* using log directory 'd:/RCompile/CRANincoming/R-devel/pythonR.Rcheck' * using R version 4.4.0 beta (2024-04-10 r86396 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * 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 ... 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'pythonR' can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See 'd:/RCompile/CRANincoming/R-devel/pythonR.Rcheck/00install.out' for details. * checking installed package size ... 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 ... OK * checking Rd files ... 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 ... [10s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [423s] ERROR Running 'testthat.R' [423s] 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") Retrieving notices: ...working... done Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 23.3.1 latest version: 24.3.0 Please update conda by running $ conda update -n base -c defaults conda Or to minimize the number of packages updated during conda update use conda install conda=24.3.0 ## Package Plan ## environment location: C:\Users\CRAN\AppData\Local\R-MINI~1 added / updated specs: - pandas The following packages will be downloaded: package | build ---------------------------|----------------- bottleneck-1.3.7 | py310h9128911_0 115 KB ca-certificates-2024.2.2 | h56e8100_0 152 KB conda-forge certifi-2024.2.2 | pyhd8ed1ab_0 157 KB conda-forge intel-openmp-2024.1.0 | h57928b3_964 1.5 MB conda-forge libblas-3.9.0 | 12_win64_mkl 4.5 MB conda-forge libcblas-3.9.0 | 12_win64_mkl 4.5 MB conda-forge liblapack-3.9.0 | 12_win64_mkl 4.5 MB conda-forge mkl-2021.4.0 | h0e2418a_729 181.7 MB conda-forge mkl-service-2.4.0 | py310h2bbff1b_0 48 KB numexpr-2.8.4 | py310hd213c9f_0 128 KB numpy-1.22.4 | py310hed7ac4c_0 6.1 MB conda-forge openssl-1.1.1w | h2bbff1b_0 5.5 MB pandas-2.2.1 | py310h5da7b33_0 11.9 MB python-dateutil-2.9.0 | pyhd8ed1ab_0 218 KB conda-forge python-tzdata-2024.1 | pyhd8ed1ab_0 141 KB conda-forge python_abi-3.10 | 2_cp310 4 KB conda-forge pytz-2024.1 | pyhd8ed1ab_0 184 KB conda-forge tbb-2021.8.0 | h59b6b97_0 149 KB ------------------------------------------------------------ Total: 221.5 MB The following NEW packages will be INSTALLED: blas pkgs/main/win-64::blas-1.0-mkl bottleneck pkgs/main/win-64::bottleneck-1.3.7-py310h9128911_0 intel-openmp conda-forge/win-64::intel-openmp-2024.1.0-h57928b3_964 libblas conda-forge/win-64::libblas-3.9.0-12_win64_mkl libcblas conda-forge/win-64::libcblas-3.9.0-12_win64_mkl liblapack conda-forge/win-64::liblapack-3.9.0-12_win64_mkl mkl conda-forge/win-64::mkl-2021.4.0-h0e2418a_729 mkl-service pkgs/main/win-64::mkl-service-2.4.0-py310h2bbff1b_0 numexpr pkgs/main/win-64::numexpr-2.8.4-py310hd213c9f_0 numpy conda-forge/win-64::numpy-1.22.4-py310hed7ac4c_0 pandas pkgs/main/win-64::pandas-2.2.1-py310h5da7b33_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/win-64::python_abi-3.10-2_cp310 pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0 tbb pkgs/main/win-64::tbb-2021.8.0-h59b6b97_0 The following packages will be UPDATED: ca-certificates pkgs/main::ca-certificates-2023.01.10~ --> conda-forge::ca-certificates-2024.2.2-h56e8100_0 certifi pkgs/main/win-64::certifi-2022.12.7-p~ --> conda-forge/noarch::certifi-2024.2.2-pyhd8ed1ab_0 openssl 1.1.1t-h2bbff1b_0 --> 1.1.1w-h2bbff1b_0 