Validation Report - chillR@0.76
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 chillR
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 0 |
| exported_namespace | 106 |
| has_vignettes | 10 |
| export_help | 106 |
| has_website | FALSE |
| has_maintainer | Eike Luedeling eike@eikeluedeling.com |
| bugs_status | package DESCRIPTION does not have a BugReports field |
| has_bug_reports_url | 0 |
| downloads_1yr | 12029 |
| reverse_dependencies | 2 |
| has_examples | 1 |
| dependencies | 35 |
| license | 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 | assertthat | Imports |
| 2 | dplyr | Imports |
| 3 | ecmwfr | Imports |
| 4 | fields | Imports |
| 5 | GenSA | Imports |
| 6 | ggplot2 | Imports |
| 7 | graphics | Imports |
| 8 | grDevices | Imports |
| 9 | httr | Imports |
| 10 | jsonlite | Imports |
| 11 | Kendall | Imports |
| 12 | keyring | Imports |
| 13 | lubridate | Imports |
| 14 | magrittr | Imports |
| 15 | metR | Imports |
| 16 | patchwork | Imports |
| 17 | pls | Imports |
| 18 | plyr | Imports |
| 19 | progress | Imports |
| 20 | purrr | Imports |
| 21 | R.utils | Imports |
| 22 | raster | Imports |
| 23 | Rcpp | Imports |
| 24 | RCurl | Imports |
| 25 | readxl | Imports |
| 26 | reshape2 | Imports |
| 27 | rlang | Imports |
| 28 | RMAWGEN | Imports |
| 29 | scales | Imports |
| 30 | stats | Imports |
| 31 | stringr | Imports |
| 32 | tidyr | Imports |
| 33 | utils | Imports |
| 34 | XML | Imports |
| 35 | Rcpp | LinkingTo |
Package dependencies
Reverse dependencies
Overall the package has 2 reverse dependencies:
ChillModels, decisionSupport
Namespace
Overall the package has 106 exported objects. 106 are documented:
add_date
TRUE
bloom_prediction
TRUE
bloom_prediction2
TRUE
bloom_prediction3
TRUE
bootstrap.phenologyFit
TRUE
check_temperature_record
TRUE
check_temperature_scenario
TRUE
chile_agromet2chillR
TRUE
chilling
TRUE
Chilling_Hours
TRUE
chilling_hourtable
TRUE
color_bar_maker
TRUE
convert_scen_information
TRUE
daily_chill
TRUE
Date2YEARMODA
TRUE
daylength
TRUE
download_baseline_cmip6_ecmwfr
TRUE
download_cmip6_ecmwfr
TRUE
Dynamic_Model
TRUE
DynModel_driver
TRUE
Empirical_daily_temperature_curve
TRUE
Empirical_hourly_temperatures
TRUE
extract_cmip6_data
TRUE
extract_differences_between_characters
TRUE
extract_temperatures_from_grids
TRUE
filter_temperatures
TRUE
fix_weather
TRUE
GDD
TRUE
GDH
TRUE
GDH_model
TRUE
gen_rel_change_scenario
TRUE
genSeason
TRUE
genSeasonList
TRUE
get_last_date
TRUE
get_weather
TRUE
getClimateWizard_scenarios
TRUE
getClimateWizardData
TRUE
handle_cimis
TRUE
handle_dwd
TRUE
handle_dwd_old
TRUE
handle_gsod
TRUE
handle_gsod_old
TRUE
handle_ucipm
TRUE
identify_common_string
TRUE
interpolate_gaps
TRUE
interpolate_gaps_hourly
TRUE
JDay_count
TRUE
JDay_earlier
TRUE
JDay_later
TRUE
leap_year
TRUE
load_ClimateWizard_scenarios
TRUE
load_temperature_scenarios
TRUE
make_all_day_table
TRUE
make_california_UCIPM_station_list
TRUE
make_chill_plot
TRUE
make_climate_scenario
TRUE
make_climate_scenario_from_files
TRUE
make_daily_chill_figures
TRUE
make_daily_chill_plot
TRUE
make_daily_chill_plot2
TRUE
make_hourly_temps
TRUE
make_JDay
TRUE
make_multi_pheno_trend_plot
TRUE
make_pheno_trend_plot
TRUE
ordered_climate_list
TRUE
patch_daily_temperatures
TRUE
patch_daily_temps
TRUE
PhenoFlex
TRUE
PhenoFlex_fixedDynModelGAUSSwrapper
TRUE
PhenoFlex_fixedDynModelwrapper
TRUE
PhenoFlex_GAUSSwrapper
TRUE
PhenoFlex_GDHwrapper
TRUE
phenologyFit
TRUE
phenologyFitter
TRUE
plot_climate_scenarios
TRUE
plot_phenology_trends
TRUE
plot_PLS
TRUE
plot_scenarios
TRUE
PLS_chill_force
TRUE
PLS_pheno
TRUE
read_tab
TRUE
RMSEP
TRUE
RPD
TRUE
RPIQ
TRUE
runn_mean
TRUE
runn_mean_pred
TRUE
save_temperature_scenarios
TRUE
select_by_file_extension
TRUE
stack_hourly_temps
TRUE
stage_transitions
TRUE
step_model
TRUE
StepChill_Wrapper
TRUE
temperature_generation
TRUE
temperature_scenario_baseline_adjustment
TRUE
temperature_scenario_from_records
TRUE
tempResponse
TRUE
tempResponse_daily_list
TRUE
tempResponse_hourtable
TRUE
test_if_equal
TRUE
UniChill_Wrapper
TRUE
UnifiedModel_Wrapper
TRUE
UniForce_Wrapper
TRUE
Utah_Model
TRUE
VIP
TRUE
weather2chillR
TRUE
YEARMODA2Date
TRUE Examples
There are 122 help pages with examples, from 122 (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 | 2025-02-16 04:13:35 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
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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 llrs-roche
GITHUB_ACTOR_ID 185338939
GITHUB_API_URL https://api.github.com
GITHUB_BASE_REF
GITHUB_ENV /home/runner/work/_temp/_runner_file_commands/set_env_6ba12b84-2f44-4ad5-be34-dae80230865f
GITHUB_EVENT_NAME schedule
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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_6ba12b84-2f44-4ad5-be34-dae80230865f
