* 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 ... [59s/67s] 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 > > 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'. trying URL 'https://github.com/conda-forge/miniforge/releases/download/24.11.3-0/Miniforge3-24.11.3-0-Linux-x86_64.sh' Content type 'application/octet-stream' length 77993651 bytes (74.4 MB) ================================================== downloaded 74.4 MB PREFIX=/tmp/check-CRAN-incoming-hornik/cache/R/basilisk/1.19.3/0 Unpacking payload ... Extracting _libgcc_mutex-0.1-conda_forge.tar.bz2 Extracting ca-certificates-2024.12.14-hbcca054_0.conda Extracting ld_impl_linux-64-2.43-h712a8e2_2.conda Extracting pybind11-abi-4-hd8ed1ab_3.tar.bz2 Extracting python_abi-3.12-5_cp312.conda Extracting tzdata-2025a-h78e105d_0.conda Extracting libgomp-14.2.0-h77fa898_1.conda Extracting _openmp_mutex-4.5-2_gnu.tar.bz2 Extracting libgcc-14.2.0-h77fa898_1.conda Extracting c-ares-1.34.4-hb9d3cd8_0.conda Extracting libexpat-2.6.4-h5888daf_0.conda Extracting libgcc-ng-14.2.0-h69a702a_1.conda Extracting liblzma-5.6.3-hb9d3cd8_1.conda Extracting libstdcxx-14.2.0-hc0a3c3a_1.conda Extracting libzlib-1.3.1-hb9d3cd8_2.conda Extracting ncurses-6.5-h2d0b736_2.conda Extracting openssl-3.4.0-h7b32b05_1.conda Extracting reproc-14.2.5.post0-hb9d3cd8_0.conda Extracting bzip2-1.0.8-h4bc722e_7.conda Extracting keyutils-1.6.1-h166bdaf_0.tar.bz2 Extracting libedit-3.1.20240808-pl5321h7949ede_0.conda Extracting libev-4.33-hd590300_2.conda Extracting libffi-3.4.2-h7f98852_5.tar.bz2 Extracting libiconv-1.17-hd590300_2.conda Extracting libnsl-2.0.1-hd590300_0.conda Extracting libsqlite-3.48.0-hee588c1_0.conda Extracting libssh2-1.11.1-hf672d98_0.conda Extracting libstdcxx-ng-14.2.0-h4852527_1.conda Extracting libuuid-2.38.1-h0b41bf4_0.conda Extracting libxcrypt-4.4.36-hd590300_1.conda Extracting lz4-c-1.10.0-h5888daf_1.conda Extracting lzo-2.10-hd590300_1001.conda Extracting readline-8.2-h8228510_1.conda Extracting reproc-cpp-14.2.5.post0-h5888daf_0.conda Extracting tk-8.6.13-noxft_h4845f30_101.conda Extracting fmt-11.0.2-h434a139_0.conda Extracting krb5-1.21.3-h659f571_0.conda Extracting libnghttp2-1.64.0-h161d5f1_0.conda Extracting libsolv-0.7.30-h3509ff9_0.conda Extracting libxml2-2.13.5-h0d44e9d_1.conda Extracting python-3.12.8-h9e4cc4f_1_cpython.conda Extracting yaml-cpp-0.8.0-h59595ed_0.conda Extracting zstd-1.5.6-ha6fb4c9_0.conda Extracting libarchive-3.7.7-h4585015_3.conda Extracting libcurl-8.11.1-h332b0f4_0.conda Extracting menuinst-2.2.0-py312h7900ff3_0.conda Extracting archspec-0.2.5-pyhd8ed1ab_0.conda Extracting boltons-24.0.0-pyhd8ed1ab_1.conda Extracting brotli-python-1.1.0-py312h2ec8cdc_2.conda Extracting certifi-2024.12.14-pyhd8ed1ab_0.conda Extracting charset-normalizer-3.4.1-pyhd8ed1ab_0.conda Extracting colorama-0.4.6-pyhd8ed1ab_1.conda Extracting distro-1.9.0-pyhd8ed1ab_1.conda Extracting frozendict-2.4.6-py312h66e93f0_0.conda Extracting hpack-4.0.0-pyhd8ed1ab_1.conda Extracting hyperframe-6.0.1-pyhd8ed1ab_1.conda