===============================
R CMD BUILD
===============================
* checking for file TSENAT/DESCRIPTION ... OK
* preparing TSENAT:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
WARNING: directory TSENAT/build is empty
* looking to see if a data/datalist file should be added
* building TSENAT_0.99.1.tar.gz
===============================
BiocCheckGitClone('TSENAT')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4107/286f8066b27b228dbedc6d8aa30d25c85be26156/TSENAT
BiocVersion: 3.23
Package: TSENAT
PackageVersion: 0.99.1
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4107/286f8066b27b228dbedc6d8aa30d25c85be26156/TSENAT.BiocCheck
BiocCheckVersion: 1.49.4
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4107/286f8066b27b228dbedc6d8aa30d25c85be26156/TSENAT
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/4107/286f8066b27b228dbedc6d8aa30d25c85be26156/TSENAT/.gitignore'
Warning in grep(filter_expr, ignore.case = TRUE, flist[["FALSE"]], value = TRUE) :
TRE pattern compilation error 'Invalid use of repetition operators'
Error in grep(filter_expr, ignore.case = TRUE, flist[["FALSE"]], value = TRUE) :
invalid regular expression '^$|^# Local R check directories and temporary package checks$|^.*\.bak$|^docs/$|^database/$|^output/$|^coverage/$|^\.DS_Store$|^\.instructions\.md$|^inst/doc/$|^/Meta/$|^__pycache__/$|^\.\.Rcheck$|^\.\.Rcheck/$|^\.Rcheck$|^\.Rcheck/$|^.*\.Rhistory$|^\.TSENAT\.Bioccheck$|^\.TSENAT\.Bioccheck/$|^\.Rhistory$|^\.Rproj\.user$|^.*\.Ruserdata$|^\.Ruserdata$|^.*\.tar\.gz$|^tmp/$|^TSENAT\.Rcheck$|^TSENAT\.Rcheck/$|^vignette/.*html$|^vignette/.*pdf$|^vignettes/ts_debug\.R$|^\.vscode/$|^Rplots\.pdf$|^# Coverage analysis files$|^.*\.gcda$|^.*\.gcno$|^# Compiled C/C++ binaries \(platform-specific, should be rebuilt locally)$|^src/.*\.o$|^src/.*\.so$|^src/.*\.dll$|^src/.*\.dylib$|^tools/$|^# Generated site$|^docs/$|^_pkgdown\.yml$|^r_dependencies_s4_interactive\.html$|^visualize_dependencies\.py$|^$|^# Exclude pkgdown templates and assets from git \(will be managed via R build)$|^inst/pkgdown/$|^$|^# Generated citations file \(restored from gh-pages when needed)$
Calls: BiocCheckGitClone -> checkBadFiles -> grep
Execution halted
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/4107/286f8066b27b228dbedc6d8aa30d25c85be26156/TSENAT.Rcheck
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-04 22:09:36 UTC
* using option --no-vignettes
* checking for file TSENAT/DESCRIPTION ... OK
* checking extension type ... Package
* this is package TSENAT version 0.99.1
* 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 TSENAT can be installed ... OK
* used C++ compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking whether startup messages can be suppressed ... [7s/7s] 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 ... [58s/58s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'calculate_effect_sizes.Rd':
\examples lines wider than 100 characters:
q = seq(0, 2, by = 0.5) # Multiple q-values for SAIT interaction analysis (5 unique: 0, 0.5, 1, 1.5, 2)
Rd file 'results.Rd':
\examples lines wider than 100 characters:
# Get diversity for specific q-value as SummarizedExperiment for downstream processing (e.g., SplicingFactory)
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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
-Werror=format-security
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in vignettes ... OK
* checking examples ... [115s/115s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_divergence_distribution 11.836 0.267 12.110
plot_sait 11.739 0.022 11.765
plot_jis_delta 10.808 0.096 10.905
calculate_effect_sizes 10.377 0.069 10.446
calculate_concordance 9.487 0.117 9.604
calculate_sait 9.336 0.050 9.387
plot_expression 9.297 0.056 9.381
* checking for unstated dependencies in tests ... WARNING
'::' or ':::' import not declared from: gtable
'library' or 'require' call not declared from: gtable
* checking tests ...
Running testthat.R [525s/528s]
[526s/528s] ERROR
Running the tests in tests/testthat.R failed.
Last 20 lines of output:
Error ('test-parallelization.R:1095:3'): nthreads parameter is properly validated
Error: Divergence calculation failed:
_R_CHECK_LIMIT_CORES_' environment variable detected, BiocParallel
workers must be <= 2 was (999)
Backtrace:
1. testthat::expect_warning(...) at test-parallelization.R:1095:3
2. testthat:::quasi_capture(...)
3. testthat (local) .capture(...)
4. base::withCallingHandlers(...)
5. rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. TSENAT (local) silent_calculate_divergence(analysis, nthreads = 999)
7. TSENAT::calculate_divergence(...) at test-parallelization.R:838:3
8. base::tryCatch(...)
9. base (local) tryCatchList(expr, classes, parentenv, handlers)
10. base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. value[[3L]](cond)
[ FAIL 11 | WARN 0 | SKIP 12 | PASS 10401 ]
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 ... [5s/5s] OK
* DONE
Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/4107/286f8066b27b228dbedc6d8aa30d25c85be26156/TSENAT.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('TSENAT_0.99.1.tar.gz')
===============================
Installing TSENAT
Package installed successfully
TSENAT session metadata
sourceDir: /tmp/Rtmp5FHroT/file254a232f979d4/TSENAT
BiocVersion: 3.23
Package: TSENAT
PackageVersion: 0.99.1
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4107/286f8066b27b228dbedc6d8aa30d25c85be26156/TSENAT.BiocCheck
BiocCheckVersion: 1.49.4
sourceDir: /tmp/Rtmp5FHroT/file254a232f979d4/TSENAT
installDir: /tmp/Rtmp5FHroT/file254a23212dd6eb
isTarBall: TRUE
platform: unix
Running BiocCheck on TSENAT
* 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 if 'Package:' field matches directory / tarball...
* 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 (16%).
* 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 TSENAT...
* Checking coding practice...
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/divergence_effect_sizes.R (line 633, column 15)
...
R/sait_helpers.R (line 1291, column 17)
* 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 196
functions greater than 50 lines.
The longest 5 functions are:
.process_assumptions_results() (R/orchestration_results.R): 309 lines
...
.lmm_interaction() (R/sait_helpers_fit.R): 195 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
TSENAT.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 10% of man
pages use at least one of these tags.
Found in files:
build_analysis.Rd
TSENAT.Rd
TSENATAnalysis-metadata.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; 4685 lines (10%) are > 80 characters long.
First few lines:
R/AllClasses.R#L24 #' @slot sait_results \code{list}. Compl ...
...
vignettes/TSENAT.Rmd#L885 35. Yulmetyev, R. M., Emelyanova, N. A., ...
i NOTE: Consider multiples of 4 spaces for line indents; 834 lines (2%) are
not.
First few lines:
R/AllClasses.R#L150 return(sprintf("@confi ...
...
vignettes/TSENAT.Rmd#L797 ACTB, etc.). These should show BALANC ...
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 v1.49.4 results
0 ERRORS | 0 WARNINGS | i 8 NOTES
i See the TSENAT.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.