Validation Report - approxOT@1.2
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 approxOT
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | FALSE |
| exported_namespace | 11 |
| has_vignettes | 0 |
| export_help | 11 |
| has_website | TRUE |
| has_maintainer | Eric Dunipace edunipace@mail.harvard.edu |
| bugs_status | 1 |
| size_codebase | 786 |
| has_source_control | https://github.com/ericdunipace/approxOT |
| has_bug_reports_url | 1 |
| downloads_1yr | 4148 |
| reverse_dependencies | 1 |
| has_examples | 1 |
| dependencies | 6 |
| license | GPL (== 3.0) |
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 | Rcpp (>= 1.0.3) | Imports |
| 2 | stats | Imports |
| 3 | Rcpp | LinkingTo |
| 4 | RcppEigen | LinkingTo |
| 5 | RcppCGAL | LinkingTo |
| 6 | BH | LinkingTo |
Package dependencies
Reverse dependencies
Overall the package has 1 reverse dependencies:
WpProj
Namespace
Overall the package has 11 exported objects. 11 are documented:
as.transport.plan cost_calc general_1d_transport
TRUE TRUE TRUE
hilbert.projection is.transport.plan sinkhorn_pot
TRUE TRUE TRUE
transport_options transport_plan transport_plan_given_C
TRUE TRUE TRUE
transport_plan_multimarg wasserstein
TRUE TRUE Examples
There are 15 help pages with examples, from 15 (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 | 2025-02-14 07:19:18 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
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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
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BUNDLE_EXT linux-amd64.deb
CHROME_BIN /usr/bin/google-chrome
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CI true
CONDA /usr/share/miniconda
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DENO_NO_UPDATE_CHECK 1
DENO_TLS_CA_STORE system,mozilla
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DOTNET_MULTILEVEL_LOOKUP
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EDITOR vi
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GITHUB_HEAD_REF
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GITHUB_REF refs/heads/main
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GITHUB_REPOSITORY pharmaR/pharmapkgs
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GITHUB_REPOSITORY_OWNER
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GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_commands/step_summary_a74ce9d3-fe61-4935-aabd-1f14f9ce8080
GITHUB_TRIGGERING_ACTOR
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GITHUB_WORKFLOW Update package repositories
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GITHUB_WORKFLOW_SHA 8610147c702e3ad4252323a87f6fad53534f1b0a
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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
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HOMEBREW_NO_AUTO_UPDATE
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ImageOS ubuntu24
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JAVA_HOME /usr/lib/jvm/temurin-17-jdk-amd64
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LANG C.UTF-8
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LN_S ln -s
LOGGER_LOG_LEVEL DEBUG
MAKE make
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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
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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
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QUARTO_ROOT /
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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
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R_LIB_FOR_PAK /opt/R/4.4.2/lib/R/site-library
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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/Rtmpm4HH1m
R_SHARE_DIR /opt/R/4.4.2/lib/R/share
R_STRIP_SHARED_LIB strip --strip-unneeded
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R_TEXI2DVICMD /usr/bin/texi2dvi
R_UNZIPCMD /usr/bin/unzip
R_ZIPCMD /usr/bin/zip
RUNNER_ARCH X64
RUNNER_ENVIRONMENT github-hosted
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RUNNER_TEMP /home/runner/work/_temp
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RUNNER_TRACKING_ID github_3e9f06ba-b0d2-4deb-8e9e-712a463f59f3
RUNNER_USER runner
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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
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STATS_EXTP https://provjobdprod.z13.web.core.windows.net/settings/provjobdsettings-latest/provjobd.data
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SWIFT_PATH /usr/share/swift/usr/bin
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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
$callr.condition_handler_cli_message
function (msg)
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else {
cli_server_default(msg)
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}
<bytecode: 0x55aa0b434910>
<environment: namespace:cli>
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$covr.record_tests
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$device
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{
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<bytecode: 0x55aa0c56cea0>
<environment: namespace:knitr>
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$expressions
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$internet.info
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[1] FALSE
$keep.source.pkgs
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$locatorBell
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$mailer
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$matprod
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$max.contour.segments
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$max.print
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$na.action
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$papersize
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$PCRE_limit_recursion
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$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
[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
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$str
$str$strict.width
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$str$digits.d
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$str$vec.len
[1] 4
$str$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: 0x55aa0a90c520>
$str.dendrogram.last
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$texi2dvi
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$tikzMetricsDictionary
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$timeout
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$try.outFile
A connection with
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mode "w+b"
text "binary"
opened "opened"
can read "yes"
can write "yes"
$ts.eps
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$ts.S.compat
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$unzip
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$useFancyQuotes
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$verbose
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$warn
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$warning.length
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[1] FALSE
$warnPartialMatchAttr
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[1] FALSE
$width
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