Downloading and Extracting Packages libblas-3.9.0 | 4.5 MB | | 0% mkl-service-2.4.0 | 48 KB | | 0%  bottleneck-1.3.7 | 115 KB | | 0%  certifi-2024.2.2 | 157 KB | | 0%  tbb-2021.8.0 | 149 KB | | 0%  intel-openmp-2024.1. | 1.5 MB | | 0%  libcblas-3.9.0 | 4.5 MB | | 0%  python-dateutil-2.9. | 218 KB | | 0%  pytz-2024.1 | 184 KB | | 0%  openssl-1.1.1w | 5.5 MB | | 0%  liblapack-3.9.0 | 4.5 MB | | 0%  python_abi-3.10 | 4 KB | | 0%  numpy-1.22.4 | 6.1 MB | | 0%  numexpr-2.8.4 | 128 KB | | 0%  mkl-2021.4.0 | 181.7 MB | | 0%  python-tzdata-2024.1 | 141 KB | | 0%  pandas-2.2.1 | 11.9 MB | | 0%  ca-certificates-2024 | 152 KB | | 0%  libblas-3.9.0 | 4.5 MB | | 0% certifi-2024.2.2 | 157 KB | # | 10%  pytz-2024.1 | 184 KB | 8 | 9%  intel-openmp-2024.1. | 1.5 MB | 1 | 1%  libcblas-3.9.0 | 4.5 MB | | 0%  python-dateutil-2.9. | 218 KB | 7 | 7%  libblas-3.9.0 | 4.5 MB | #####5 | 55% tbb-2021.8.0 | 149 KB | ########## | 100%  mkl-service-2.4.0 | 48 KB | ########## | 100%  tbb-2021.8.0 | 149 KB | ########## | 100%  mkl-service-2.4.0 | 48 KB | ########## | 100%  openssl-1.1.1w | 5.5 MB | | 0%  intel-openmp-2024.1. | 1.5 MB | #########8 | 98%  libcblas-3.9.0 | 4.5 MB | ###3 | 33%  liblapack-3.9.0 | 4.5 MB | | 0%  libblas-3.9.0 | 4.5 MB | #########3 | 93% python_abi-3.10 | 4 KB | ########## | 100%  openssl-1.1.1w | 5.5 MB | ##1 | 21%  numexpr-2.8.4 | 128 KB | #2 | 13%  numpy-1.22.4 | 6.1 MB | | 0%  liblapack-3.9.0 | 4.5 MB | ##9 | 30%  libcblas-3.9.0 | 4.5 MB | ######3 | 63%  mkl-2021.4.0 | 181.7 MB | | 0%  certifi-2024.2.2 | 157 KB | ########## | 100%  certifi-2024.2.2 | 157 KB | ########## | 100%  numpy-1.22.4 | 6.1 MB | #8 | 19%  openssl-1.1.1w | 5.5 MB | ####4 | 44%  libcblas-3.9.0 | 4.5 MB | #########4 | 95%  liblapack-3.9.0 | 4.5 MB | ######1 | 62%  mkl-2021.4.0 | 181.7 MB | | 1%  python-tzdata-2024.1 | 141 KB | #1 | 11%  bottleneck-1.3.7 | 115 KB | ########## | 100%  bottleneck-1.3.7 | 115 KB | ########## | 100%  openssl-1.1.1w | 5.5 MB | ######8 | 69%  numpy-1.22.4 | 6.1 MB | ###9 | 40%  liblapack-3.9.0 | 4.5 MB | #########2 | 92%  pandas-2.2.1 | 11.9 MB | | 0%  mkl-2021.4.0 | 181.7 MB | 1 | 2%  ca-certificates-2024 | 152 KB | # | 11%  numpy-1.22.4 | 6.1 MB | ######5 | 65%  openssl-1.1.1w | 5.5 MB | #########5 | 95%  pandas-2.2.1 | 11.9 MB | #2 | 12%  mkl-2021.4.0 | 181.7 MB | 2 | 3%  python-dateutil-2.9. | 218 KB | ########## | 100%  python-dateutil-2.9. | 218 KB | ########## | 100%  numpy-1.22.4 | 6.1 MB | #########3 | 94%  pandas-2.2.1 | 11.9 MB | ###2 | 32%  mkl-2021.4.0 | 181.7 MB | 4 | 4%  pandas-2.2.1 | 11.9 MB | #####2 | 53%  mkl-2021.4.0 | 181.7 MB | 5 | 6%  pandas-2.2.1 | 11.9 MB | #######9 | 79%  mkl-2021.4.0 | 181.7 MB | 7 | 7%  intel-openmp-2024.1. | 1.5 MB | ########## | 100%  python_abi-3.10 | 4 KB | ########## | 100%  mkl-2021.4.0 | 181.7 MB | # | 11%  mkl-2021.4.0 | 181.7 MB | #3 | 14%  numexpr-2.8.4 | 128 KB | ########## | 100%  numexpr-2.8.4 | 128 KB | ########## | 100%  mkl-2021.4.0 | 181.7 MB | #7 | 17%  mkl-2021.4.0 | 181.7 MB | ##1 | 21%  mkl-2021.4.0 | 181.7 MB | ##5 | 26%  mkl-2021.4.0 | 181.7 MB | ### | 30%  mkl-2021.4.0 | 181.7 MB | ###4 | 35%  mkl-2021.4.0 | 181.7 MB | ###9 | 39%  mkl-2021.4.0 | 181.7 MB | ####3 | 43%  pytz-2024.1 | 184 KB | ########## | 100%  pytz-2024.1 | 184 KB | ########## | 100%  mkl-2021.4.0 | 181.7 MB | ####8 | 49%  