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R CMD BUILD
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* 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
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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
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* 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.