GITHUB_PATH /home/runner/work/_temp/_runner_file_commands/add_path_6ba12b84-2f44-4ad5-be34-dae80230865f
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 13351230359
GITHUB_RUN_NUMBER 93
GITHUB_SERVER_URL https://github.com
GITHUB_SHA b7796ef4941f135c4d61c83d399bb9fa3a477379
GITHUB_STATE /home/runner/work/_temp/_runner_file_commands/save_state_6ba12b84-2f44-4ad5-be34-dae80230865f
GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_commands/step_summary_6ba12b84-2f44-4ad5-be34-dae80230865f
GITHUB_TRIGGERING_ACTOR
llrs-roche
GITHUB_WORKFLOW Update package repositories
GITHUB_WORKFLOW_REF pharmaR/pharmapkgs/.github/workflows/update-repos.yml@refs/heads/main
GITHUB_WORKFLOW_SHA b7796ef4941f135c4d61c83d399bb9fa3a477379
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 cea0ff53850b49ce839e8b7d02d05041
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 8:7454
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 1000
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/RtmpCk6Ofc
POWERSHELL_DISTRIBUTION_CHANNEL
GitHub-Actions-ubuntu24
PROCESSX_PS1bc379e775d6_1739679210
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/RtmpKyqCE7
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 9
RUNNER_OS Linux
RUNNER_PERFLOG /home/runner/perflog
RUNNER_TEMP /home/runner/work/_temp
RUNNER_TOOL_CACHE /opt/hostedtoolcache
RUNNER_TRACKING_ID github_d0120492-4873-4b13-9ede-fb6d0d82420b
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
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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 829
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: 0x55adb4e97910>
<environment: namespace:cli>
$catch.script.errors
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$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"
$covr.record_tests
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$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: 0x55adb4617640>
<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
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$help.search.types
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$help.try.all.packages
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$htmltools.preserve.raw
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$HTTPUserAgent
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$internet.info
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$keep.parse.data
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$keep.parse.data.pkgs
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$keep.source
[1] FALSE
$keep.source.pkgs
[1] FALSE
$knitr.in.progress
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$locatorBell
[1] TRUE
$mailer
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$matprod
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$max.contour.segments
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$max.print
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$na.action
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$Ncpus
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$nwarnings
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$OutDec
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$papersize
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$PCRE_limit_recursion
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$PCRE_study
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$PCRE_use_JIT
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$pdfviewer
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$pkgType
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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
<environment: R_GlobalEnv>
$scipen
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$show.coef.Pvalues
[1] TRUE
$show.error.messages
[1] TRUE
$show.signif.stars
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$showErrorCalls
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$showNCalls
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$showWarnCalls
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$str
$str$strict.width
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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
NULL
$str$drop.deparse.attr
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$str$formatNum
function (x, ...)
format(x, trim = TRUE, drop0trailing = TRUE, ...)
<environment: 0x55adb436f520>
$str.dendrogram.last
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$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
$warn
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$warning.length
[1] 1000
$warnPartialMatchArgs
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$warnPartialMatchAttr
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$warnPartialMatchDollar
[1] FALSE
$width
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