Validation Report - dendextend@1.19.0
Context
This report is fully automated and builds on rhub/ref-image image. Documents the installation of this package on an open source R environment, focusing on:
- Installation environment description
- Testing coverage
It is limited to assess whether unit tests and documentation are present and can execute without error. An assessment would be required that the tests and documentation are meaningful.
Package dendextend
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 151 |
| has_vignettes | 8 |
| export_help | 151 |
| has_website | TRUE |
| has_maintainer | Tal Galili tal.galili@gmail.com |
| bugs_status | subscript out of bounds |
| has_source_control | https://github.com/talgalili/dendextend/ |
| has_bug_reports_url | 1 |
| downloads_1yr | 852163 |
| reverse_dependencies | 92 |
| has_examples | 0.9927007 |
| dependencies | 6 |
| license | GPL-2 | GPL-3 |
Package general assessment: Coverage, check results, size, download the last year, reverse dependencies and number of dependencies.
Dependencies
Overall the package has these dependencies:
| package | type | |
|---|---|---|
| 1 | utils | Imports |
| 2 | stats | Imports |
| 3 | datasets | Imports |
| 4 | magrittr (>= 1.0.1) | Imports |
| 5 | ggplot2 | Imports |
| 6 | viridis | Imports |
Package dependencies
Reverse dependencies
Overall the package has 92 reverse dependencies:
adjclust, AntMAN, aqp, archeofrag.gui, BasketballAnalyzeR, BiBitR, CALANGO, celda, celltrackR, CellTrails, ChAMP, CHETAH, CINNA, circlize, Cluster.OBeu, cola, ComplexHeatmap, conos, consensusDE, COTAN, DAPAR, DatabionicSwarm, dbscan, DEGreport, DeMixT, didec, ecan, EGAnet, elaborator, EnsCat, evaluomeR, factoextra, FCPS, GeneNMF, GeneTonic, GlobalAncova, GOpro, GSEAmining, HCD, heatmaply, hfr, HGC, ILoReg, IncDTW, INFOSET, InterCellar, isocat, kanjistat, kmer, ldaPrototype, MAGeCKFlute, mappoly, mdendro, Mercator, metaprotr, mFD, Momocs, moRphomenses, multiClust, numbat, omXplore, packFinder, PdPDB, PhosR, phylogram, plotly, ProjectionBasedClustering, pRoloc, protti, rainette, rare, rnmamod, rSAFE, sarp.snowprofile.alignment, scGPS, segregation, seriation, SISIR, sits, SlideCNA, spatialHeatmap, spiralize, tidyHeatmap, TreeAndLeaf, tsibbletalk, uclust, variancePartition, VecDep, ViSEAGO, visxhclust, Xplortext, YAPSA
Namespace
Overall the package has 151 exported objects. 150 are documented:
%>% all_couple_rotations_at_k
FALSE TRUE
all_unique as_hclust_fixed
TRUE TRUE
as.dendlist as.ggdend
TRUE TRUE
assign_dendextend_options assign_values_to_branches_edgePar
TRUE TRUE
assign_values_to_leaves_edgePar assign_values_to_leaves_nodePar
TRUE TRUE
assign_values_to_nodes_nodePar Bk
TRUE TRUE
Bk_permutations Bk_plot
TRUE TRUE
branches_attr_by_clusters branches_attr_by_labels
TRUE TRUE
branches_attr_by_lists branches_color
TRUE TRUE
circlize_dendrogram click_rotate
TRUE TRUE
collapse_branch collapse_labels
TRUE TRUE
color_branches color_labels
TRUE TRUE
color_unique_labels colored_bars
TRUE TRUE
colored_dots colour_branches
TRUE TRUE
common_subtrees_clusters cor_bakers_gamma
TRUE TRUE
cor_common_nodes cor_cophenetic
TRUE TRUE
cor_FM_index cor.dendlist
TRUE TRUE
count_terminal_nodes cut_lower_fun
TRUE TRUE
cutree cutree_1h.dendrogram
TRUE TRUE
cutree_1k.dendrogram dend_diff
TRUE TRUE
dend_expend dendbackback
TRUE TRUE
dendextend_options dendlist
TRUE TRUE
DendSer.dendrogram dist_long
TRUE TRUE
dist.dendlist distinct_edges
TRUE TRUE
duplicate_leaf entanglement
TRUE TRUE
fac2num find_dend
TRUE TRUE
find_dendrogram find_k
TRUE TRUE
fix_members_attr.dendrogram flatten.dendrogram
TRUE TRUE
flip_leaves FM_index
TRUE TRUE
FM_index_permutation FM_index_R
TRUE TRUE
get_branches_heights get_childrens_heights
TRUE TRUE
get_leaves_attr get_leaves_branches_attr
TRUE TRUE
get_leaves_branches_col get_leaves_edgePar
TRUE TRUE
get_leaves_nodePar get_nodes_attr
TRUE TRUE
get_nodes_xy get_root_branches_attr
TRUE TRUE
get_subdendrograms ggdend
TRUE TRUE
hang.dendrogram has_component_in_attribute
TRUE TRUE
has_edgePar has_nodePar
TRUE TRUE
heights_per_k.dendrogram highlight_branches
TRUE TRUE
highlight_branches_col highlight_branches_lwd
TRUE TRUE
highlight_distinct_edges intersect_trees
TRUE TRUE
is.dendlist is.dendrogram
TRUE TRUE
is.dist is.hclust
TRUE TRUE
is.natural.number is.phylo
TRUE TRUE
labels_cex labels_cex<-
TRUE TRUE
labels_col labels_colors
TRUE TRUE
labels_colors<- labels<-
TRUE TRUE
ladderize leaf_colors
TRUE TRUE
leaf_Colors lowest_common_branch
TRUE TRUE
match_order_by_labels match_order_dendrogram_by_old_order
TRUE TRUE
max_depth min_depth
TRUE TRUE
na_locf nleaves
TRUE TRUE
nnodes noded_with_condition
TRUE TRUE
order.dendrogram<- order.hclust
TRUE TRUE
partition_leaves place_labels