Extracting idna-3.10-pyhd8ed1ab_1.conda Extracting jsonpointer-3.0.0-py312h7900ff3_1.conda Extracting libmamba-1.5.12-h49b8a8d_0.conda Extracting packaging-24.2-pyhd8ed1ab_2.conda Extracting platformdirs-4.3.6-pyhd8ed1ab_1.conda Extracting pluggy-1.5.0-pyhd8ed1ab_1.conda Extracting pycosat-0.6.6-py312h66e93f0_2.conda Extracting pycparser-2.22-pyh29332c3_1.conda Extracting pysocks-1.7.1-pyha55dd90_7.conda Extracting ruamel.yaml.clib-0.2.8-py312h66e93f0_1.conda Extracting setuptools-75.8.0-pyhff2d567_0.conda Extracting truststore-0.10.0-pyhd8ed1ab_0.conda Extracting wheel-0.45.1-pyhd8ed1ab_1.conda Extracting cffi-1.17.1-py312h06ac9bb_0.conda Extracting h2-4.1.0-pyhd8ed1ab_1.conda Extracting jsonpatch-1.33-pyhd8ed1ab_1.conda Extracting libmambapy-1.5.12-py312hbaee817_0.conda Extracting pip-24.3.1-pyh8b19718_2.conda Extracting ruamel.yaml-0.18.10-py312h66e93f0_0.conda Extracting tqdm-4.67.1-pyhd8ed1ab_1.conda Extracting zstandard-0.23.0-py312hef9b889_1.conda Extracting conda-package-streaming-0.11.0-pyhd8ed1ab_0.conda Extracting urllib3-2.3.0-pyhd8ed1ab_0.conda Extracting requests-2.32.3-pyhd8ed1ab_1.conda Extracting conda-package-handling-2.4.0-pyh7900ff3_2.conda Extracting conda-24.11.3-py312h7900ff3_0.conda Extracting conda-libmamba-solver-24.9.0-pyhd8ed1ab_0.conda Extracting mamba-1.5.12-py312h9460a1c_0.conda Installing base environment... Transaction Prefix: /tmp/check-CRAN-incoming-hornik/cache/R/basilisk/1.19.3/0 Updating specs: - conda-forge/linux-64::_libgcc_mutex==0.1=conda_forge[md5=d7c89558ba9fa0495403155b64376d81] - conda-forge/linux-64::ca-certificates==2024.12.14=hbcca054_0[md5=720523eb0d6a9b0f6120c16b2aa4e7de] - conda-forge/linux-64::ld_impl_linux-64==2.43=h712a8e2_2[md5=048b02e3962f066da18efe3a21b77672] - conda-forge/noarch::pybind11-abi==4=hd8ed1ab_3[md5=878f923dd6acc8aeb47a75da6c4098be] - conda-forge/linux-64::python_abi==3.12=5_cp312[md5=0424ae29b104430108f5218a66db7260] - conda-forge/noarch::tzdata==2025a=h78e105d_0[md5=dbcace4706afdfb7eb891f7b37d07c04] - conda-forge/linux-64::libgomp==14.2.0=h77fa898_1[md5=cc3573974587f12dda90d96e3e55a702] - conda-forge/linux-64::_openmp_mutex==4.5=2_gnu[md5=73aaf86a425cc6e73fcf236a5a46396d] - conda-forge/linux-64::libgcc==14.2.0=h77fa898_1[md5=3cb76c3f10d3bc7f1105b2fc9db984df] - conda-forge/linux-64::c-ares==1.34.4=hb9d3cd8_0[md5=e2775acf57efd5af15b8e3d1d74d72d3] - conda-forge/linux-64::libexpat==2.6.4=h5888daf_0[md5=db833e03127376d461e1e13e76f09b6c] - conda-forge/linux-64::libgcc-ng==14.2.0=h69a702a_1[md5=e39480b9ca41323497b05492a63bc35b] - conda-forge/linux-64::liblzma==5.6.3=hb9d3cd8_1[md5=2ecf2f1c7e4e21fcfe6423a51a992d84] - conda-forge/linux-64::libstdcxx==14.2.0=hc0a3c3a_1[md5=234a5554c53625688d51062645337328] - conda-forge/linux-64::libzlib==1.3.1=hb9d3cd8_2[md5=edb0dca6bc32e4f4789199455a1dbeb8] - conda-forge/linux-64::ncurses==6.5=h2d0b736_2[md5=04b34b9a40cdc48cfdab261ab176ff74] - conda-forge/linux-64::openssl==3.4.0=h7b32b05_1[md5=4ce6875f75469b2757a65e10a5d05e31] - conda-forge/linux-64::reproc==14.2