CRAN Package Check Results for Maintainer ‘Paul Boutros <PBoutros at sbpdiscovery.org>’

Last updated on 2026-03-11 01:54:09 CET.

Package	ERROR	NOTE	OK
ApplyPolygenicScore	1		13
bedr			14
BoutrosLab.plotting.general	1		13
OmicsQC	1		13
OutSeekR		2	12
SeqKat		1	13
VennDiagram			14

Package ApplyPolygenicScore

Current CRAN status: ERROR: 1, OK: 13

Version: 4.0.2
Check: tests
Result: ERROR Running 'testthat.R' [163s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat); > library(ApplyPolygenicScore); > > test_check('ApplyPolygenicScore'); Input data passed validation Input data passed validation Saving _problems/test-pgs-statistics-371.R Skipping test for >12 PGS columns as 'scales' package is available and will be used. Saving _problems/test-pgs-statistics-559.R Saving _problems/test-plotting-136.R Saving _problems/test-plotting-431.R Saving _problems/test-plotting-741.R [1] "springgreen3" [1] "darkturquoise" _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices 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_cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices [1] "springgreen3" [1] "darkturquoise" _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices Saving _problems/test-plotting-995.R _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices _cairo_win32_scaled_font_ucs4_to_index:GetGlyphIndices [ FAIL 6 | WARN 87 | SKIP 0 | PASS 625 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-pgs-statistics.R:363:9'): analyze.pgs.binary.predictiveness validates binary phenotype columns ── Error in `basename(x)`: a character vector argument expected Backtrace: ▆ 1. ├─testthat::expect_warning(...) at test-pgs-statistics.R:363:9 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─ApplyPolygenicScore::analyze.pgs.binary.predictiveness(...) 8. └─BoutrosLab.plotting.general::create.multipanelplot(...) 9. └─BoutrosLab.plotting.general:::get.legend.height(...) 10. └─tools::file_ext(filename) 11. ├─base::ifelse(...) 12. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x)) 13. │ └─base::is.factor(x) 14. └─base::basename(x) ── Error ('test-pgs-statistics.R:552:9'): analyze.pgs.binary.predictiveness correctly formats outputs ── Error in `basename(x)`: a character vector argument expected Backtrace: ▆ 1. └─ApplyPolygenicScore::analyze.pgs.binary.predictiveness(...) at test-pgs-statistics.R:552:9 2. └─BoutrosLab.plotting.general::create.multipanelplot(...) 3. └─BoutrosLab.plotting.general:::get.legend.height(...) 4. └─tools::file_ext(filename) 5. ├─base::ifelse(...) 6. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x)) 7. │ └─base::is.factor(x) 8. └─base::basename(x) ── Error ('test-plotting.R:132:9'): create.pgs.density.plot runs with no error with basic inputs ── Error in `basename(x)`: a character vector argument expected Backtrace: ▆ 1. └─ApplyPolygenicScore::create.pgs.density.plot(...) at test-plotting.R:132:9 2. └─BoutrosLab.plotting.general::create.multipanelplot(...) 3. └─BoutrosLab.plotting.general:::get.legend.height(...) 4. └─tools::file_ext(filename) 5. ├─base::ifelse(...) 6. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x)) 7. │ └─base::is.factor(x) 8. └─base::basename(x) ── Error ('test-plotting.R:426:9'): create.pgs.with.continuous.phenotype.plot runs with no error with basic inputs ── Error in `basename(x)`: a character vector argument expected Backtrace: ▆ 1. └─ApplyPolygenicScore::create.pgs.with.continuous.phenotype.plot(...) at test-plotting.R:426:9 2. └─BoutrosLab.plotting.general::create.multipanelplot(...) 3. └─BoutrosLab.plotting.general:::get.legend.height(...) 4. └─tools::file_ext(filename) 5. ├─base::ifelse(...) 6. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x)) 7. │ └─base::is.factor(x) 8. └─base::basename(x) ── Error ('test-plotting.R:737:9'): create.pgs.rank.plot runs with no error with basic inputs ── Error in `basename(x)`: a character vector argument expected Backtrace: ▆ 1. └─ApplyPolygenicScore::create.pgs.rank.plot(...) at test-plotting.R:737:9 2. └─BoutrosLab.plotting.general::create.multipanelplot(...) 3. └─BoutrosLab.plotting.general:::get.legend.height(...) 4. └─tools::file_ext(filename) 5. ├─base::ifelse(...) 6. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x)) 7. │ └─base::is.factor(x) 8. └─base::basename(x) ── Error ('test-plotting.R:991:9'): create.pgs.boxplot runs with no error with basic inputs ── Error in `basename(x)`: a character vector argument expected Backtrace: ▆ 1. └─ApplyPolygenicScore::create.pgs.boxplot(...) at test-plotting.R:991:9 2. └─BoutrosLab.plotting.general::create.multipanelplot(...) 3. └─BoutrosLab.plotting.general:::get.legend.height(...) 4. └─tools::file_ext(filename) 5. ├─base::ifelse(...) 6. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x)) 7. │ └─base::is.factor(x) 8. └─base::basename(x) [ FAIL 6 | WARN 87 | SKIP 0 | PASS 625 ] Error: ! Test failures. Execution halted Flavor: r-devel-windows-x86_64

