===============================
BiocCheckGitClone('CycleMix')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4252/CycleMix_20260518181402/CycleMix
→ BiocVersion: 3.23
→ Package: CycleMix
→ PackageVersion: 0.99.00
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4252/CycleMix_20260518181402/CycleMix.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4252/CycleMix_20260518181402/CycleMix
→ 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 remote package usage...
* Checking NAMESPACE...
* Checking for valid maintainer...
✖ ERROR: Do not use Author/Maintainer fields. Use Authors@R.
* 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 v1.49.6 results ───────────────────────────────────────────────────
✖ 1 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/4252/CycleMix_20260518181402/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: 2026-05-18 18:17:40 UTC
* using option ‘--no-vignettes’
* checking for file ‘CycleMix/DESCRIPTION’ ... OK
* this is package ‘CycleMix’ version ‘0.99.00’
* 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [11s/11s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘methods’
Namespace in Imports field not imported from: ‘scater’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [36s/36s] NOTE
checkFit : <anonymous>: no visible global function definition for
‘rnorm’
checkFit: no visible global function definition for ‘ks.test’
downloadEnsemblData: no visible binding for global variable ‘HGeneSets’
downloadEnsemblData: no visible binding for global variable ‘MGeneSets’
knnSmooth: no visible global function definition for ‘new’
Undefined global functions or variables:
HGeneSets MGeneSets ks.test new rnorm
Consider adding
importFrom("methods", "new")
importFrom("stats", "ks.test", "rnorm")
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 ... [15s/15s] ERROR
Running examples in ‘CycleMix-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: checkFit
> ### Title: Check Goodness of Fit of the GMM
> ### Aliases: checkFit
> ### Keywords: goodness of fit
>
> ### ** Examples
>
> require(SingleCellExperiment)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: ‘MatrixGenerics’
The following objects are masked from ‘package:matrixStats’:
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘Biobase’
The following object is masked from ‘package:MatrixGenerics’:
rowMedians
The following objects are masked from ‘package:matrixStats’:
anyMissing, rowMedians
> classification <- classifyCells(Ex, MGeneSets$Cyclone, do.scale=TRUE, allow.multi=FALSE, symbol_column="feature_symbol");
Warning in prepData(obj, do.scale = do.scale, expr_name = expr_name, symbol_column = symbol_column) :
Excluding 14 duplicated genes.
> good.fit.allres <- checkFit(classification, 100, summarize=FALSE)
Error in checkFit(classification, 100, summarize = FALSE) :
could not find function "checkFit"
Execution halted
* 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 ERROR, 1 WARNING, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4252/CycleMix_20260518181402/CycleMix.Rcheck/00check.log’
for details.
===============================
BiocCheck('CycleMix_0.99.00.tar.gz')
===============================
── Installing CycleMix ─────────────────────────────────────────────────────────
✔ Package installed successfully
── CycleMix session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpF2yuMi/file2c691126007bc6/CycleMix
→ BiocVersion: 3.23
→ Package: CycleMix
→ PackageVersion: 0.99.00
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4252/CycleMix_20260518181402/CycleMix.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /tmp/RtmpF2yuMi/file2c691126007bc6/CycleMix
→ installDir: /tmp/RtmpF2yuMi/file2c691179fd811c
→ 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
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 if 'Package:' field matches directory / tarball...
* Checking for Version: field...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (25%).
* 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...
✖ ERROR: 'VignetteBuilder' listed in DESCRIPTION but not found as
'VignetteEngine' in any vignettes:
• BiocStyle
• rmarkdown
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 303, column 17)
• print() in R/Analysis.R (line 342, column 17)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/Analysis.R (line 162, column 17)
• ...
• R/Ensembl_Stuff.R (line 96, column 25)
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 T/F variables; If logical, use TRUE/FALSE
Found 3 times:
• T in R/Ensembl_Stuff.R (line 3, column 75)
• T in R/Ensembl_Stuff.R (line 5, column 43)
• F in R/Ensembl_Stuff.R (line 6, column 65)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
Found in files:
• Analysis.R (line 5, column 27)
• ...
• Analysis.R (line 350, 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): 66 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; 189 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; 542 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#L183 }) ...
• ...
• 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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.6 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 2 WARNINGS | i 20 NOTES
i See the CycleMix.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.