Validation Report - AMR@2.1.1
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 AMR
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 222 |
| has_vignettes | 2 |
| export_help | 222 |
| has_website | TRUE |
| has_maintainer | Matthijs S. Berends m.s.berends@umcg.nl |
| bugs_status | subscript out of bounds |
| size_codebase | 19744 |
| has_source_control | https://github.com/msberends/AMR |
| has_bug_reports_url | 1 |
| downloads_1yr | 22502 |
| reverse_dependencies | 2 |
| has_examples | 0.9827586 |
| dependencies | 0 |
| license | GPL-2 | file LICENSE |
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 |
|---|
Package dependencies
Reverse dependencies
Overall the package has 2 reverse dependencies:
MIC, MIMER
Namespace
Overall the package has 222 exported objects. 218 are documented:
%like_case% %like%
FALSE FALSE
%unlike_case% %unlike%
FALSE FALSE
ab_atc ab_atc_group1
TRUE TRUE
ab_atc_group2 ab_cid
TRUE TRUE
ab_class ab_ddd
TRUE TRUE
ab_ddd_units ab_from_text
TRUE TRUE
ab_group ab_info
TRUE TRUE
ab_loinc ab_name
TRUE TRUE
ab_property ab_selector
TRUE TRUE
ab_synonyms ab_tradenames
TRUE TRUE
ab_url add_custom_antimicrobials
TRUE TRUE
add_custom_microorganisms administrable_iv
TRUE TRUE
administrable_per_os age
TRUE TRUE
age_groups all_antimicrobials
TRUE TRUE
aminoglycosides aminopenicillins
TRUE TRUE
amr_distance_from_row anti_join_microorganisms
TRUE TRUE
antibiogram antifungals
TRUE TRUE
antimicrobials_equal antimycobacterials
TRUE TRUE
as.ab as.av
TRUE TRUE
as.disk as.mic
TRUE TRUE
as.mo as.rsi
TRUE TRUE
as.sir atc_online_ddd
TRUE TRUE
atc_online_ddd_units atc_online_groups
TRUE TRUE
atc_online_property av_atc
TRUE TRUE
av_cid av_ddd
TRUE TRUE
av_ddd_units av_from_text
TRUE TRUE
av_group av_info
TRUE TRUE
av_loinc av_name
TRUE TRUE
av_property av_synonyms
TRUE TRUE
av_tradenames av_url
TRUE TRUE
availability betalactams
TRUE TRUE
brmo bug_drug_combinations
TRUE TRUE
carbapenems cephalosporins
TRUE TRUE
cephalosporins_1st cephalosporins_2nd
TRUE TRUE
cephalosporins_3rd cephalosporins_4th
TRUE TRUE
cephalosporins_5th clear_custom_antimicrobials
TRUE TRUE
clear_custom_microorganisms count_all
TRUE TRUE
count_df count_I
TRUE TRUE
count_IR count_R
TRUE TRUE
count_resistant count_S
TRUE TRUE
count_SI count_susceptible
TRUE TRUE
custom_eucast_rules custom_mdro_guideline
TRUE TRUE
eucast_dosage eucast_exceptional_phenotypes
TRUE TRUE
eucast_rules facet_rsi
TRUE TRUE
facet_sir filter_first_isolate
