Logger producing unknown binary symbols
Closed this issue · 6 comments
nlarusstone commented
Here's my logger setup (this is in a file called logger.R).
library(glue)
library(logger)
layout <- layout_glue_generator(format = "{user}/{namespace}/{pid}/{fn} [{time}] {level}: {msg}")
log_layout(layout)
# Log INFO or above to console
log_threshold(INFO)
# Log everything to file
log_threshold(TRACE, index = 2)
log_file <- file.path("logs", format(as.POSIXct(Sys.time()), "%m-%d-%Y-%H:%M:%S"))
log_appender(appender_file(log_file), index = 2)
log_layout(layout, index = 2)
When I source this file from another script I run, I get strange binary symbols in an output file (NOT the log file). Here's the relevant part of the script that runs:
write(group_vars, here::here("pipeline", experiment, "group_vars.txt"), ncolumns = 1)
log_info("Finished preprocess.R")
And this is part of group_vars.txt:
nlarusstone commented
Here's my environment info:
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 3.6.1 (2019-07-05)
os Ubuntu 16.04.6 LTS
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Los_Angeles
date 2021-06-28
─ Packages ───────────────────────────────────────────────────────────────────
package * version date lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 3.6.1)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.1)
cachem 1.0.1 2021-01-21 [1] CRAN (R 3.6.1)
callr 3.5.1 2020-10-13 [1] CRAN (R 3.6.1)
car 3.0-10 2020-09-29 [1] CRAN (R 3.6.1)
carData 3.0-4 2020-05-22 [1] CRAN (R 3.6.1)
cellranger 1.1.0 2016-07-27 [2] CRAN (R 3.5.1)
cli 2.5.0 2021-04-26 [1] CRAN (R 3.6.1)
codetools 0.2-18 2020-11-04 [1] CRAN (R 3.6.1)
colorspace 2.0-1 2021-05-04 [1] CRAN (R 3.6.1)
crayon 1.4.1 2021-02-08 [1] CRAN (R 3.6.1)
curl 4.3.1 2021-04-30 [1] CRAN (R 3.6.1)
data.table 1.14.0 2021-02-21 [1] CRAN (R 3.6.1)
DBI 1.1.1 2021-01-15 [1] CRAN (R 3.6.1)
desc 1.3.0 2021-03-05 [1] CRAN (R 3.6.1)
devtools * 2.3.2 2020-09-18 [1] CRAN (R 3.6.1)
dplyr 1.0.4 2021-02-02 [1] CRAN (R 3.6.1)
drc 3.0-1 2016-08-30 [1] CRAN (R 3.6.1)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 3.6.1)
fansi 0.5.0 2021-05-25 [1] CRAN (R 3.6.1)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 3.6.1)
forcats 0.5.1 2021-01-27 [1] CRAN (R 3.6.1)
foreign 0.8-72 2019-08-02 [4] CRAN (R 3.6.1)
fs 1.5.0 2020-07-31 [1] CRAN (R 3.6.1)
generics 0.1.0 2020-10-31 [1] CRAN (R 3.6.1)
glue 1.4.1.9000 2021-02-02 [1] Github (tidyverse/glue@f0a7b2a)
gtools 3.9.2 2021-06-06 [1] CRAN (R 3.6.1)
haven 2.3.1 2020-06-01 [1] CRAN (R 3.6.1)
hms 1.0.0 2021-01-13 [1] CRAN (R 3.6.1)
lattice 0.20-41 2020-04-02 [1] CRAN (R 3.6.1)
lifecycle 1.0.0 2021-02-15 [1] CRAN (R 3.6.1)
logger 0.2.0 2021-03-04 [1] Github (daroczig/logger@e88153b)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 3.6.1)
MASS 7.3-53 2020-09-09 [1] CRAN (R 3.6.1)
Matrix 1.3-2 2021-01-06 [1] CRAN (R 3.6.1)
memoise 2.0.0 2021-01-26 [1] CRAN (R 3.6.1)
multcomp 1.4-16 2021-02-08 [1] CRAN (R 3.6.1)
munsell 0.5.0 2018-06-12 [2] CRAN (R 3.5.1)
