* using log directory 'd:/Rcompile/CRANpkg/local/4.6/RNAseqQC.Rcheck' * using R Under development (unstable) (2025-06-11 r88304 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'RNAseqQC/DESCRIPTION' ... OK * this is package 'RNAseqQC' version '0.2.1' * 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 'RNAseqQC' 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [9s] OK * checking whether the package can be loaded with stated dependencies ... [9s] OK * checking whether the package can be unloaded cleanly ... [9s] OK * checking whether the namespace can be loaded with stated dependencies ... [9s] OK * checking whether the namespace can be unloaded cleanly ... [9s] OK * checking loading without being on the library search path ... [9s] 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 ... [21s] OK * checking Rd files ... [1s] 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 ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... [9s] 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 ... [19s] ERROR Running examples in 'RNAseqQC-Ex.R' failed The error most likely occurred in: > ### Name: plot_chromosome > ### Title: Plot gene expression along a chromosome > ### Aliases: plot_chromosome > > ### ** Examples > > library("DESeq2") Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > chr1 <- T47D[which(mcols(T47D)$chromosome=="1"),] > vsd <- vst(chr1) > plot_chromosome(vsd, chr="1") Error in Cairo(width, height, type = "png", file = filename, pointsize = pointsize, : Graphics API version mismatch Error: The size of the temporary image for rasterization is too huge (311 x 476 px) that it is cannot be handled by the device function `Cairo:CairoPNG()`. Please reduce the maximal size of temporary image by setting proper values for `ht_opt$raster_temp_image_max_width` and `ht_opt$raster_temp_image_max_height`. Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [34s] ERROR Error(s) in re-building vignettes: --- re-building 'data.Rmd' using rmarkdown --- finished re-building 'data.Rmd' --- re-building 'introduction.Rmd' using rmarkdown Quitting from introduction.Rmd:123-125 [unnamed-chunk-13] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! The size of the temporary image for rasterization is too huge (324 x 331 px) that it is cannot be handled by the device function `Cairo:CairoPNG()`. Please reduce the maximal size of temporary image by setting proper values for `ht_opt$raster_temp_image_max_width` and `ht_opt$raster_temp_image_max_height`. --- Backtrace: ▆ 1. └─tools:::.buildOneVignette(...) 2. ├─base::tryCatch(...) 3. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) 6. └─engine$weave(file, quiet = quiet, encoding = enc) 7. └─knitr:::vweave_rmarkdown(...) 8. └─rmarkdown::render(...) 9. └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 10. └─knitr:::process_file(text, output) 11. ├─xfun:::handle_error(...) 12. ├─base::withCallingHandlers(...) 13. └─knitr:::process_group(group) 14. └─knitr:::call_block(x) 15. └─knitr:::block_exec(params) 16. └─knitr:::eng_r(options) 17. ├─knitr:::in_input_dir(...) 18. │ └─knitr:::in_dir(input_dir(), expr) 19. └─knitr (local) evaluate(...) 20. └─evaluate::evaluate(...) 21. ├─base::withRestarts(...) 22. │ └─base (local) withRestartList(expr, restarts) 23. │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]]) 24. │ │ └─base (local) doWithOneRestart(return(expr), restart) 25. │ └─base (local) withRestartList(expr, restarts[-nr]) 26. │ └─base (local) withOneRestart(expr, restarts[[1L]]) 27. │ └─base (local) doWithOneRestart(return(expr), restart) 28. ├─evaluate:::with_handlers(...) 29. │ ├─base::eval(call) 30. │ │ └─base::eval(call) 31. │ └─base::withCallingHandlers(...) 32. └─watcher$print_value(ev$value, ev$visible, envir) 33. ├─base::withVisible(handle_value(handler, value, visible, envir)) 34. └─evaluate:::handle_value(handler, value, visible, envir) 35. └─handler$value(value, visible) 36. └─knitr (local) fun(x, options = options) 37. ├─base::withVisible(knit_print(x, ...)) 38. ├─knitr::knit_print(x, ...) 39. └─knitr:::knit_print.default(x, ...) 40. └─knitr::normal_print(x) 41. ├─base::print(x) 42. └─base::print.default(x) 43. ├─methods (local) ``(``) 44. └─ComplexHeatmap (local) ``(``) 45. ├─ComplexHeatmap::draw(object) 46. └─ComplexHeatmap::draw(object) 47. └─ComplexHeatmap (local) .local(object, ...) 48. ├─ComplexHeatmap::draw(ht_list, ...) 49. └─ComplexHeatmap::draw(ht_list, ...) 50. └─ComplexHeatmap (local) .local(object, ...) 51. ├─base::eval(code) 52. │ └─base::eval(code) 53. └─ht_graphic_fun_list[[j]](object) 54. ├─ComplexHeatmap::draw_heatmap_list(object) 55. └─ComplexHeatmap::draw_heatmap_list(object) 56. └─ComplexHeatmap (local) .local(object, ...) 57. ├─ComplexHeatmap::draw(ht, internal = TRUE) 58. └─ComplexHeatmap::draw(ht, internal = TRUE) 59. └─ComplexHeatmap (local) .local(object, ...) 60. └─ht_graphic_fun_list[[j]](object) 61. ├─ComplexHeatmap::draw_heatmap_body(...) 62. └─ComplexHeatmap::draw_heatmap_body(...) 63. └─ComplexHeatmap (local) .local(object, ...) 64. └─ComplexHeatmap:::stop_wrap(qq("The size of the temporary image for rasterization is too huge (@{temp_image_width} x @{temp_image_height} px) that it is cannot be handled by the device function `@{device_info[1]}:@{raster_device}()`. Please reduce the maximal size of temporary image by setting proper values for `ht_opt$raster_temp_image_max_width` and `ht_opt$raster_temp_image_max_height`.")) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'introduction.Rmd' failed with diagnostics: The size of the temporary image for rasterization is too huge (324 x 331 px) that it is cannot be handled by the device function `Cairo:CairoPNG()`. Please reduce the maximal size of temporary image by setting proper values for `ht_opt$raster_temp_image_max_width` and `ht_opt$raster_temp_image_max_height`. --- 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 ... [20s] OK * checking HTML version of manual ... [4s] OK * DONE Status: 2 ERRORs