* using log directory 'd:/Rcompile/CRANpkg/local/4.0/tidyHeatmap.Rcheck' * using R version 4.0.5 (2021-03-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'tidyHeatmap/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'tidyHeatmap' version '1.6.0' * package encoding: UTF-8 * 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 'tidyHeatmap' can be installed ... OK * checking installed package size ... OK * checking package directory ... 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 R 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 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 ... [17s] OK * checking Rd files ... OK * checking Rd metadata ... 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 ... WARNING Warning: parse error in file 'lines': 19: unexpected '>' 389: 390: tidyHeatmap::N52 |> ^ * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [36s] ERROR Running examples in 'tidyHeatmap-Ex.R' failed The error most likely occurred in: > ### Name: wrap_heatmap > ### Title: Wrap tidyHeatmap (ComplexHeatmap) in a patchwork-compliant patch > ### Aliases: wrap_heatmap wrap_heatmap,InputHeatmap-method > > ### ** Examples > > > > tidyHeatmap::N52 |> Error: unexpected '>' in "tidyHeatmap::N52 |>" Execution halted * checking for unstated dependencies in 'tests' ... WARNING Warning: parse error in file 'testthat/tests.R': 47:20: unexpected '>' 46: .value = `read count normalised log` 47: ) |> ^ * checking tests ... [7s] ERROR Running 'testthat.R' [6s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(tidyHeatmap) ======================================== tidyHeatmap version 1.6.0 If you use tidyHeatmap in published research, please cite: 1) Mangiola et al. tidyHeatmap: an R package for modular heatmap production based on tidy principles. JOSS 2020. 2) Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 2016. This message can be suppressed by: suppressPackageStartupMessages(library(tidyHeatmap)) ======================================== Attaching package: 'tidyHeatmap' The following object is masked from 'package:stats': heatmap > > test_check("tidyHeatmap") Error in parse(con, n = -1, srcfile = srcfile, encoding = "UTF-8") : tests.R:47:20: unexpected '>' 46: .value = `read count normalised log` 47: ) |> ^ Calls: test_check ... doTryCatch -> lapply -> FUN -> source_file -> parse Execution halted * checking for unstated dependencies in vignettes ... NOTE Warning: parse error in file 'd:/RCompile/CRANpkg/lib/4.0/tidyHeatmap/doc/introduction.R': /RCompile/CRANpkg/lib/4.0/tidyHeatmap/doc/introduction.R:20:17: unexpected '>' 19: mtcars_tidy <- 20: mtcars |> ^ * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [7s] WARNING Error(s) in re-building vignettes: --- re-building 'introduction.Rmd' using rmarkdown ## Citation Mangiola et al., (2020). tidyHeatmap: an R package for modular heatmap production based on tidy principles. Journal of Open Source Software, 5(52), 2472, https://doi.org/10.21105/joss.02472 Please have a look also to - [tidygate](https://github.com/stemangiola/tidygate/) for adding custom gate information to your tibble - [tidySingleCellExperiment](https://stemangiola.github.io/tidySingleCellExperiment/) for tidy manipulation of Seurat objects - [tidyseurat](https://stemangiola.github.io/tidyseurat/) for tidy manipulation of Seurat objects - [tidybulk](https://stemangiola.github.io/tidybulk/) for tidy high-level data analysis and manipulation - [tidySummarizedExperiment](https://stemangiola.github.io/tidySummarizedExperiment/) for heatmaps produced with tidy principles website: [stemangiola.github.io/tidyHeatmap](https://stemangiola.github.io/tidyHeatmap/) `tidyHeatmap` is a package that introduces tidy principles to the creation of information-rich heatmaps. This package uses [ComplexHeatmap](https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html) as graphical engine. **Advantages:** - Modular annotation with just specifying column names - Custom grouping of rows is easy to specify providing a grouped tbl. For example `df |> group_by(...)` - Labels size adjusted by row and column total number - Default use of Brewer and Viridis palettes ## Functions/utilities available Function | Description ------------ | ------------- `heatmap` | Plots base heatmap `add_tile` | Adds tile annotation to the heatmap `add_point` | Adds point annotation to the heatmap `add_bar` | Adds bar annotation to the heatmap `add_line` | Adds line annotation to the heatmap `layer_point` | Adds layer of symbols on top of the heatmap `layer_square` | Adds layer of symbols on top of the heatmap `layer_diamond` | Adds layer of symbols on top of the heatmap `layer_arrow_up` | Adds layer of symbols on top of the heatmap `layer_arrow_down` | Add layer of symbols on top of the heatmap `split_rows` | Splits the rows based on the dendogram `split_columns` | Splits the columns based on the dendogram `save_pdf` | Saves the PDF of the heatmap ## Installation To install the most up-to-date version ```r devtools::install_github("stemangiola/tidyHeatmap") ``` To install the most stable version (however please keep in mind that this package is under a maturing lifecycle stage) ```r install.packages("tidyHeatmap") ``` ## Contribution If you want to contribute to the software, report issues or problems with the software or seek support please open an issue [here](https://github.com/stemangiola/tidyHeatmap/issues) ## Input data frame The heatmaps visualise a multi-element, multi-feature dataset, annotated with independent variables. Each observation is a element-feature pair (e.g., person-physical characteristics). element | feature | value | independent_variables ------------ | ------------- | ------------- | ------------- `chr` or `fctr` | `chr` or `fctr` | `numeric` | ... Let's transform the mtcars dataset into a tidy "element-feature-independent variables" data frame. Where the independent variables in this case are 'hp' and 'vs'. Quitting from lines 85-96 (./../man/fragments/intro.Rmd) Quitting from lines 48-52 (./../man/fragments/intro.Rmd) Error: processing vignette 'introduction.Rmd' failed with diagnostics: :2:17: unexpected '>' 1: mtcars_tidy <- 2: mtcars |> ^ --- failed re-building 'introduction.Rmd' SUMMARY: processing the following file failed: 'introduction.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 3 WARNINGs, 1 NOTE