Validation Report - fmcmc@0.5.2
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 fmcmc
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 56 |
| has_vignettes | 6 |
| export_help | 56 |
| has_website | TRUE |
| has_maintainer | George Vega Yon g.vegayon@gmail.com |
| bugs_status | subscript out of bounds |
| assess_size_codebase | 1777 |
| has_source_control | https://github.com/USCbiostats/fmcmc |
| has_bug_reports_url | 1 |
| downloads_1yr | 3866 |
| reverse_dependencies | 2 |
| has_examples | 1 |
| dependencies | 6 |
| license | MIT + 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 | |
|---|---|---|
| 1 | parallel | Imports |
| 2 | coda | Imports |
| 3 | stats | Imports |
| 4 | methods | Imports |
| 5 | MASS | Imports |
| 6 | Matrix | Imports |
Package dependencies
Reverse dependencies
Overall the package has 2 reverse dependencies:
aphylo, ergmito
Namespace
Overall the package has 56 exported objects. 56 are documented:
append_chains check_initial convergence_auto
TRUE TRUE TRUE
convergence_data_get convergence_data_set convergence_gelman
TRUE TRUE TRUE
convergence_geweke convergence_heildel convergence_msg_get
TRUE TRUE TRUE
convergence_msg_set cov_recursive get_
TRUE TRUE TRUE
get_burnin get_chain_id get_cl
TRUE TRUE TRUE
get_conv_checker get_draws get_elapsed
TRUE TRUE TRUE
get_fun get_initial get_kernel
TRUE TRUE TRUE
get_logpost get_multicore get_nchains
TRUE TRUE TRUE
get_nsteps get_progress get_seed
TRUE TRUE TRUE
get_thin get_userdata ith_step
TRUE TRUE TRUE
kernel_adapt kernel_am kernel_new
TRUE TRUE TRUE
kernel_nmirror kernel_normal kernel_normal_reflective
TRUE TRUE TRUE
kernel_ram kernel_umirror kernel_unif
TRUE TRUE TRUE
kernel_unif_reflective last_ LAST_CONV_CHECK
TRUE TRUE TRUE
last_conv_checker last_elapsed last_kernel
TRUE TRUE TRUE
LAST_MCMC last_nchains last_nsteps
TRUE TRUE TRUE
MCMC MCMC_OUTPUT MCMC_without_conv_checker
TRUE TRUE TRUE
mean_recursive new_progress_bar plan_update_sequence
TRUE TRUE TRUE
reflect_on_boundaries set_userdata
TRUE TRUE Examples
There are 18 help pages with examples, from 18 (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 | 2025-03-04 08:54:06 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_1.49 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
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ANT_HOME /usr/share/ant
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BOOTSTRAP_HASKELL_NONINTERACTIVE
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GITHUB_TRIGGERING_ACTOR
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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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INVOCATION_ID 34f2cdb0c0f043c99198fad4c4387f28
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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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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
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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
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QUARTO_PROJECT_ROOT /home/runner/work/pharmapkgs/pharmapkgs
QUARTO_ROOT /
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R_PLATFORM x86_64-pc-linux-gnu
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R_RD4PDF times,inconsolata,hyper
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RUNNER_ARCH X64
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TZ UTC
USER runner
VCPKG_INSTALLATION_ROOT
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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
$callr.condition_handler_cli_message
function (msg)
{
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else {
cli_server_default(msg)
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}
<bytecode: 0x555f76070330>
<environment: namespace:cli>
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<bytecode: 0x555f7563eea0>
<environment: namespace:knitr>
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$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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$str
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$str$list.len
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$str$deparse.lines
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$str$drop.deparse.attr
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$str$formatNum
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<environment: 0x555f7554b688>
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$tikzMetricsDictionary
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A connection with
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can write "yes"
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