TRUE TRUE
first_isolate fluoroquinolones
TRUE TRUE
full_join_microorganisms g.test
TRUE TRUE
geom_rsi geom_sir
TRUE TRUE
get_AMR_locale get_episode
TRUE TRUE
get_mo_source ggplot_pca
TRUE TRUE
ggplot_rsi ggplot_rsi_predict
TRUE TRUE
ggplot_sir ggplot_sir_predict
TRUE TRUE
glycopeptides guess_ab_col
TRUE TRUE
inner_join_microorganisms is_new_episode
TRUE TRUE
is_sir_eligible is.ab
TRUE TRUE
is.av is.disk
TRUE TRUE
is.mic is.mo
TRUE TRUE
is.rsi is.rsi.eligible
TRUE TRUE
is.sir italicise_taxonomy
TRUE TRUE
italicize_taxonomy key_antimicrobials
TRUE TRUE
kurtosis labels_rsi_count
TRUE TRUE
labels_sir_count left_join_microorganisms
TRUE TRUE
like lincosamides
TRUE TRUE
lipoglycopeptides macrolides
TRUE TRUE
mdr_cmi2012 mdr_tb
TRUE TRUE
mdro mean_amr_distance
TRUE TRUE
mo_authors mo_class
TRUE TRUE
mo_cleaning_regex mo_current
TRUE TRUE
mo_domain mo_failures
TRUE TRUE
mo_family mo_fullname
TRUE TRUE
mo_gbif mo_genus
TRUE TRUE
mo_gramstain mo_info
TRUE TRUE
mo_is_anaerobic mo_is_gram_negative
TRUE TRUE
mo_is_gram_positive mo_is_intrinsic_resistant
TRUE TRUE
mo_is_yeast mo_kingdom
TRUE TRUE
mo_lpsn mo_matching_score
TRUE TRUE
mo_name mo_order
TRUE TRUE
mo_oxygen_tolerance mo_pathogenicity
TRUE TRUE
mo_phylum mo_property
TRUE TRUE
mo_rank mo_ref
TRUE TRUE
mo_renamed mo_reset_session
TRUE TRUE
mo_shortname mo_snomed
TRUE TRUE
mo_species mo_status
TRUE TRUE
mo_subspecies mo_synonyms
TRUE TRUE
mo_taxonomy mo_type
TRUE TRUE
mo_uncertainties mo_url
TRUE TRUE
mo_year mrgn
TRUE TRUE
n_rsi n_sir
TRUE TRUE
NA_disk_ NA_mic_
TRUE TRUE
NA_rsi_ NA_sir_
TRUE TRUE
not_intrinsic_resistant oxazolidinones
TRUE TRUE
pca penicillins
TRUE TRUE
polymyxins proportion_df
TRUE TRUE
proportion_I proportion_IR
TRUE TRUE
proportion_R proportion_S
TRUE TRUE
proportion_SI quinolones
TRUE TRUE
random_disk random_mic
TRUE TRUE
random_rsi random_sir
TRUE TRUE
reset_AMR_locale resistance
TRUE TRUE
resistance_predict right_join_microorganisms
TRUE TRUE
rsi_df rsi_predict
TRUE TRUE
scale_rsi_colours scale_sir_colours
TRUE TRUE
scale_y_percent semi_join_microorganisms
TRUE TRUE
set_ab_names set_AMR_locale
TRUE TRUE
set_mo_source sir_confidence_interval
TRUE TRUE
sir_df sir_interpretation_history
TRUE TRUE
sir_predict skewness
TRUE TRUE
streptogramins susceptibility
TRUE TRUE
tetracyclines theme_rsi
TRUE TRUE
theme_sir translate_AMR
TRUE TRUE
trimethoprims ureidopenicillins
TRUE TRUE Examples
There are 57 help pages with examples, from 58 (98.28 %).
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 | 2025-02-14 06:53:04 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
/opt/actionarchivecache
AGENT_TOOLSDIRECTORY /opt/hostedtoolcache
ANDROID_HOME /usr/local/lib/android/sdk
ANDROID_NDK /usr/local/lib/android/sdk/ndk/27.2.12479018
ANDROID_NDK_HOME /usr/local/lib/android/sdk/ndk/27.2.12479018
ANDROID_NDK_LATEST_HOME
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ANDROID_NDK_ROOT /usr/local/lib/android/sdk/ndk/27.2.12479018
ANDROID_SDK_ROOT /usr/local/lib/android/sdk
ANT_HOME /usr/share/ant
AZURE_EXTENSION_DIR /opt/az/azcliextensions
BOOTSTRAP_HASKELL_NONINTERACTIVE
1
BUNDLE_EXT linux-amd64.deb
CHROME_BIN /usr/bin/google-chrome
CHROMEWEBDRIVER /usr/local/share/chromedriver-linux64
CI true
CONDA /usr/share/miniconda
DEBIAN_FRONTEND noninteractive
DENO_DOM_PLUGIN /opt/quarto/bin/tools/x86_64/deno_dom/libplugin.so
DENO_NO_UPDATE_CHECK 1
DENO_TLS_CA_STORE system,mozilla
DEPLOYMENT_BASEPATH /opt/runner
DOTNET_MULTILEVEL_LOOKUP
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DOTNET_NOLOGO 1
DOTNET_SKIP_FIRST_TIME_EXPERIENCE
1
EDGEWEBDRIVER /usr/local/share/edge_driver
EDITOR vi
GECKOWEBDRIVER /usr/local/share/gecko_driver
GHCUP_INSTALL_BASE_PREFIX
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GITHUB_ACTION __run
GITHUB_ACTION_REF
GITHUB_ACTION_REPOSITORY
GITHUB_ACTIONS true
GITHUB_ACTOR Gotfrid
GITHUB_ACTOR_ID 8464262
GITHUB_API_URL https://api.github.com
GITHUB_BASE_REF
GITHUB_ENV /home/runner/work/_temp/_runner_file_commands/set_env_f6c8d8cb-0607-4376-9ed1-89a505373e7d
GITHUB_EVENT_NAME workflow_dispatch
GITHUB_EVENT_PATH /home/runner/work/_temp/_github_workflow/event.json
GITHUB_GRAPHQL_URL https://api.github.com/graphql
GITHUB_HEAD_REF
GITHUB_JOB main
GITHUB_OUTPUT /home/runner/work/_temp/_runner_file_commands/set_output_f6c8d8cb-0607-4376-9ed1-89a505373e7d
GITHUB_PATH /home/runner/work/_temp/_runner_file_commands/add_path_f6c8d8cb-0607-4376-9ed1-89a505373e7d
GITHUB_REF refs/heads/main
GITHUB_REF_NAME main
GITHUB_REF_PROTECTED false
GITHUB_REF_TYPE branch
GITHUB_REPOSITORY pharmaR/pharmapkgs
GITHUB_REPOSITORY_ID 798326913
GITHUB_REPOSITORY_OWNER
pharmaR
GITHUB_REPOSITORY_OWNER_ID
42115094
GITHUB_RETENTION_DAYS 90
GITHUB_RUN_ATTEMPT 1
GITHUB_RUN_ID 13323516711
GITHUB_RUN_NUMBER 86
GITHUB_SERVER_URL https://github.com
GITHUB_SHA d790b87bd807399b7640c7bca6ec67a96a6b839e
GITHUB_STATE /home/runner/work/_temp/_runner_file_commands/save_state_f6c8d8cb-0607-4376-9ed1-89a505373e7d
GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_commands/step_summary_f6c8d8cb-0607-4376-9ed1-89a505373e7d
GITHUB_TRIGGERING_ACTOR
Gotfrid
GITHUB_WORKFLOW Update package repositories
GITHUB_WORKFLOW_REF pharmaR/pharmapkgs/.github/workflows/update-repos.yml@refs/heads/main
GITHUB_WORKFLOW_SHA d790b87bd807399b7640c7bca6ec67a96a6b839e
GITHUB_WORKSPACE /home/runner/work/pharmapkgs/pharmapkgs
GOROOT_1_21_X64 /opt/hostedtoolcache/go/1.21.13/x64
GOROOT_1_22_X64 /opt/hostedtoolcache/go/1.22.12/x64
GOROOT_1_23_X64 /opt/hostedtoolcache/go/1.23.6/x64
GRADLE_HOME /usr/share/gradle-8.12.1
HOME /home/runner
HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS
3650
HOMEBREW_NO_AUTO_UPDATE
1
ImageOS ubuntu24
ImageVersion 20250209.1.0
INVOCATION_ID 173b090202a445c984b291dd28076462
JAVA_HOME /usr/lib/jvm/temurin-17-jdk-amd64
JAVA_HOME_11_X64 /usr/lib/jvm/temurin-11-jdk-amd64
