CRAN Package Check Results for Maintainer ‘Michael J. Kane <michael.kane at yale.edu>’

Last updated on 2025-10-10 11:51:44 CEST.

Package ERROR NOTE
basket 13
listdown 9 4
preference 13

Package basket

Current CRAN status: NOTE: 13

Version: 0.10.11
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘Michael J. Kane <michael.kane@yale.edu>’ Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.10.11
Check: Rd files
Result: NOTE checkRd: (-1) basket-package.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) basket-package.Rd:23-24: Lost braces in \itemize; meant \describe ? checkRd: (-1) basket-package.Rd:25-26: Lost braces in \itemize; meant \describe ? checkRd: (-1) basket-package.Rd:27-28: Lost braces in \itemize; meant \describe ? checkRd: (-1) basket-package.Rd:29-30: Lost braces in \itemize; meant \describe ? checkRd: (-1) basket-package.Rd:31-32: Lost braces in \itemize; meant \describe ? checkRd: (-1) basket-package.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) basket-package.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) basket-package.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) basket-package.Rd:36-37: Lost braces in \itemize; meant \describe ? checkRd: (-1) basket-package.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) basket-package.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) basket-package.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_map.Rd:26-30: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_map.Rd:31-32: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_map.Rd:33-34: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_map.Rd:35-36: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_map.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_map.Rd:38-39: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_map.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_map.Rd:41-42: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_map.Rd:43-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_pep.Rd:26-35: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_pep.Rd:31: Lost braces 31 | \item{[text_color]}{A text string setting the color of the exchangeability | ^ checkRd: (-1) plot_pep.Rd:31-32: Lost braces 31 | \item{[text_color]}{A text string setting the color of the exchangeability | ^ checkRd: (-1) plot_pep.Rd:33: Lost braces 33 | \item{[tile_color]}{A text string setting the color of the edges of the | ^ checkRd: (-1) plot_pep.Rd:33-34: Lost braces 33 | \item{[tile_color]}{A text string setting the color of the edges of the | ^ checkRd: (-1) plot_pep.Rd:36-37: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_pep.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_pep.Rd:39-40: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_pep.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_pep.Rd:42-43: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_pep.Rd:44-45: Lost braces in \itemize; meant \describe ? checkRd: (-1) vemu.Rd:20: Lost braces; missing escapes or markup? 20 | concluded that nonmelanoma tumor types harboring $BRAF^{V600}$ mutations | ^ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Package listdown

