Validation Report - CDMConnector@1.7.0
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 CDMConnector
Metric based risk assessment
The following metrics are derived from the riskmetric R package.
| has_news | 1 |
| news_current | TRUE |
| exported_namespace | 107 |
| has_vignettes | 13 |
| export_help | 107 |
| has_website | TRUE |
| has_maintainer | Adam Black black@ohdsi.org |
| bugs_status | subscript out of bounds |
| has_source_control | https://github.com/darwin-eu/CDMConnector |
| has_bug_reports_url | 1 |
| downloads_1yr | 15386 |
| reverse_dependencies | 14 |
| has_examples | 0.9811321 |
| dependencies | 19 |
| 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 | dplyr | Imports |
| 2 | dbplyr (>= 2.5.0) | Imports |
| 3 | DBI (>= 0.3.0) | Imports |
| 4 | checkmate | Imports |
| 5 | cli | Imports |
| 6 | purrr | Imports |
| 7 | rlang | Imports |
| 8 | tidyselect | Imports |
| 9 | glue | Imports |
| 10 | methods | Imports |
| 11 | withr | Imports |
| 12 | lifecycle | Imports |
| 13 | stringr | Imports |
| 14 | stringi | Imports |
| 15 | generics | Imports |
| 16 | tidyr | Imports |
| 17 | jsonlite | Imports |
| 18 | readr | Imports |
| 19 | omopgenerics (>= 0.1.2) | Imports |
Package dependencies
Reverse dependencies
Overall the package has 14 reverse dependencies:
CodelistGenerator, CohortCharacteristics, CohortConstructor, CohortSurvival, CohortSymmetry, DrugExposureDiagnostics, DrugUtilisation, IncidencePrevalence, OmopSketch, OmopViewer, PatientProfiles, PhenotypeR, TestGenerator, TreatmentPatterns
Namespace
Overall the package has 107 exported objects. 106 are documented:
%>% append_permanent
FALSE TRUE
appendPermanent as_date
TRUE TRUE
asDate assert_tables
TRUE TRUE
assert_write_schema assertTables
TRUE TRUE
assertWriteSchema attrition
TRUE TRUE
benchmarkCDMConnector bind
TRUE TRUE
cdm_disconnect cdm_flatten
TRUE TRUE
cdm_from_con cdm_from_environment
TRUE TRUE
cdm_from_files cdm_from_tables
TRUE TRUE
cdm_name cdm_sample
TRUE TRUE
cdm_select_tbl cdm_subset
TRUE TRUE
cdm_subset_cohort cdmCon
TRUE TRUE
cdmDisconnect cdmFlatten
TRUE TRUE
cdmFromCon cdmFromEnvironment
TRUE TRUE
cdmFromFiles cdmFromTables
TRUE TRUE
cdmName cdmSample
TRUE TRUE
cdmSelect cdmSelectTbl
TRUE TRUE
cdmSubset cdmSubsetCohort
TRUE TRUE
cdmVersion cdmWriteSchema
TRUE TRUE
cohort_attrition cohort_count
TRUE TRUE
cohort_erafy cohort_set
TRUE TRUE
cohort_union cohortAttrition
TRUE TRUE
cohortCodelist cohortCount
TRUE TRUE
cohortErafy cohortSet
TRUE TRUE
cohortUnion compute
TRUE TRUE
compute_query computeQuery
TRUE TRUE
copy_cdm_to copyCdmTo
TRUE TRUE
dateadd datediff
TRUE TRUE
datepart dbms
TRUE TRUE
dbSource download_eunomia_data
TRUE TRUE
downloadEunomiaData dropSourceTable
TRUE TRUE
dropTable eunomia_dir
TRUE TRUE
eunomia_is_available eunomiaDir
TRUE TRUE
eunomiaIsAvailable example_datasets
TRUE TRUE
exampleDatasets generate_cohort_set
TRUE TRUE
generate_concept_cohort_set generateCohortSet
TRUE TRUE
generateConceptCohortSet in_schema
TRUE TRUE
inSchema insertTable
TRUE TRUE
intersect_cohorts intersectCohorts
TRUE TRUE
list_tables listSourceTables
TRUE TRUE
listTables new_generated_cohort_set
TRUE TRUE
newCohortTable newGeneratedCohortSet
TRUE TRUE
read_cohort_set readCohortSet
TRUE TRUE
readSourceTable record_cohort_attrition
TRUE TRUE
recordCohortAttrition require_eunomia
TRUE TRUE
requireEunomia settings
TRUE TRUE
snapshot stow
TRUE TRUE
summarise_quantile summariseQuantile
TRUE TRUE
summarize_quantile summarizeQuantile
TRUE TRUE
tbl_group tblGroup
TRUE TRUE
union_cohorts unionCohorts
TRUE TRUE
unique_table_name uniqueTableName
TRUE TRUE
validate_cdm validateCdm
TRUE TRUE
version
TRUE Examples
There are 52 help pages with examples, from 53 (98.11 %).
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 | 2025-02-16 03:56:57 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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PHARMAPKGS_EXCLUDED_METRICS
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$browser
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$callr.condition_handler_cli_message
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<bytecode: 0x55945d6e3910>
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