mvtnorm 1.1-2 2021-06-07 [1] CRAN (R 3.6.1)
openxlsx 4.2.3 2020-10-27 [1] CRAN (R 3.6.1)
pillar 1.5.0 2021-02-22 [1] CRAN (R 3.6.1)
pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 3.6.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.1)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 3.6.1)
plotrix 3.8-1 2021-01-21 [1] CRAN (R 3.6.1)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.1)
processx 3.5.2 2021-04-30 [1] CRAN (R 3.6.1)
ps 1.6.0 2021-02-28 [1] CRAN (R 3.6.1)
purrr 0.3.4 2020-04-17 [1] CRAN (R 3.6.1)
R6 2.5.0 2020-10-28 [1] CRAN (R 3.6.1)
Rcpp 1.0.6 2021-01-15 [1] CRAN (R 3.6.1)
readxl 1.3.1 2019-03-13 [1] CRAN (R 3.6.1)
remotes 2.4.0 2021-06-02 [1] CRAN (R 3.6.1)
rio 0.5.26 2021-03-01 [1] CRAN (R 3.6.1)
rlang 0.4.11 2021-04-30 [1] CRAN (R 3.6.1)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 3.6.1)
sandwich 3.0-0 2020-10-02 [1] CRAN (R 3.6.1)
scales 1.1.1 2020-05-11 [1] CRAN (R 3.6.1)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.1)
stringi 1.6.2 2021-05-17 [1] CRAN (R 3.6.1)
survival 3.2-7 2020-09-28 [1] CRAN (R 3.6.1)
testthat 3.0.1 2020-12-17 [1] CRAN (R 3.6.1)
TH.data 1.0-10 2019-01-21 [1] CRAN (R 3.6.1)
tibble 3.0.6 2021-01-29 [1] CRAN (R 3.6.1)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 3.6.1)
usethis * 2.0.0 2020-12-10 [1] CRAN (R 3.6.1)
utf8 1.2.1 2021-03-12 [1] CRAN (R 3.6.1)
vctrs 0.3.6 2020-12-17 [1] CRAN (R 3.6.1)
withr 2.4.2 2021-04-18 [1] CRAN (R 3.6.1)
zip 2.2.0 2021-05-31 [1] CRAN (R 3.6.1)
zoo 1.8-9 2021-03-09 [1] CRAN (R 3.6.1)
[1] /data/home/nicholas/R/x86_64-pc-linux-gnu-library/3.6
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library
daroczig commented
Can you please update with a reproducible minimal example, e.g. a minimal second script sourcing the first one so that I can run and check what's going on? I was not able to reproduce as per the description on my own.
nlarusstone commented
Here's a reprex:
#!/usr/bin/env Rscript
library(here)
# local files
source(here::here("src", "logger.R"))
group_vars <- c("foo", "bar", "baz")
write(group_vars, here::here("pipeline", "foo", "group_vars.txt"), ncolumns = 1)
log_info("Finished preprocess.R")
Gives me:
foo
bar
baz
�����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������nicholas/global/17962/NA [2021-06-29 11:55:59] INFO: Finished preprocess.R
nlarusstone commented
Note that this happens regardless of whether or not the logger.R file is sourced or if that code is directly in this file.
nlarusstone commented
This is NOT happening in R 4.0.3 on my Mac by the way -- just on 3.6.1 on Linux
daroczig commented
Sorry for the late reply, I did not have any clues on what might have been going on there -- but now taking another look, I suspect there might have been something in your .Rprofile file or similar setting a custom layout, or something is missing from the minimal example?
I am closing this, as I suppose it's not relevant anymore, but please feel free to reopen if you can still reproduce and can provide more info.