===============================
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_0.99.11.tar.gz’
===============================
BiocCheckGitClone('TSENAT')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4107/2d6ddada916cf45de80f353a835d3c52137554a5/TSENAT
→ BiocVersion: 3.23
→ Package: TSENAT
→ PackageVersion: 0.99.11
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4107/2d6ddada916cf45de80f353a835d3c52137554a5/TSENAT.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4107/2d6ddada916cf45de80f353a835d3c52137554a5/TSENAT
→ 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 remote package usage...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4107/2d6ddada916cf45de80f353a835d3c52137554a5/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: 2026-05-05 03:06:16 UTC
* using option ‘--no-vignettes’
* checking for file ‘TSENAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TSENAT’ version ‘0.99.11’
* 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] OK
* checking whether startup messages can be suppressed ... [8s/8s] 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 ... [62s/62s] 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 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 ... [70s/70s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_jis_delta 10.591 0.049 10.639
plot_divergence_distribution 10.501 0.074 10.576
plot_expression 9.261 0.084 9.345
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [464s/469s]
[465s/469s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-parallelization.R:1096:3'): 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. ├─base::suppressWarnings(...) at test-parallelization.R:1096:3
2. │ └─base::withCallingHandlers(...)
3. └─TSENAT (local) silent_calculate_divergence(analysis, nthreads = 999)
4. └─TSENAT::calculate_divergence(...) at test-parallelization.R:838:3
5. └─base::tryCatch(...)
6. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
[ FAIL 3 | WARN 0 | SKIP 308 | PASS 9911 ]
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 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4107/2d6ddada916cf45de80f353a835d3c52137554a5/TSENAT.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('TSENAT_0.99.11.tar.gz')
===============================
── Installing TSENAT ───────────────────────────────────────────────────────────
✔ Package installed successfully
── TSENAT session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpRL4kNG/filee173162e23a87/TSENAT
→ BiocVersion: 3.23
→ Package: TSENAT
→ PackageVersion: 0.99.11
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4107/2d6ddada916cf45de80f353a835d3c52137554a5/TSENAT.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpRL4kNG/filee173162e23a87/TSENAT
→ installDir: /tmp/RtmpRL4kNG/filee173140f8fac9
→ 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.
• calculate_concordance.Rd
• ...
• TSENAT.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 17% of man
pages use at least one of these tags.
Found in files:
• calculate_effect_sizes.Rd
• ...
• TSENATAnalysis-metadata.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• calculate_effect_sizes.Rd
• calculate_sait.Rd
• plot_sait.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
i NOTE: skip_on_bioc() found in testthat files:
test-core-functions-divergence_effect_sizes.R test-integration-workflow.R
test-visualization-expression.R test-visualization.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 4682 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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 502 Bad Gateway.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 10 NOTES
i See the TSENAT.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.