CRAN Package Check Results for Package dendextend

Last updated on 2019-03-14 00:46:32 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.9.0 15.23 247.88 263.11 ERROR
r-devel-linux-x86_64-debian-gcc 1.9.0 11.19 234.88 246.07 ERROR
r-devel-linux-x86_64-fedora-clang 1.9.0 363.95 ERROR
r-devel-linux-x86_64-fedora-gcc 1.9.0 360.28 ERROR
r-devel-windows-ix86+x86_64 1.9.0 31.00 287.00 318.00 ERROR
r-patched-linux-x86_64 1.9.0 8.74 271.47 280.21 ERROR
r-patched-solaris-x86 1.9.0 462.20 WARN
r-release-linux-x86_64 ERROR
r-release-windows-ix86+x86_64 1.9.0 27.00 349.00 376.00 OK
r-release-osx-x86_64 1.9.0 WARN
r-oldrel-windows-ix86+x86_64 1.9.0 21.00 381.00 402.00 WARN
r-oldrel-osx-x86_64 1.9.0 WARN

Check Details

Version: 1.9.0
Check: tests
Result: ERROR
     Running 'test-all.R' [13s/14s]
    Running the tests in 'tests/test-all.R' failed.
    Complete output:
     > library(testthat)
     >
     > library(dendextend)
    
     ---------------------
     Welcome to dendextend version 1.9.0
     Type citation('dendextend') for how to cite the package.
    
     Type browseVignettes(package = 'dendextend') for the package vignette.
     The github page is: https://github.com/talgalili/dendextend/
    
     Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
     Or contact: <tal.galili@gmail.com>
    
     To suppress this message use: suppressPackageStartupMessages(library(dendextend))
     ---------------------
    
    
     Attaching package: 'dendextend'
    
     The following object is masked from 'package:stats':
    
     cutree
    
     > test_check("dendextend")
     -- 1. Failure: FM_index_R works (@test-bk_method.R#134) -----------------------
     round(as.vector(tmp_index), 2) not identical to 0.38.
     1/1 mismatches
     [1] 0.37 - 0.38 == -0.01
    
     -- 2. Failure: cor_bakers_gamma works (@test-cor_bakers_gamma.R#27) -----------
     round(cor_bakers_gamma(dend1, dend2), 2) not identical to 0.57.
     1/1 mismatches
     [1] 0.35 - 0.57 == -0.22
    
     -- 3. Failure: labels options works (@test-set.dendrogram.R#45) ---------------
     dend %>% set("labels_color") %>% labels_colors not equal to `new_col_labels`.
     Names: 9 string mismatches
    
     -- 4. Failure: leaves options works (@test-set.dendrogram.R#90) ---------------
     attr(tmp, "height") not equal to 0.9030533.
     1/1 mismatches
     [1] 1.42 - 0.903 == 0.518
    
     -- 5. Failure: shuffle works (@test-untangle.R#15) ----------------------------
     round(entanglement(dend, dend2), 3) not identical to 0.398.
     1/1 mismatches
     [1] 0.775 - 0.398 == 0.377
    
     -- 6. Failure: untangle_step_rotate_1side work (@test-untangle.R#57) ----------
     round(entanglement(dend1, dend2, L = 2), 2) not identical to 0.47.
     1/1 mismatches
     [1] 0.04 - 0.47 == -0.43
    
     == testthat results ===========================================================
     OK: 400 SKIPPED: 0 FAILED: 6
     1. Failure: FM_index_R works (@test-bk_method.R#134)
     2. Failure: cor_bakers_gamma works (@test-cor_bakers_gamma.R#27)
     3. Failure: labels options works (@test-set.dendrogram.R#45)
     4. Failure: leaves options works (@test-set.dendrogram.R#90)
     5. Failure: shuffle works (@test-untangle.R#15)
     6. Failure: untangle_step_rotate_1side work (@test-untangle.R#57)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.9.0
Check: tests
Result: ERROR
     Running ‘test-all.R’ [16s/22s]
    Running the tests in ‘tests/test-all.R’ failed.
    Complete output:
     > library(testthat)
     >
     > library(dendextend)
    
     ---------------------
     Welcome to dendextend version 1.9.0
     Type citation('dendextend') for how to cite the package.
    
