colorout package interferes with pkg output, causes missing line breaks
slowkow opened this issue · 5 comments
colorout is interfering with the output from pkg, so line breaks are not appearing as they should.
I think I should stop using colorout now that crayon is gaining more usage.
With library(colorout) in my ~/.Rprofile:
Loading required package: colorout
> pkg::pkg_install("AnnotationDbi")
ℹ Checking for package metadata updates
✔ All 10 metadata files are current.
ℹ Loading session disk cached package metadata✔ Loading session disk cached package metadata✔ Using cached package metadata
Found 20 deps for 1/1 pkgs [⠙] Checking installed packagesFound 20 deps for 1/1 pkgs [⠹] Checking installed packagesFound 43 deps for 1/1 pkgs [⠸] Resolving standard (CRAN/BioC) packagesFound 43 deps for 1/1 pkgs [⠼] Resolving standard (CRAN/BioC) packages✔ 1 + 16 pkgs | kept 17, updated 0, new 0 | downloaded 0 (0 B) [4.4s]
Without colorout:
> pkg::pkg_install("AnnotationDbi")
ℹ Checking for package metadata updates
✔ All 10 metadata files are current.
✔ Loading session disk cached package metadata
✔ Using cached package metadata
✔ 1 + 16 pkgs | kept 17, updated 0, new 0 | downloaded 0 (0 B) [4.6s]
Details
iTerm2 Build 3.2.7
> devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 3.5.1 (2018-07-02)
os macOS High Sierra 10.13.6
system x86_64, darwin15.6.0
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2019-01-23
─ Packages ───────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.0 2017-04-11 [1] CRAN (R 3.5.0)
backports 1.1.3 2018-12-14 [1] CRAN (R 3.5.0)
callr 3.1.1 2018-12-21 [1] CRAN (R 3.5.0)
cli 1.0.1 2018-09-25 [1] CRAN (R 3.5.0)
colorout * 1.2-0 2019-01-01 [1] local
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.0)
curl 3.3 2019-01-10 [1] CRAN (R 3.5.2)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.0)
devtools * 2.0.1 2018-10-26 [1] CRAN (R 3.5.1)
digest 0.6.18 2018-10-10 [1] CRAN (R 3.5.0)
filelock 1.0.2 2018-10-05 [1] CRAN (R 3.5.0)
fs 1.2.6 2018-08-23 [1] CRAN (R 3.5.0)
glue 1.3.0 2018-07-17 [1] CRAN (R 3.5.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.0)
memoise 1.1.0.9000 2019-01-18 [1] Github (hadley/memoise@1650ad7)
pkg * 0.1.1.9000 2019-01-23 [1] Github (r-lib/pkg@582d0d5)
pkgbuild 1.0.2 2018-10-16 [1] CRAN (R 3.5.0)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.5.0)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.0)
processx 3.2.1 2018-12-05 [1] CRAN (R 3.5.0)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.5.0)
R6 2.3.0 2018-10-04 [1] CRAN (R 3.5.0)
Rcpp 1.0.0 2018-11-07 [1] CRAN (R 3.5.0)
remotes 2.0.2 2018-10-30 [1] CRAN (R 3.5.0)
rlang 0.3.1.9000 2019-01-23 [1] Github (r-lib/rlang@02bff45)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.0)
testthat 2.0.1 2018-10-13 [1] CRAN (R 3.5.0)
usethis * 1.4.0 2018-08-14 [1] CRAN (R 3.5.0)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.0)
[1] /Library/Frameworks/R.framework/Versions/3.5/Resources/library
Colorout already checks whether the string is colorized by another package:
https://github.com/jalvesaq/colorout/blob/master/src/colorout.c#L254
But it seems that R's output does not come in a single string. R breaks it in many pieces, and an ANSI color code might have been output in a previous string and still be active. So, I will not be surprised if colorout interferes in the colorizing made by other packages, but it should not mess with line breaks.
Perhaps the problem is here:
https://github.com/jalvesaq/colorout/blob/master/src/colorout.c#L261
Maybe a workaround: define a hook for every call of the problematic function (in your case the pkg_install).
I tried with the devtools::install_github function. From my .Rprofile:
# modify a function from a package as soon as the package is loaded
setHook(hookName=packageEvent(pkgname="devtools", event="attach"),
value=function(...) {
# save the function to be overwritten
original_install_github <- devtools::install_github
# define new function
my_install_github <- function(...) {
# first detach colorout if loaded
if (any(search() == "package:colorout")) {
message("setHook: detach colorout package ... ", appendLF=F)
detach(package:colorout, unload=T)
if (!any(search() == "package:colorout")) {
message("SUCCESS")
} else {
message("FAILED")
}
}
# run the original function
message("setHook: now run devtools::install_github ...")
original_install_github(...)
# reload colorout package
message("setHook: reload colorout package ... ", appendLF=F)
suppressMessages(suppressWarnings(require("colorout", character.only=T)))
if (any(search() == "package:colorout")) {
message("SUCCESS")
} else {
message("FAILED")
}
}
# overwrite the original function of the package
unlockBinding("install_github", as.environment("package:devtools"))
assign("install_github", my_install_github, "package:devtools")
} # hook function
) # setHook
Now, within R, there are 2 install_github functions:
> getAnywhere(install_github)
2 differing objects matching ‘install_github’ were found
in the following places
package:devtools
namespace:remotes
Use [] to view one of them
The original function is unchanged and interferes with the colorout package in an undesired way:
> any(search() == "package:colorout")
[1] TRUE
> devtools::install_github('rstudio/bookdown', force=T)
Downloading GitHub repo rstudio/bookdown@master
32m✔39m 38;5;247mchecking for file ‘/tmp/RtmpbU5ARO/remotes3da26e4a1da2/rstudio-bookdown-44af2c0/DESCRIPTION’39m36m39m
38;5;247m─39m38;5;247m 39m38;5;247mpreparing ‘bookdown’:39m36m39m
32m✔39m 38;5;247mchecking DESCRIPTION meta-information39m36m39m
38;5;247m─39m38;5;247m 39m38;5;247mchecking for LF line-endings in source and make files and shell scripts39m36m39m
38;5;247m─39m38;5;247m 39m38;5;247mchecking for empty or unneeded directories39m36m39m
38;5;247m─39m38;5;247m 39m38;5;247mbuilding ‘bookdown_0.9.1.tar.gz’39m36m39m
...
Through the hook, however, we can use our own function instead:
> any(search() == "package:colorout")
[1] TRUE
> install_github('rstudio/bookdown', force=T)
setHook: detach colorout package ... SUCCESS
setHook: now run devtools:install_github ...
Downloading GitHub repo rstudio/bookdown@master
✔ checking for file ‘/tmp/RtmpbU5ARO/remotes3da239ca9904/rstudio-bookdown-44af2c0/DESCRIPTION’ ...
─ preparing ‘bookdown’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘bookdown_0.9.1.tar.gz’
...
setHook: reload colorout package ... SUCCESS
Maybe this helps as a workaround? Good luck with your thesis ...
You may call the function noColorOut() to disable the colorizing of R output, and ColorOut() to enable it again. This will be faster than detaching colorout and attaching it again.
Good point ty!
I guess this bug is finally fixed on the branch fix_nl.
When the output already had colors, it was always printed on stdout.