Validation Report - apsimx@2.8.235
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 apsimx
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | FALSE |
| exported_namespace | 86 |
| has_vignettes | 8 |
| export_help | 86 |
| has_website | FALSE |
| has_maintainer | Fernando Miguez femiguez@iastate.edu |
| bugs_status | 0.6333333 |
| assess_size_codebase | 14028 |
| has_bug_reports_url | 1 |
| downloads_1yr | 9602 |
| reverse_dependencies | 3 |
| has_examples | 1 |
| dependencies | 7 |
| 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 | DBI | Imports |
| 2 | jsonlite | Imports |
| 3 | knitr | Imports |
| 4 | RSQLite | Imports |
| 5 | tools | Imports |
| 6 | utils | Imports |
| 7 | xml2 | Imports |
Package dependencies
Reverse dependencies
Overall the package has 3 reverse dependencies:
metrica, pacu, weatherOz
Namespace
Overall the package has 86 exported objects. 86 are documented:
add_column_apsim_met amp_apsim_met
TRUE TRUE
apsim apsim_example
TRUE TRUE
apsim_options apsim_version
TRUE TRUE
apsim.options apsimx
TRUE TRUE
apsimx_example apsimx_filetype
TRUE TRUE
apsimx_options apsimx_soil_profile
TRUE TRUE
apsimx.options as_apsim_met
TRUE TRUE
auto_detect_apsim_examples auto_detect_apsimx_examples
TRUE TRUE
available_water_content carbon_stocks
TRUE TRUE
check_apsim_met check_apsimx
TRUE TRUE
check_apsimx_soil_profile compare_apsim
TRUE TRUE
compare_apsim_met compare_apsim_soil_profile
TRUE TRUE
date2doy doy2date
TRUE TRUE
edit_apsim edit_apsim_replace_soil_profile
TRUE TRUE
edit_apsim_xml edit_apsimx
TRUE TRUE
edit_apsimx_batch edit_apsimx_replace_soil_profile
TRUE TRUE
edit_apsimx_replacement extract_data_apsimx
TRUE TRUE
extract_values_apsimx get_apsimx_json
TRUE TRUE
get_chirps_apsim_met get_daymet_apsim_met
TRUE TRUE
get_daymet2_apsim_met get_gsod_apsim_met
TRUE TRUE
get_iem_apsim_met get_iemre_apsim_met
TRUE TRUE
get_isric_soil_profile get_power_apsim_met
TRUE TRUE
get_slga_soil get_slga_soil_profile
TRUE TRUE
get_ssurgo_soil_profile get_ssurgo_tables
TRUE TRUE
get_worldmodeler_apsim_met get_worldmodeler_soil_profile
TRUE TRUE
grep_json_list impute_apsim_met
TRUE TRUE
initialwater_parms insert_replacement_node
TRUE TRUE
inspect_apsim inspect_apsim_xml
TRUE TRUE
inspect_apsimx inspect_apsimx_json
TRUE TRUE
inspect_apsimx_replacement mcmc.apsim.env
TRUE TRUE
mcmc.apsimx.env napad_apsim_met
TRUE TRUE
optim_apsim optim_apsimx
TRUE TRUE
read_apsim read_apsim_all
TRUE TRUE
read_apsim_met read_apsim_soils
TRUE TRUE
read_apsimx read_apsimx_all
TRUE TRUE
remove_column_apsim_met sens_apsim
TRUE TRUE
sens_apsimx soilorganicmatter_parms
TRUE TRUE
soilwat_parms solutes_parms
TRUE TRUE
ssurgo2sp swim_parms
TRUE TRUE
tav_apsim_met tt_apsim_met
TRUE TRUE
unit_conv view_apsim
TRUE TRUE
view_apsim_xml view_apsimx
TRUE TRUE
write_apsim_met xargs_apsimx
TRUE TRUE Examples
There are 88 help pages with examples, from 88 (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 | 2025-03-14 03:26:24 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
/opt/actionarchivecache
AGENT_TOOLSDIRECTORY /opt/hostedtoolcache
ANDROID_HOME /usr/local/lib/android/sdk
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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
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DENO_TLS_CA_STORE system,mozilla
DEPLOYMENT_BASEPATH /opt/runner
DOTNET_MULTILEVEL_LOOKUP
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GITHUB_PATH /home/runner/work/_temp/_runner_file_commands/add_path_35fa6bbb-61f7-46c6-bfa7-b11c9a45dd6b
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GITHUB_REF_TYPE branch
GITHUB_REPOSITORY pharmaR/pharmapkgs
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GITHUB_REPOSITORY_OWNER
pharmaR
GITHUB_REPOSITORY_OWNER_ID
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GITHUB_RUN_ATTEMPT 1
GITHUB_RUN_ID 13849192039
GITHUB_RUN_NUMBER 128
GITHUB_SERVER_URL https://github.com
GITHUB_SHA cd2aa3d897be31c10b200e93da24712e8b0fbab1
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GITHUB_STEP_SUMMARY /home/runner/work/_temp/_runner_file_commands/step_summary_35fa6bbb-61f7-46c6-bfa7-b11c9a45dd6b
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 cd2aa3d897be31c10b200e93da24712e8b0fbab1
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
3650
HOMEBREW_NO_AUTO_UPDATE
1
ImageOS ubuntu24
ImageVersion 20250309.1.0
INVOCATION_ID 9d113ec6dfde453695a0e16866091f43
JAVA_HOME /usr/lib/jvm/temurin-17-jdk-amd64
JAVA_HOME_11_X64 /usr/lib/jvm/temurin-11-jdk-amd64
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JAVA_HOME_21_X64 /usr/lib/jvm/temurin-21-jdk-amd64
JAVA_HOME_8_X64 /usr/lib/jvm/temurin-8-jdk-amd64
JOURNAL_STREAM 8:6519
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
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 100
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/Rtmp41A9Dr
POWERSHELL_DISTRIBUTION_CHANNEL
GitHub-Actions-ubuntu24
PROCESSX_PS1d7462e30b1e_1741922780
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
R_HOME /opt/R/4.4.3/lib/R
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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/RtmpaQ64Di
R_SHARE_DIR /opt/R/4.4.3/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-1000000483
RUNNER_OS Linux
RUNNER_PERFLOG /home/runner/perflog
RUNNER_TEMP /home/runner/work/_temp
RUNNER_TOOL_CACHE /opt/hostedtoolcache
RUNNER_TRACKING_ID github_935ddd69-831d-48e1-b9b2-8be6628fe0df
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 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: 0x55725222b330>
<environment: namespace:cli>
$catch.script.errors
[1] FALSE
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$continue
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$contrasts
unordered ordered
"contr.treatment" "contr.poly"
$covr.record_tests
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$defaultPackages
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$demo.ask
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$device
function (width = 7, height = 7, ...)
{
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}
<bytecode: 0x55725170f1a8>
<environment: namespace:knitr>
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$digits
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$expressions
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$internet.info
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[1] TRUE
$keep.parse.data.pkgs
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$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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$na.action
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$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
"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
$showErrorCalls
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$showNCalls
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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
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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: 0x557251706688>
$str.dendrogram.last
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$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
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$verbose
[1] FALSE
$warn
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$warning.length
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$warnPartialMatchArgs
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$warnPartialMatchAttr
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$warnPartialMatchDollar
[1] FALSE
$width
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