* using log directory ‘/srv/hornik/tmp/CRAN/microdiluteR.Rcheck’ * using R Under development (unstable) (2024-05-06 r86526) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.4 (1) Debian flang-new version 18.1.4 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘microdiluteR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘microdiluteR’ version ‘1.0.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Silvia Eckert ’ New submission Possibly misspelled words in DESCRIPTION: Microdilution (3:26) microdilution (8:46) Found the following (possibly) invalid URLs: URL: https://github.com/silvia-eckert/microdiluteR From: inst/doc/tidy_photometer_data.html Status: 404 Message: Not Found * 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 ‘microdiluteR’ can be installed ... [3s/3s] 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking whether startup messages can be suppressed ... [1s/1s] 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 ... [4s/4s] 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [2s/2s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [3s/3s] ERROR Running ‘testthat.R’ [3s/3s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(microdiluteR) > > test_check("microdiluteR") Enter concentration of row A: Enter concentration of row B: Enter concentration of row C: Enter concentration of row D: Enter concentration of row E: Enter concentration of row F: Enter concentration of row G: Enter concentration of row H: Enter concentration of column 1: Enter concentration of column 2: Enter concentration of column 3: Enter concentration of column 4: Enter concentration of column 5: Enter concentration of column 6: Enter concentration of column 7: Enter concentration of column 8: Enter concentration of column 9: Enter concentration of column 10: Enter concentration of column 11: Enter concentration of column 12: Enter treatment of row A: Enter treatment of row B: Enter treatment of row C: Enter treatment of row D: Enter treatment of row E: Enter treatment of row F: Enter treatment of row G: Enter treatment of row H: Enter treatment of column 1: Enter treatment of column 2: Enter treatment of column 3: Enter treatment of column 4: Enter treatment of column 5: Enter treatment of column 6: Enter treatment of column 7: Enter treatment of column 8: Enter treatment of column 9: Enter treatment of column 10: Enter treatment of column 11: Enter treatment of column 12: Enter concentration of row A: Enter concentration of row B: Enter concentration of row C: Enter concentration of row D: Enter concentration of row E: Enter concentration of row F: Enter concentration of row G: Enter concentration of row H: Enter concentration of column 1: Enter concentration of column 2: Enter concentration of column 3: Enter concentration of column 4: Enter concentration of column 5: Enter concentration of column 6: Enter concentration of column 7: Enter concentration of column 8: Enter concentration of column 9: Enter concentration of column 10: Enter concentration of column 11: Enter concentration of column 12: Enter experiment identifier for exp1: Enter experiment identifier for exp1: Enter experiment identifier for exp2: Enter group name for grp1: Enter group name for grp1: Enter group name for grp2: Enter well positions (e.g. A-2) of invalid samples separated by spaces: Enter threshold for distinguishing valid from invalid samples: Enter threshold for distinguishing valid from invalid samples: Enter treatment of row A: Enter treatment of row B: Enter treatment of row C: Enter treatment of row D: Enter treatment of row E: Enter treatment of row F: Enter treatment of row G: Enter treatment of row H: Enter treatment of column 1: Enter treatment of column 2: Enter treatment of column 3: Enter treatment of column 4: Enter treatment of column 5: Enter treatment of column 6: Enter treatment of column 7: Enter treatment of column 8: Enter treatment of column 9: Enter treatment of column 10: Enter treatment of column 11: Enter treatment of column 12: Enter 'threshold' for specifying a threshold or 'samples' for directly providing invalid samples: Enter 'threshold' for specifying a threshold or 'samples' for directly providing invalid samples: Enter 'threshold' for specifying a threshold or 'samples' for directly providing invalid samples: All groups have monotonic behavior. Returning original input data. Do you want to see all plots? (y/n): Non-monotonic well positions detected for case: b . Do you want to set this group as valid? (y/n): Continuing without changes for case: b Non-monotonic well positions detected for case: c . Do you want to set this group as valid? (y/n): Continuing without changes for case: c Non-monotonic groups detected: b, c Returning subset of data containing non-monotonic groups. Non-monotonic well positions detected for case: b . Do you want to set this group as valid? (y/n): Continuing without changes for case: b Non-monotonic well positions detected for case: c . Do you want to set this group as valid? (y/n): Continuing without changes for case: c Non-monotonic groups detected: b, c Returning subset of data containing non-monotonic groups. Non-monotonic well positions detected for case: A.b . Do you want to set this group as valid? (y/n): Continuing without changes for case: A.b Non-monotonic well positions detected for case: B.b . Do you want to set this group as valid? (y/n): Continuing