Last updated on 2026-03-26 05:51:08 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.0 | 36.76 | 91.63 | 128.39 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.0 | 31.11 | 63.94 | 95.05 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.0 | 51.00 | 140.58 | 191.58 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.2.0 | 78.00 | 151.29 | 229.29 | OK | |
| r-devel-macos-arm64 | 0.2.0 | 9.00 | 25.00 | 34.00 | OK | |
| r-devel-windows-x86_64 | 0.2.0 | 60.00 | 156.00 | 216.00 | OK | |
| r-patched-linux-x86_64 | 0.2.0 | 41.07 | 83.30 | 124.37 | OK | |
| r-release-linux-x86_64 | 0.2.0 | 40.38 | 82.40 | 122.78 | OK | |
| r-release-macos-arm64 | 0.2.0 | 8.00 | 24.00 | 32.00 | OK | |
| r-release-macos-x86_64 | 0.2.0 | 33.00 | 227.00 | 260.00 | OK | |
| r-release-windows-x86_64 | 0.2.0 | 58.00 | 142.00 | 200.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.0 | 8.00 | 28.00 | 36.00 | OK | |
| r-oldrel-macos-x86_64 | 0.2.0 | 32.00 | 201.00 | 233.00 | OK | |
| r-oldrel-windows-x86_64 | 0.2.0 | 71.00 | 166.00 | 237.00 | WARN |
Version: 0.2.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘RcppTskit_intro.qmd’ using html
<1b>[31m
processing file: RcppTskit_intro.qmd
<1b>[39m
Information on package 'RcppTskit'
Description:
Type: Package
Package: RcppTskit
Title: 'R' Access to the 'tskit C' API
Version: 0.2.0
Date: 2026-01-27
Authors@R: c( person("Gregor", "Gorjanc", ,
"gregor.gorjanc@gmail.com", role = c("aut",
"cre", "cph"), comment = c(ORCID =
"0000-0001-8008-2787")), person("Tskit
Developers", role = "cph", comment =
"Authors of included tskit C library") )
Description: 'Tskit' enables efficient storage,
manipulation, and analysis of ancestral
recombination graphs (ARGs) using succinct
tree sequence encoding. The tree sequence
encoding of an ARG is described in Wong et
al. (2024) <doi:10.1093/genetics/iyae100>,
while `tskit` project is described in
Jeffrey et al. (2026)
<doi:10.48550/arXiv.2602.09649>. See also
<https://tskit.dev> for project news,
documentation, and tutorials. 'Tskit'
provides 'Python', 'C', and 'Rust'
application programming interfaces (APIs).
The 'Python' API can be called from 'R' via
the 'reticulate' package to load and analyse
tree sequences as described at
<https://tskit.dev/tutorials/tskitr.html>.
'RcppTskit' provides 'R' access to the
'tskit C' API for cases where the
'reticulate' option is not optimal; for
example, high-performance or low-level work
with tree sequences. Currently, 'RcppTskit'
provides a limited set of 'R' functions
because the 'Python' API and 'reticulate'
already covers most needs.
License: MIT + file LICENSE
URL: https://github.com/HighlanderLab/RcppTskit
BugReports: https://github.com/HighlanderLab/RcppTskit/issues
Depends: R (>= 4.0.0)
Imports: methods, R6, Rcpp (>= 1.0.8), reticulate (>=
1.43.0)
Suggests: covr, knitr, quarto, spelling, testthat (>=
3.0.0)
LinkingTo: Rcpp (>= 0.12.10)
VignetteBuilder: quarto
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-GB
RoxygenNote: 7.3.3
NeedsCompilation: yes
Packaged: 2026-02-22 09:34:21 UTC; ggorjanc
Author: Gregor Gorjanc [aut, cre, cph] (ORCID:
<https://orcid.org/0000-0001-8008-2787>),
Tskit Developers [cph] (Authors of included
tskit C library)
Maintainer: Gregor Gorjanc <gregor.gorjanc@gmail.com>
Repository: CRAN
Date/Publication: 2026-02-27 16:02:24 UTC
Built: R 4.6.0; x86_64-pc-linux-gnu; 2026-03-25
10:13:23 UTC; unix
Index:
TableCollection Table collection R6 class (TableCollection)
TreeSequence Succinct tree sequence R6 class (TreeSequence)
get_tskit_py Get the reticulate 'tskit' Python module
kastore_version Report the version of installed kastore C API
tc_load Load a table collection from a file
tc_py_to_r Transfer a table collection from reticulate
Python to R
ts_load Load a tree sequence from a file
ts_py_to_r Transfer a tree sequence from reticulate Python
to R
tskit_version Report the version of installed 'tskit' C API
Further information is available in the following vignettes in
directory
'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppTskit/doc':
RcppTskit_intro: RcppTskit: Working with tree sequences in R (source,
pdf)
<1b>[31mError:
! /tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so - /tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so: cannot enable executable stack as shared object requires: Invalid argument
Backtrace:
▆
1. ├─ts$r_to_py()
2. │ └─RcppTskit:::ts_ptr_r_to_py(...)
