CRAN Package Check Results for Package dataquieR

Last updated on 2022-10-05 05:57:00 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.10 22.04 416.92 438.96 OK
r-devel-linux-x86_64-debian-gcc 1.0.10 15.38 240.87 256.25 ERROR
r-devel-linux-x86_64-fedora-clang 1.0.10 557.09 OK
r-devel-linux-x86_64-fedora-gcc 1.0.10 538.24 OK
r-devel-windows-x86_64 1.0.10 220.00 462.00 682.00 OK
r-patched-linux-x86_64 1.0.10 32.51 372.83 405.34 OK
r-release-linux-x86_64 1.0.10 18.54 376.24 394.78 OK
r-release-macos-arm64 1.0.10 121.00 OK
r-release-macos-x86_64 1.0.10 197.00 OK
r-release-windows-x86_64 1.0.10 211.00 443.00 654.00 OK
r-oldrel-macos-arm64 1.0.10 104.00 OK
r-oldrel-macos-x86_64 1.0.10 201.00 OK
r-oldrel-windows-ix86+x86_64 1.0.10 41.00 464.00 505.00 WARN

Check Details

Version: 1.0.10
Check: examples
Result: ERROR
    Running examples in ‘dataquieR-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: con_detection_limits
    > ### Title: con_detection_limits
    > ### Aliases: con_detection_limits
    >
    > ### ** Examples
    >
    > load(system.file("extdata", "study_data.RData", package = "dataquieR"))
    > load(system.file("extdata", "meta_data.RData", package = "dataquieR"))
    >
    > # make things a bit more complicated for the function, giving datetimes
    > # as numeric
    > study_data[,
    + vapply(study_data, inherits, "POSIXct", FUN.VALUE = logical(1))] <-
    + lapply(study_data[, vapply(study_data, inherits, "POSIXct",
    + FUN.VALUE = logical(1))], as.numeric)
    >
    > MyValueLimits <- con_limit_deviations(
    + resp_vars = NULL,
    + label_col = "LABEL",
    + study_data = study_data,
    + meta_data = meta_data,
    + limits = "HARD_LIMITS"
    + )
    Warning: In con_limit_deviations: All variables with HARD_LIMITS in the metadata are used.
    > con_limit_deviations(resp_vars = NULL, label_col = "LABEL", study_data = study_data,
     meta_data = meta_data, limits = "HARD_LIMITS")
    
    Error in .POSIXct(x, tz, ...) : unused argument (origin = 0)
    Calls: con_limit_deviations -> lapply -> FUN -> as.POSIXct -> as.POSIXct.default
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.10
Check: tests
Result: ERROR
     Running ‘testthat.R’ [132s/223s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(dataquieR)
     > testthat::test_check("dataquieR")
     Error : In suppressWarnings: Metadata do not contain the column KEY_STUDY_SEGMENT.
     > suppressWarnings(dq_report(sd0, md0, cores = 1, label_col = LABEL,
     dimensions = c("Completeness"), check_table = read.csv(system.file("extdata",
    
     Error : In suppressWarnings: Missing check_table -- cannot apply contradictions checks w/o contradiction rules
     > suppressWarnings(dq_report(sd0, md0, cores = 1, label_col = LABEL,
     dimensions = c("Completeness", "Consistency", "Accuracy"),
    
     Error : In suppressWarnings: Missing check_table -- cannot apply contradictions checks w/o contradiction rules
     > suppressWarnings(dq_report(sd0, md0, resp_vars = "SBP_0", cores = 1,
     label_col = LABEL, dimensions = c("Completeness", "Consistency",
    
     list()
     [1] "SEX_0"
     [ FAIL 4 | WARN 0 | SKIP 31 | PASS 710 ]
    
     ══ Skipped tests ═══════════════════════════════════════════════════════════════
     • On CRAN (31)
    