.5.post0=hb9d3cd8_0[md5=69fbc0a9e42eb5fe6733d2d60d818822] - conda-forge/linux-64::bzip2==1.0.8=h4bc722e_7[md5=62ee74e96c5ebb0af99386de58cf9553] - conda-forge/linux-64::keyutils==1.6.1=h166bdaf_0[md5=30186d27e2c9fa62b45fb1476b7200e3] - conda-forge/linux-64::libedit==3.1.20240808=pl5321h7949ede_0[md5=8247f80f3dc464d9322e85007e307fe8] - conda-forge/linux-64::libev==4.33=hd590300_2[md5=172bf1cd1ff8629f2b1179945ed45055] - conda-forge/linux-64::libffi==3.4.2=h7f98852_5[md5=d645c6d2ac96843a2bfaccd2d62b3ac3] - conda-forge/linux-64::libiconv==1.17=hd590300_2[md5=d66573916ffcf376178462f1b61c941e] - conda-forge/linux-64::libnsl==2.0.1=hd590300_0[md5=30fd6e37fe21f86f4bd26d6ee73eeec7] - conda-forge/linux-64::libsqlite==3.48.0=hee588c1_0[md5=84bd1c9a82b455e7a2f390375fb38f90] - conda-forge/linux-64::libssh2==1.11.1=hf672d98_0[md5=be2de152d8073ef1c01b7728475f2fe7] - conda-forge/linux-64::libstdcxx-ng==14.2.0=h4852527_1[md5=8371ac6457591af2cf6159439c1fd051] - conda-forge/linux-64::libuuid==2.38.1=h0b41bf4_0[md5=40b61aab5c7ba9ff276c41cfffe6b80b] - conda-forge/linux-64::libxcrypt==4.4.36=hd590300_1[md5=5aa797f8787fe7a17d1b0821485b5adc] - conda-forge/linux-64::lz4-c==1.10.0=h5888daf_1[md5=9de5350a85c4a20c685259b889aa6393] - conda-forge/linux-64::lzo==2.10=hd590300_1001[md5=ec7398d21e2651e0dcb0044d03b9a339] - conda-forge/linux-64::readline==8.2=h8228510_1[md5=47d31b792659ce70f470b5c82fdfb7a4] - conda-forge/linux-64::reproc-cpp==14.2.5.post0=h5888daf_0[md5=828302fca535f9cfeb598d5f7c204323] - conda-forge/linux-64::tk==8.6.13=noxft_h4845f30_101[md5=d453b98d9c83e71da0741bb0ff4d76bc] - conda-forge/linux-64::fmt==11.0.2=h434a139_0[md5=995f7e13598497691c1dc476d889bc04] - conda-forge/linux-64::krb5==1.21.3=h659f571_0[md5=3f43953b7d3fb3aaa1d0d0723d91e368] - conda-forge/linux-64::libnghttp2==1.64.0=h161d5f1_0[md5=19e57602824042dfd0446292ef90488b] - conda-forge/linux-64::libsolv==0.7.30=h3509ff9_0[md5=02539b77d25aa4f65b20246549e256c3] - conda-forge/linux-64::libxml2==2.13.5=h0d44e9d_1[md5=f5b05674697ae7d2c5932766695945e1] - conda-forge/linux-64::python==3.12.8=h9e4cc4f_1_cpython[md5=7fd2fd79436d9b473812f14e86746844] - conda-forge/linux-64::yaml-cpp==0.8.0=h59595ed_0[md5=965eaacd7c18eb8361fd12bb9e7a57d7] - conda-forge/linux-64::zstd==1.5.6=ha6fb4c9_0[md5=4d056880988120e29d75bfff282e0f45] - conda-forge/linux-64::libarchive==3.7.7=h4585015_3[md5=a28808eae584c7f519943719b2a2b386] - conda-forge/linux-64::libcurl==8.11.1=h332b0f4_0[md5=2b3e0081006dc21e8bf53a91c83a055c] - conda-forge/linux-64::menuinst==2.2.0=py312h7900ff3_0[md5=f22f8e77b36e67297feffe03eefd5375] - conda-forge/noarch::archspec==0.2.5=pyhd8ed1ab_0[md5=845b38297fca2f2d18a29748e2ece7fa] - conda-forge/noarch::boltons==24.0.0=pyhd8ed1ab_1[md5=d88c38e66d85ecc9c7e2c4110676bbf4] - conda-forge/linux-64::brotli-python==1.1.0=py312h2ec8cdc_2[md5=b0b867af6fc74b2a0aa206da29c0f3cf] - conda-forge/noarch::certifi==2024.12.14=pyhd8ed1ab_0[md5=6feb87357ecd66733be3279f16a8c400] - conda-forge/noarch::charset-normalizer==3.4.1=pyhd8ed1ab_0[md5=e83a31202d1c0a000fce3e9cf3825875] - conda-forge/noarch::colorama==0.4.6=pyhd8ed1ab_1[md5=962b9857ee8e7018c22f2776ffa0b2d7] - conda-forge/noarch::distro==1.9.0=pyhd8ed1ab_1[md5=0a2014fd9860f8b1eaa0b1f3d3771a08] - conda-forge/linux-64::frozendict==2.4.6=py312h66e93f0_0[md5=9fa8408745a0621314b7751d11fecc18] - conda-forge/noarch::hpack==4.0.0=pyhd8ed1ab_1[md5=2aa5ff7fa34a81b9196532c84c10d865] - conda-forge/noarch::hyperframe==6.0.1=pyhd8ed1ab_1[md5=566e75c90c1d0c8c459eb0ad9833dc7a] - conda-forge/noarch::idna==3.10=pyhd8ed1ab_1[md5=39a4f67be3286c86d696df570b1201b7] - conda-forge/linux-64::jsonpointer==3.0.0=py312h7900ff3_1[md5=6b51f7459ea4073eeb5057207e2e1e3d] - conda-forge/linux-64::libmamba==1.5.12=h49b8a8d_0[md5=d6aec145c4f2473c09c2699d74f6dfc0] - conda-forge/noarch::packaging==24.2=pyhd8ed1ab_2[md5=3bfed7e6228ebf2f7b9eaa47f1b4e2aa] - conda-forge/noarch::platformdirs==4.3.6=pyhd8ed1ab_1[md5=577852c7e53901ddccc7e6a9959ddebe] - conda-forge/noarch::pluggy==1.5.0=pyhd8ed1ab_1[md5=e9dcbce5f45f9ee500e728ae58b605b6] - conda-forge/linux-64::pycosat==0.6.6=py312h66e93f0_2[md5=08223e6a73e0bca5ade16ec4cebebf23] - conda-forge/noarch::pycparser==2.22=pyh29332c3_1[md5=12c566707c80111f9799308d9e265aef] - conda-forge/noarch::pysocks==1.7.1=pyha55dd90_7[md5=461219d1a5bd61342293efa2c0c90eac] - conda-forge/linux-64::ruamel.yaml.clib==0.2.8=py312h66e93f0_1[md5=532c3e5d0280be4fea52396ec1fa7d5d] - conda-forge/noarch::setuptools==75.8.0=pyhff2d567_0[md5=8f28e299c11afdd79e0ec1e279dcdc52] - conda-forge/noarch::truststore==0.10.0=pyhd8ed1ab_0[md5=ad1c20cd193e3044bcf17798c33b9d67] - conda-forge/noarch::wheel==0.45.1=pyhd8ed1ab_1[md5=75cb7132eb58d97896e173ef12ac9986] - conda-forge/linux-64::cffi==1.17.1=py312h06ac9bb_0[md5=a861504bbea4161a9170b85d4d2be840] - conda-forge/noarch::h2==4.1.0=pyhd8ed1ab_1[md5=825927dc7b0f287ef8d4d0011bb113b1] - conda-forge/noarch::jsonpatch==1.33=pyhd8ed1ab_1[md5=cb60ae9cf02b9fcb8004dec4089e5691] - conda-forge/linux-64::libmambapy==1.5.12=py312hbaee817_0[md5=88dd983e44c86cdde2817ecfa7d84d5a] - conda-forge/noarch::pip==24.3.1=pyh8b19718_2[md5=04e691b9fadd93a8a9fad87a81d4fd8f] - conda-forge/linux-64::ruamel.yaml==0.18.10=py312h66e93f0_0[md5=5260b7fb19694ee5bc4ed0ee7a2a769f] - conda-forge/noarch::tqdm==4.67.1=pyhd8ed1ab_1[md5=9efbfdc37242619130ea42b1cc4ed861] - conda-forge/linux-64::zstandard==0.23.0=py312hef9b889_1[md5=8b7069e9792ee4e5b4919a7a306d2e67] - conda-forge/noarch::conda-package-streaming==0.11.0=pyhd8ed1ab_0[md5=bc9533d8616a97551ed144789bf9c1cd] - conda-forge/noarch::urllib3==2.3.0=pyhd8ed1ab_0[md5=32674f8dbfb7b26410ed580dd3c10a29] - conda-forge/noarch::requests==2.32.3=pyhd8ed1ab_1[md5=a9b9368f3701a417eac9edbcae7cb737] - conda-forge/noarch::conda-package-handling==2.4.0=pyh7900ff3_2[md5=32c158f481b4fd7630c565030f7bc482] - conda-forge/linux-64::conda==24.11.3=py312h7900ff3_0[md5=bdaca5d82db98d8b5639f058a818ff03] - conda-forge/noarch::conda-libmamba-solver==24.9.0=pyhd8ed1ab_0[md5=45378d089c5f72c9c0d63d58414c645d] - conda-forge/linux-64::mamba==1.5.12=py312h9460a1c_0[md5=59a9360536caad98732fdfdc320e41dc] Package