Validation Report - admiral@1.2.0
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 admiral
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 144 |
| has_vignettes | 30 |
| export_help | 144 |
| has_website | TRUE |
| has_maintainer | Ben Straub ben.x.straub@gsk.com |
| bugs_status | subscript out of bounds |
| size_codebase | 7033 |
| has_source_control | https://github.com/pharmaverse/admiral |
| has_bug_reports_url | 1 |
| downloads_1yr | 14733 |
| reverse_dependencies | 6 |
| has_examples | 0.9877301 |
| dependencies | 12 |
| license | Apache License (>= 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 | admiraldev (>= 1.2.0) | Imports |
| 2 | cli (>= 3.6.2) | Imports |
| 3 | dplyr (>= 1.0.5) | Imports |
| 4 | hms (>= 0.5.3) | Imports |
| 5 | lifecycle (>= 0.1.0) | Imports |
| 6 | lubridate (>= 1.7.4) | Imports |
| 7 | magrittr (>= 1.5) | Imports |
| 8 | purrr (>= 0.3.3) | Imports |
| 9 | rlang (>= 0.4.4) | Imports |
| 10 | stringr (>= 1.4.0) | Imports |
| 11 | tidyr (>= 1.0.2) | Imports |
| 12 | tidyselect (>= 1.1.0) | Imports |
Package dependencies
Reverse dependencies
Overall the package has 6 reverse dependencies:
admiralmetabolic, admiralonco, admiralophtha, admiralpeds, admiralvaccine, psm3mkv
Namespace
Overall the package has 144 exported objects. 143 are documented:
%>% ae_event
FALSE TRUE
ae_gr1_event ae_gr2_event
TRUE TRUE
ae_gr3_event ae_gr35_event
TRUE TRUE
ae_gr4_event ae_gr5_event
TRUE TRUE
ae_ser_event ae_sev_event
TRUE TRUE
ae_wd_event basket_select
TRUE TRUE
call_derivation call_user_fun
TRUE TRUE
censor_source chr2vars
TRUE TRUE
compute_age_years compute_bmi
TRUE TRUE
compute_bsa compute_dtf
TRUE TRUE
compute_duration compute_egfr
TRUE TRUE
compute_framingham compute_map
TRUE TRUE
compute_qtc compute_qual_imputation
TRUE TRUE
compute_qual_imputation_dec compute_rr
TRUE TRUE
compute_scale compute_tmf
TRUE TRUE
consolidate_metadata convert_blanks_to_na
TRUE TRUE
convert_date_to_dtm convert_dtc_to_dt
TRUE TRUE
convert_dtc_to_dtm convert_na_to_blanks
TRUE TRUE
count_vals create_period_dataset
TRUE TRUE
create_query_data create_single_dose_dataset
TRUE TRUE
date_source death_event
TRUE TRUE
default_qtc_paramcd derivation_slice
TRUE TRUE
derive_basetype_records derive_expected_records
TRUE TRUE
derive_extreme_event derive_extreme_records
TRUE TRUE
derive_locf_records derive_param_bmi
TRUE TRUE
derive_param_bsa derive_param_computed
TRUE TRUE
derive_param_doseint derive_param_exist_flag
TRUE TRUE
derive_param_exposure derive_param_extreme_record
TRUE TRUE
derive_param_framingham derive_param_map
TRUE TRUE
derive_param_qtc derive_param_rr
TRUE TRUE
derive_param_tte derive_param_wbc_abs
TRUE TRUE
derive_summary_records derive_var_age_years
TRUE TRUE
derive_var_analysis_ratio derive_var_anrind
TRUE TRUE
derive_var_atoxgr derive_var_atoxgr_dir
TRUE TRUE
derive_var_base derive_var_chg
TRUE TRUE
derive_var_dthcaus derive_var_extreme_dt
TRUE TRUE
derive_var_extreme_dtm derive_var_extreme_flag
TRUE TRUE
derive_var_joined_exist_flag derive_var_merged_ef_msrc
TRUE TRUE
derive_var_merged_exist_flag derive_var_merged_summary
TRUE TRUE
derive_var_obs_number derive_var_ontrtfl
TRUE TRUE
derive_var_pchg derive_var_relative_flag
TRUE TRUE
derive_var_shift derive_var_trtdurd
TRUE TRUE
derive_var_trtemfl derive_vars_aage
TRUE TRUE
derive_vars_atc derive_vars_cat
TRUE TRUE
derive_vars_computed derive_vars_crit_flag
TRUE TRUE
derive_vars_dt derive_vars_dtm
TRUE TRUE
derive_vars_dtm_to_dt derive_vars_dtm_to_tm
TRUE TRUE
derive_vars_duration derive_vars_dy
TRUE TRUE
derive_vars_extreme_event derive_vars_joined
TRUE TRUE
derive_vars_merged derive_vars_merged_lookup
TRUE TRUE
derive_vars_period derive_vars_query
TRUE TRUE
derive_vars_transposed desc
TRUE TRUE
dthcaus_source event
TRUE TRUE
event_joined event_source
TRUE TRUE
exprs extract_duplicate_records
TRUE TRUE
extract_unit filter_exist
TRUE TRUE
filter_extreme filter_joined
TRUE TRUE
filter_not_exist filter_relative
TRUE TRUE
flag_event get_admiral_option
TRUE TRUE
get_duplicates_dataset get_flagged_records
TRUE TRUE
get_many_to_one_dataset get_not_mapped
TRUE TRUE
get_one_to_many_dataset get_summary_records
TRUE TRUE
get_vars_query impute_dtc_dt
TRUE TRUE
impute_dtc_dtm lastalive_censor
TRUE TRUE
list_all_templates list_tte_source_objects
TRUE TRUE
max_cond min_cond
TRUE TRUE
negate_vars params
TRUE TRUE
print_named_list query
TRUE TRUE
records_source restrict_derivation
TRUE TRUE
set_admiral_options signal_duplicate_records
TRUE TRUE
slice_derivation transform_range
TRUE TRUE
use_ad_template yn_to_numeric
TRUE TRUE Examples
There are 161 help pages with examples, from 163 (98.77 %).
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 06:38:13 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
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FALSE
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RUNNER_PERFLOG
PHARMAPKGS_EXCLUDED_METRICS
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TZ UTC
USER runner
VCPKG_INSTALLATION_ROOT
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$callr.condition_handler_cli_message
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<bytecode: 0x562fc41b5910>
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$rlang_trace_top_env
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