===============================
R CMD BUILD
===============================
* checking for file ‘CENTRE/DESCRIPTION’ ... OK
* preparing ‘CENTRE’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘CENTRE_0.99.0.tar.gz’
===============================
BiocCheckGitClone('CENTRE')
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→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3927/CENTRE_20250904151702/CENTRE
→ BiocVersion: 3.22
→ Package: CENTRE
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3927/CENTRE_20250904151702/CENTRE.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3927/CENTRE_20250904151702/CENTRE
→ 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 NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.45.18 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/3927/CENTRE_20250904151702/CENTRE.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CENTRE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CENTRE’ version ‘0.99.0’
* 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 ‘CENTRE’ 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 ... [14s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the package can be unloaded cleanly ... [13s/13s] 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 ... [14s/14s] 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 ... [39s/39s] NOTE
centrePrediction: no visible binding for global variable ‘distance’
centrePrediction: no visible binding for global variable ‘crup_cor’
centrePrediction: no visible binding for global variable
‘combined_tests’
centrePrediction: no visible binding for global variable ‘pair’
centrePrediction: no visible binding for global variable ‘gene_id1’
centrePrediction: no visible binding for global variable ‘enhancer_id’
computeCrupRegDistanceEnh: no visible binding for global variable
‘Var1’
computeCrupRegDistanceEnh: no visible binding for global variable ‘.’
computeCrupRegDistanceEnh: no visible binding for global variable
‘pair’
computeCrupRegDistanceProm: no visible binding for global variable
‘Var1’
computeCrupRegDistanceProm: no visible binding for global variable ‘.’
computeCrupRegDistanceProm: no visible binding for global variable
‘pair’
computeDistances: no visible binding for global variable ‘enhancer_id’
computeDistances: no visible binding for global variable ‘gene_id1’
computeGenericFeatures: no visible binding for global variable ‘pair’
computeGenericFeatures: no visible binding for global variable
‘cor_CRUP’
computeGenericFeatures: no visible binding for global variable
‘gene_id1’
computeGenericFeatures: no visible binding for global variable
‘enhancer_id’
computeGenericFeatures: no visible binding for global variable
‘distance’
computeGenericFeatures: no visible binding for global variable
‘crup_cor’
computeGenericFeatures: no visible binding for global variable
‘combined_tests’
createRegionsDf: no visible binding for global variable ‘enhancer_id’
createRegionsDf: no visible binding for global variable ‘gene_id1’
getEPFeatures: no visible binding for global variable ‘enhancer_id’
getEPFeatures: no visible binding for global variable ‘gene_id1’
getPPFeatures: no visible binding for global variable ‘enhancer_id’
getPPFeatures: no visible binding for global variable ‘gene_id1’
getRNAseq: no visible binding for global variable ‘gene_id1’
reformatDf: no visible binding for global variable ‘gene_id1’
reformatDf: no visible binding for global variable ‘enhancer_id’
reformatDf: no visible binding for global variable ‘EP_prob_enh.1’
reformatDf: no visible binding for global variable ‘EP_prob_enh.2’
reformatDf: no visible binding for global variable ‘EP_prob_enh.3’
reformatDf: no visible binding for global variable ‘EP_prob_enh.4’
reformatDf: no visible binding for global variable ‘EP_prob_enh.5’
reformatDf: no visible binding for global variable ‘EP_prob_gene.1’
reformatDf: no visible binding for global variable ‘EP_prob_gene.2’
reformatDf: no visible binding for global variable ‘EP_prob_gene.3’
reformatDf: no visible binding for global variable ‘EP_prob_gene.4’
reformatDf: no visible binding for global variable ‘EP_prob_gene.5’
reformatDf: no visible binding for global variable ‘reg_dist_enh’
reformatDf: no visible binding for global variable ‘norm_reg_dist_enh’
reformatDf: no visible binding for global variable ‘PP_prob_enh.1’
reformatDf: no visible binding for global variable ‘PP_prob_enh.2’
reformatDf: no visible binding for global variable ‘PP_prob_enh.3’
reformatDf: no visible binding for global variable ‘PP_prob_enh.4’
reformatDf: no visible binding for global variable ‘PP_prob_enh.5’
reformatDf: no visible binding for global variable ‘PP_prob_gene.1’
reformatDf: no visible binding for global variable ‘PP_prob_gene.2’
reformatDf: no visible binding for global variable ‘PP_prob_gene.3’
reformatDf: no visible binding for global variable ‘PP_prob_gene.4’
reformatDf: no visible binding for global variable ‘PP_prob_gene.5’
reformatDf: no visible binding for global variable ‘reg_dist_prom’
reformatDf: no visible binding for global variable ‘norm_reg_dist_prom’
reformatDf: no visible binding for global variable ‘TPM’
reformatDf: no visible binding for global variable ‘.’