Current CRAN status: ERROR: 9, NOTE: 4

Version: 0.5.7
Check: Rd files
Result: NOTE checkRd: (-1) ld_build_html_site.Rd:41: Lost braces 41 | directory specified by `rmd_dir`. Note that this is an {{rmarkdown}} | ^ checkRd: (-1) ld_create_doc.Rd:29: Lost braces 29 | directory specified by `rmd_dir`. Note that this is an {{rmarkdown}} | ^ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 0.5.7
Check: examples
Result: ERROR Running examples in ‘listdown-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: as_ld_yml > ### Title: Turn a Computational Component List into YAML with Class > ### Information > ### Aliases: as_ld_yml > > ### ** Examples > > if (require("ggplot2")) { + + cc_list <- list( + Linear = ggplot(anscombe, aes(x = x1, y = y1)) + geom_point(), + `Non Linear` = ggplot(anscombe, aes(x = x2, y = y2)) + geom_point(), + `Outlier Vertical`= ggplot(anscombe, aes(x = x3, y = y3)) + geom_point(), + `Outlier Horizontal` = ggplot(anscombe, aes(x = x4, y = y4)) + + geom_point()) + + as_ld_yml(cc_list) + } Loading required package: ggplot2 Error in parse(text = paste("x", loc, " <<- list(paste(", deparse(class(elem)), : <text>:2:1: unexpected symbol 1: x [[1]] <<- list(paste( c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg" , collapse = ":")) 2: x ^ Calls: as_ld_yml -> depth_first_copy -> eval -> parse Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.5.7
Check: tests
Result: ERROR Running ‘testthat.r’ [24s/30s] Running the tests in ‘tests/testthat.r’ failed. Complete output: > library(testthat) > library(listdown) > > test_check("listdown") [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-create-doc.r:27:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-as-yml.r:20:3'): Writing a yml file works. ───────────────────── Error in `parse(text = paste("x", loc, " <<- list(paste(", deparse(class(elem)), ", collapse = \":\"))"))`: <text>:2:1: unexpected symbol 1: x [[1]] <<- list(paste( c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg" , collapse = ":")) 2: x ^ Backtrace: ▆ 1. ├─testthat::expect_equal(as_ld_yml(cc_list), read_reference("as-yml.rds")) at test-as-yml.r:20:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─listdown::as_ld_yml(cc_list) 5. └─listdown (local) depth_first_copy() 6. ├─base::eval(...) 7. └─base::parse(...) ── Failure ('test-cc-dendro.r:20:3'): Dendrograms work. ──────────────────────── ld_cc_dendro(cc_list) not equal to read_reference("cc-dendro.rds"). 4 string mismatches [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.5.7
Check: tests
Result: ERROR Running ‘testthat.r’ [17s/22s] Running the tests in ‘tests/testthat.r’ failed. Complete output: > library(testthat) > library(listdown) > > test_check("listdown") [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-create-doc.r:27:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-as-yml.r:20:3'): Writing a yml file works. ───────────────────── Error in `parse(text = paste("x", loc, " <<- list(paste(", deparse(class(elem)), ", collapse = \":\"))"))`: <text>:2:1: unexpected symbol 1: x [[1]] <<- list(paste( c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg" , collapse = ":")) 2: x ^ Backtrace: ▆ 1. ├─testthat::expect_equal(as_ld_yml(cc_list), read_reference("as-yml.rds")) at test-as-yml.r:20:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─listdown::as_ld_yml(cc_list) 5. └─listdown (local) depth_first_copy() 6. ├─base::eval(...) 7. └─base::parse(...) ── Failure ('test-cc-dendro.r:20:3'): Dendrograms work. ──────────────────────── ld_cc_dendro(cc_list) not equal to read_reference("cc-dendro.rds"). 4 string mismatches [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.5.7
Check: examples