     Type browseVignettes(package = 'dendextend') for the package vignette.
     The github page is: https://github.com/talgalili/dendextend/
    
     Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
     Or contact: <tal.galili@gmail.com>
    
     To suppress this message use: suppressPackageStartupMessages(library(dendextend))
     ---------------------
    
    
     Attaching package: 'dendextend'
    
     The following object is masked from 'package:stats':
    
     cutree
    
     > test_check("dendextend")
     ── 1. Failure: FM_index_R works (@test-bk_method.R#134) ───────────────────────
     round(as.vector(tmp_index), 2) not identical to 0.38.
     1/1 mismatches
     [1] 0.37 - 0.38 == -0.01
    
     ── 2. Failure: cor_bakers_gamma works (@test-cor_bakers_gamma.R#27) ───────────
     round(cor_bakers_gamma(dend1, dend2), 2) not identical to 0.57.
     1/1 mismatches
     [1] 0.35 - 0.57 == -0.22
    
     ── 3. Failure: labels options works (@test-set.dendrogram.R#45) ───────────────
     dend %>% set("labels_color") %>% labels_colors not equal to `new_col_labels`.
     Names: 9 string mismatches
    
     ── 4. Failure: leaves options works (@test-set.dendrogram.R#90) ───────────────
     attr(tmp, "height") not equal to 0.9030533.
     1/1 mismatches
     [1] 1.42 - 0.903 == 0.518
    
     ── 5. Failure: shuffle works (@test-untangle.R#15) ────────────────────────────
     round(entanglement(dend, dend2), 3) not identical to 0.398.
     1/1 mismatches
     [1] 0.775 - 0.398 == 0.377
    
     ── 6. Failure: untangle_step_rotate_1side work (@test-untangle.R#57) ──────────
     round(entanglement(dend1, dend2, L = 2), 2) not identical to 0.47.
     1/1 mismatches
     [1] 0.04 - 0.47 == -0.43
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 400 SKIPPED: 0 FAILED: 6
     1. Failure: FM_index_R works (@test-bk_method.R#134)
     2. Failure: cor_bakers_gamma works (@test-cor_bakers_gamma.R#27)
     3. Failure: labels options works (@test-set.dendrogram.R#45)
     4. Failure: leaves options works (@test-set.dendrogram.R#90)
     5. Failure: shuffle works (@test-untangle.R#15)
     6. Failure: untangle_step_rotate_1side work (@test-untangle.R#57)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.9.0
Check: tests
Result: ERROR
     Running ‘test-all.R’ [23s/28s]
    Running the tests in ‘tests/test-all.R’ failed.
    Complete output:
     > library(testthat)
     >
     > library(dendextend)
    
     ---------------------
     Welcome to dendextend version 1.9.0
     Type citation('dendextend') for how to cite the package.
    
     Type browseVignettes(package = 'dendextend') for the package vignette.
     The github page is: https://github.com/talgalili/dendextend/
    
     Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
     Or contact: <tal.galili@gmail.com>
    
     To suppress this message use: suppressPackageStartupMessages(library(dendextend))
     ---------------------
    
    
     Attaching package: 'dendextend'
    
     The following object is masked from 'package:stats':
    
     cutree
    
     > test_check("dendextend")
     ── 1. Failure: FM_index_R works (@test-bk_method.R#134) ───────────────────────
     round(as.vector(tmp_index), 2) not identical to 0.38.
     1/1 mismatches
     [1] 0.37 - 0.38 == -0.01
    
     ── 2. Failure: cor_bakers_gamma works (@test-cor_bakers_gamma.R#27) ───────────
     round(cor_bakers_gamma(dend1, dend2), 2) not identical to 0.57.
     1/1 mismatches
     [1] 0.35 - 0.57 == -0.22
    
     ── 3. Failure: labels options works (@test-set.dendrogram.R#45) ───────────────
     dend %>% set("labels_color") %>% labels_colors not equal to `new_col_labels`.
     Names: 9 string mismatches
    
     ── 4. Failure: leaves options works (@test-set.dendrogram.R#90) ───────────────
     attr(tmp, "height") not equal to 0.9030533.
     1/1 mismatches
     [1] 1.42 - 0.903 == 0.518
    
     ── 5. Failure: shuffle works (@test-untangle.R#15) ────────────────────────────
     round(entanglement(dend, dend2), 3) not identical to 0.398.
     1/1 mismatches
     [1] 0.775 - 0.398 == 0.377
    
