Bug: Warning() at end of file overrides result #160
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What happened?
It looks like warning() function overrides the final result from the script.
FYI @kodesiba @nicholas-masel
Session Information
This log was generated using logrx 0.2.1.0.0.0.1675442722
logrx package version: 0.2.1.0.0.0.1675442722
logrx build: RSPM (R 4.2.1)
logrx link to repository: https://github.com/pharmaverse/logrx
─ Session info ─────────────────────────────────────────────────────────────────
setting value
version R version 4.2.1 (2022-06-23)
os Red Hat Enterprise Linux
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2023-02-09
rstudio 2022.02.3+492.pro3 Prairie Trillium (server)
pandoc 2.17.1.1 @ /usr/lib/rstudio-server/bin/quarto/bin/ (via rmarkdown)
─ Packages ─────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
admiral * 0.9.1 2022-12-23 [1] RSPM (R 4.2.1)
admiraldev 0.2.0 2022-12-01 [1] RSPM (R 4.2.1)
assertthat 0.2.1 2019-03-21 [2] RSPM (R 4.2.1)
cachem 1.0.6 2021-08-19 [2] RSPM (R 4.2.1)
callr 3.7.1 2022-07-13 [2] RSPM (R 4.2.1)
cli 3.3.0 2022-04-25 [2] RSPM (R 4.2.1)
crayon 1.5.1 2022-03-26 [2] RSPM (R 4.2.1)
cyclocomp 1.1.0 2016-09-10 [1] RSPM (R 4.2.1)
DBI 1.1.3 2022-06-18 [2] RSPM (R 4.2.1)
desc 1.4.1 2022-03-06 [2] RSPM (R 4.2.1)
devtools * 2.4.3 2021-11-30 [2] RSPM (R 4.2.1)
digest 0.6.29 2021-12-01 [2] RSPM (R 4.2.1)
dplyr 1.0.9 2022-04-28 [2] RSPM (R 4.2.1)
ellipsis 0.3.2 2021-04-29 [2] RSPM (R 4.2.1)
evaluate 0.15 2022-02-18 [2] RSPM (R 4.2.1)
fansi 1.0.3 2022-03-24 [2] RSPM (R 4.2.1)
fastmap 1.1.0 2021-01-25 [2] RSPM (R 4.2.1)
fs 1.5.2 2021-12-08 [2] RSPM (R 4.2.1)
generics 0.1.3 2022-07-05 [2] RSPM (R 4.2.1)
glue 1.6.2 2022-02-24 [2] RSPM (R 4.2.1)
hms 1.1.1 2021-09-26 [2] RSPM (R 4.2.1)
htmltools 0.5.2 2021-08-25 [2] RSPM (R 4.2.1)
httpuv 1.6.5 2022-01-05 [2] RSPM (R 4.2.1)
knitr 1.39 2022-04-26 [2] RSPM (R 4.2.1)
later 1.3.0 2021-08-18 [2] RSPM (R 4.2.1)
lazyeval 0.2.2 2019-03-15 [2] RSPM (R 4.2.1)
lifecycle 1.0.1 2021-09-24 [2] RSPM (R 4.2.1)
lintr 3.0.0 2022-06-13 [1] RSPM (R 4.2.1)
logrx 0.2.1.0.0.0.1675442722 2023-02-03 [1] RSPM (R 4.2.1)
lubridate 1.8.0 2021-10-07 [2] RSPM (R 4.2.1)
magrittr 2.0.3 2022-03-30 [2] RSPM (R 4.2.1)
memoise 2.0.1 2021-11-26 [2] RSPM (R 4.2.1)
mime 0.12 2021-09-28 [2] RSPM (R 4.2.1)
miniUI 0.1.1.1 2018-05-18 [2] RSPM (R 4.2.1)
pillar 1.7.0 2022-02-01 [2] RSPM (R 4.2.1)
pkgbuild 1.3.1 2021-12-20 [2] RSPM (R 4.2.1)
pkgconfig 2.0.3 2019-09-22 [2] RSPM (R 4.2.1)
pkgload 1.3.0 2022-06-27 [2] RSPM (R 4.2.1)
prettyunits 1.1.1 2020-01-24 [2] RSPM (R 4.2.1)
processx 3.7.0 2022-07-07 [2] RSPM (R 4.2.1)
promises 1.2.0.1 2021-02-11 [2] RSPM (R 4.2.1)
ps 1.7.1 2022-06-18 [2] RSPM (R 4.2.1)
purrr 0.3.4 2020-04-17 [2] RSPM (R 4.2.1)
R6 2.5.1 2021-08-19 [2] RSPM (R 4.2.1)
Rcpp 1.0.9.0.0.0.1657464909 2022-07-15 [2] RSPM (R 4.2.1)