Undefined global functions or variables:
. EP_prob_enh.1 EP_prob_enh.2 EP_prob_enh.3 EP_prob_enh.4
EP_prob_enh.5 EP_prob_gene.1 EP_prob_gene.2 EP_prob_gene.3
EP_prob_gene.4 EP_prob_gene.5 PP_prob_enh.1 PP_prob_enh.2
PP_prob_enh.3 PP_prob_enh.4 PP_prob_enh.5 PP_prob_gene.1
PP_prob_gene.2 PP_prob_gene.3 PP_prob_gene.4 PP_prob_gene.5 TPM Var1
combined_tests cor_CRUP crup_cor distance enhancer_id gene_id1
norm_reg_dist_enh norm_reg_dist_prom pair reg_dist_enh reg_dist_prom
* checking Rd files ... [0s/0s] OK
* 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 ... [433s/443s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
centrePrediction 172.730 29.301 205.203
computeCellTypeFeatures 158.621 23.549 185.345
computeGenericFeatures 23.171 1.409 27.043
createPairs 5.015 0.263 6.759
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [116s/126s]
[117s/127s] 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: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3927/CENTRE_20250904151702/CENTRE.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('CENTRE_0.99.0.tar.gz')
===============================
── Installing CENTRE ───────────────────────────────────────────────────────────
✔ Package installed successfully
── CENTRE session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmppFPGRt/file4c5ab1825474c/CENTRE
→ BiocVersion: 3.22
→ Package: CENTRE
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3927/CENTRE_20250904151702/CENTRE.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/RtmppFPGRt/file4c5ab1825474c/CENTRE
→ installDir: /tmp/RtmppFPGRt/file4c5ab68eb00c4
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CENTRE ─────────────────────────────────────────────────
* 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...
i NOTE: Consider adding these automatically suggested biocViews: Sequencing,
SingleCell
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 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 (54%).
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of CENTRE...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• functionsComputeCellType.R (line 97, column 27)
• ...
• functionsComputeCellType.R (line 168, column 27)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/centrePrediction.R (line 133, column 13)
• ...
• R/createPairs.R (line 52, column 13)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/computeCellTypeFeatures.R (line 118, column 13)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
• suppressMessages() in R/functions.R (line 198, column 5)
• suppressMessages() in R/functions.R (line 283, column 5)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
The longest 5 functions are:
• geneCenteredPairs() (R/functions.R): 87 lines
• ...
• centrePrediction() (R/centrePrediction.R): 63 lines
* Checking man page documentation...
* 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; 23 lines (1%) are > 80 characters long.
First few lines:
• R/functions.R#L131 # extend the enhancer region 500Kb t ...
• ...
• vignettes/CENTRE_vignette.Rmd#L254 by a `_` of the corresponding pair and t
...
i NOTE: Consider multiples of 4 spaces for line indents; 1 lines (0%) are not.
First few lines:
• vignettes/CENTRE_vignette.Rmd#L47 `computeCellTypeFeatures()` -> `centreC ...
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 v1.45.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 9 NOTES
i See the CENTRE.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.