TRUE TRUE
plot_horiz.dendrogram prepare.ggdend
TRUE TRUE
prune prune_common_subtrees.dendlist
TRUE TRUE
prune_leaf pvclust_edges
TRUE TRUE
pvclust_show_signif pvclust_show_signif_gradient
TRUE TRUE
pvrect2 raise.dendrogram
TRUE TRUE
rank_branches rank_order.dendrogram
TRUE TRUE
rank_values_with_clusters rect.dendrogram
TRUE TRUE
reindex_dend remove_branches_edgePar
TRUE TRUE
remove_leaves_nodePar remove_nodes_nodePar
TRUE TRUE
rotate rotate_DendSer
TRUE TRUE
sample.dendrogram seriate_dendrogram
TRUE TRUE
set set_labels
TRUE TRUE
shuffle sort_2_clusters_vectors
TRUE TRUE
sort_dist_mat sort_levels_values
TRUE TRUE
tanglegram theme_dendro
TRUE TRUE
unbranch unclass_dend
TRUE TRUE
untangle untangle_DendSer
TRUE TRUE
untangle_labels untangle_random_search
TRUE TRUE
untangle_step_rotate_1side untangle_step_rotate_2side
TRUE TRUE
untangle_step_rotate_both_side which_leaf
TRUE TRUE
which_node
TRUE Examples
There are 136 help pages with examples, from 137 (99.27 %).
NEWS
The package has NEWS file and it is current.
License
The package uses .
Installation environment
System Info
| Field | Value |
|---|---|
| Image | rhub/ref-image |
| OS | Ubuntu 24.04.1 LTS |
| Platform | x86_64-pc-linux-gnu |
| System | x86_64, linux-gnu |
| Execution Time | 2025-02-18 03:40:44 UTC |
System information. Table about the system used to check the package.
R Session Info
Information about the R environment and capabilities:
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: UTC
tzcode source: system (glibc)
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
loaded via a namespace (and not attached):
[1] riskreports_0.0.0.9003 compiler_4.4.2 fastmap_1.2.0
[4] cli_3.6.4 htmltools_0.5.8.1 yaml_2.3.10
[7] rmarkdown_2.29 knitr_1.49 jsonlite_1.8.9
[10] xfun_0.50 digest_0.6.37 rlang_1.1.5
[13] evaluate_1.0.3 Platform used:
OS.type file.sep dynlib.ext GUI endian pkgType path.sep
"unix" "/" ".so" "X11" "little" "source" ":"
r_arch
"" R’s capabilities:
jpeg png tiff tcltk X11 aqua
TRUE TRUE TRUE TRUE FALSE FALSE
http/ftp sockets libxml fifo cledit iconv
TRUE TRUE FALSE TRUE FALSE TRUE
NLS Rprof profmem cairo ICU long.double
TRUE TRUE TRUE TRUE TRUE TRUE
libcurl
TRUE External software:
zlib
"1.3"
bzlib
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xz
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libdeflate
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PCRE
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ICU
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TRE
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iconv
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readline
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BLAS
"/usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3" Graphics external software:
cairo cairoFT pango
"1.18.0" "" "1.52.1"
libpng jpeg libtiff
"1.6.43" "8.0" "LIBTIFF, Version 4.5.1" Numerical characteristics of the machine:
double.eps double.neg.eps double.xmin
2.220446e-16 1.110223e-16 2.225074e-308
double.xmax double.base double.digits
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double.rounding double.guard double.ulp.digits
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double.neg.ulp.digits double.exponent double.min.exp
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double.max.exp integer.max sizeof.long
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sizeof.longlong sizeof.longdouble sizeof.pointer
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sizeof.time_t longdouble.eps longdouble.neg.eps
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longdouble.digits longdouble.rounding longdouble.guard
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longdouble.min.exp longdouble.max.exp
-1.638200e+04 1.638400e+04 Random number generation process:
[1] "Mersenne-Twister" "Inversion" "Rejection" Information about the environment
Environmental and options variables affect how package checks and software in it might behave. Here is the environmental variables when running this report
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ACCEPT_EULA Y
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RUNNER_PERFLOG
PHARMAPKGS_EXCLUDED_METRICS
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$browser
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$callr.condition_handler_cli_message
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<bytecode: 0x558a797a5910>
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[1] FALSE
$unzip
[1] "/usr/bin/unzip"
$useFancyQuotes
[1] FALSE
$verbose
[1] FALSE
$warn
[1] 0
$warning.length
[1] 1000
$warnPartialMatchArgs
[1] FALSE
$warnPartialMatchAttr
[1] FALSE
$warnPartialMatchDollar
[1] FALSE
$width
[1] 80