Version Build Channel Size ───────────────────────────────────────────────────────────────────────────────────── Install: ───────────────────────────────────────────────────────────────────────────────────── + _libgcc_mutex 0.1 conda_forge conda-forge + ca-certificates 2024.12.14 hbcca054_0 conda-forge + ld_impl_linux-64 2.43 h712a8e2_2 conda-forge + pybind11-abi 4 hd8ed1ab_3 conda-forge + python_abi 3.12 5_cp312 conda-forge + tzdata 2025a h78e105d_0 conda-forge + libgomp 14.2.0 h77fa898_1 conda-forge + _openmp_mutex 4.5 2_gnu conda-forge + libgcc 14.2.0 h77fa898_1 conda-forge + c-ares 1.34.4 hb9d3cd8_0 conda-forge + libexpat 2.6.4 h5888daf_0 conda-forge + libgcc-ng 14.2.0 h69a702a_1 conda-forge + liblzma 5.6.3 hb9d3cd8_1 conda-forge + libstdcxx 14.2.0 hc0a3c3a_1 conda-forge + libzlib 1.3.1 hb9d3cd8_2 conda-forge + ncurses 6.5 h2d0b736_2 conda-forge + openssl 3.4.0 h7b32b05_1 conda-forge + reproc 14.2.5.post0 hb9d3cd8_0 conda-forge + bzip2 1.0.8 h4bc722e_7 conda-forge + keyutils 1.6.1 h166bdaf_0 conda-forge + libedit 3.1.20240808 pl5321h7949ede_0 conda-forge + libev 4.33 hd590300_2 conda-forge + libffi 3.4.2 h7f98852_5 conda-forge + libiconv 1.17 hd590300_2 conda-forge + libnsl 2.0.1 hd590300_0 conda-forge + libsqlite 3.48.0 hee588c1_0 conda-forge + libssh2 1.11.1 hf672d98_0 conda-forge + libstdcxx-ng 14.2.0 h4852527_1 conda-forge + libuuid 2.38.1 h0b41bf4_0 conda-forge + libxcrypt 4.4.36 hd590300_1 conda-forge + lz4-c 1.10.0 h5888daf_1 conda-forge + lzo 2.10 hd590300_1001 conda-forge + readline 8.2 h8228510_1 conda-forge + reproc-cpp 14.2.5.post0 h5888daf_0 conda-forge + tk 8.6.13 noxft_h4845f30_101 conda-forge + fmt 11.0.2 h434a139_0 conda-forge + krb5 1.21.3 h659f571_0 conda-forge + libnghttp2 1.64.0 h161d5f1_0 conda-forge + libsolv 0.7.30 h3509ff9_0 conda-forge + libxml2 2.13.5 h0d44e9d_1 conda-forge + python 3.12.8 h9e4cc4f_1_cpython conda-forge + yaml-cpp 0.8.0 h59595ed_0 conda-forge + zstd 1.5.6 ha6fb4c9_0 conda-forge + libarchive 3.7.7 h4585015_3 conda-forge + libcurl 8.11.1 h332b0f4_0 conda-forge + menuinst 2.2.0 py312h7900ff3_0 conda-forge + archspec 0.2.5 pyhd8ed1ab_0 conda-forge + boltons 24.0.0 pyhd8ed1ab_1 conda-forge + brotli-python 1.1.0 py312h2ec8cdc_2 conda-forge + certifi 2024.12.14 pyhd8ed1ab_0 conda-forge + charset-normalizer 3.4.1 pyhd8ed1ab_0 conda-forge + colorama 0.4.6 pyhd8ed1ab_1 conda-forge + distro 1.9.0 pyhd8ed1ab_1 conda-forge + frozendict 2.4.6 py312h66e93f0_0 conda-forge + hpack 4.0.0 pyhd8ed1ab_1 conda-forge + hyperframe 6.0.1 pyhd8ed1ab_1 conda-forge + idna 3.10 pyhd8ed1ab_1 conda-forge + jsonpointer 3.0.0 py312h7900ff3_1 conda-forge + libmamba 1.5.12 h49b8a8d_0 conda-forge + packaging 24.2 pyhd8ed1ab_2 conda-forge + platformdirs 4.3.6 pyhd8ed1ab_1 conda-forge + pluggy 1.5.0 pyhd8ed1ab_1 conda-forge + pycosat 0.6.6 py312h66e93f0_2 conda-forge + pycparser 2.22 pyh29332c3_1 conda-forge + pysocks 1.7.1 pyha55dd90_7 conda-forge + ruamel.yaml.clib 0.2.8 py312h66e93f0_1 conda-forge + setuptools 75.8.0 