3. │ ├─tskit_module$load
4. │ └─reticulate:::`$.python.builtin.module`(tskit_module, "load")
5. │ └─reticulate::py_get_attr(x, name, TRUE)
6. └─reticulate (local) `<fn>`()
7. └─reticulate:::initialize_python()
8. └─base::tryCatch(...)
9. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. └─value[[3L]](cond)
<1b>[39m<1b>[31m
Quitting from RcppTskit_intro.qmd:244-295 [use_case_2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[39m<1b>[31m~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! /tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x8<1b>[39m<1b>[31m6_64-gnu/lib/libpython3.12.so - /tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib<1b>[39m<1b>[31m/libpython3.12.so: cannot enable executable stack as shared object requires: Invalid argument
---
Backtrace:
▆
1. ├─ts$r_to_py()
2. │ └─RcppTskit:::ts_ptr_r_to_py(...)
3. │ ├─tskit_module$load
4. │ └─reticulate:::`$.python.builtin.module`(tskit_module, "load")
5. │ └─reticulate::py_get_attr(x, name, TRUE)
6. └─reticulate (local) `<fn>`()
7. └─reticulate:::initialize_python()
8. └─base::tryCatch(...)
9. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Execution halted
<1b>[39m<1b>[33mWARN: Error encountered when rendering files<1b>[39m
Error: processing vignette 'RcppTskit_intro.qmd' failed with diagnostics:
! Error running quarto CLI from R.
Caused by error in `quarto_render()`:
✖ Error returned by quarto CLI.
-----------------------------
processing file: RcppTskit_intro.qmd
Information on package 'RcppTskit'
Description:
Type: Package
Package: RcppTskit
Title: 'R' Access to the 'tskit C' API
Version: 0.2.0
Date: 2026-01-27
Authors@R: c( person("Gregor", "Gorjanc", ,
"gregor.gorjanc@gmail.com", role = c("aut",
"cre", "cph"), comment = c(ORCID =
"0000-0001-8008-2787")), person("Tskit
Developers", role = "cph", comment =
"Authors of included tskit C library") )
Description: 'Tskit' enables efficient storage,
manipulation, and analysis of ancestral
recombination graphs (ARGs) using succinct
tree sequence encoding. The tree sequence
encoding of an ARG is described in Wong et
al. (2024) <doi:10.1093/genetics/iyae100>,
while `tskit` project is described in
Jeffrey et al. (2026)
<doi:10.48550/arXiv.2602.09649>. See also
<https://tskit.dev> for project news,
documentation, and tutorials. 'Tskit'
provides 'Python', 'C', and 'Rust'
application programming interfaces (APIs).
The 'Python' API can be called from 'R' via
the 'reticulate' package to load and analyse
tree sequences as described at
<https://tskit.dev/tutorials/tskitr.html>.
'RcppTskit' provides 'R' access to the
'tskit C' API for cases where the
'reticulate' option is not optimal; for
example, high-performance or low-level work
with tree sequences. Currently, 'RcppTskit'
provides a limited set of 'R' functions
because the 'Python' API and 'reticulate'
already covers most needs.
