE, allow.multi=FALSE, symbol_column="feat ... [TRUNCATED]
classification <- classifyCells(esc_Smartseq_example, MGeneSets$Cyclone, do.scale=FALSE, allow.multi=TRUE, symbol_column="feat ... [TRUNCATED]
Rd file 'CheckFit.Rd':
\examples lines wider than 100 characters:
classification <- classifyCells(esc_Smartseq_example, MGeneSets$Cyclone, do.scale=TRUE, allow.multi=FALSE, symbol_column="feat ... [TRUNCATED]
Rd file 'PlotMixture.Rd':
\examples lines wider than 100 characters:
classification <- classifyCells(esc_Smartseq_example, MGeneSets$Cyclone, do.scale=TRUE, allow.multi=FALSE, symbol_column="feat ... [TRUNCATED]
Rd file 'PrepData.Rd':
\examples lines wider than 100 characters:
expr_mat <- prepData(esc_Smartseq_example, symbol_column="feature_symbol") # esc_Smartseq_example = SingleCellExperiment Object
Rd file 'RegressCycle.Rd':
\usage lines wider than 90 characters:
regressCyclePartial(expr_mat, classification, type=c("counts","norm"), method=c("scores", "phase"), phases=c("G2M", "G1S"), allow_neg ... [TRUNCATED]
\examples lines wider than 100 characters:
classification <- classifyCells(esc_Smartseq_example, MGeneSets$Cyclone, do.scale=TRUE, allow.multi=FALSE, symbol_column="feat ... [TRUNCATED]
regressed_counts1 <- regressCyclePartial(counts(esc_Smartseq_example), classification, type="counts", method="scores", phases=c ... [TRUNCATED]
regressed_counts2 <- regressCyclePartial(counts(esc_Smartseq_example), classification, type="counts", method="phase", phases=c( ... [TRUNCATED]
regressed_lognorm1 <- regressCyclePartial(logcounts(esc_Smartseq_example), classification, type="norm", method="scores", phases ... [TRUNCATED]
regressed_lognorm2 <- regressCyclePartial(logcounts(esc_Smartseq_example), classification, type="norm", method="phase", phases= ... [TRUNCATED]
Rd file 'knnSmooth.Rd':
\examples lines wider than 100 characters:
classification <- classifyCells(esc_Smartseq_example, MGeneSets$Cyclone, do.scale=TRUE, allow.multi=FALSE, symbol_column="feat ... [TRUNCATED]
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [6s/6s] OK
* checking LazyData ... NOTE
'LazyDataCompression' is specified without 'LazyData'
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [59s/58s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
RegressCycle 37.735 0.332 38.069
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [14s/14s]
[15s/14s] 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/4252/CycleMix_20261027133936/CycleMix.Rcheck/00check.log’
for details.
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BiocCheck('CycleMix_0.99.51.tar.gz')
===============================
── Installing CycleMix ─────────────────────────────────────────────────────────
✔ Package installed successfully
── CycleMix session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmplEtcBb/file153c764e85b6d5/CycleMix
→ BiocVersion: 3.23
→ Package: CycleMix
→ PackageVersion: 0.99.51
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4252/CycleMix_20261027133936/CycleMix.BiocCheck
→ BiocCheckVersion: 1.49.33
→ sourceDir: /tmp/RtmplEtcBb/file153c764e85b6d5/CycleMix
→ installDir: /tmp/RtmplEtcBb/file153c76e6d873d/lib
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CycleMix ───────────────────────────────────────────────
* 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 4.6.0
* 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: SingleCell,
Classification, Regression
i Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking DESCRIPTION readability...
* Checking validity of DESCRIPTION fields...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for whitespace in DESCRIPTION field names...
* Checking for proper Description: field...
i NOTE: The Description field in the DESCRIPTION is made up of less than 3
sentences. Provide a more detailed description of the package.
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (17%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i 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 CITATION...
i (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()'.
* 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:
• CycleMix.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of CycleMix...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/Analysis.R (line 102, column 25)
• ...
• R/Analysis.R (line 135, column 32)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• Analysis.R (line 67, column 40)
• ...
• Plotting.R (line 57, column 26)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/Analysis.R (line 295, column 17)
• print() in R/Analysis.R (line 358, column 17)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/Analysis.R (line 220, column 24)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/Analysis.R (line 34, column 25)
• R/Analysis.R (line 45, column 23)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/Analysis.R (line 45, column 29)
• ...
• R/Analysis.R (line 232, column 22)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in vignettes/CycleMix.Rmd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
• suppressWarnings() in R/Analysis.R (line 126, column 32)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 3
functions greater than 50 lines.
The longest 5 functions are:
• glm_discrete() (R/Analysis.R): 70 lines
• knnSmooth() (R/Analysis.R): 67 lines
• regressCyclePartial() (R/Analysis.R): 66 lines
* Checking man page documentation...
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 181 lines (16%) are > 80 characters long.
First few lines:
• R/Analysis.R#L2 prepData <- function(obj, expr_name="log ...
• ...
• vignettes/CycleMix.Rmd#L298 Jack Edward Peplinski, Tallulah S Andrew ...
i NOTE: Consider 4 spaces instead of tabs; 459 lines (42%) contain tabs.
First few lines:
• R/Analysis.R#L3 gene_names <- rownames(obj) ...
• ...
• man/RegressCycle.Rd#L35 regressed_lognorm2 <- regressCycleParti ...
i NOTE: Consider multiples of 4 spaces for line indents; 43 lines (4%) are not.
First few lines:
• R/Analysis.R#L189 }) ...
• ...
• man/RegressCycle.Rd#L17 \item{subsample_cells}{how many cells ...
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 'cyclemix' is already in your 'Watched Tags' on the Support Site.
── BiocCheck v1.49.33 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 17 NOTES
i See the CycleMix.BiocCheck folder and run
`browseVignettes(package = 'BiocCheck')`
for details.