Package bedr

Current CRAN status: OK: 14

Package BoutrosLab.plotting.general

Current CRAN status: ERROR: 1, OK: 13

Version: 7.1.5
Check: examples
Result: ERROR Running examples in 'BoutrosLab.plotting.general-Ex.R' failed The error most likely occurred in: > ### Name: create.multipanelplot > ### Title: Joins plots together > ### Aliases: create.multipanelplot > ### Keywords: hplot > > ### ** Examples > > set.seed(12345); > # begin by creating the individual plots which will be combined into a multiplot > dist <- data.frame( + a = rnorm(100, 1), + b = rnorm(100, 3), + c = rnorm(100, 5) + ); > > simple.data <- data.frame( + x = c(dist$a, dist$b, dist$c), + y = rep(LETTERS[1:3], each = 100) + ); > fill.squares <- matrix(c(1, 0, 0, 0, 1, 0, 0, 0, 1), ncol = 3, byrow = TRUE); > rownames(fill.squares) <- c("Drug I only", "Drug II only" , "Drugs I & II"); > colnames(fill.squares) <- levels(factor(simple.data$y)); > > # Create plot # 1 > simple.boxplot <- create.boxplot( + formula = x ~ y, + data = simple.data, + xaxis.lab = c('','',''), + main.x = 0.57, + ylab.label = 'Sugar Level', + xlab.label = '', + col = 'lightgrey', + xaxis.tck = c(0,0), + yaxis.tck = c(1,0), + yaxis.lab = seq(-1,8,2) , + yat = seq(-1,8,2), + left.padding = 0, + right.padding = 0, + lwd = 2 + ); > > # Create plot # 2 > simple.heatmap <- create.heatmap( + x = t(fill.squares), + clustering.method = 'none', + shrink = 0.8, + yaxis.lab = c(3,2,3), + yaxis.tck = 1, + xaxis.lab = c('A','B','C'), + ylab.label = 'Drug Regimen', + xlab.label = 'Patient Group', + colour.scheme = c("white", "grey20"), + fill.colour = "white", + print.colour.key = FALSE, + left.padding = 0, + xaxis.tck = c(1,0), + right.padding = 0, + xaxis.rot = 0 + ); > > create.multipanelplot( + # filename = tempfile(pattern = 'Multipanelplot_Simple', fileext = '.tiff'), + plot.objects = list(simple.boxplot,simple.heatmap), + y.spacing = 1, + ylab.axis.padding = 2, + main = 'Simple', + top.padding = 2, + resolution = 200 + ); Error in basename(x) : a character vector argument expected Calls: create.multipanelplot ... file_ext -> ifelse -> grepl -> is.factor -> basename Execution halted Flavor: r-devel-windows-x86_64

Version: 7.1.5
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'PlottingGuide.Rnw' using knitr_notangle Warning in remind_sweave(if (in.file) input, sweave_lines) : It seems you are using the Sweave-specific syntax in line(s) 2303, 2363; you may need Sweave2knitr("PlottingGuide.Rnw") to convert it to knitr Quitting from PlottingGuide.Rnw:2303-2353 [auto-axis-scaling] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `basename()`: ! a character vector argument expected --- Backtrace: x 1. \-global create.auto.axis.examples() 2. \-BoutrosLab.plotting.general::create.multipanelplot(...) 3. \-BoutrosLab.plotting.general:::get.legend.height(...) 4. \-tools::file_ext(filename) 5. +-base::ifelse(...) 6. +-base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x)) 7. | \-base::is.factor(x) 8. \-base::basename(x) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'PlottingGuide.Rnw' failed with diagnostics: a character vector argument expected --- failed re-building 'PlottingGuide.Rnw' SUMMARY: processing the following file failed: 'PlottingGuide.Rnw' Error: Vignette re-building failed. Execution halted Flavor: r-devel-windows-x86_64

Package OmicsQC

Current CRAN status: ERROR: 1, OK: 13

Version: 1.1.1
Check: tests
Result: ERROR Running 'testthat.R' [5s] Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat); > > test_check('OmicsQC') Loading required package: OmicsQC Saving _problems/test-plotting-127.R [ FAIL 1 | WARN 0 | SKIP 0 | PASS 66 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-plotting.R:124:3'): get.qc.multipanelplot ──────────────────── Expected `get.qc.multipanelplot(barplot = bp, heatmap = hm)` not to throw any errors. Actually got a <simpleError> with message: a character vector argument expected Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-plotting.R:124:3 2. │ └─testthat:::expect_condition_matching_(...) 3. │ └─testthat:::quasi_capture(...) 4. │ ├─testthat (local) .capture(...) 5. │ │ └─base::withCallingHandlers(...) 6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. └─OmicsQC::get.qc.multipanelplot(barplot = bp, heatmap = hm) 8. └─BoutrosLab.plotting.general::create.multipanelplot(...) 9. └─BoutrosLab.plotting.general:::get.legend.height(...) 10. └─tools::file_ext(filename) 11. ├─base::ifelse(...) 12. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x)) 13. │ └─base::is.factor(x) 14. └─base::basename(x) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 66 ] Error: ! Test failures. Execution halted Flavor: r-devel-windows-x86_64

Package OutSeekR

Current CRAN status: NOTE: 2, OK: 12

Version: 1.1.0
Check: dependencies in R code
Result: NOTE Namespaces in Imports field not imported from: ‘future’ ‘truncnorm’ All declared Imports should be used. Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Package SeqKat

Current CRAN status: NOTE: 1, OK: 13

Version: 0.0.9
Check: package dependencies
Result: NOTE Package suggested but not available for checking: 'doMC' Flavor: r-oldrel-windows-x86_64

Package VennDiagram

Current CRAN status: OK: 14