* using log directory ‘/srv/hornik/tmp/CRAN_pretest/bolt4jr.Rcheck’ * using R Under development (unstable) (2025-01-15 r87581) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.6 (1+b1) Debian flang-new version 19.1.6 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘bolt4jr/DESCRIPTION’ ... OK * this is package ‘bolt4jr’ version ‘1.2.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/5s] NOTE Maintainer: ‘Wanjun Gu ’ New submission Possibly misspelled words in DESCRIPTION: bioinformatics (7:360) * 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 ‘bolt4jr’ can be installed ... [1s/1s] OK * 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking whether startup messages can be suppressed ... [0s/0s] 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 ... [2s/2s] 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 ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [49s/47s] ERROR Running examples in ‘bolt4jr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: setup_bolt4jr > ### Title: Set up the Conda environment for bolt4jr > ### Aliases: setup_bolt4jr > > ### ** Examples > > setup_bolt4jr() No Conda binary found. Installing Miniconda... Warning in check_forbidden_install("Miniconda") : cannot install Miniconda during R CMD check * Installing Miniconda -- please wait a moment ... * Downloading 'https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh' ... trying URL 'https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh' Content type 'application/octet-stream' length 147784736 bytes (140.9 MB) ================================================== downloaded 140.9 MB + /usr/bin/bash /tmp/RtmpqAduou/working_dir/RtmpCU5Gdr/Miniconda3-latest-Linux-x86_64.sh -b -u -p '/tmp/check-CRAN-incoming-hornik/data/R/reticulate/miniconda' PREFIX=/tmp/check-CRAN-incoming-hornik/data/R/reticulate/miniconda Unpacking payload ... Installing base environment... Preparing transaction: ...working... done Executing transaction: ...working... done installation finished. + /tmp/check-CRAN-incoming-hornik/data/R/reticulate/miniconda/bin/conda update --yes --name base conda Channels: - defaults Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /tmp/check-CRAN-incoming-hornik/data/R/reticulate/miniconda added / updated specs: - conda The following packages will be downloaded: package | build ---------------------------|----------------- ca-certificates-2024.12.31 | h06a4308_0 128 KB certifi-2024.12.14 | py312h06a4308_0 161 KB ------------------------------------------------------------ Total: 289 KB The following packages will be UPDATED: ca-certificates 2024.11.26-h06a4308_0 --> 2024.12.31-h06a4308_0 certifi 2024.8.30-py312h06a4308_0 --> 2024.12.14-py312h06a4308_0 Downloading and Extracting Packages: ...working... certifi-2024.12.14 | 161 KB | | 0% ca-certificates-2024 | 128 KB | | 0%  ca-certificates-2024 | 128 KB | ########## | 100%  certifi-2024.12.14 | 161 KB | ########## | 100% ca-certificates-2024 | 128 KB | ########## | 100%  certifi-2024.12.14 | 161 KB | ########## | 100%  done Preparing transaction: - done Verifying transaction: | done Executing transaction: - done Warning in check_forbidden_install("Conda Environments") : cannot install Conda Environments during R CMD check + /tmp/check-CRAN-incoming-hornik/data/R/reticulate/miniconda/bin/conda create --yes --name r-reticulate 'python=3.10' numpy --quiet -c conda-forge Channels: - conda-forge - defaults Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /tmp/check-CRAN-incoming-hornik/data/R/reticulate/miniconda/envs/r-reticulate added / updated specs: - numpy - python=3.10 The following packages will be downloaded: package | build ---------------------------|----------------- _libgcc_mutex-0.1 | conda_forge 3 KB conda-forge _openmp_mutex-4.5 | 2_gnu 23 KB conda-forge bzip2-1.0.8 | h4bc722e_7 247 KB conda-forge ca-certificates-2024.12.14 | hbcca054_0 153 KB conda-forge ld_impl_linux-64-2.43 | h712a8e2_2 654 KB conda-forge libblas-3.9.0 |26_linux64_openblas 16 KB conda-forge libcblas-3.9.0 |26_linux64_openblas 16 KB conda-forge libffi-3.4.2 | h7f98852_5 57 KB conda-forge libgcc-14.2.0 | h77fa898_1 829 KB conda-forge libgcc-ng-14.2.0 | h69a702a_1 53 KB conda-forge libgfortran-14.2.0 | h69a702a_1 53 KB conda-forge libgfortran5-14.2.0 | hd5240d6_1 1.4 MB conda-forge libgomp-14.2.0 | h77fa898_1 450 KB conda-forge liblapack-3.9.0 |26_linux64_openblas 16 KB conda-forge liblzma-5.6.3 | hb9d3cd8_1 109 KB conda-forge libnsl-2.0.1 | hd590300_0 33 KB conda-forge libopenblas-0.3.28 |pthreads_h94d23a6_1 5.3 MB conda-forge libsqlite-3.47.2 | hee588c1_0 853 KB conda-forge libstdcxx-14.2.0 | hc0a3c3a_1 3.7 MB conda-forge libuuid-2.38.1 | h0b41bf4_0 33 KB conda-forge libxcrypt-4.4.36 | hd590300_1 98 KB conda-forge libzlib-1.3.1 | hb9d3cd8_2 60 KB conda-forge ncurses-6.5 | h2d0b736_2 873 KB conda-forge numpy-2.2.1 | py310h5851e9f_0 7.5 MB conda-forge openssl-3.4.0 | h7b32b05_1 2.8 MB conda-forge pip-24.3.1 | pyh8b19718_2 1.2 MB conda-forge python-3.10.16 |he725a3c_1_cpython 24.0 MB conda-forge python_abi-3.10 | 5_cp310 6 KB conda-forge readline-8.2 | h8228510_1 275 KB conda-forge setuptools-75.8.0 | pyhff2d567_0 757 KB conda-forge tk-8.6.13 |noxft_h4845f30_101 3.2 MB conda-forge tzdata-2024b | hc8b5060_0 119 KB conda-forge wheel-0.45.1 | pyhd8ed1ab_1 61 KB conda-forge ------------------------------------------------------------ Total: 54.9 MB The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 ca-certificates conda-forge/linux-64::ca-certificates-2024.12.14-hbcca054_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_2 libblas conda-forge/linux-64::libblas-3.9.0-26_linux64_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-26_linux64_openblas libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5 libgcc conda-forge/linux-64::libgcc-14.2.0-h77fa898_1 libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_1 libgfortran conda-forge/linux-64::libgfortran-14.2.0-h69a702a_1 libgfortran5 conda-forge/linux-64::libgfortran5-14.2.0-hd5240d6_1 libgomp conda-forge/linux-64::libgomp-14.2.0-h77fa898_1 liblapack conda-forge/linux-64::liblapack-3.9.0-26_linux64_openblas liblzma conda-forge/linux-64::liblzma-5.6.3-hb9d3cd8_1 libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libopenblas conda-forge/linux-64::libopenblas-0.3.28-pthreads_h94d23a6_1 libsqlite conda-forge/linux-64::libsqlite-3.47.2-hee588c1_0 libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-hc0a3c3a_1 libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 ncurses conda-forge/linux-64::ncurses-6.5-h2d0b736_2 numpy conda-forge/linux-64::numpy-2.2.1-py310h5851e9f_0 openssl conda-forge/linux-64::openssl-3.4.0-h7b32b05_1 pip conda-forge/noarch::pip-24.3.1-pyh8b19718_2 python conda-forge/linux-64::python-3.10.16-he725a3c_1_cpython python_abi conda-forge/linux-64::python_abi-3.10-5_cp310 readline conda-forge/linux-64::readline-8.2-h8228510_1 setuptools conda-forge/noarch::setuptools-75.8.0-pyhff2d567_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0 wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done * Miniconda has been successfully installed at "/tmp/check-CRAN-incoming-hornik/data/R/reticulate/miniconda". Creating Conda environment: bolt4jr Warning in check_forbidden_install("Conda Environments") : cannot install Conda Environments during R CMD check + /tmp/check-CRAN-incoming-hornik/data/R/reticulate/miniconda/bin/conda create --yes --name bolt4jr 'python=3.9' --quiet -c conda-forge Channels: - conda-forge - defaults Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /tmp/check-CRAN-incoming-hornik/data/R/reticulate/miniconda/envs/bolt4jr added / updated specs: - python=3.9 The following packages will be downloaded: package | build ---------------------------|----------------- python-3.9.21 |h9c0c6dc_1_cpython 22.5 MB conda-forge ------------------------------------------------------------ Total: 22.5 MB The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-64::bzip2-1.0.8-h4bc722e_7 ca-certificates conda-forge/linux-64::ca-certificates-2024.12.14-hbcca054_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_2 libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5 libgcc conda-forge/linux-64::libgcc-14.2.0-h77fa898_1 libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_1 libgomp conda-forge/linux-64::libgomp-14.2.0-h77fa898_1 liblzma conda-forge/linux-64::liblzma-5.6.3-hb9d3cd8_1 libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libsqlite conda-forge/linux-64::libsqlite-3.47.2-hee588c1_0 libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 ncurses conda-forge/linux-64::ncurses-6.5-h2d0b736_2 openssl conda-forge/linux-64::openssl-3.4.0-h7b32b05_1 pip conda-forge/noarch::pip-24.3.1-pyh8b19718_2 python conda-forge/linux-64::python-3.9.21-h9c0c6dc_1_cpython readline conda-forge/linux-64::readline-8.2-h8228510_1 setuptools conda-forge/noarch::setuptools-75.8.0-pyhff2d567_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0 wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Installing 'neo4j' in environment: bolt4jr Warning in check_forbidden_install("Python packages") : cannot install Python packages during R CMD check + . /tmp/check-CRAN-incoming-hornik/data/R/reticulate/miniconda/bin/activate + conda activate 'bolt4jr' + '/tmp/check-CRAN-incoming-hornik/data/R/reticulate/miniconda/envs/bolt4jr/bin/python' -m pip install --upgrade --no-user neo4j ERROR: Could not find an activated virtualenv (required). Error: Error installing package(s): 'neo4j' Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE