Validation Report - breakaway@4.8.4
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 breakaway
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 0 |
| exported_namespace | 45 |
| has_vignettes | 9 |
| export_help | 45 |
| has_website | TRUE |
| has_maintainer | Amy D Willis adwillis@uw.edu |
| bugs_status | subscript out of bounds |
| has_bug_reports_url | 1 |
| downloads_1yr | 11718 |
| reverse_dependencies | 1 |
| has_examples | 1 |
| dependencies | 9 |
| license | GPL-2 |
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 | ggplot2 | Imports |
| 2 | graphics | Imports |
| 3 | lme4 | Imports |
| 4 | magrittr | Imports |
| 5 | MASS | Imports |
| 6 | phyloseq | Imports |
| 7 | stats | Imports |
| 8 | tibble | Imports |
| 9 | utils | Imports |
Package dependencies
Reverse dependencies
Overall the package has 1 reverse dependencies:
VDJdive
Namespace
Overall the package has 45 exported objects. 44 are documented:
%>% alpha_estimate
FALSE TRUE
alpha_estimates betta
TRUE TRUE
betta_lincom betta_pic
TRUE TRUE
betta_random breakaway
TRUE TRUE
breakaway_nof1 build_frequency_count_tables
TRUE TRUE
chao_bunge chao_shen
TRUE TRUE
chao1 chao1_bc
TRUE TRUE
convert F_test
TRUE TRUE
good_turing kemp
TRUE TRUE
make_design_matrix make_frequency_count_table
TRUE TRUE
objective_bayes_geometric objective_bayes_mixedgeo
TRUE TRUE
objective_bayes_negbin objective_bayes_poisson
TRUE TRUE
poisson_model poisson_model_nof1
TRUE TRUE
proportions_instead rnbinomtable
TRUE TRUE
rztnbinomtable sample_inverse_simpson
TRUE TRUE
sample_richness sample_shannon
TRUE TRUE
sample_shannon_e sample_simpson
TRUE TRUE
sample_size_estimate sample_size_figure
TRUE TRUE
test_submodel true_gini
TRUE TRUE
true_hill true_inverse_simpson
TRUE TRUE
true_shannon true_shannon_e
TRUE TRUE
true_simpson wlrm_transformed
TRUE TRUE
wlrm_untransformed
TRUE Examples
There are 58 help pages with examples, from 58 (100.00 %).
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 | 2025-02-15 04:42:40 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
"1.0.8, 13-Jul-2019"
xz
"5.4.5"
libdeflate
"1.19"
PCRE
"10.42 2022-12-11"
ICU
"74.2"
TRE
"TRE 0.8.0 R_fixes (BSD)"
iconv
"glibc 2.39"
readline
"8.2"
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
1.797693e+308 2.000000e+00 5.300000e+01
double.rounding double.guard double.ulp.digits
5.000000e+00 0.000000e+00 -5.200000e+01
double.neg.ulp.digits double.exponent double.min.exp
-5.300000e+01 1.100000e+01 -1.022000e+03
double.max.exp integer.max sizeof.long
1.024000e+03 2.147484e+09 8.000000e+00
sizeof.longlong sizeof.longdouble sizeof.pointer
8.000000e+00 1.600000e+01 8.000000e+00
sizeof.time_t longdouble.eps longdouble.neg.eps
8.000000e+00 1.084202e-19 5.421011e-20
longdouble.digits longdouble.rounding longdouble.guard
6.400000e+01 5.000000e+00 0.000000e+00
longdouble.ulp.digits longdouble.neg.ulp.digits longdouble.exponent
-6.300000e+01 -6.400000e+01 1.500000e+01
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
_R_CHECK_SYSTEM_CLOCK_
FALSE
ACCEPT_EULA Y
ACTIONS_RUNNER_ACTION_ARCHIVE_CACHE
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ANT_HOME /usr/share/ant
AZURE_EXTENSION_DIR /opt/az/azcliextensions
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GITHUB_TRIGGERING_ACTOR
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GRADLE_HOME /usr/share/gradle-8.12.1
HOME /home/runner
HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS
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HOMEBREW_NO_AUTO_UPDATE
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ImageOS ubuntu24
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LOGGER_LOG_LEVEL DEBUG
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PERFLOG_LOCATION_SETTING
RUNNER_PERFLOG
PHARMAPKGS_EXCLUDED_METRICS
assess_covr_coverage,assess_r_cmd_check
PHARMAPKGS_LIMIT 1000
PHARMAPKGS_PLATFORM ubuntu-22.04
PHARMAPKGS_R_VERSION 4.4
PHARMAPKGS_REMOTE_REPO
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PIPX_HOME /opt/pipx
PKGCACHE_HTTP_VERSION 2
PKGLOAD_PARENT_TEMPDIR
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POWERSHELL_DISTRIBUTION_CHANNEL
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YES
PWD /home/runner/work/pharmapkgs/pharmapkgs
QUARTO_BIN_PATH /opt/quarto/bin
QUARTO_DENO /opt/quarto/bin/tools/x86_64/deno
QUARTO_DOCUMENT_PATH /home/runner/work/pharmapkgs/pharmapkgs/inst/report
QUARTO_PROFILE
QUARTO_PROJECT_DIR /home/runner/work/pharmapkgs/pharmapkgs
QUARTO_PROJECT_ROOT /home/runner/work/pharmapkgs/pharmapkgs
QUARTO_ROOT /
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R_PLATFORM x86_64-pc-linux-gnu
R_PRINTCMD /usr/bin/lpr
R_RD4PDF times,inconsolata,hyper
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RUNNER_ARCH X64
RUNNER_ENVIRONMENT github-hosted
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SGX_AESM_ADDR 1
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STATS_D true
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TZ UTC
USER runner
VCPKG_INSTALLATION_ROOT
/usr/local/share/vcpkg
XDG_CONFIG_HOME /home/runner/.config
XDG_RUNTIME_DIR /run/user/1001These are the options set to generate the report:
$add.smooth
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$bitmapType
[1] "cairo"
$browser
[1] "xdg-open"
$browserNLdisabled
[1] FALSE
$callr.condition_handler_cli_message
function (msg)
{
custom_handler <- getOption("cli.default_handler")
if (is.function(custom_handler)) {
custom_handler(msg)
}
else {
cli_server_default(msg)
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}
<bytecode: 0x55894c075910>
<environment: namespace:cli>
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unordered ordered
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$demo.ask
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$device
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{
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<bytecode: 0x55894c078b38>
<environment: namespace:knitr>
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$internet.info
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$locatorBell
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$matprod
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$pdfviewer
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$printcmd
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$prompt
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$repos
CRAN
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$rl_word_breaks
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$rlang_trace_top_env
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$scipen
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$show.coef.Pvalues
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$show.error.messages
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$show.signif.stars
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$showErrorCalls
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$showNCalls
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$str
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$str$digits.d
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$str$vec.len
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$str$list.len
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$str$deparse.lines
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$str$drop.deparse.attr
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$str$formatNum
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format(x, trim = TRUE, drop0trailing = TRUE, ...)
<environment: 0x55894b54d520>
$str.dendrogram.last
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$texi2dvi
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$tikzMetricsDictionary
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$try.outFile
A connection with
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mode "w+b"
text "binary"
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can read "yes"
can write "yes"
$ts.eps
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$ts.S.compat
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$unzip
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$warn
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$width
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