Result: ERROR Running examples in ‘listdown-Ex.R’ failed The error most likely occurred in: > ### Name: as_ld_yml > ### Title: Turn a Computational Component List into YAML with Class > ### Information > ### Aliases: as_ld_yml > > ### ** Examples > > if (require("ggplot2")) { + + cc_list <- list( + Linear = ggplot(anscombe, aes(x = x1, y = y1)) + geom_point(), + `Non Linear` = ggplot(anscombe, aes(x = x2, y = y2)) + geom_point(), + `Outlier Vertical`= ggplot(anscombe, aes(x = x3, y = y3)) + geom_point(), + `Outlier Horizontal` = ggplot(anscombe, aes(x = x4, y = y4)) + + geom_point()) + + as_ld_yml(cc_list) + } Loading required package: ggplot2 Error in parse(text = paste("x", loc, " <<- list(paste(", deparse(class(elem)), : <text>:2:1: unexpected symbol 1: x [[1]] <<- list(paste( c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg" , collapse = ":")) 2: x ^ Calls: as_ld_yml -> depth_first_copy -> eval -> parse Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 0.5.7
Check: tests
Result: ERROR Running ‘testthat.r’ [35s/54s] Running the tests in ‘tests/testthat.r’ failed. Complete output: > library(testthat) > library(listdown) > > test_check("listdown") [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-create-doc.r:27:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-as-yml.r:20:3'): Writing a yml file works. ───────────────────── Error in `parse(text = paste("x", loc, " <<- list(paste(", deparse(class(elem)), ", collapse = \":\"))"))`: <text>:2:1: unexpected symbol 1: x [[1]] <<- list(paste( c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg" , collapse = ":")) 2: x ^ Backtrace: ▆ 1. ├─testthat::expect_equal(as_ld_yml(cc_list), read_reference("as-yml.rds")) at test-as-yml.r:20:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─listdown::as_ld_yml(cc_list) 5. └─listdown (local) depth_first_copy() 6. ├─base::eval(...) 7. └─base::parse(...) ── Failure ('test-cc-dendro.r:20:3'): Dendrograms work. ──────────────────────── ld_cc_dendro(cc_list) not equal to read_reference("cc-dendro.rds"). 4 string mismatches [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.5.7
Check: tests
Result: ERROR Running ‘testthat.r’ [34s/45s] Running the tests in ‘tests/testthat.r’ failed. Complete output: > library(testthat) > library(listdown) > > test_check("listdown") [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-create-doc.r:27:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-as-yml.r:20:3'): Writing a yml file works. ───────────────────── Error in `parse(text = paste("x", loc, " <<- list(paste(", deparse(class(elem)), ", collapse = \":\"))"))`: <text>:2:1: unexpected symbol 1: x [[1]] <<- list(paste( c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg" , collapse = ":")) 2: x ^ Backtrace: ▆ 1. ├─testthat::expect_equal(as_ld_yml(cc_list), read_reference("as-yml.rds")) at test-as-yml.r:20:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─listdown::as_ld_yml(cc_list) 5. └─listdown (local) depth_first_copy() 6. ├─base::eval(...) 7. └─base::parse(...) ── Failure ('test-cc-dendro.r:20:3'): Dendrograms work. ──────────────────────── ld_cc_dendro(cc_list) not equal to read_reference("cc-dendro.rds"). 4 string mismatches [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ] Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.5.7
Check: tests
Result: ERROR Running 'testthat.r' [21s] Running the tests in 'tests/testthat.r' failed. Complete output: > library(testthat) > library(listdown) > > test_check("listdown") [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-create-doc.r:27:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-as-yml.r:20:3'): Writing a yml file works. ───────────────────── Error in `parse(text = paste("x", loc, " <<- list(paste(", deparse(class(elem)), ", collapse = \":\"))"))`: <text>:2:1: unexpected symbol 1: x [[1]] <<- list(paste( c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg" , collapse = ":")) 2: x ^ Backtrace: ▆ 1. ├─testthat::expect_equal(as_ld_yml(cc_list), read_reference("as-yml.rds")) at test-as-yml.r:20:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─listdown::as_ld_yml(cc_list) 5. └─listdown (local) depth_first_copy() 6. ├─base::eval(...) 7. └─base::parse(...) ── Failure ('test-cc-dendro.r:20:3'): Dendrograms work. ──────────────────────── ld_cc_dendro(cc_list) not equal to read_reference("cc-dendro.rds"). 4 string mismatches [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ] Error: Test failures Execution halted Flavors: r-devel-windows-x86_64, r-release-windows-x86_64

