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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 (it is needed 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_0.99.4.tar.gz’
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BiocCheckGitClone('CENTRE')
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→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3927/1772b09887bcc88cd59a8eb3f79972ce1e03595a/CENTRE
→ BiocVersion: 3.23
→ Package: CENTRE
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3927/1772b09887bcc88cd59a8eb3f79972ce1e03595a/CENTRE.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3927/1772b09887bcc88cd59a8eb3f79972ce1e03595a/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 v1.47.1 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/3927/1772b09887bcc88cd59a8eb3f79972ce1e03595a/CENTRE.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘0.99.4’
* 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 ... [13s/13s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/13s] OK
* checking loading without being on the library search path ... [13s/13s] 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 ... [40s/40s] OK
* 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 ... [32s/35s] ERROR
Running examples in ‘CENTRE-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: centrePrediction
> ### Title: CENTRE predicton
> ### Aliases: centrePrediction
>
> ### ** Examples
>
> pairs <- readRDS(file = system.file("extdata",
+ "input_cellType_pairs.rds",
+ package = "CENTRE"
+ ))
>
> generic_features <- computeGenericFeatures(pairs)
Computing CENTRE generic features
Computing distance features...
loading from cache
loading from cache
Removing all pairs that are not in the same chromosome.
Removing pairs with distance over 500 Kb.
Getting Wilcoxon tests and CRUP correlations...
Load Wilcoxon tests from ExperimentHub.
Load CRUP correlations from ExperimentHub.
time: 21.65967 secs
>
> celltype_features <- readRDS(file = system.file("extdata",
+ "expected_cellType_HeLa_reduced.rds",
+ package = "CENTRE"
+ ))
> # Finally compute the predictions
> predictions <- centrePrediction(celltype_features, generic_features)
Computing CENTRE predictions...
Error in xgb.get.handle(object) :
'xgb.Booster' object is corrupted or is from an incompatible XGBoost version.
Calls: centrePrediction ... predict.xgb.Booster -> xgb.best_iteration -> xgb.attr -> xgb.get.handle
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [79s/88s]
[79s/88s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
loading from cache
time: 4.255233 secs
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_centrePrediction.R:21:5'): compute centrePrediction function runs as expected ──
Error in `xgb.get.handle(object)`: 'xgb.Booster' object is corrupted or is from an incompatible XGBoost version.
Backtrace:
▆
1. └─CENTRE::centrePrediction(celltype_features, generic_features) at test_centrePrediction.R:21:5
2. ├─stats::predict(xgb_model, feature_matrix)
3. └─xgboost:::predict.xgb.Booster(xgb_model, feature_matrix)
4. └─xgboost:::xgb.best_iteration(object)
5. └─xgboost::xgb.attr(bst, "best_iteration")
6. └─xgboost:::xgb.get.handle(object)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ]
Error:
! Test failures.
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: 2 ERRORs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3927/1772b09887bcc88cd59a8eb3f79972ce1e03595a/CENTRE.Rcheck/00check.log’
for details.
===============================
BiocCheck('CENTRE_0.99.4.tar.gz')
===============================
── Installing CENTRE ───────────────────────────────────────────────────────────
✔ Package installed successfully
── CENTRE session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpueeUBC/file1649505ceada02/CENTRE
→ BiocVersion: 3.23
→ Package: CENTRE
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3927/1772b09887bcc88cd59a8eb3f79972ce1e03595a/CENTRE.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /tmp/RtmpueeUBC/file1649505ceada02/CENTRE
→ installDir: /tmp/RtmpueeUBC/file1649502dc918e0
→ 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...
i NOTE: Update R version dependency from 4.5.0 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...
* 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...
! WARNING: Evaluate more vignette chunks.
i 4 out of 8 code chunks = 50% unevaluated
i 0 non-exec code chunk(s) (e.g., '```r')
* 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 123, column 27)
• ...
• functionsComputeCellType.R (line 194, column 27)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/centrePrediction.R (line 99, 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 121, 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 199, column 5)
• suppressMessages() in R/functions.R (line 284, 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): 65 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
• computeCellTypeFeatures.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 25% of man
pages use at least one of these tags.
Found in files:
• computeCellTypeFeatures.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• computeCellTypeFeatures.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; 23 lines (1%) are > 80 characters long.
First few lines:
• R/functions.R#L132 # extend the enhancer region 500Kb t ...
• ...
• vignettes/CENTRE_vignette.Rmd#L251 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 v1.47.1 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | i 11 NOTES
i See the CENTRE.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.