pyhff2d567_0 conda-forge + truststore 0.10.0 pyhd8ed1ab_0 conda-forge + wheel 0.45.1 pyhd8ed1ab_1 conda-forge + cffi 1.17.1 py312h06ac9bb_0 conda-forge + h2 4.1.0 pyhd8ed1ab_1 conda-forge + jsonpatch 1.33 pyhd8ed1ab_1 conda-forge + libmambapy 1.5.12 py312hbaee817_0 conda-forge + pip 24.3.1 pyh8b19718_2 conda-forge + ruamel.yaml 0.18.10 py312h66e93f0_0 conda-forge + tqdm 4.67.1 pyhd8ed1ab_1 conda-forge + zstandard 0.23.0 py312hef9b889_1 conda-forge + conda-package-streaming 0.11.0 pyhd8ed1ab_0 conda-forge + urllib3 2.3.0 pyhd8ed1ab_0 conda-forge + requests 2.32.3 pyhd8ed1ab_1 conda-forge + conda-package-handling 2.4.0 pyh7900ff3_2 conda-forge + conda 24.11.3 py312h7900ff3_0 conda-forge + conda-libmamba-solver 24.9.0 pyhd8ed1ab_0 conda-forge + mamba 1.5.12 py312h9460a1c_0 conda-forge Summary: Install: 84 packages Total download: 0 B ───────────────────────────────────────────────────────────────────────────────────── Transaction starting Transaction finished To activate this environment, use: micromamba activate /tmp/check-CRAN-incoming-hornik/cache/R/basilisk/1.19.3/0 Or to execute a single command in this environment, use: micromamba run -p /tmp/check-CRAN-incoming-hornik/cache/R/basilisk/1.19.3/0 mycommand installation finished. + /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 packages will be downloaded: package | build ---------------------------|----------------- ca-certificates-2025.1.31 | hbcca054_0 154 KB conda-forge ld_impl_linux-64-2.43 | h712a8e2_4 656 KB conda-forge libffi-3.4.6 | h2dba641_1 56 KB conda-forge libgcc-14.2.0 | h767d61c_2 828 KB conda-forge libgcc-ng-14.2.0 | h69a702a_2 52 KB conda-forge libgomp-14.2.0 | h767d61c_2 449 KB conda-forge liblzma-5.8.1 | hb9d3cd8_0 110 KB conda-forge liblzma-devel-5.8.1 | hb9d3cd8_0 431 KB conda-forge libsqlite-3.49.1 | hee588c1_2 897 KB conda-forge ncurses-6.5 | h2d0b736_3 871 KB conda-forge openssl-3.4.1 | h7b32b05_0 2.8 MB conda-forge pip-25.0.1 | pyh8b19718_0 1.2 MB conda-forge python-3.10.5 |ha86cf86_0_cpython 28.7 MB conda-forge readline-8.2 | h8c095d6_2 276 KB conda-forge setuptools-78.1.0 | pyhff2d567_0 768 KB conda-forge sqlite-3.49.1 | h9eae976_2 839 KB conda-forge tzdata-2025b | h78e105d_0 120 KB conda-forge xz-5.8.1 | hbcc6ac9_0 23 KB conda-forge xz-gpl-tools-5.8.1 | hbcc6ac9_0 33 KB conda-forge xz-tools-5.8.1 | hb9d3cd8_0 94 KB conda-forge ------------------------------------------------------------ Total: 39.2 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-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 packages will be downloaded: package | build ---------------------------|----------------- cached-property-1.5.2 | hd8ed1ab_1 4 KB conda-forge cached_property-1.5.2 | pyha770c72_1 11 KB conda-forge dtw-python-1.2.2 | py310h5764c6d_0 276 KB conda-forge h5py-3.6.0 |nompi_py310he751f51_100 6.7 MB conda-forge hdf5-1.12.1 |nompi_h4df4325_104 3.6 MB conda-forge joblib-1.4.2 | pyhd8ed1ab_1 215 KB conda-forge libblas-3.9.0 |20_linux64_openblas 14 KB conda-forge libcblas-3.9.0 |20_linux64_openblas 