* using log directory ‘/srv/hornik/tmp/CRAN_pretest/CASSIA.Rcheck’ * using R Under development (unstable) (2025-12-07 r89119) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 21.1.6 (2) Debian flang version 21.1.6 (2) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘CASSIA/DESCRIPTION’ ... OK * this is package ‘CASSIA’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/6s] NOTE Maintainer: ‘Elliot Yixuan Xie ’ New submission Possibly misspelled words in DESCRIPTION: reticulate (8:13) The Title field should be in title case. Current version is: ‘Collaborative agent system for single-cell interpretable annotation’ In title case that is: ‘Collaborative Agent System for Single-Cell Interpretable Annotation’ The Description field should not start with the package name, 'This package' or similar. * 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 whether package ‘CASSIA’ can be installed ... [12s/12s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE Non-standard file/directory found at top level: ‘cran-comments.md’ * 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 ... [4s/4s] ERROR Initial setup failed, attempting automatic environment setup... Using existing virtualenv: cassia_env Using virtual environment 'cassia_env' ... ============================================================ CASSIA Setup Error ============================================================ PROBLEM: Failed to create the CASSIA Python environment. Error: Failed to set up CASSIA Python environment with method: auto WHY THIS MATTERS: This may be due to permission issues or network problems. HOW TO FIX: Try these solutions: 1. Ensure python3-venv is installed: sudo apt install python3-venv 2. Check your internet connection 3. Try manually creating the environment: python3 -m venv ~/.virtualenvs/cassia_env ============================================================ Warning messages: 1: In check_forbidden_install("Python packages") : cannot install Python packages during R CMD check 2: In system2(python, c("-c", shQuote(command)), stdout = TRUE, stderr = TRUE) : running command ''/tmp/check-CRAN-incoming-hornik/.virtualenvs/cassia_env/bin/python' -c 'import sys; import pip; sys.stdout.write(pip.__version__)' 2>&1' had status 1 3: In value[[3L]](cond) : Virtualenv setup failed: the condition has length > 1 It looks like this package has a loading problem: see the messages for details. * checking whether the package can be loaded with stated dependencies ... [4s/4s] WARNING Initial setup failed, attempting automatic environment setup... Using existing virtualenv: cassia_env Using virtual environment 'cassia_env' ... ============================================================ CASSIA Setup Error ============================================================ PROBLEM: Failed to create the CASSIA Python environment. Error: Failed to set up CASSIA Python environment with method: auto WHY THIS MATTERS: This may be due to permission issues or network problems. HOW TO FIX: Try these solutions: 1. Ensure python3-venv is installed: sudo apt install python3-venv 2. Check your internet connection 3. Try manually creating the environment: python3 -m venv ~/.virtualenvs/cassia_env ============================================================ Warning messages: 1: In check_forbidden_install("Python packages") : cannot install Python packages during R CMD check 2: In system2(python, c("-c", shQuote(command)), stdout = TRUE, stderr = TRUE) : running command ''/tmp/check-CRAN-incoming-hornik/.virtualenvs/cassia_env/bin/python' -c 'import sys; import pip; sys.stdout.write(pip.__version__)' 2>&1' had status 1 3: In value[[3L]](cond) : Virtualenv setup failed: the condition has length > 1 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 ... [4s/4s] OK * checking whether the namespace can be loaded with stated dependencies ... [3s/3s] NOTE Warning in check_forbidden_install("Python packages") : cannot install Python packages during R CMD check Using virtual environment 'cassia_env' ... Warning in system2(python, c("-c", shQuote(command)), stdout = TRUE, stderr = TRUE) : running command ''/tmp/check-CRAN-incoming-hornik/.virtualenvs/cassia_env/bin/python' -c 'import sys; import pip; sys.stdout.write(pip.__version__)' 2>&1' had status 1 Warning in value[[3L]](cond) : Virtualenv setup failed: the condition has length > 1 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 ... [4s/4s] OK * checking loading without being on the library search path ... [4s/4s] WARNING Initial setup failed, attempting automatic environment setup... Using existing virtualenv: cassia_env Using virtual environment 'cassia_env' ... ============================================================ CASSIA Setup Error ============================================================ PROBLEM: Failed to create the CASSIA Python environment. Error: Failed to set up CASSIA Python environment with method: auto WHY THIS MATTERS: This may be due to permission issues or network problems. HOW TO FIX: Try these solutions: 1. Ensure python3-venv is installed: sudo apt install python3-venv 2. Check your internet connection 3. Try manually creating the environment: python3 -m venv ~/.virtualenvs/cassia_env ============================================================ Warning messages: 1: In check_forbidden_install("Python packages") : cannot install Python packages during R CMD check 2: In system2(python, c("-c", shQuote(command)), stdout = TRUE, stderr = TRUE) : running command ''/tmp/check-CRAN-incoming-hornik/.virtualenvs/cassia_env/bin/python' -c 'import sys; import pip; sys.stdout.write(pip.__version__)' 2>&1' had status 1 3: In value[[3L]](cond) : Virtualenv setup failed: the condition has length > 1 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 ... [4s/4s] NOTE Using existing virtualenv: cassia_env Using virtual environment 'cassia_env' ... ============================================================ CASSIA Setup Error ============================================================ PROBLEM: Failed to create the CASSIA Python environment. Error: Failed to set up CASSIA Python environment with method: auto WHY THIS MATTERS: This may be due to permission issues or network problems. HOW TO FIX: Try these solutions: 1. Ensure python3-venv is installed: sudo apt install python3-venv 2. Check your internet connection 3. Try manually creating the environment: python3 -m venv ~/.virtualenvs/cassia_env ============================================================ 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 ... [17s/17s] NOTE File ‘CASSIA/R/annotator.R’: .onLoad calls: packageStartupMessage("CASSIA Python environment not found. Setting up automatically...") packageStartupMessage("CASSIA loaded successfully! Happy annotating!") packageStartupMessage("Initial setup failed, attempting automatic environment setup...") packageStartupMessage("CASSIA loaded successfully! Happy annotating!") See section ‘Good practice’ in '?.onAttach'. Using virtual environment 'cassia_env' ... * 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 examples ... [9s/9s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [4s/4s] OK Running ‘testthat.R’ [4s/4s] * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 WARNINGs, 5 NOTEs