* using log directory ‘/srv/hornik/tmp/CRAN_pretest/SUMO.Rcheck’ * using R Under development (unstable) (2025-04-07 r88118) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘SUMO/DESCRIPTION’ ... OK * this is package ‘SUMO’ version ‘0.2.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/5s] NOTE Maintainer: ‘Bernard Isekah Osang'ir ’ Possibly misspelled words in DESCRIPTION: Benchmarking (2:56) MOFA (12:314) Package has a FOSS license but eventually depends on the following package which may restrict use: MOFA2 The Description field should not start with the package name, 'This package' or similar. Found the following \keyword or \concept entries which likely give several index terms: File ‘SUMO.Rd’: \keyword{benchmarking,} \keyword{data,} \keyword{multi-omics,} \keyword{simulation,} * 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 ‘SUMO’ can be installed ... [15s/15s] OK * checking package directory ... OK * checking for future file timestamps ... 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 ... [4s/4s] OK * checking whether the package can be loaded with stated dependencies ... [4s/4s] OK * checking whether the package can be unloaded cleanly ... [4s/4s] OK * checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK * checking whether the namespace can be unloaded cleanly ... [4s/4s] OK * checking loading without being on the library search path ... [4s/4s] 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 ... [22s/22s] 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 examples ... [34s/34s] ERROR Running examples in ‘SUMO-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: demo_multiomics_analysis > ### Title: Demonstration of SUMO Utility in Multi-Omics Analysis using > ### MOFA2 > ### Aliases: demo_multiomics_analysis > > ### ** Examples > > if (requireNamespace("MOFAdata", quietly = TRUE)) { + demo_multiomics_analysis("SUMO", export_pptx = FALSE) + } Processing SUMO-generated data... Multi-omics demo mode activated! Simulation Available for 2 Latent Factors Creating MOFA object from a list of matrices (features as rows, sample as columns)... Checking data options... Checking training options... Checking model options... Connecting to the mofapy2 package using basilisk. Set 'use_basilisk' to FALSE if you prefer to manually set the python binary using 'reticulate'. + /tmp/check-CRAN-incoming-hornik/cache/R/basilisk/1.19.3/0/bin/conda create --yes --prefix /tmp/check-CRAN-incoming-hornik/cache/R/basilisk/1.19.3/MOFA2/1.17.0/mofa_env 'python=3.10.5' --quiet -c conda-forge --override-channels Channels: - conda-forge Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /tmp/check-CRAN-incoming-hornik/cache/R/basilisk/1.19.3/MOFA2/1.17.0/mofa_env added / updated specs: - python=3.10.5 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-2025.1.31-hbcca054_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.43-h712a8e2_4 libffi conda-forge/linux-64::libffi-3.4.6-h2dba641_1 libgcc conda-forge/linux-64::libgcc-14.2.0-h767d61c_2 libgcc-ng conda-forge/linux-64::libgcc-ng-14.2.0-h69a702a_2 libgomp conda-forge/linux-64::libgomp-14.2.0-h767d61c_2 liblzma conda-forge/linux-64::liblzma-5.8.1-hb9d3cd8_0 liblzma-devel conda-forge/linux-64::liblzma-devel-5.8.1-hb9d3cd8_0 libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libsqlite conda-forge/linux-64::libsqlite-3.49.1-hee588c1_2 libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2 ncurses conda-forge/linux-64::ncurses-6.5-h2d0b736_3 openssl conda-forge/linux-64::openssl-3.4.1-h7b32b05_0 pip conda-forge/noarch::pip-25.0.1-pyh8b19718_0 python conda-forge/linux-64::python-3.10.5-ha86cf86_0_cpython readline conda-forge/linux-64::readline-8.2-h8c095d6_2 setuptools conda-forge/noarch::setuptools-78.1.0-pyhff2d567_0 sqlite conda-forge/linux-64::sqlite-3.49.1-h9eae976_2 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 tzdata conda-forge/noarch::tzdata-2025b-h78e105d_0 wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 xz conda-forge/linux-64::xz-5.8.1-hbcc6ac9_0 xz-gpl-tools conda-forge/linux-64::xz-gpl-tools-5.8.1-hbcc6ac9_0 xz-tools conda-forge/linux-64::xz-tools-5.8.1-hb9d3cd8_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done + /tmp/check-CRAN-incoming-hornik/cache/R/basilisk/1.19.3/0/bin/conda install --yes --prefix /tmp/check-CRAN-incoming-hornik/cache/R/basilisk/1.19.3/MOFA2/1.17.0/mofa_env 'python=3.10.5' -c conda-forge --override-channels Channels: - conda-forge Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.11.3 latest version: 25.3.1 Please update conda by running $ conda update -n base -c conda-forge conda # All requested packages already installed. + /tmp/check-CRAN-incoming-hornik/cache/R/basilisk/1.19.3/0/bin/conda install --yes --prefix /tmp/check-CRAN-incoming-hornik/cache/R/basilisk/1.19.3/MOFA2/1.17.0/mofa_env -c conda-forge 'python=3.10.5' 'python=3.10.5' 'numpy=1.23.1' 'scipy=1.8.1' 'pandas=1.4.3' 'h5py=3.6.0' 'scikit-learn=1.1.1' 'dtw-python=1.2.2' --override-channels Channels: - conda-forge Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.11.3 latest version: 25.3.1 Please update conda by running $ conda update -n base -c conda-forge conda ## Package Plan ## environment location: /tmp/check-CRAN-incoming-hornik/cache/R/basilisk/1.19.3/MOFA2/1.17.0/mofa_env added / updated specs: - dtw-python=1.2.2 - h5py=3.6.0 - numpy=1.23.1 - pandas=1.4.3 - python[version='3.10.5.*,3.10.5.*'] - scikit-learn=1.1.1 - scipy=1.8.1 The following NEW packages will be INSTALLED: c-ares conda-forge/linux-64::c-ares-1.34.4-hb9d3cd8_0 cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1 cached_property conda-forge/noarch::cached_property-1.5.2-pyha770c72_1 dtw-python conda-forge/linux-64::dtw-python-1.2.2-py310h5764c6d_0 h5py conda-forge/linux-64::h5py-3.6.0-nompi_py310he751f51_100 hdf5 conda-forge/linux-64::hdf5-1.12.1-nompi_h4df4325_104 joblib conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_1 keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0 krb5 conda-forge/linux-64::krb5-1.21.3-h659f571_0 libblas conda-forge/linux-64::libblas-3.9.0-20_linux64_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-20_linux64_openblas libcurl conda-forge/linux-64::libcurl-8.8.0-hca28451_1 libedit conda-forge/linux-64::libedit-3.1.20250104-pl5321h7949ede_0 libev conda-forge/linux-64::libev-4.33-hd590300_2 libgfortran conda-forge/linux-64::libgfortran-14.2.0-h69a702a_2 libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.2.0-h69a702a_2 libgfortran5 conda-forge/linux-64::libgfortran5-14.2.0-hf1ad2bd_2 liblapack conda-forge/linux-64::liblapack-3.9.0-20_linux64_openblas libnghttp2 conda-forge/linux-64::libnghttp2-1.58.0-h47da74e_1 libopenblas conda-forge/linux-64::libopenblas-0.3.25-pthreads_h413a1c8_0 libssh2 conda-forge/linux-64::libssh2-1.11.0-h0841786_0 libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-h8f9b012_2 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-14.2.0-h4852527_2 numpy conda-forge/linux-64::numpy-1.23.1-py310h53a5b5f_0 pandas conda-forge/linux-64::pandas-1.4.3-py310h769672d_0 python-dateutil conda-forge/noarch::python-dateutil-2.9.0.post0-pyhff2d567_1 python_abi conda-forge/linux-64::python_abi-3.10-6_cp310 pytz conda-forge/noarch::pytz-2025.2-pyhd8ed1ab_0 scikit-learn conda-forge/linux-64::scikit-learn-1.1.1-py310hffb9edd_0 scipy conda-forge/linux-64::scipy-1.8.1-py310hdfbd76f_3 six conda-forge/noarch::six-1.17.0-pyhd8ed1ab_0 threadpoolctl conda-forge/noarch::threadpoolctl-3.6.0-pyhecae5ae_0 zlib conda-forge/linux-64::zlib-1.2.13-h4ab18f5_6 zstd conda-forge/linux-64::zstd-1.5.6-ha6fb4c9_0 The following packages will be DOWNGRADED: libsqlite 3.49.1-hee588c1_2 --> 3.46.0-hde9e2c9_0 libzlib 1.3.1-hb9d3cd8_2 --> 1.2.13-h4ab18f5_6 sqlite 3.49.1-h9eae976_2 --> 3.46.0-h6d4b2fc_0 Downloading and Extracting Packages: ...working... done Preparing transaction: - \ done Verifying transaction: / - \ | / - done Executing transaction: | / - \ | / - \ | / - \ done ERROR: Could not find an activated virtualenv (required). Error in setupBasiliskEnv(envpath, packages = .getPackages(env), channels = .getChannels(env), : failed to install additional packages via pip Calls: demo_multiomics_analysis -> run_mofa_analysis Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [7s/7s] OK Running ‘testthat.R’ [7s/7s] * checking PDF version of manual ... [2s/2s] 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