JAVA_HOME_17_X64 /usr/lib/jvm/temurin-17-jdk-amd64
JAVA_HOME_21_X64 /usr/lib/jvm/temurin-21-jdk-amd64
JAVA_HOME_8_X64 /usr/lib/jvm/temurin-8-jdk-amd64
JOURNAL_STREAM 8:7727
LANG C.UTF-8
LD_LIBRARY_PATH /opt/R/4.4.2/lib/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/temurin-17-jdk-amd64/lib/server:/opt/R/4.4.2/lib/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/temurin-17-jdk-amd64/lib/server
LN_S ln -s
LOGGER_LOG_LEVEL DEBUG
MAKE make
MEMORY_PRESSURE_WATCH /sys/fs/cgroup/system.slice/runner-provisioner.service/memory.pressure
MEMORY_PRESSURE_WRITE c29tZSAyMDAwMDAgMjAwMDAwMAA=
NOT_CRAN true
NVM_DIR /home/runner/.nvm
PAGER /usr/bin/pager
PATH /snap/bin:/home/runner/.local/bin:/opt/pipx_bin:/home/runner/.cargo/bin:/home/runner/.config/composer/vendor/bin:/usr/local/.ghcup/bin:/home/runner/.dotnet/tools:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
PERFLOG_LOCATION_SETTING
RUNNER_PERFLOG
PHARMAPKGS_EXCLUDED_METRICS
assess_covr_coverage,assess_r_cmd_check
PHARMAPKGS_LIMIT 500
PHARMAPKGS_PLATFORM ubuntu-22.04
PHARMAPKGS_R_VERSION 4.4
PHARMAPKGS_REMOTE_REPO
https://cloud.r-project.org/
PIPX_BIN_DIR /opt/pipx_bin
PIPX_HOME /opt/pipx
PKGCACHE_HTTP_VERSION 2
PKGLOAD_PARENT_TEMPDIR
/tmp/RtmpBUYGbc
POWERSHELL_DISTRIBUTION_CHANNEL
GitHub-Actions-ubuntu24
PROCESSX_PS726d4e8f9e65_1739515981
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 /
QUARTO_SHARE_PATH /opt/quarto/share
R_ARCH
R_BROWSER xdg-open
R_BZIPCMD /usr/bin/bzip2
R_DOC_DIR /opt/R/4.4.2/lib/R/doc
R_GZIPCMD /usr/bin/gzip
R_HOME /opt/R/4.4.2/lib/R
R_INCLUDE_DIR /opt/R/4.4.2/lib/R/include
R_LIB_FOR_PAK /opt/R/4.4.2/lib/R/site-library
R_LIBS_SITE /opt/R/4.4.2/lib/R/site-library
R_LIBS_USER /home/runner/work/_temp/Library
R_PAPERSIZE letter
R_PAPERSIZE_USER letter
R_PDFVIEWER /usr/bin/xdg-open
R_PLATFORM x86_64-pc-linux-gnu
R_PRINTCMD /usr/bin/lpr
R_RD4PDF times,inconsolata,hyper
R_SESSION_TMPDIR /tmp/RtmpPZDv0D
R_SHARE_DIR /opt/R/4.4.2/lib/R/share
R_STRIP_SHARED_LIB strip --strip-unneeded
R_STRIP_STATIC_LIB strip --strip-debug
R_TEXI2DVICMD /usr/bin/texi2dvi
R_UNZIPCMD /usr/bin/unzip
R_ZIPCMD /usr/bin/zip
RUNNER_ARCH X64
RUNNER_ENVIRONMENT github-hosted
RUNNER_NAME GitHub Actions 13
RUNNER_OS Linux
RUNNER_PERFLOG /home/runner/perflog
RUNNER_TEMP /home/runner/work/_temp
RUNNER_TOOL_CACHE /opt/hostedtoolcache
RUNNER_TRACKING_ID github_05609c14-ef8b-4640-9d49-0f5a08371745
RUNNER_USER runner
RUNNER_WORKSPACE /home/runner/work/pharmapkgs
SED /usr/bin/sed
SELENIUM_JAR_PATH /usr/share/java/selenium-server.jar
SGX_AESM_ADDR 1
SHLVL 1
STATS_D true
STATS_D_D true
STATS_D_TC true
STATS_EXT true
STATS_EXTP https://provjobdprod.z13.web.core.windows.net/settings/provjobdsettings-latest/provjobd.data
STATS_PIP false
STATS_RDCL true
STATS_TRP true
STATS_UE true
STATS_V3PS true
STATS_VMD true
STATS_VMFE true
SWIFT_PATH /usr/share/swift/usr/bin
SYSTEMD_EXEC_PID 831
TAR /usr/bin/tar
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
[1] TRUE
$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)
}
}
<bytecode: 0x55b67cd46910>
<environment: namespace:cli>
$catch.script.errors
[1] FALSE
$CBoundsCheck
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$check.bounds
[1] FALSE
$citation.bibtex.max
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$continue
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$contrasts
unordered ordered