     ── 6. Failure: untangle_step_rotate_1side work (@test-untangle.R#57) ──────────
     round(entanglement(dend1, dend2, L = 2), 2) not identical to 0.47.
     1/1 mismatches
     [1] 0.04 - 0.47 == -0.43
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 400 SKIPPED: 0 FAILED: 6
     1. Failure: FM_index_R works (@test-bk_method.R#134)
     2. Failure: cor_bakers_gamma works (@test-cor_bakers_gamma.R#27)
     3. Failure: labels options works (@test-set.dendrogram.R#45)
     4. Failure: leaves options works (@test-set.dendrogram.R#90)
     5. Failure: shuffle works (@test-untangle.R#15)
     6. Failure: untangle_step_rotate_1side work (@test-untangle.R#57)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.9.0
Check: tests
Result: ERROR
     Running ‘test-all.R’ [23s/52s]
    Running the tests in ‘tests/test-all.R’ failed.
    Complete output:
     > library(testthat)
     >
     > library(dendextend)
    
     ---------------------
     Welcome to dendextend version 1.9.0
     Type citation('dendextend') for how to cite the package.
    
     Type browseVignettes(package = 'dendextend') for the package vignette.
     The github page is: https://github.com/talgalili/dendextend/
    
     Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
     Or contact: <tal.galili@gmail.com>
    
     To suppress this message use: suppressPackageStartupMessages(library(dendextend))
     ---------------------
    
    
     Attaching package: 'dendextend'
    
     The following object is masked from 'package:stats':
    
     cutree
    
     > test_check("dendextend")
     ── 1. Failure: FM_index_R works (@test-bk_method.R#134) ───────────────────────
     round(as.vector(tmp_index), 2) not identical to 0.38.
     1/1 mismatches
     [1] 0.37 - 0.38 == -0.01
    
     ── 2. Failure: cor_bakers_gamma works (@test-cor_bakers_gamma.R#27) ───────────
     round(cor_bakers_gamma(dend1, dend2), 2) not identical to 0.57.
     1/1 mismatches
     [1] 0.35 - 0.57 == -0.22
    
     ── 3. Failure: labels options works (@test-set.dendrogram.R#45) ───────────────
     dend %>% set("labels_color") %>% labels_colors not equal to `new_col_labels`.
     Names: 9 string mismatches
    
     ── 4. Failure: leaves options works (@test-set.dendrogram.R#90) ───────────────
     attr(tmp, "height") not equal to 0.9030533.
     1/1 mismatches
     [1] 1.42 - 0.903 == 0.518
    
     ── 5. Failure: shuffle works (@test-untangle.R#15) ────────────────────────────
     round(entanglement(dend, dend2), 3) not identical to 0.398.
     1/1 mismatches
     [1] 0.775 - 0.398 == 0.377
    
     ── 6. Failure: untangle_step_rotate_1side work (@test-untangle.R#57) ──────────
     round(entanglement(dend1, dend2, L = 2), 2) not identical to 0.47.
     1/1 mismatches
     [1] 0.04 - 0.47 == -0.43
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 400 SKIPPED: 0 FAILED: 6
     1. Failure: FM_index_R works (@test-bk_method.R#134)
     2. Failure: cor_bakers_gamma works (@test-cor_bakers_gamma.R#27)
     3. Failure: labels options works (@test-set.dendrogram.R#45)
     4. Failure: leaves options works (@test-set.dendrogram.R#90)
     5. Failure: shuffle works (@test-untangle.R#15)
     6. Failure: untangle_step_rotate_1side work (@test-untangle.R#57)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.9.0
Check: tests
Result: ERROR
     Running 'test-all.R' [16s]
    Running the tests in 'tests/test-all.R' failed.
    Complete output:
     > library(testthat)
     >
     > library(dendextend)
    
     ---------------------
     Welcome to dendextend version 1.9.0
     Type citation('dendextend') for how to cite the package.
    
     Type browseVignettes(package = 'dendextend') for the package vignette.
     The github page is: https://github.com/talgalili/dendextend/
    
     Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
     Or contact: <tal.galili@gmail.com>
    
     To suppress this message use: suppressPackageStartupMessages(library(dendextend))
     ---------------------
    
    
     Attaching package: 'dendextend'
    
     The following object is masked from 'package:stats':
    
     cutree
    
     > test_check("dendextend")
     -- 1. Failure: FM_index_R works (@test-bk_method.R#134) -----------------------
     round(as.vector(tmp_index), 2) not identical to 0.38.
     1/1 mismatches
     [1] 0.37 - 0.38 == -0.01
    
     -- 2. Failure: cor_bakers_gamma works (@test-cor_bakers_gamma.R#27) -----------
     round(cor_bakers_gamma(dend1, dend2), 2) not identical to 0.57.
     1/1 mismatches
     [1] 0.35 - 0.57 == -0.22
    
