* using log directory ‘/srv/hornik/tmp/CRAN/pythonR.Rcheck’ * using R Under development (unstable) (2024-04-10 r86396) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘pythonR/DESCRIPTION’ ... OK * this is package ‘pythonR’ version ‘0.1.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/4s] NOTE Maintainer: ‘Kyle Barrett ’ New submission Possibly misspelled words in DESCRIPTION: reticulate (9:92) The Title field should be in title case. Current version is: ‘Helper functions for using Python in R’ In title case that is: ‘Helper Functions for using Python in R’ * 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 ‘pythonR’ can be installed ... [39s/36s] NOTE Found the following notes/warnings: Non-staged installation was used See ‘/srv/hornik/tmp/CRAN/pythonR.Rcheck/00install.out’ 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 ... [4s/2s] OK * checking whether the package can be loaded with stated dependencies ... [4s/2s] OK * checking whether the package can be unloaded cleanly ... [4s/2s] 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 ... [4s/2s] OK * checking whether startup messages can be suppressed ... [4s/2s] 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 ... NOTE Documented arguments not in \usage in Rd file 'miniconda_is_installed.Rd': ‘path’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 ... [5s/2s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [78s/51s] ERROR Running ‘testthat.R’ [78s/51s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(dplyr) Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union > library(testthat) Attaching package: 'testthat' The following object is masked from 'package:dplyr': matches > library(pythonR) > > test_check("pythonR") 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-miniconda added / updated specs: - pandas The following packages will be downloaded: package | build ---------------------------|----------------- certifi-2024.2.2 | pyhd8ed1ab_0 157 KB conda-forge conda-24.3.0 | py312h7900ff3_0 1.1 MB conda-forge libexpat-2.5.0 | hcb278e6_1 76 KB conda-forge numpy-1.26.4 | py312heda63a1_0 7.1 MB conda-forge pandas-2.2.2 | py312hfb8ada1_0 14.7 MB conda-forge python-3.12.2 |hab00c5b_0_cpython 30.8 MB conda-forge python-dateutil-2.9.0 | pyhd8ed1ab_0 218 KB conda-forge python-tzdata-2024.1 | pyhd8ed1ab_0 141 KB conda-forge python_abi-3.12 | 4_cp312 6 KB conda-forge pytz-2024.1 | pyhd8ed1ab_0 184 KB conda-forge six-1.16.0 | pyh6c4a22f_0 14 KB conda-forge zlib-1.2.13 | hd590300_5 91 KB conda-forge ------------------------------------------------------------ Total: 54.7 MB The following NEW packages will be INSTALLED: libblas conda-forge/linux-64::libblas-3.9.0-22_linux64_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-22_linux64_openblas libexpat conda-forge/linux-64::libexpat-2.5.0-hcb278e6_1 libgfortran-ng conda-forge/linux-64::libgfortran-ng-13.2.0-h69a702a_5 libgfortran5 conda-forge/linux-64::libgfortran5-13.2.0-ha4646dd_5 liblapack conda-forge/linux-64::liblapack-3.9.0-22_linux64_openblas libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_h413a1c8_0 libsqlite conda-forge/linux-64::libsqlite-3.45.2-h2797004_0 libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 libzlib conda-forge/linux-64::libzlib-1.2.13-hd590300_5 numpy conda-forge/linux-64::numpy-1.26.4-py312heda63a1_0 pandas conda-forge/linux-64::pandas-2.2.2-py312hfb8ada1_0 python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0 python-tzdata conda-forge/noarch::python-tzdata-2024.1-pyhd8ed1ab_0 python_abi conda-forge/linux-64::python_abi-3.12-4_cp312 pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 The following packages will be UPDATED: libgcc-ng pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-13.2.0-h807b86a_5 libgomp pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-13.2.0-h807b86a_5 libstdcxx-ng pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-13.2.0-h7e041cc_5 libuuid pkgs/main::libuuid-1.41.5-h5eee18b_0 --> conda-forge::libuuid-2.38.1-h0b41bf4_0 openssl pkgs/main::openssl-3.0.13-h7f8727e_0 --> conda-forge::openssl-3.2.1-hd590300_1 python pkgs/main::python-3.12.1-h996f2a0_0 --> conda-forge::python-3.12.2-hab00c5b_0_cpython tk pkgs/main::tk-8.6.12-h1ccaba5_0 --> conda-forge::tk-8.6.13-noxft_h4845f30_101 zlib pkgs/main::zlib-1.2.13-h5eee18b_0 --> conda-forge::zlib-1.2.13-hd590300_5 The following packages will be SUPERSEDED by a higher-priority channel: _libgcc_mutex pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge _openmp_mutex pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_gnu certifi pkgs/main/linux-64::certifi-2024.2.2-~ --> conda-forge/noarch::certifi-2024.2.2-pyhd8ed1ab_0 conda pkgs/main::conda-24.3.0-py312h06a4308~ --> conda-forge::conda-24.3.0-py312h7900ff3_0 Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done 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-miniconda added / updated specs: - scipy The following packages will be downloaded: package | build ---------------------------|----------------- scipy-1.13.0 | py312heda63a1_0 16.6 MB conda-forge ------------------------------------------------------------ Total: 16.6 MB The following NEW packages will be INSTALLED: scipy conda-forge/linux-64::scipy-1.13.0-py312heda63a1_0 Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done [ FAIL 4 | WARN 5 | SKIP 1 | PASS 10 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • pandas not available for testing (1): 'test-examples.R:23:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-import-py-pkgs.R:7:3'): importing python packages - unit ───── exists("pandas") is not TRUE `actual`: FALSE `expected`: TRUE ── Error ('test-import-py-pkgs.R:8:3'): importing python packages - unit ─────── Error in `eval(code, test_env)`: object 'pandas' not found Backtrace: ▆ 1. ├─testthat::expect_true(inherits(pandas, "python.builtin.module")) at test-import-py-pkgs.R:8:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─base::inherits(pandas, "python.builtin.module") ── Error ('test-import-py-pkgs.R:26:5'): importing python packages - integration ── Error in `check_py_pkgs_installed(required_py_pkgs)`: ✖ The following python modules are not available: pandas, scipy ℹ Reason(s): `NA` `No module named 'scipy'` Backtrace: ▆ 1. └─pythonR:::py_array() at test-import-py-pkgs.R:43:3 2. ├─checkmate::assert_true(check_py_pkgs_installed(required_py_pkgs)) at test-import-py-pkgs.R:26:5 3. │ └─checkmate::checkTRUE(x, na.ok) 4. │ └─base::isTRUE(x) 5. └─pythonR::check_py_pkgs_installed(required_py_pkgs) 6. └─cli (local) alert_fn(...) 7. └─rlang::abort(...) ── Error ('test-setup-python-pkgs.R:16:3'): python setup - setup_py_env: conda ── Error in `check_py_pkgs_installed(c("pandas", "numpy"))`: ✖ The following python modules are not available: pandas ℹ Reason(s): `NA` Backtrace: ▆ 1. ├─testthat::expect_true(check_py_pkgs_installed(c("pandas", "numpy"))) at test-setup-python-pkgs.R:16:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─pythonR::check_py_pkgs_installed(c("pandas", "numpy")) 5. └─cli (local) alert_fn(...) 6. └─rlang::abort(...) [ FAIL 4 | WARN 5 | SKIP 1 | PASS 10 ] Error: Test failures 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, 3 NOTEs