License: MIT + file LICENSE
URL: https://github.com/HighlanderLab/RcppTskit
BugReports: https://github.com/HighlanderLab/RcppTskit/issues
Depends: R (>= 4.0.0)
Imports: methods, R6, Rcpp (>= 1.0.8), reticulate (>=
1.43.0)
Suggests: covr, knitr, quarto, spelling, testthat (>=
3.0.0)
LinkingTo: Rcpp (>= 0.12.10)
VignetteBuilder: quarto
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-GB
RoxygenNote: 7.3.3
NeedsCompilation: yes
Packaged: 2026-02-22 09:34:21 UTC; ggorjanc
Author: Gregor Gorjanc [aut, cre, cph] (ORCID:
<https://orcid.org/0000-0001-8008-2787>),
Tskit Developers [cph] (Authors of included
tskit C library)
Maintainer: Gregor Gorjanc <gregor.gorjanc@gmail.com>
Repository: CRAN
Date/Publication: 2026-02-27 16:02:24 UTC
Built: R 4.6.0; x86_64-pc-linux-gnu; 2026-03-25
10:13:23 UTC; unix
Index:
TableCollection Table collection R6 class (TableCollection)
TreeSequence Succinct tree sequence R6 class (TreeSequence)
get_tskit_py Get the reticulate 'tskit' Python module
kastore_version Report the version of installed kastore C API
tc_load Load a table collection from a file
tc_py_to_r Transfer a table collection from reticulate
Python to R
ts_load Load a tree sequence from a file
ts_py_to_r Transfer a tree sequence from reticulate Python
to R
tskit_version Report the version of installed 'tskit' C API
Further information is available in the following vignettes in
directory
'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppTskit/doc':
RcppTskit_intro: RcppTskit: Working with tree sequences in R (source,
pdf)
<1b>[31mError:<1b>[39m
!
/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so
-
/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so:
cannot enable executable stack as shared object requires: Invalid argument
Backtrace:
▆
1. ├─ts$r_to_py()
2. │ └─RcppTskit:::ts_ptr_r_to_py(...)
3. │ ├─tskit_module$load
4. │ └─reticulate:::`$.python.builtin.module`(tskit_module, "load")
5. │ └─reticulate::py_get_attr(x, name, TRUE)
6. └─reticulate (local) `<fn>`()
7. └─reticulate:::initialize_python()
8. └─base::tryCatch(...)
9. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. └─value[[3L]](cond)
Quitting from RcppTskit_intro.qmd:244-295 [use_case_2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<1b>[31m~~~~~~~~~~~~~~<1b>[39m
<error/rlang_error>
Error:
!
/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x8<1b>[31m6_64-gnu/lib/libpython3.12.so<1b>[39m
<1b>[31m-<1b>[39m
<1b>[31m/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so:<1b>[39m
<1b>[31mcannot enable executable stack as shared object requires: Invalid argument<1b>[39m
---
Backtrace:
▆
1. ├─ts$r_to_py()
2. │ └─RcppTskit:::ts_ptr_r_to_py(...)
3. │ ├─tskit_module$load
4. │ └─reticulate:::`$.python.builtin.module`(tskit_module, "load")
5. │ └─reticulate::py_get_attr(x, name, TRUE)
6. └─reticulate (local) `<fn>`()
7. └─reticulate:::initialize_python()
8. └─base::tryCatch(...)
9. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
11. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Execution halted
<1b>[33mWARN: Error encountered when rendering files<1b>[39m
Caused by error:
! System command 'quarto' failed
--- failed re-building ‘RcppTskit_intro.qmd’
SUMMARY: processing the following file failed:
‘RcppTskit_intro.qmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.0
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
tskit/kastore.c:1157:32: warning: unknown conversion type character 'z' in format [-Wformat=]
tskit/kastore.c:1157:18: warning: too many arguments for format [-Wformat-extra-args]
tskit/kastore.c:1158:32: warning: unknown conversion type character 'z' in format [-Wformat=]
tskit/kastore.c:1158:18: warning: too many arguments for format [-Wformat-extra-args]
tskit/kastore.c:1165:40: warning: unknown conversion type character 'z' in format [-Wformat=]
tskit/kastore.c:1165:53: warning: unknown conversion type character 'z' in format [-Wformat=]
tskit/kastore.c:1165:62: warning: format '%p' expects argument of type 'void *', but argument 6 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
tskit/kastore.c:1165:13: warning: unknown conversion type character 'z' in format [-Wformat=]
tskit/kastore.c:1165:13: warning: format '%p' expects argument of type 'void *', but argument 7 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
tskit/kastore.c:1165:13: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.4/RcppTskit.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* used C++ compiler: 'g++.exe (GCC) 13.3.0'
Flavor: r-oldrel-windows-x86_64