     -- 3. Failure: labels options works (@test-set.dendrogram.R#45) ---------------
     dend %>% set("labels_color") %>% labels_colors not equal to `new_col_labels`.
     Names: 9 string mismatches
    
     -- 4. Failure: leaves options works (@test-set.dendrogram.R#90) ---------------
     attr(tmp, "height") not equal to 0.9030533.
     1/1 mismatches
     [1] 1.42 - 0.903 == 0.518
    
     -- 5. Failure: shuffle works (@test-untangle.R#15) ----------------------------
     round(entanglement(dend, dend2), 3) not identical to 0.398.
     1/1 mismatches
     [1] 0.775 - 0.398 == 0.377
    
     -- 6. Failure: untangle_step_rotate_1side work (@test-untangle.R#57) ----------
     round(entanglement(dend1, dend2, L = 2), 2) not identical to 0.47.
     1/1 mismatches
     [1] 0.04 - 0.47 == -0.43
    
     == testthat results ===========================================================
     OK: 400 SKIPPED: 0 FAILED: 6
     1. Failure: FM_index_R works (@test-bk_method.R#134)
     2. Failure: cor_bakers_gamma works (@test-cor_bakers_gamma.R#27)
     3. Failure: labels options works (@test-set.dendrogram.R#45)
     4. Failure: leaves options works (@test-set.dendrogram.R#90)
     5. Failure: shuffle works (@test-untangle.R#15)
     6. Failure: untangle_step_rotate_1side work (@test-untangle.R#57)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.9.0
Check: examples
Result: ERROR
    Running examples in ‘dendextend-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: collapse_branch
    > ### Title: Collapse branches under a tolerance level
    > ### Aliases: collapse_branch
    >
    > ### ** Examples
    >
    >
    > # # ladderize is like sort(..., type = "node")
    > dend <- iris[1:5,-5] %>% dist %>% hclust %>% as.dendrogram
    > par(mfrow = c(1,3))
    > dend %>% ladderize %>% plot(horiz = TRUE); abline(v = .2, col = 2, lty = 2)
    > dend %>% collapse_branch(tol = 0.2) %>% ladderize %>% plot(horiz = TRUE)
    > dend %>% collapse_branch(tol = 0.2) %>% ladderize %>%
    + hang.dendrogram(hang = 0) %>% plot(horiz = TRUE)
    >
    > par(mfrow = c(1,2))
    > dend %>% collapse_branch(tol = 0.2, lower = FALSE) %>% plot(horiz = TRUE, main = "dendrogram")
    > library(ape)
    
    Attaching package: ‘ape’
    
    The following objects are masked from ‘package:dendextend’:
    
     ladderize, rotate
    
    > dend %>% as.phylo %>% di2multi(tol = 0.2) %>% plot(main = "phylo")
    Error in UseMethod("as.phylo") :
     no applicable method for 'as.phylo' applied to an object of class "dendrogram"
    Calls: %>% ... eval -> _fseq -> freduce -> <Anonymous> -> as.phylo
    Execution halted
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.9.0
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    
    ---------------------
    Welcome to dendextend version 1.9.0
    Type citation('dendextend') for how to cite the package.
    
    Type browseVignettes(package = 'dendextend') for the package vignette.
    The github page is: https://github.com/talgalili/dendextend/
    
    Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
    Or contact: <tal.galili@gmail.com>
    
     To suppress this message use: suppressPackageStartupMessages(library(dendextend))
    ---------------------
    
    
    Attaching package: 'dendextend'
    
    The following object is masked from 'package:stats':
    
     cutree
    
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    
    Attaching package: 'gplots'
    
    The following objects are masked from 'package:seriation':
    
     bluered, greenred
    
    The following object is masked from 'package:stats':
    
     lowess
    
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    Quitting from lines 931-933 (introduction.Rmd)
    Error: processing vignette 'introduction.Rmd' failed with diagnostics:
    cannot open the connection
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.9.0
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    
     cutree
    
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    
    Attaching package: 'gplots'
    
    The following objects are masked from 'package:seriation':
    
     bluered, greenred
    
    The following object is masked from 'package:stats':
    
     lowess
    
    PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
    Quitting from lines 931-933 (introduction.Rmd)
    Error: processing vignette 'introduction.Rmd' failed with diagnostics:
    cannot open the connection
    Execution halted
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 1.9.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
Flavor: r-oldrel-windows-ix86+x86_64

Version: 1.9.0
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘WGCNA’
Flavor: r-oldrel-osx-x86_64