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BiocCheckGitClone('CycleMix')
===============================
── Running Git clone checks on CycleMix ────────────────────────────────────────
* Checking valid files...
* 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()'.
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R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4252/75ad0ff7fc7f874f285aa18652521270bfe60025/CycleMix.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* 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: 2026-06-18 16:19:45 UTC
* using option ‘--no-vignettes’
* checking for file ‘CycleMix/DESCRIPTION’ ... OK
* this is package ‘CycleMix’ version ‘0.99.03’
* 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 ... 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 ... [13s/13s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/13s] OK
* checking loading without being on the library search path ... [13s/13s] 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 ... [38s/38s] NOTE
downloadEnsemblData: no visible binding for global variable ‘HGeneSets’
downloadEnsemblData: no visible binding for global variable ‘MGeneSets’
prepData: no visible global function definition for ‘is’
Undefined global functions or variables:
HGeneSets MGeneSets is
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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:
classification <- classifyCells(Ex, MGeneSets$Cyclone, do.scale=TRUE, allow.multi=FALSE, symbol_column="feature_symbol")
classification <- classifyCells(Ex, MGeneSets$Cyclone, do.scale=FALSE, allow.multi=TRUE, symbol_column="feature_symbol")
Rd file 'CheckFit.Rd':
\examples lines wider than 100 characters:
classification <- classifyCells(Ex, MGeneSets$Cyclone, do.scale=TRUE, allow.multi=FALSE, symbol_column="feature_symbol");
Rd file 'EnsemblStuff.Rd':
\usage lines wider than 90 characters:
mapGeneNames(maps, genes, in.org=c("Hsap","Mmus"), in.name=c("symbol","ensg"), out.org=c("Hsap","Mmus"), out.name=c("symbol","ensg"))
\examples lines wider than 100 characters:
#MGeneSets$Whitfield$Gene <- mapGeneNames(maps, as.character(MGeneSets$Whitfield$Gene), in.org="Hsap", in.name="symbol", out.or ... [TRUNCATED]
#MGeneSets$Whitfield <- MGeneSets$Whitfield[MGeneSets$Whitfield$Gene != "",] #remove genes without orthologs.
Rd file 'PlotMixture.Rd':
\examples lines wider than 100 characters:
classification <- classifyCells(Ex, MGeneSets$Cyclone, do.scale=TRUE, allow.multi=FALSE, symbol_column="feature_symbol")
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(Ex, MGeneSets$Cyclone, do.scale=TRUE, allow.multi=FALSE, symbol_column="feature_symbol");
regressed_counts1 <- regressCyclePartial(counts(Ex), classification, type="counts", method="scores", phases=c("S", "G2M"), allo ... [TRUNCATED]
regressed_counts2 <- regressCyclePartial(counts(Ex), classification, type="counts", method="phase", phases=c("S", "G2M"), allow ... [TRUNCATED]
regressed_lognorm1 <- regressCyclePartial(logcounts(Ex), classification, type="norm", method="scores", phases=c("G1", "S", "G2M ... [TRUNCATED]
regressed_lognorm2 <- regressCyclePartial(logcounts(Ex), classification, type="norm", method="phase", phases=c("G1", "S", "G2M" ... [TRUNCATED]
Rd file 'knnSmooth.Rd':
\examples lines wider than 100 characters:
classification <- classifyCells(Ex, MGeneSets$Cyclone, do.scale=TRUE, allow.multi=FALSE, symbol_column="feature_symbol");
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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [62s/62s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
RegressCycle 38.696 0.253 38.952
* 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/4252/75ad0ff7fc7f874f285aa18652521270bfe60025/CycleMix.Rcheck/00check.log’
for details.
===============================
BiocCheck('CycleMix_0.99.03.tar.gz')
===============================
── Installing CycleMix ─────────────────────────────────────────────────────────
✔ Package installed successfully
── CycleMix session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpRjeHwk/file1817d6460cb4a0/CycleMix
→ BiocVersion: 3.23
→ Package: CycleMix
→ PackageVersion: 0.99.03
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4252/75ad0ff7fc7f874f285aa18652521270bfe60025/CycleMix.BiocCheck
→ BiocCheckVersion: 1.49.17
→ sourceDir: /tmp/RtmpRjeHwk/file1817d6460cb4a0/CycleMix
→ installDir: /tmp/RtmpRjeHwk/file1817d6404472bf
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CycleMix ───────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* 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 for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* 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 (17%).
* 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:
• Vignette.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 99, column 25)
• ...
• R/Analysis.R (line 131, column 32)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• Analysis.R (line 65, column 40)
• ...
• Plotting.R (line 55, column 26)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/Analysis.R (line 286, column 17)
• print() in R/Analysis.R (line 325, column 17)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/Analysis.R (line 214, column 24)
• ...
• R/Ensembl_Stuff.R (line 92, column 21)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/Analysis.R (line 33, column 25)
• ...
• R/Ensembl_Stuff.R (line 32, column 25)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/Analysis.R (line 43, column 29)
• ...
• R/Ensembl_Stuff.R (line 31, column 25)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
Found in files:
• Analysis.R (line 212, column 35)
• Analysis.R (line 296, column 33)
• Analysis.R (line 333, column 33)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in vignettes/Vignette.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 122, 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:
• knnSmooth() (R/Analysis.R): 67 lines
• regressCyclePartial() (R/Analysis.R): 65 lines
• downloadEnsemblData() (R/Ensembl_Stuff.R): 53 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• EnsemblStuff.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 185 lines (16%) are > 80 characters long.
First few lines:
• R/Analysis.R#L1 prepData <- function(obj, expr_name="log ...
• ...
• vignettes/Vignette.Rmd#L225 Note that even non-proliferating cells a ...
i NOTE: Consider 4 spaces instead of tabs; 531 lines (47%) contain tabs.
First few lines:
• R/Analysis.R#L2 gene_names <- rownames(obj) ...
• ...
• man/RegressCycle.Rd#L33 regressed_lognorm2 <- regressCycleParti ...
i NOTE: Consider multiples of 4 spaces for line indents; 53 lines (5%) are not.
First few lines:
• R/Analysis.R#L184 }) ...
• ...
• 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 v1.49.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 20 NOTES
i See the CycleMix.BiocCheck folder and run
`browseVignettes(package = 'BiocCheck')`
for details.