Version: 0.5.7
Check: tests
Result: ERROR Running ‘testthat.r’ [23s/27s] Running the tests in ‘tests/testthat.r’ failed. Complete output: > library(testthat) > library(listdown) > > test_check("listdown") [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-create-doc.r:27:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-as-yml.r:20:3'): Writing a yml file works. ───────────────────── Error in `parse(text = paste("x", loc, " <<- list(paste(", deparse(class(elem)), ", collapse = \":\"))"))`: <text>:2:1: unexpected symbol 1: x [[1]] <<- list(paste( c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg" , collapse = ":")) 2: x ^ Backtrace: ▆ 1. ├─testthat::expect_equal(as_ld_yml(cc_list), read_reference("as-yml.rds")) at test-as-yml.r:20:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─listdown::as_ld_yml(cc_list) 5. └─listdown (local) depth_first_copy() 6. ├─base::eval(...) 7. └─base::parse(...) ── Failure ('test-cc-dendro.r:20:3'): Dendrograms work. ──────────────────────── ld_cc_dendro(cc_list) not equal to read_reference("cc-dendro.rds"). 4 string mismatches [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ] Error: Test failures Execution halted Flavor: r-patched-linux-x86_64

Version: 0.5.7
Check: tests
Result: ERROR Running ‘testthat.r’ [24s/31s] Running the tests in ‘tests/testthat.r’ failed. Complete output: > library(testthat) > library(listdown) > > test_check("listdown") [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-create-doc.r:27:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-as-yml.r:20:3'): Writing a yml file works. ───────────────────── Error in `parse(text = paste("x", loc, " <<- list(paste(", deparse(class(elem)), ", collapse = \":\"))"))`: <text>:2:1: unexpected symbol 1: x [[1]] <<- list(paste( c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg" , collapse = ":")) 2: x ^ Backtrace: ▆ 1. ├─testthat::expect_equal(as_ld_yml(cc_list), read_reference("as-yml.rds")) at test-as-yml.r:20:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─listdown::as_ld_yml(cc_list) 5. └─listdown (local) depth_first_copy() 6. ├─base::eval(...) 7. └─base::parse(...) ── Failure ('test-cc-dendro.r:20:3'): Dendrograms work. ──────────────────────── ld_cc_dendro(cc_list) not equal to read_reference("cc-dendro.rds"). 4 string mismatches [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ] Error: Test failures Execution halted Flavor: r-release-linux-x86_64

Version: 0.5.7
Check: tests
Result: ERROR Running 'testthat.r' [29s] Running the tests in 'tests/testthat.r' failed. Complete output: > library(testthat) > library(listdown) > > test_check("listdown") [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • On CRAN (1): 'test-create-doc.r:27:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-as-yml.r:20:3'): Writing a yml file works. ───────────────────── Error in `parse(text = paste("x", loc, " <<- list(paste(", deparse(class(elem)), ", collapse = \":\"))"))`: <text>:2:1: unexpected symbol 1: x [[1]] <<- list(paste( c("ggplot2::ggplot", "ggplot", "ggplot2::gg", "S7_object", "gg" , collapse = ":")) 2: x ^ Backtrace: ▆ 1. ├─testthat::expect_equal(as_ld_yml(cc_list), read_reference("as-yml.rds")) at test-as-yml.r:20:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─listdown::as_ld_yml(cc_list) 5. └─listdown (local) depth_first_copy() 6. ├─base::eval(...) 7. └─base::parse(...) ── Failure ('test-cc-dendro.r:20:3'): Dendrograms work. ──────────────────────── ld_cc_dendro(cc_list) not equal to read_reference("cc-dendro.rds"). 4 string mismatches [ FAIL 2 | WARN 0 | SKIP 1 | PASS 34 ] Error: Test failures Execution halted Flavor: r-oldrel-windows-x86_64

Package preference

Current CRAN status: NOTE: 13

Version: 1.1.6
Check: Rd files
Result: NOTE checkRd: (-1) preference-package.Rd:48-49: Lost braces in \itemize; meant \describe ? checkRd: (-1) preference-package.Rd:50-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) preference-package.Rd:52-53: Lost braces in \itemize; meant \describe ? checkRd: (-1) preference-package.Rd:58-60: Lost braces in \itemize; meant \describe ? checkRd: (-1) preference-package.Rd:61-63: Lost braces in \itemize; meant \describe ? checkRd: (-1) preference-package.Rd:68-69: Lost braces in \itemize; meant \describe ? checkRd: (-1) preference-package.Rd:70-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) preference-package.Rd:72-73: Lost braces in \itemize; meant \describe ? checkRd: (-1) preference-package.Rd:78-79: Lost braces in \itemize; meant \describe ? checkRd: (-1) preference-package.Rd:80-81: Lost braces in \itemize; meant \describe ? checkRd: (-1) preference.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) preference.Rd:22-23: Lost braces in \itemize; meant \describe ? checkRd: (-1) preference.Rd:24-25: Lost braces in \itemize; meant \describe ? checkRd: (-1) preference.Rd:26-27: Lost braces in \itemize; meant \describe ? Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

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