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processing file: RcppTskit_intro.qmd
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		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 4.7.0; x86_64-pc-linux-gnu; 2026-03-29
                           09:13:12 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)

[31mError:
! /tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so - /tm[39m[31mp/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so: cannot enable ex[39m[31mecutable stack as shared object requires: Invalid argument
Backtrace:
     ▆
  1. ├─ts$r_to_py()
  2. │ └─RcppTskit:[39m[31m::ts_ptr_r_to_py(...)
  3. │   ├─tskit_module$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]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! /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)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
[39m[33mWARN: Error encountered when rendering files[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 4.7.0; x86_64-pc-linux-gnu; 2026-03-29
  09:13:12 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)
  
  [31mError:[39m
  !
  /tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so
  -
  /tm[31mp/check-CRAN-regular-hornik/cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so:[39m
  [31mcannot enable executable stack as shared object requires: Invalid argument[39m
  Backtrace:
  ▆
  1. ├─ts$r_to_py()
  2. │ └─RcppTskit:[31m::ts_ptr_r_to_py(...)[39m
  3. │ ├─tskit_module$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]
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  <error/rlang_error>
  Error:
  !
  /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)
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  
  Execution halted
  [33mWARN: Error encountered when rendering files[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