Validation Report - GB2@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 GB2
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 0 |
| exported_namespace | 92 |
| has_vignettes | 0 |
| export_help | 92 |
| has_website | FALSE |
| has_maintainer | Desislava Nedyalkova desislava.nedyalkova@gmail.com |
| bugs_status | package DESCRIPTION does not have a BugReports field |
| assess_size_codebase | 1268 |
| has_bug_reports_url | 0 |
| downloads_1yr | 3918 |
| reverse_dependencies | 4 |
| has_examples | 1 |
| dependencies | 6 |
| 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 | cubature | Imports |
| 2 | hypergeo | Imports |
| 3 | laeken | Imports |
| 4 | numDeriv | Imports |
| 5 | stats | Imports |
| 6 | survey | Imports |
Package dependencies
Reverse dependencies
Overall the package has 4 reverse dependencies:
GB2group, Kernelheaping, PRSim, sdPrior
Namespace
Overall the package has 92 exported objects. 92 are documented:
arpr.cgb2 arpr.gb2 arpt.cgb2 arpt.gb2 contindic.gb2
TRUE TRUE TRUE TRUE TRUE
contprof.gb2 d2logf.gb2 dcgb2 derivind.cgb2 derivind.gb2
TRUE TRUE TRUE TRUE TRUE
desvar.cavgb2 desvar.cgb2 dgb2 dl.cgb2 dlogf.gb2
TRUE TRUE TRUE TRUE TRUE
dplot.cavgb2 dplot.cgb2 el.gb2 fg.cgb2 fisk
TRUE TRUE TRUE TRUE TRUE
fiskh gb2.gini gini.b2 gini.dag gini.gb2
TRUE TRUE TRUE TRUE TRUE
gini.sm hess.cavgb2 hess.cgb2 incompl.cgb2 incompl.gb2
TRUE TRUE TRUE TRUE TRUE
info.gb2 kl.gb2 lambda0.cavgb2 logf.gb2 logl.cavgb2
TRUE TRUE TRUE TRUE TRUE
logl.cgb2 loglh.gb2 loglp.gb2 main.cgb2 main.emp
TRUE TRUE TRUE TRUE TRUE
main.gb2 main2.gb2 mkl.cgb2 ml.cavgb2 ml.cgb2
TRUE TRUE TRUE TRUE TRUE
ml.gb2 mlfit.gb2 mlh.gb2 moment.cgb2 moment.gb2
TRUE TRUE TRUE TRUE TRUE
nlsfit.gb2 pcgb2 pgb2 pkl.cavgb2 pl.cgb2
TRUE TRUE TRUE TRUE TRUE
plotsML.gb2 pofv.cgb2 prcgb2 prof.gb2 proflogl.gb2
TRUE TRUE TRUE TRUE TRUE
profml.gb2 profscores.gb2 qcgb2 qgb2 qsr.cgb2
TRUE TRUE TRUE TRUE TRUE
qsr.gb2 rcgb2 rgb2 rmpg.cgb2 rmpg.gb2
TRUE TRUE TRUE TRUE TRUE
robwts saveplot scores.cavgb2 scores.cgb2 scoresh.gb2
TRUE TRUE TRUE TRUE TRUE
scoresp.gb2 scoreU.cavgb2 scoreU.cgb2 scorez.cavgb2 sl.gb2
TRUE TRUE TRUE TRUE TRUE
Thomae varscore.cavgb2 varscore.cgb2 varscore.gb2 veind.cavgb2
TRUE TRUE TRUE TRUE TRUE
veind.cgb2 veind.gb2 vepar.cavgb2 vepar.cgb2 vepar.gb2
TRUE TRUE TRUE TRUE TRUE
vl.gb2 vofp.cgb2
TRUE TRUE Examples
There are 28 help pages with examples, from 28 (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 24.04.2 LTS |
| Platform | x86_64-pc-linux-gnu |
| System | x86_64, linux-gnu |
| Execution Time | 2025-03-20 03:27:58 UTC |
System information. Table about the system used to check the package.
R Session Info
Information about the R environment and capabilities:
R version 4.4.3 (2025-02-28)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.2 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_4.4.3 fastmap_1.2.0
[4] cli_3.6.4 htmltools_0.5.8.1 yaml_2.3.10
[7] rmarkdown_2.29 knitr_1.50 jsonlite_1.9.1
[10] xfun_0.51 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
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ANDROID_HOME /usr/local/lib/android/sdk
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ANDROID_NDK_LATEST_HOME
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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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CI true
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DOTNET_MULTILEVEL_LOOKUP
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GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_commands/step_summary_e2677645-7247-452d-9419-c7d8ef0de7ca
GITHUB_TRIGGERING_ACTOR
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GITHUB_WORKFLOW Update package repositories
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GITHUB_WORKFLOW_SHA 120caef21b98097a79a664a46bd1302fa5a31744
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/1.23.7/x64
GRADLE_HOME /usr/share/gradle-8.13
HOME /home/runner
HOMEBREW_CLEANUP_PERIODIC_FULL_DAYS
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HOMEBREW_NO_AUTO_UPDATE
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JOURNAL_STREAM 8:6584
LANG C.UTF-8
LD_LIBRARY_PATH /opt/R/4.4.3/lib/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/temurin-17-jdk-amd64/lib/server:/opt/R/4.4.3/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
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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 100
PHARMAPKGS_PLATFORM ubuntu-22.04
PHARMAPKGS_R_VERSION 4.4
PHARMAPKGS_REMOTE_REPO
https://cloud.r-project.org/
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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 /
QUARTO_SHARE_PATH /opt/quarto/share
R_ARCH
R_BROWSER xdg-open
R_BZIPCMD /usr/bin/bzip2
R_DOC_DIR /opt/R/4.4.3/lib/R/doc
R_GZIPCMD /usr/bin/gzip
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R_PAPERSIZE letter
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R_PLATFORM x86_64-pc-linux-gnu
R_PRINTCMD /usr/bin/lpr
R_RD4PDF times,inconsolata,hyper
R_SESSION_TMPDIR /tmp/RtmpqsJ9Pk
R_SHARE_DIR /opt/R/4.4.3/lib/R/share
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R_TEXI2DVICMD /usr/bin/texi2dvi
R_UNZIPCMD /usr/bin/unzip
R_ZIPCMD /usr/bin/zip
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RUNNER_ENVIRONMENT github-hosted
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SED /usr/bin/sed
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SGX_AESM_ADDR 1
SHLVL 1
STATS_D true
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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)
{
custom_handler <- getOption("cli.default_handler")
if (is.function(custom_handler)) {
custom_handler(msg)
}
else {
cli_server_default(msg)
}
}
<bytecode: 0x558bd7502330>
<environment: namespace:cli>
$catch.script.errors
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$continue
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$contrasts
unordered ordered
"contr.treatment" "contr.poly"
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$demo.ask
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$device
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{
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<bytecode: 0x558bd6ad97d0>
<environment: namespace:knitr>
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$locatorBell
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$matprod
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CRAN
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$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
[1] TRUE
$show.signif.stars
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$showErrorCalls
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$str
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$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: 0x558bd69dd688>
$str.dendrogram.last
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$texi2dvi
[1] "/usr/bin/texi2dvi"
$tikzMetricsDictionary
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$try.outFile
A connection with
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can read "yes"
can write "yes"
$ts.eps
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$unzip
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$width
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