without changes for case: B.b Non-monotonic well positions detected for case: A.c . Do you want to set this group as valid? (y/n): Continuing without changes for case: A.c Non-monotonic well positions detected for case: B.c . Do you want to set this group as valid? (y/n): Continuing without changes for case: B.c Non-monotonic groups detected: A.b, B.b, A.c, B.c Returning subset of data containing non-monotonic groups. Enter group name for grp1: Enter experiment identifier for exp1: Enter 'threshold' for specifying a threshold or 'samples' for directly providing invalid samples: Enter well positions (e.g. A-2) of invalid samples separated by spaces: Enter treatment of column 1: Enter treatment of column 2: Enter treatment of column 3: Enter treatment of column 4: Enter treatment of column 5: Enter treatment of column 6: Enter treatment of column 7: Enter treatment of column 8: Enter treatment of column 9: Enter treatment of column 10: Enter treatment of column 11: Enter treatment of column 12: Enter concentration of column 1: Enter concentration of column 2: Enter concentration of column 3: Enter concentration of column 4: Enter concentration of column 5: Enter concentration of column 6: Enter concentration of column 7: Enter concentration of column 8: Enter concentration of column 9: Enter concentration of column 10: Enter concentration of column 11: Enter concentration of column 12: Enter group name for grp1: Enter experiment identifier for exp1: Enter 'threshold' for specifying a threshold or 'samples' for directly providing invalid samples: Enter threshold for distinguishing valid from invalid samples: Enter treatment of row A: Enter treatment of row B: Enter treatment of row C: Enter treatment of row D: Enter treatment of row E: Enter treatment of row F: Enter treatment of row G: Enter treatment of row H: Enter concentration of row A: Enter concentration of row B: Enter concentration of row C: Enter concentration of row D: Enter concentration of row E: Enter concentration of row F: Enter concentration of row G: Enter concentration of row H: Enter group name for grp1: Enter experiment identifier for exp1: Enter 'threshold' for specifying a threshold or 'samples' for directly providing invalid samples: Enter threshold for distinguishing valid from invalid samples: Enter treatment of row A: Enter treatment of row B: Enter treatment of row C: Enter treatment of row D: Enter treatment of row E: Enter treatment of row F: Enter treatment of row G: Enter treatment of row H: Enter concentration of row A: Enter concentration of row B: Enter concentration of row C: Enter concentration of row D: Enter concentration of row E: Enter concentration of row F: Enter concentration of row G: Enter concentration of row H: Enter group name for grp1: Enter experiment identifier for exp1: Enter 'threshold' for specifying a threshold or 'samples' for directly providing invalid samples: Enter well positions (e.g. A-2) of invalid samples separated by spaces: Enter treatment of column 1: Enter treatment of column 2: Enter treatment of column 3: Enter treatment of column 4: Enter treatment of column 5: Enter treatment of column 6: Enter treatment of column 7: Enter treatment of column 8: Enter treatment of column 9: Enter treatment of column 10: Enter treatment of column 11: Enter treatment of column 12: Enter concentration of column 1: Enter concentration of column 2: Enter concentration of column 3: Enter concentration of column 4: Enter concentration of column 5: Enter concentration of column 6: Enter concentration of column 7: Enter concentration of column 8: Enter concentration of column 9: Enter concentration of column 10: Enter concentration of column 11: Enter concentration of column 12: Enter group name for grp1: Enter experiment identifier for exp1: Enter 'threshold' for specifying a threshold or 'samples' for directly providing invalid samples: Enter well positions (e.g. A-2) of invalid samples separated by spaces: Enter treatment of column 1: Enter treatment of column 2: Enter treatment of column 3: Enter treatment of column 4: Enter treatment of column 5: Enter treatment of column 6: Enter treatment of column 7: Enter treatment of column 8: Enter treatment of column 9: Enter treatment of column 10: Enter treatment of column 11: Enter treatment of column 12: Enter concentration of column 1: Enter concentration of column 2: Enter concentration of column 3: Enter concentration of column 4: Enter concentration of column 5: Enter concentration of column 6: Enter concentration of column 7: Enter concentration of column 8: Enter concentration of column 9: Enter concentration of column 10: Enter concentration of column 11: Enter concentration of column 12: [ FAIL 1 | WARN 0 | SKIP 0 | PASS 121 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-plot_growth_performance.R:30:3'): plot_growth_performance() produces expected output ── Error in `sym(y_var) < 0`: comparison (<) is not possible for language types Backtrace: ▆ 1. └─microdiluteR::plot_growth_performance(input_data = test_summarized_data) at test-plot_growth_performance.R:30:3 2. ├─ggplot2::geom_text(...) 3. │ ├─ggplot2::layer(...) 4. │ └─rlang::list2(...) 5. └─base::ifelse(!!sym(y_var) < 0, -0.5, 0.5) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 121 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [2s/2s] 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