     ══ Failed tests ════════════════════════════════════════════════════════════════
     ── Error (test-con_limit_deviations.R:7:3): con_limit_deviations works ─────────
     Error in `.POSIXct(x, tz, ...)`: unused argument (origin = 0)
     Backtrace:
     ▆
     1. ├─testthat::expect_warning(...) at test-con_limit_deviations.R:7:2
     2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
     3. │ ├─testthat (local) .capture(...)
     4. │ │ └─base::withCallingHandlers(...)
     5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     6. └─dataquieR::con_limit_deviations(...)
     7. └─base::lapply(...) at dataquieR/R/con_limit_deviations.R:164:2
     8. ├─base (local) FUN(X[[i]], ...)
     9. └─base::as.POSIXct.default(X[[i]], ...)
     ── Error (test-con_limit_deviations.R:57:3): con_limit_deviations and timevars with < 20 integer sec-values ok ──
     Error in `.POSIXct(x, tz, ...)`: unused argument (origin = 0)
     Backtrace:
     ▆
     1. └─dataquieR::con_limit_deviations(...) at test-con_limit_deviations.R:57:2
     2. └─base::lapply(...) at dataquieR/R/con_limit_deviations.R:233:2
     3. └─dataquieR (local) FUN(X[[i]], ...)
     4. ├─base::as.POSIXct(...) at dataquieR/R/con_limit_deviations.R:457:8
     5. └─base::as.POSIXct.default(...)
     ── Error (test-con_limit_deviations.R:99:3): con_limit_deviations works w/o resp_vars ──
     Error in `.POSIXct(x, tz, ...)`: unused argument (origin = 0)
     Backtrace:
     ▆
     1. ├─testthat::expect_warning(...) at test-con_limit_deviations.R:99:2
     2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
     3. │ ├─testthat (local) .capture(...)
     4. │ │ └─base::withCallingHandlers(...)
     5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     6. └─dataquieR::con_limit_deviations(...)
     7. └─base::lapply(...) at dataquieR/R/con_limit_deviations.R:164:2
     8. ├─base (local) FUN(X[[i]], ...)
     9. └─base::as.POSIXct.default(X[[i]], ...)
     ── Error (test-con_limit_deviations.R:186:3): con_limit_deviations handles errors ──
     Error in `.POSIXct(x, tz, ...)`: unused argument (origin = 0)
     Backtrace:
     ▆
     1. ├─testthat::expect_warning(...) at test-con_limit_deviations.R:186:2
     2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
     3. │ ├─testthat (local) .capture(...)
     4. │ │ └─base::withCallingHandlers(...)
     5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     6. └─dataquieR::con_limit_deviations(...)
     7. └─base::lapply(...) at dataquieR/R/con_limit_deviations.R:164:2
     8. ├─base (local) FUN(X[[i]], ...)
     9. └─base::as.POSIXct.default(X[[i]], ...)
    