"contr.treatment" "contr.poly"
$covr.record_tests
[1] TRUE
$defaultPackages
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$demo.ask
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$deparse.cutoff
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$device
function (width = 7, height = 7, ...)
{
grDevices::pdf(NULL, width, height, ...)
}
<bytecode: 0x55b67de7eea0>
<environment: namespace:knitr>
$device.ask.default
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$digits
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$dvipscmd
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$echo
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$editor
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$encoding
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$example.ask
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$expressions
[1] 5000
$help.search.types
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$help.try.all.packages
[1] FALSE
$htmltools.preserve.raw
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$HTTPUserAgent
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$internet.info
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$keep.parse.data
[1] TRUE
$keep.parse.data.pkgs
[1] FALSE
$keep.source
[1] FALSE
$keep.source.pkgs
[1] FALSE
$knitr.in.progress
[1] TRUE
$locatorBell
[1] TRUE
$mailer
[1] "mailto"
$matprod
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$max.contour.segments
[1] 25000
$max.print
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$menu.graphics
[1] TRUE
$na.action
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$Ncpus
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$nwarnings
[1] 50
$OutDec
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$pager
[1] "/opt/R/4.4.2/lib/R/bin/pager"
$papersize
[1] "letter"
$PCRE_limit_recursion
[1] NA
$PCRE_study
[1] FALSE
$PCRE_use_JIT
[1] TRUE
$pdfviewer
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$pkgType
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$printcmd
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$prompt
[1] "> "
$repos
CRAN
"https://cran.rstudio.com"
$rl_word_breaks
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$rlang_trace_top_env
<environment: R_GlobalEnv>
$scipen
[1] 0
$show.coef.Pvalues
[1] TRUE
$show.error.messages
[1] TRUE
$show.signif.stars
[1] TRUE
$showErrorCalls
[1] TRUE
$showNCalls
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$showWarnCalls
[1] FALSE
$str
$str$strict.width
[1] "no"
$str$digits.d
[1] 3
$str$vec.len
[1] 4
$str$list.len
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$str$deparse.lines
NULL
$str$drop.deparse.attr
[1] TRUE
$str$formatNum
function (x, ...)
format(x, trim = TRUE, drop0trailing = TRUE, ...)
<environment: 0x55b67c21e520>
$str.dendrogram.last
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$texi2dvi
[1] "/usr/bin/texi2dvi"
$tikzMetricsDictionary
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$timeout
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$try.outFile
A connection with
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class "file"
mode "w+b"
text "binary"
opened "opened"
can read "yes"
can write "yes"
$ts.eps
[1] 1e-05
$ts.S.compat
[1] FALSE
$unzip
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$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