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medizininformatik-initiative / Projectathon7-VHF

Repository für den 7. MII Projectathon
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analysis fails with error `missing value where TRUE/FALSE needed` #15

Open joundso opened 6 months ago

joundso commented 6 months ago 
$ dupctl analyze --dup vhf
2024/02/29 11:04:15 Using config file: config.toml
latest: Pulling from smith-phep/dup/vhf-analysis
43f89b94cd7d: Already exists
6e4412f9416b: Already exists
586b4a75d153: Already exists
e0f9f11c18f0: Already exists
2612c5821234: Already exists
e815b42127f1: Already exists
f5d986b6ee5b: Already exists  
e0319e802593: Pulling fs layer
e1083254dd3b: Pulling fs layer
521be9c9a122: Pulling fs layer
5d2db17c092f: Pulling fs layer
5d2db17c092f: Waiting
e0319e802593: Verifying Checksum
e0319e802593: Download complete 
e1083254dd3b: Download complete 
e0319e802593: Pull complete     
521be9c9a122: Verifying Checksum
521be9c9a122: Download complete
e1083254dd3b: Pull complete
521be9c9a122: Pull complete
5d2db17c092f: Verifying Checksum
5d2db17c092f: Download complete
5d2db17c092f: Pull complete
Digest: sha256:4dadb05e0d845368707fce0314f4c0b540970a3d619e23f15a55a3a4d901ce3f
Status: Downloaded newer image for registry.gitlab.com/smith-phep/dup/vhf-analysis:latest
Loading required package: data.table
Loading required package: rmarkdown
Loading required package: knitr
Loading required package: dataquieR
Loading required package: lubridate

Attaching package: ‘lubridate’

The following objects are masked from ‘package:data.table’:

    hour, isoweek, mday, minute, month, quarter, second, wday, week,
    yday, year

The following objects are masked from ‘package:base’:

    date, intersect, setdiff, union

Loading required package: Epi
Loading required package: gmodels
Loading required package: xfun

Attaching package: ‘xfun’

The following objects are masked from ‘package:base’:

    attr, isFALSE

Loading required package: pointblank

Attaching package: ‘pointblank’

The following object is masked from ‘package:data.table’:

    between

Loading required package: digest
Loading required package: ggplot2
Run Analysis with Parameters:
-----------------------------
              DEBUG = FALSE
DATA_QUALITY_REPORT = TRUE
 DECENTRAL_ANALSYIS = TRUE
    OUTPUT_DIR_BASE = /mnt
Start Analysis at 2024-02-29 10:04:42.44051

SessionInfo:
R version 4.3.1 (2023-06-16)Platform: x86_64-pc-linux-gnu (64-bit)Running under: Ubuntu 22.04.3 LTSMatrix products: defaultBLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0locale: [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               [3] LC_TIME=en_US.UTF-8    
    LC_COLLATE=en_US.UTF-8     [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  [9] LC_ADDRESS=C               LC_TELEPHONE=C            [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       time zone: Etc/UTCtzcode source: system (glibc)attached base packages:[1] stats     graphics  grDevices utils     datasets  methods   base     other attached packages: [1] ggplot2_3.4.4     digest_0.6.33     pointblank_0.11.4 xfun_0.40         [5] gmodels_2.18.1.1  Epi_2.47.1        lubridate_1.9.3   dataquieR_2.0.1   [9] knitr_1.44        rmarkdown_2.25    data.table_1.14.8loaded via a namespace (and not attached): [1] utf8_1.2.4          generics_0.1.3      gtools_3.9.4        [4] lattice_0.21-8      magrittr_2.0.3      evaluate_0.22       [7] grid_4.3.1          timechange_0.2.0    pkgload_1.3.3      [10] fastmap_1.1.1       plyr_1.8.9          Matrix_1.5-4.1     [13] reshape_0.8.9       survival_3.5-5      mgcv_1.8-42        [16] fansi_1.0.5         scales_1.2.1        numDeriv_2016.8-1.1[19] cli_3.6.1           rlang_1.1.1         munsell_0.5.0      [22] 
splines_4.3.1       withr_2.5.1         tools_4.3.1        [25] parallel_4.3.1      dplyr_1.1.3         colorspace_2.1-0   [28] etm_1.1.1           MultinomialCI_1.2   vctrs_0.6.4        [31] R6_2.5.1            zoo_1.8-12          lifecycle_1.0.3    [34] MASS_7.3-60         pkgconfig_2.0.3     pillar_1.9.0       [37] gtable_0.3.4        glue_1.6.2          Rcpp_1.0.11       
 [40] tibble_3.2.1        tidyselect_1.2.0    htmltools_0.5.6.1  [43] nlme_3.1-162        cmprsk_2.2-11       patchwork_1.1.3    [46] gdata_3.0.0         qmrparser_0.1.6     compiler_4.3.1 
    [49] blastula_0.3.4

processing file: report.Rmd
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output file: /mnt/outputLocal/VHF/report.knit.md

/usr/bin/pandoc +RTS -K512m -RTS /mnt/outputLocal/VHF/report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /mnt/outputGlobal/VHF/DQ-Report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpbEuLr2/rmarkdown-str15f00bfe2.html

Output created: /mnt/outputGlobal/VHF/DQ-Report.html
data-quality/report.Rmd finished at 2024-02-29 10:08:14.711609.
Rmd script execution took 3.49 mins.

Full Cohort NTProBNP values:
    total before cleanup: 12345
                      NA: 123 (removed)
                     < 0: 0 (removed)
                     < 1: 0
                     > 0: 12345
                 > 10000: 12345
                 > 20000: 12345
                 > 30000: 12345
                 > 40000: 0
                 > 50000: 0
                 > 60000: 0
                 > 70000: 0
                 > 80000: 0
                 > 90000: 0
                 > 1e+05: 0
     total after cleanup: 12345

Start Cohort Analysis: 2024-02-29 10:08:17.692899
Cohort: Full Cohort
Atrial Fibrillation incl. all other diagnoses (all NTproBNP values have no comparator):
Error in if (all(con == first_con)) { : 
  missing value where TRUE/FALSE needed
Calls: writeCohortAnalysisFiles -> analyzeCohort -> cohortAnalysis -> analyze
Execution halted
astruebi commented 6 months ago

Der Fehler sollte jetzt behoben sein. Bitte mal testen.