===============================
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_0.99.7.tar.gz’
===============================
BiocCheckGitClone('TSENAT')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4107/320776700cdd8b8137e56961456582ad0166b77c/TSENAT
→ BiocVersion: 3.23
→ Package: TSENAT
→ PackageVersion: 0.99.7
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4107/320776700cdd8b8137e56961456582ad0166b77c/TSENAT.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4107/320776700cdd8b8137e56961456582ad0166b77c/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/4107/320776700cdd8b8137e56961456582ad0166b77c/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 01:14:21 UTC
* using option ‘--no-vignettes’
* checking for file ‘TSENAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TSENAT’ version ‘0.99.7’
* 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 ... [6s/6s] 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 ... [55s/55s] 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 ... ERROR
Warning: parse error in file 'TSENAT-Ex.R':
2: unexpected symbol
359:
360: \dontrun
^
** will not attempt to run examples
* 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 ... WARNING
Found the following file(s) containing GNU extensions:
src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... NOTE
PKG_CFLAGS set in ‘src/Makevars’ without any corresponding files
PKG_CFLAGS set in ‘src/Makevars.win’ without any corresponding files
* 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 ... SKIPPED
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [458s/462s]
[459s/462s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
workers must be <= 2 was (999)
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-parallelization.R:1096:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─TSENAT (local) silent_calculate_divergence(analysis, nthreads = 999)
10. └─TSENAT::calculate_divergence(...) at test-parallelization.R:838:3
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─value[[3L]](cond)
[ FAIL 3 | WARN 0 | SKIP 312 | PASS 9905 ]
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: 2 ERRORs, 1 WARNING, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4107/320776700cdd8b8137e56961456582ad0166b77c/TSENAT.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('TSENAT_0.99.7.tar.gz')
===============================
── Installing TSENAT ───────────────────────────────────────────────────────────
✔ Package installed successfully
── TSENAT session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpaGgQPH/filecadfe6bb867b1/TSENAT
→ BiocVersion: 3.23
→ Package: TSENAT
→ PackageVersion: 0.99.7
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4107/320776700cdd8b8137e56961456582ad0166b77c/TSENAT.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpaGgQPH/filecadfe6bb867b1/TSENAT
→ installDir: /tmp/RtmpaGgQPH/filecadfebb3a826
→ 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...
Error in parse(outfile, keep.source = TRUE) :
/tmp/RtmpaGgQPH/filecadfe54305511/parseFile.tmp:8:2: unexpected symbol
7:
8: \dontrun
^
Calls: BiocCheck -> BiocCheckRun -> parseFiles -> parseFile -> parse
Execution halted