mkl-2021.4.0 | 181.7 MB | #####3 | 54%  mkl-2021.4.0 | 181.7 MB | #####8 | 58%  mkl-2021.4.0 | 181.7 MB | ######2 | 63%  mkl-2021.4.0 | 181.7 MB | ######6 | 67%  libblas-3.9.0 | 4.5 MB | ########## | 100% mkl-2021.4.0 | 181.7 MB | ####### | 71%  mkl-2021.4.0 | 181.7 MB | #######4 | 75%  mkl-2021.4.0 | 181.7 MB | #######8 | 79%  mkl-2021.4.0 | 181.7 MB | ########2 | 82%  mkl-2021.4.0 | 181.7 MB | ########5 | 86%  libcblas-3.9.0 | 4.5 MB | ########## | 100%  mkl-2021.4.0 | 181.7 MB | ########9 | 89%  ca-certificates-2024 | 152 KB | ########## | 100%  ca-certificates-2024 | 152 KB | ########## | 100%  mkl-2021.4.0 | 181.7 MB | #########2 | 93%  mkl-2021.4.0 | 181.7 MB | #########6 | 96%  python-tzdata-2024.1 | 141 KB | ########## | 100%  python-tzdata-2024.1 | 141 KB | ########## | 100%  openssl-1.1.1w | 5.5 MB | ########## | 100%  liblapack-3.9.0 | 4.5 MB | ########## | 100%  numpy-1.22.4 | 6.1 MB | ########## | 100%  pandas-2.2.1 | 11.9 MB | ########## | 100%  pandas-2.2.1 | 11.9 MB | ########## | 100%  mkl-2021.4.0 | 181.7 MB | ########## | 100%  mkl-2021.4.0 | 181.7 MB | ########## | 100%                   Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 23.3.1 latest version: 24.3.0 Please update conda by running $ conda update -n base -c defaults conda Or to minimize the number of packages updated during conda update use conda install conda=24.3.0 ## Package Plan ## environment location: C:\Users\CRAN\AppData\Local\R-MINI~1 added / updated specs: - scipy The following packages will be downloaded: package | build ---------------------------|----------------- pandas-2.0.3 | py310h4ed8f06_0 9.8 MB scipy-1.7.3 | py310h33db832_0 24.6 MB conda-forge ------------------------------------------------------------ Total: 34.5 MB The following NEW packages will be INSTALLED: m2w64-gcc-libgfor~ conda-forge/win-64::m2w64-gcc-libgfortran-5.3.0-6 m2w64-gcc-libs conda-forge/win-64::m2w64-gcc-libs-5.3.0-7 m2w64-gcc-libs-co~ conda-forge/win-64::m2w64-gcc-libs-core-5.3.0-7 m2w64-gmp conda-forge/win-64::m2w64-gmp-6.1.0-2 m2w64-libwinpthre~ conda-forge/win-64::m2w64-libwinpthread-git-5.0.0.4634.697f757-2 msys2-conda-epoch conda-forge/win-64::msys2-conda-epoch-20160418-1 scipy conda-forge/win-64::scipy-1.7.3-py310h33db832_0 The following packages will be DOWNGRADED: pandas 2.2.1-py310h5da7b33_0 --> 2.0.3-py310h4ed8f06_0 Downloading and Extracting Packages scipy-1.7.3 | 24.6 MB | | 0% pandas-2.0.3 | 9.8 MB | | 0%  pandas-2.0.3 | 9.8 MB | 4 | 4%  scipy-1.7.3 | 24.6 MB | | 0% scipy-1.7.3 | 24.6 MB | 6 | 7% scipy-1.7.3 | 24.6 MB | ##6 | 26% scipy-1.7.3 | 24.6 MB | #######4 | 74% pandas-2.0.3 | 9.8 MB | ########## | 100%  pandas-2.0.3 | 9.8 MB | ########## | 100%  scipy-1.7.3 | 24.6 MB | ########## | 100% scipy-1.7.3 | 24.6 MB | ########## | 100%  Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done [ FAIL 1 | WARN 2 | SKIP 1 | PASS 13 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • scipy not available for testing (1): 'test-examples.R:24:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── 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: scipy ℹ Reason(s): `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(...) [ FAIL 1 | WARN 2 | SKIP 1 | PASS 13 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [28s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR, 3 NOTEs