     [ FAIL 4 | WARN 0 | SKIP 31 | PASS 710 ]
     Deleting unused snapshots:
     • acc_distributions/ecdf-plot-for-sbp0-ok.svg
     • acc_end_digits/enddigits-plot-for-crp-0-ok.svg
     • acc_loess/loess-combined-plot-for-crp-0-both-ok.svg
     • acc_loess/loess-combined-plot-for-crp-0-combined-ok.svg
     • acc_loess/loess-combined-plot-for-crp-0-ok.svg
     • acc_loess/loess-combined-plot-for-crp-0-with-covars-ok.svg
     • acc_loess/loess-facets-plot-for-crp-0-both-ok.svg
     • acc_loess/loess-facets-plot-for-crp-0-facets-ok.svg
     • acc_loess/loess-facets-plot-for-crp-0-ok.svg
     • acc_loess/loess-facets-plot-for-crp-0-with-covars-ok.svg
     • acc_loess/loess-plot-for-crp-0-auto1-ok.svg
     • acc_loess/loess-plot-for-crp-0-auto2-ok.svg
     • acc_margins/margins-plot-for-crp-0-ok.svg
     • acc_multivariate_outlier/acc-mv-outliercrp0globheava0.svg
     • acc_shape_or_scale/shape-or-scale-plot-for-crp-0-ok.svg
     • com_item_missingness/item-missingness-plot-with-labels-ok.svg
     • com_item_missingness/item-missingness-plot-without-labels-ok.svg
     • com_segment_missingness/segment-missingness-plot-ok.svg
     • con_contradictions/one-cat-contradiction-plot-ok.svg
     • con_contradictions/summary-contradiction-plot-ok.svg
     • con_limit_deviations/con-limit-deviations-4-hists-1-val.svg
     • con_limit_deviations/con-limit-deviations-for-reverse-order-ok.svg
     • con_limit_deviations/con-limit-deviations-histgrms-misscds.svg
     • con_limit_deviations/con-limit-deviations-quest-dt-0.svg
     • con_limit_deviations/con-limit-deviations-rev-order-w-1-0-max-ok.svg
     • int_datatype_matrix/intdtv10000.svg
     • int_datatype_matrix/intdtv20000.svg
     • int_datatype_matrix/intdtv30000.svg
     • int_datatype_matrix/intdtv40000.svg
     • int_datatype_matrix/intdtv50000.svg
     • int_datatype_matrix/integrity-datatype.svg
     • print/app-ex-repsumtab.svg
     • print/im-empty-repsumtab.svg
     • print/im-ex1-repsumtab.svg
     • print/im-ex2-repsumtab.svg
     • pro_applicability_matrix/appmatrix-plot-for-segment-v10000-ok.svg
     • pro_applicability_matrix/appmatrix-plot-ok.svg
     • util_heatmap_1th/util-heatmap-1th-1.svg
     • util_heatmap_1th/util-heatmap-1th-2.svg
     • util_heatmap_1th/util-heatmap-1th-3.svg
     Error: Test failures
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.10
Check: re-building of vignette outputs
Result: ERROR
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘DQ-report-example.Rmd’ using rmarkdown
    Warning: In com_segment_missingness: Study variables: "AGE_GROUP_0", "ARM_CIRC_0", "ARM_CIRC_DISC_0", "ARM_CUFF_0", "USR_VO2_0", "USR_BP_0", "EXAM_DT_0", "DEV_NO_0", "LAB_DT_0", "USR_SOCDEM_0", "INT_DT_0", "QUEST_DT_0" are not considered due to their VARIABLE_ROLE.
    > com_segment_missingness(study_data = sd1, meta_data = md1, label_col = "LABEL",
     threshold_value = 5, direction = "high", exclude_roles = c("secondary",
    
    Loading required package: lubridate
    
    Attaching package: 'lubridate'
    
    The following objects are masked from 'package:base':
    
     date, intersect, setdiff, union
    
    Warning: In com_segment_missingness: Study variables: "AGE_GROUP_0", "ARM_CIRC_0", "ARM_CIRC_DISC_0", "ARM_CUFF_0", "USR_VO2_0", "USR_BP_0", "EXAM_DT_0", "DEV_NO_0", "LAB_DT_0", "USR_SOCDEM_0", "INT_DT_0", "QUEST_DT_0" are not considered due to their VARIABLE_ROLE.
    > com_segment_missingness(study_data = sd2, meta_data = MD_TMP,
     group_vars = "EXAM_MONTH", label_col = "LABEL", threshold_value = 1,
    
    Warning: In com_item_missingness: Setting suppressWarnings to its default FALSE
    > com_item_missingness(study_data = sd1, meta_data = meta_data,
     label_col = "LABEL", show_causes = TRUE, cause_label_df = code_labels,
    
    Warning: In con_limit_deviations: All variables with HARD_LIMITS in the metadata are used.
    > con_limit_deviations(resp_vars = NULL, label_col = "LABEL", study_data = sd1,
     meta_data = md1, limits = "HARD_LIMITS")
    
    Quitting from lines 192-197 (DQ-report-example.Rmd)
    Error: processing vignette ‘DQ-report-example.Rmd’ failed with diagnostics:
    unused argument (origin = 0)
    --- failed re-building ‘DQ-report-example.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘DQ-report-example.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.10
Check: for unstated dependencies in ‘tests’
Result: WARN
    Warning: unable to access index for repository https://bioconductor.org/packages/3.14/bioc/src/contrib:
     cannot open URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/PACKAGES'
    Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/src/contrib:
     cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PACKAGES'
    Warning: unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/src/contrib:
     cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/PACKAGES'
Flavor: r-oldrel-windows-ix86+x86_64