===============================
R CMD BUILD
===============================
* checking for file ‘Coralysis/DESCRIPTION’ ... OK
* preparing ‘Coralysis’:
* 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
* building ‘Coralysis_0.99.3.tar.gz’
===============================
BiocCheckGitClone('Coralysis')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3729/1561f694dcda17ded6540000004e16c880bd727c/Coralysis
→ BiocVersion: 3.21
→ Package: Coralysis
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3729/1561f694dcda17ded6540000004e16c880bd727c/Coralysis.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3729/1561f694dcda17ded6540000004e16c880bd727c/Coralysis
→ 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 valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.43.12 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/3729/1561f694dcda17ded6540000004e16c880bd727c/Coralysis.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Coralysis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Coralysis’ version ‘0.99.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘Coralysis’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘Matrix::det’ by ‘SparseM::det’ when loading ‘Coralysis’
See ‘/home/pkgbuild/packagebuilder/workers/jobs/3729/1561f694dcda17ded6540000004e16c880bd727c/Coralysis.Rcheck/00install.out’ for details.
* 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] 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 ... [33s/33s] OK
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) SampleClusterBatchProbs.Rd:17: Lost braces; missing escapes or markup?
17 | quantile (numeric). By default {0.5}, i.e., median.}
| ^
checkRd: (-1) SampleClusterProbs.Rd:15: Lost braces; missing escapes or markup?
15 | quantile (numeric). By default {0.5}, i.e., median.}
| ^
checkRd: (-1) SamplePCACells.Rd:27: Lost braces; missing escapes or markup?
27 | quantile (numeric). By default {0.5}, i.e., median.}
| ^
* 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 ... [61s/171s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
AggregateDataByBatch 18.849 0.722 27.886
RunUMAP 2.447 0.100 12.661
ReferenceMapping 2.104 0.063 11.983
PCAElbowPlot 1.437 0.050 11.528
SummariseCellClusterProbability 1.318 0.065 11.401
PlotClusterTree 1.212 0.013 12.021
RunParallelDivisiveICP 1.124 0.063 11.354
RunPCA 1.077 0.051 11.177
CellClusterProbabilityDistribution 0.857 0.009 11.650
GetFeatureCoefficients 0.355 0.009 11.086
GetCellClusterProbability 0.310 0.022 10.345
* 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 ... [4s/4s] OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3729/1561f694dcda17ded6540000004e16c880bd727c/Coralysis.Rcheck/00check.log’
for details.
===============================
BiocCheck('Coralysis_0.99.3.tar.gz')
===============================
── Installing Coralysis ────────────────────────────────────────────────────────
✔ Package installed successfully
── Coralysis session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp7Rez4A/filebc63d24c53ed9/Coralysis
→ BiocVersion: 3.21
→ Package: Coralysis
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3729/1561f694dcda17ded6540000004e16c880bd727c/Coralysis.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /tmp/Rtmp7Rez4A/filebc63d24c53ed9/Coralysis
→ installDir: /tmp/Rtmp7Rez4A/filebc63d52809703
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Coralysis ──────────────────────────────────────────────
* 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 4.2.0 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (14%).
* 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 .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 Coralysis...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/CoreMethods.R (line 1251, column 17)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• AllGenerics.R (line 219, column 21)
• ...
• VizMethods.R (line 658, column 38)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/Utils.R (line 483, column 21)
• cat() in R/Utils.R (line 644, column 9)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/CoreMethods.R (line 42, column 14)
• ...
• R/Utils.R (line 608, column 25)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/CoreMethods.R (line 42, column 20)
• ...
• R/Utils.R (line 484, column 17)
! WARNING: Remove set.seed usage (found 3 times)
• set.seed() in R/VizMethods.R (line 192, column 11)
• set.seed() in R/VizMethods.R (line 420, column 11)
• set.seed() in R/VizMethods.R (line 747, column 15)
* 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 14
functions greater than 50 lines.
The longest 5 functions are:
• RunParallelDivisiveICP.SingleCellExperiment() (R/IntegrationMethods.R): 335
lines
• ...
• FindAllClusterMarkers.SingleCellExperiment() (R/CoreMethods.R): 136 lines
* Checking man page documentation...
Warning: replacing previous import ‘Matrix::det’ by ‘SparseM::det’ when loading ‘Coralysis’
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• BinCellClusterProbability.Rd
• ...
• TabulateCellBinsByGroup.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 11% of man
pages use at least one of these tags.
Found in files:
• BinCellClusterProbability.Rd
• ...
• TabulateCellBinsByGroup.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• MajorityVotingFeatures.Rd
* Checking package NEWS...
* 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; 522 lines (8%) are > 80 characters long.
First few lines:
• R/AllGenerics.R#L208 select.icp.models = metadat ...
• ...
• vignettes/RefMap.Rmd#L313 Wickham H (2016). "ggplot2: Elegant Grap ...
i NOTE: Consider multiples of 4 spaces for line indents; 146 lines (2%) are
not.
First few lines:
• R/AllGenerics.R#L13 batch.label, ...
• ...
• vignettes/RefMap.Rmd#L306 ...
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 v1.43.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 14 NOTES
i See the Coralysis.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.