14 KB conda-forge libcurl-8.8.0 | hca28451_1 401 KB conda-forge libedit-3.1.20250104 | pl5321h7949ede_0 132 KB conda-forge libgfortran-14.2.0 | h69a702a_2 52 KB conda-forge libgfortran-ng-14.2.0 | h69a702a_2 53 KB conda-forge libgfortran5-14.2.0 | hf1ad2bd_2 1.4 MB conda-forge liblapack-3.9.0 |20_linux64_openblas 14 KB conda-forge libnghttp2-1.58.0 | h47da74e_1 617 KB conda-forge libopenblas-0.3.25 |pthreads_h413a1c8_0 5.3 MB conda-forge libsqlite-3.46.0 | hde9e2c9_0 845 KB conda-forge libssh2-1.11.0 | h0841786_0 265 KB conda-forge libstdcxx-14.2.0 | h8f9b012_2 3.7 MB conda-forge libstdcxx-ng-14.2.0 | h4852527_2 53 KB conda-forge libzlib-1.2.13 | h4ab18f5_6 60 KB conda-forge numpy-1.23.1 | py310h53a5b5f_0 7.0 MB conda-forge pandas-1.4.3 | py310h769672d_0 12.5 MB conda-forge python-dateutil-2.9.0.post0| pyhff2d567_1 217 KB conda-forge python_abi-3.10 | 6_cp310 7 KB conda-forge pytz-2025.2 | pyhd8ed1ab_0 185 KB conda-forge scikit-learn-1.1.1 | py310hffb9edd_0 8.3 MB conda-forge scipy-1.8.1 | py310hdfbd76f_3 25.0 MB conda-forge six-1.17.0 | pyhd8ed1ab_0 16 KB conda-forge sqlite-3.46.0 | h6d4b2fc_0 840 KB conda-forge threadpoolctl-3.6.0 | pyhecae5ae_0 23 KB conda-forge zlib-1.2.13 | h4ab18f5_6 91 KB conda-forge ------------------------------------------------------------ Total: 77.7 MB 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... scipy-1.8.1 | 25.0 MB | | 0% pandas-1.4.3 | 12.5 MB | | 0%  scikit-learn-1.1.1 | 8.3 MB | | 0%  numpy-1.23.1 | 7.0 MB | | 0%  h5py-3.6.0 | 6.7 MB | | 0%  libopenblas-0.3.25 | 5.3 MB | | 0%  libstdcxx-14.2.0 | 3.7 MB | | 0%  hdf5-1.12.1 | 3.6 MB | | 0%  libgfortran5-14.2.0 | 1.4 MB | | 0%  libsqlite-3.46.0 | 845 KB | | 0%  sqlite-3.46.0 | 840 KB | | 0%  libnghttp2-1.58.0 | 617 KB | | 0%  libcurl-8.8.0 | 401 KB | | 0%  dtw-python-1.2.2 | 276 KB | | 0%  libssh2-1.11.0 | 265 KB | | 0%  python-dateutil-2.9. | 217 KB | | 0%  joblib-1.4.2 | 215 KB | | 0%  pytz-2025.2 | 185 KB | | 0%  libedit-3.1.20250104 | 132 KB | | 0%  ... (more hidden) ... scipy-1.8.1 | 25.0 MB | 4 | 4% scikit-learn-1.1.1 | 8.3 MB | ##8 | 28%  pandas-1.4.3 | 12.5 MB | 4 | 5%  h5py-3.6.0 | 6.7 MB | #1 | 12%  numpy-1.23.1 | 7.0 MB | | 0%  scipy-1.8.1 | 25.0 MB | #4 | 15% scikit-learn-1.1.1 | 8.3 MB | ###### | 61%  pandas-1.4.3 | 12.5 MB | ##1 | 22%  h5py-3.6.0 | 6.7 MB | #### | 41%  numpy-1.23.1 | 7.0 MB | ##3 | 23%  scipy-1.8.1 | 25.0 MB | ##3 | 23% pandas-1.4.3 | 12.5 MB | ####1 | 42%  h5py-3.6.0 | 6.7 MB | #######5 | 75%  numpy-1.23.1 | 7.0 MB | #####4 | 54%  scikit-learn-1.1.1 | 8.3 MB | #########1 | 91%  scipy-1.8.1 | 25.0 MB | ###4 | 34% pandas-1.4.3 | 12.5 MB | ######4 | 65%  scikit-learn-1.1.1 | 8.3 MB | ########## | 100%  numpy-1.23.1 | 7.0 MB | #########5 | 95%  h5py-3.6.0 | 6.7 MB | ########## | 100%  libopenblas-0.3.25 | 5.3 MB | | 0%  numpy-1.23.1 | 7.0 MB | ########## | 100%  libstdcxx-14.2.0 | 3.7 MB | | 0%  hdf5-1.12.1 | 3.6 MB | | 0%  scipy-1.8.1 | 25.0 MB | ##### | 50% pandas-1.4.3 | 12.5 MB | #########7 | 98%  libopenblas-0.3.25 | 5.3 MB | ###3 | 34%  