remotes 2.4.2 2021-11-30 [2] RSPM (R 4.2.1)
rex 1.2.1 2021-11-26 [2] RSPM (R 4.2.1)
rlang 1.0.4 2022-07-12 [2] RSPM (R 4.2.1)
rmarkdown 2.14 2022-04-25 [2] RSPM (R 4.2.1)
rprojroot 2.0.3 2022-04-02 [2] RSPM (R 4.2.1)
rstudioapi 0.13 2020-11-12 [2] RSPM (R 4.2.1)
sessioninfo 1.2.2 2021-12-06 [2] RSPM (R 4.2.1)
shiny 1.7.1 2021-10-02 [2] RSPM (R 4.2.1)
stringi 1.7.8 2022-07-11 [2] RSPM (R 4.2.1)
stringr 1.4.0 2019-02-10 [2] RSPM (R 4.2.1)
tibble * 3.1.7 2022-05-03 [2] RSPM (R 4.2.1)
tidyr 1.2.0 2022-02-01 [2] RSPM (R 4.2.1)
tidyselect 1.1.2 2022-02-21 [2] RSPM (R 4.2.1)
usethis * 2.1.6 2022-05-25 [2] RSPM (R 4.2.1)
utf8 1.2.2 2021-07-24 [2] RSPM (R 4.2.1)
vctrs 0.4.1 2022-04-13 [2] RSPM (R 4.2.1)
waiter 0.2.5 2022-01-03 [1] RSPM (R 4.2.1)
withr 2.5.0 2022-03-03 [2] RSPM (R 4.2.1)
xfun 0.31 2022-05-10 [2] RSPM (R 4.2.1)
xml2 1.3.3 2021-11-30 [2] RSPM (R 4.2.1)
xtable 1.8-4 2019-04-21 [2] RSPM (R 4.2.1)
yaml 2.3.5 2022-02-21 [2] RSPM (R 4.2.1)
[1] /shared-scratch/area/bs832471/R/libs/4.2.1
[2] /shared-app/R-4.2.1/lib64/R/library
─ External software ────────────────────────────────────────────────────────────
setting value
cairo 1.15.12
cairoFT
pango 1.42.3
png 1.5.13
jpeg 6.2
tiff LIBTIFF, Version 4.0.3
tcl 8.5.13
curl 7.29.0
zlib 1.2.7
bzlib 1.0.6, 6-Sept-2010
xz 5.2.2
PCRE 10.23 2017-02-14
ICU 50.1.2
TRE TRE 0.8.0 R_fixes (BSD)
iconv glibc 2.17
readline 6.2
BLAS /usr/lib64/libblas.so.3.4.2
lapack /usr/lib64/liblapack.so.3.4.2
lapack_version 3.4.2
─ Python configuration ─────────────────────────────────────────────────────────
Python is not available
────────────────────────────────────────────────────────────────────────────────
function
%>%from {package:admiral} by package:tibblefunction
plotfrom {package:base} by package:graphicsfunction
body<-from {package:base} by package:methodsfunction
kroneckerfrom {package:base} by package:methods{package:admiral} derive_extreme_records, vars
{package:base} library, message, warning
{package:tibble} tribble
Start time: 2023-02-09 14:17:50 EST
End time: 2023-02-09 14:17:50 EST
Run time: 0 seconds
Errors:
Warnings:
Warning - Ship is under attack!
Warning - Loosing result
Messages:
Hello R4GxP!
Result:
[1] "Warning - Loosing result"
Log name: demo_script2.log
Log path: /shared-scratch/area/bs832471/logrx_demo
Reproducible Example
library(admiral)
library(tibble)
adlb <- tribble(
~USUBJID, ~AVISITN, ~AVAL, ~LBSEQ,
"1", 1, 113, 1,
"1", 2, 113, 2,
"1", 3, 117, 3,
"2", 1, 101, 1,
"2", 2, 101, 2,
"2", 3, 95, 3
)
message("Hello R4GxP!")
warning("Warning - Ship is under attack!")
derive_extreme_records(
adlb,
by_vars = vars(USUBJID),
order = vars(AVISITN),
mode = "last",
set_values_to = vars(
AVISITN = 99,
DTYPE = "LOV"
)
)
warning("Warning - Losing result if warning is at bottom of script")
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