===============================
R CMD BUILD
===============================
* checking for file ‘vmrseq/DESCRIPTION’ ... OK
* preparing ‘vmrseq’:
* checking DESCRIPTION meta-information ... OK
* installing the package 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘vmrseq_0.99.6.tar.gz’
===============================
BiocCheckGitClone('vmrseq')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3455/1e91584e537a8a6f14377d5750813f504f46d3d1/vmrseq
→ BiocVersion: 3.21
→ Package: vmrseq
→ PackageVersion: 0.99.6
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3455/1e91584e537a8a6f14377d5750813f504f46d3d1/vmrseq.BiocCheck
→ BiocCheckVersion: 1.43.4
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3455/1e91584e537a8a6f14377d5750813f504f46d3d1/vmrseq
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.43.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3455/1e91584e537a8a6f14377d5750813f504f46d3d1/vmrseq.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘vmrseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘vmrseq’ version ‘0.99.6’
* 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 ... NOTE
Found the following hidden files and directories:
.github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘vmrseq’ 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 ... NOTE
License stub is invalid DCF.
* 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 ... [16s/16s] OK
* checking whether the package can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the package can be unloaded cleanly ... [14s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the namespace can be unloaded cleanly ... [15s/15s] OK
* checking loading without being on the library search path ... [16s/16s] 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 ... [51s/51s] NOTE
.computeProb1Unit : .computeLag: no visible binding for global variable
‘chr’
.computeProb1Unit : .computeLag: no visible binding for global variable
‘state’
.computeProb1Unit : .computeLag: no visible binding for global variable
‘state_lag’
.computeProb1Unit : .computeLag: no visible binding for global variable
‘dist_bp’
.computeProb1Unit: no visible binding for global variable ‘dist_bp’
.computeProb1Unit: no visible binding for global variable ‘N_00’
.computeProb1Unit: no visible binding for global variable ‘N_10’
.computeProb1Unit: no visible binding for global variable ‘N_01’
.computeProb1Unit: no visible binding for global variable ‘N_11’
.computeProb1Unit: no visible binding for global variable ‘p_00’
.computeProb1Unit: no visible binding for global variable ‘p_01’
.estimTransitProbsFromSummary: no visible binding for global variable
‘dist_bp’
.estimTransitProbsFromSummary: no visible binding for global variable
‘p_00’
.estimTransitProbsFromSummary: no visible binding for global variable
‘p_01’
.estimTransitProbsFromSummary: no visible binding for global variable
‘p_10’
.estimTransitProbsFromSummary: no visible binding for global variable
‘p_11’
.estimTransitProbsFromSummary : .selectCols: no visible binding for
global variable ‘dist_bp’
HDF5NAdrop2matrix: no visible global function definition for ‘as’
computeVar : varByCluster: no visible global function definition for
‘as’
computeVarCutoff: no visible global function definition for ‘quantile’
extractInfo: no visible binding for global variable ‘meth’
extractInfo: no visible binding for global variable ‘total’
extractInfo: no visible binding for global variable ‘bool’
tpPlot: no visible binding for global variable ‘dist_bp’
tpPlot: no visible binding for global variable ‘pbar’
tpPlot: no visible binding for global variable ‘phat’
vmrseqFit: no visible binding for global variable ‘bpWindow’
Undefined global functions or variables:
N_00 N_01 N_10 N_11 as bool bpWindow chr dist_bp meth p_00 p_01 p_10
p_11 pbar phat quantile state state_lag total
Consider adding
importFrom("methods", "as")
importFrom("stats", "quantile")
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 'poolData.Rd':
\examples lines wider than 100 characters:
poolData(cellFiles = your_cell_file_list, sep = ",", chrNames = "chr1", writeDir = "your/write/path")
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 ... [3s/3s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [93s/72s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
vmrseqFit 15.411 0.765 19.683
vmrseqSmooth 5.874 0.911 6.906
regionSummary 4.783 0.387 4.834
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [15s/15s]
[16s/16s] 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: 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3455/1e91584e537a8a6f14377d5750813f504f46d3d1/vmrseq.Rcheck/00check.log’
for details.
===============================
BiocCheck('vmrseq_0.99.6.tar.gz')
===============================
── Installing vmrseq ───────────────────────────────────────────────────────────
✔ Package installed successfully
── vmrseq session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpvk5RL5/file3867d62b607193/vmrseq
→ BiocVersion: 3.21
→ Package: vmrseq
→ PackageVersion: 0.99.6
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3455/1e91584e537a8a6f14377d5750813f504f46d3d1/vmrseq.BiocCheck
→ BiocCheckVersion: 1.43.4
→ sourceDir: /tmp/Rtmpvk5RL5/file3867d62b607193/vmrseq
→ installDir: /tmp/Rtmpvk5RL5/file3867d65582dd80
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on vmrseq ─────────────────────────────────────────────────
* 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...
* 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 (50%).
* Checking for pinned package versions in DESCRIPTION...
* 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 vmrseq...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• helper_functions.R (line 374, column 42)
• ...
• vmrseqFit.R (line 185, column 42)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/poolData.R (line 76, column 13)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
The longest 5 functions are:
• vmrseqFit() (R/vmrseqFit.R): 118 lines
• ...
• searchVMR() (R/helper_functions.R): 75 lines
* Checking man page documentation...
Registered S3 methods overwritten by 'proxy':
method from
print.registry_field registry
print.registry_entry registry
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• poolData.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
Found in files:
• poolData.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; 214 lines (9%) are > 80 characters long.
First few lines:
• R/HDF5NAdrop2matrix.R#L14 #' toy.se <- HDF5Array::loadHDF5Summariz ...
• ...
• vignettes/vmrseq-vignette.Rmd#L247 We have created the GitHub repo [vmrseq-
...
i NOTE: Consider multiples of 4 spaces for line indents; 698 lines (31%) are
not.
First few lines:
• R/HDF5NAdrop2matrix.R#L21 mat <- hdf5_assay |> as("matrix") |> a ...
• ...
• vignettes/vmrseq-vignette.Rmd#L221 6. `bb_params`: Beta-binomial paramete ...
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 v1.43.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 8 NOTES
i See the vmrseq.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.