libstdcxx-14.2.0 | 3.7 MB | #####5 | 56%  hdf5-1.12.1 | 3.6 MB | ########2 | 82%  scipy-1.8.1 | 25.0 MB | ######3 | 63% libopenblas-0.3.25 | 5.3 MB | #######1 | 72%  scipy-1.8.1 | 25.0 MB | ########1 | 81% hdf5-1.12.1 | 3.6 MB | ########## | 100%  libstdcxx-14.2.0 | 3.7 MB | ########## | 100%  libstdcxx-14.2.0 | 3.7 MB | ########## | 100%  pandas-1.4.3 | 12.5 MB | ########## | 100%  libgfortran5-14.2.0 | 1.4 MB | 1 | 1%  libopenblas-0.3.25 | 5.3 MB | ########## | 100%  libopenblas-0.3.25 | 5.3 MB | ########## | 100%  sqlite-3.46.0 | 840 KB | 1 | 2%  libsqlite-3.46.0 | 845 KB | 1 | 2%  libnghttp2-1.58.0 | 617 KB | 2 | 3%  sqlite-3.46.0 | 840 KB | ########## | 100%  libnghttp2-1.58.0 | 617 KB | ########## | 100%  libsqlite-3.46.0 | 845 KB | ########## | 100%  libgfortran5-14.2.0 | 1.4 MB | ########## | 100%  libcurl-8.8.0 | 401 KB | 3 | 4%  libssh2-1.11.0 | 265 KB | 6 | 6%  libcurl-8.8.0 | 401 KB | ########## | 100%  libssh2-1.11.0 | 265 KB | ########## | 100%  python-dateutil-2.9. | 217 KB | 7 | 7%  python-dateutil-2.9. | 217 KB | ########## | 100%  joblib-1.4.2 | 215 KB | 7 | 7%  pytz-2025.2 | 185 KB | 8 | 9%  joblib-1.4.2 | 215 KB | ########## | 100%  pytz-2025.2 | 185 KB | ########## | 100%  libedit-3.1.20250104 | 132 KB | #2 | 12%  libedit-3.1.20250104 | 132 KB | ########## | 100%  ... (more hidden) ... ... (more hidden) ... dtw-python-1.2.2 | 276 KB | 5 | 6%  dtw-python-1.2.2 | 276 KB | ########## | 100%  scipy-1.8.1 | 25.0 MB | ########## | 100% scipy-1.8.1 | 25.0 MB | ########## | 100% h5py-3.6.0 | 6.7 MB | ########## | 100%  hdf5-1.12.1 | 3.6 MB | ########## | 100%  libstdcxx-14.2.0 | 3.7 MB | ########## | 100%  numpy-1.23.1 | 7.0 MB | ########## | 100%  libopenblas-0.3.25 | 5.3 MB | ########## | 100%  sqlite-3.46.0 | 840 KB | ########## | 100%  sqlite-3.46.0 | 840 KB | ########## | 100%  libnghttp2-1.58.0 | 617 KB | ########## | 100%  libnghttp2-1.58.0 | 617 KB | ########## | 100%  libsqlite-3.46.0 | 845 KB | ########## | 100%  libsqlite-3.46.0 | 845 KB | ########## | 100%  scikit-learn-1.1.1 | 8.3 MB | ########## | 100%  libcurl-8.8.0 | 401 KB | ########## | 100%  libcurl-8.8.0 | 401 KB | ########## | 100%  libgfortran5-14.2.0 | 1.4 MB | ########## | 100%  libgfortran5-14.2.0 | 1.4 MB | ########## | 100%  python-dateutil-2.9. | 217 KB | ########## | 100%  python-dateutil-2.9. | 217 KB | ########## | 100%  libssh2-1.11.0 | 265 KB | ########## | 100%  libssh2-1.11.0 | 265 KB | ########## | 100%  joblib-1.4.2 | 215 KB | ########## | 100%  joblib-1.4.2 | 215 KB | ########## | 100%  libedit-3.1.20250104 | 132 KB | ########## | 100%  libedit-3.1.20250104 | 132 KB | ########## | 100%  ... (more hidden) ... ... (more hidden) ... dtw-python-1.2.2 | 276 KB | ########## | 100%  dtw-python-1.2.2 | 276 KB | ########## | 100%  pytz-2025.2 | 185 KB | ########## | 100%  pytz-2025.2 | 185 KB | ########## | 100%  pandas-1.4.3 | 12.5 MB | ########## | 100%  scipy-1.8.1 | 25.0 MB | ########## | 100%                                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