• using R Under development (unstable) (2025-07-15 r88411)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-19) 14.2.0     GNU Fortran (Debian 14.2.0-19) 14.2.0
• running under: Debian GNU/Linux 13 (trixie)
• using session charset: UTF-8
• checking for file ‘sjSDM/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘sjSDM’ version ‘1.0.6’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/1s] OK
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking serialization versions ... OK
• checking whether package ‘sjSDM’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... 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 ... [3s/4s] ERROR ── Attaching sjSDM ──────────────────────────────────────────────────── 1.0.6 ── Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpv35f2X/bin/python': No such file. In addition: Warning message: In normalizePath(python_home) :   path[1]="/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpv35f2X/bin": No such file or directory Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpGN1n5d/bin/python': No such file. In addition: Warning message: In normalizePath(python_home) :   path[1]="/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpGN1n5d/bin": No such file or directory Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpafzMz2/bin/python': No such file. In addition: Warning message: In normalizePath(python_home) :   path[1]="/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpafzMz2/bin": No such file or directory Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpTqcJJh/bin/python': No such file. In addition: Warning message: In normalizePath(python_home) :   path[1]="/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpTqcJJh/bin": No such file or directory ✖ torch ✖ torch_optimizer ✖ pyro ✖ madgrad Torch or other dependencies not found:  1. Use install_sjSDM() to install Pytorch and conda automatically  2. Installation trouble shooting guide: ?installation_help  3. If 1) and 2) did not help, please create an issue on <https://github.com/TheoreticalEcology/s-jSDM/issues> (see ?install_diagnostic) It looks like this package has a loading problem: see the messages for details.
• checking whether the package can be loaded with stated dependencies ... [3s/4s] WARNING ── Attaching sjSDM ──────────────────────────────────────────────────── 1.0.6 ── Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpjGBpam/bin/python': No such file. In addition: Warning message: In normalizePath(python_home) :   path[1]="/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpjGBpam/bin": No such file or directory Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmp5KhFdD/bin/python': No such file. In addition: Warning message: In normalizePath(python_home) :   path[1]="/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmp5KhFdD/bin": No such file or directory Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpMAm2H9/bin/python': No such file. In addition: Warning message: In normalizePath(python_home) :   path[1]="/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpMAm2H9/bin": No such file or directory Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpZ4EVSv/bin/python': No such file. In addition: Warning message: In normalizePath(python_home) :   path[1]="/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpZ4EVSv/bin": No such file or directory ✖ torch ✖ torch_optimizer ✖ pyro ✖ madgrad Torch or other dependencies not found:  1. Use install_sjSDM() to install Pytorch and conda automatically  2. Installation trouble shooting guide: ?installation_help  3. If 1) and 2) did not help, please create an issue on <https://github.com/TheoreticalEcology/s-jSDM/issues> (see ?install_diagnostic) It looks like this package (or one of its dependent packages) has an unstated dependence on a standard package. All dependencies must be declared in DESCRIPTION. See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
• checking whether the package can be unloaded cleanly ... [3s/4s] WARNING ---- unloading
• checking whether the namespace can be loaded with stated dependencies ... [3s/3s] WARNING Warning in normalizePath(python_home) :   path[1]="/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpMYG8o4/bin": No such file or directory Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpMYG8o4/bin/python': No such file. Warning in normalizePath(python_home) :   path[1]="/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmp5lJDbn/bin": No such file or directory Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmp5lJDbn/bin/python': No such file. Warning in normalizePath(python_home) :   path[1]="/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpkvM9XV/bin": No such file or directory Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpkvM9XV/bin/python': No such file. Warning in normalizePath(python_home) :   path[1]="/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpKdNzzD/bin": No such file or directory Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpKdNzzD/bin/python': No such file. A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file.
• checking whether the namespace can be unloaded cleanly ... [3s/4s] WARNING ---- unloading
• checking loading without being on the library search path ... [3s/4s] WARNING ── Attaching sjSDM ──────────────────────────────────────────────────── 1.0.6 ── Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmp1BWTlU/bin/python': No such file. In addition: Warning message: In normalizePath(python_home) :   path[1]="/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmp1BWTlU/bin": No such file or directory Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmp4oT4Nr/bin/python': No such file. In addition: Warning message: In normalizePath(python_home) :   path[1]="/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmp4oT4Nr/bin": No such file or directory Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpUDqwVm/bin/python': No such file. In addition: Warning message: In normalizePath(python_home) :   path[1]="/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpUDqwVm/bin": No such file or directory Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpS9qVg6/bin/python': No such file. In addition: Warning message: In normalizePath(python_home) :   path[1]="/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpS9qVg6/bin": No such file or directory ✖ torch ✖ torch_optimizer ✖ pyro ✖ madgrad Torch or other dependencies not found:  1. Use install_sjSDM() to install Pytorch and conda automatically  2. Installation trouble shooting guide: ?installation_help  3. If 1) and 2) did not help, please create an issue on <https://github.com/TheoreticalEcology/s-jSDM/issues> (see ?install_diagnostic) It looks like this package has a loading problem when not on .libPaths: see the messages for details.
• checking whether startup messages can be suppressed ... [3s/4s] NOTE Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpjUdkBy/bin/python': No such file. Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpoUv7TG/bin/python': No such file. Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpNCplqj/bin/python': No such file. Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpxN1xdx/bin/python': No such file. It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage.
• 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 ... [19s/25s] NOTE Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpnQqN87/bin/python': No such file. Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpJDIS21/bin/python': No such file. Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpLxFwQa/bin/python': No such file. Error in python_config_impl(python) :   Error running '/tmp/check-CRAN-regular-hornik/cache/R/reticulate/uv/cache/builds-v0/.tmpM6G2Z1/bin/python': No such file.
• checking Rd files ... [1s/1s] 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 LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [3s/4s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [4s/6s] OK   Running ‘testthat.R’ [4s/6s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [2s/2s] OK
• checking PDF version of manual ... [5s/6s] OK
• checking HTML version of manual ... [2s/3s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 5 WARNINGs, 2 NOTEs