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lcolladotor/debug_pkgdown.R

Created May 21, 2020 23:38
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Weird issue with finding gitconfig with git on Windows through processx (used internally by pkgdown)
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debug_pkgdown.R
##################### Steps for reproducing this problem ######################
## Create a package
usethis::create_package("~/Desktop/testgit")
## Set up git and say yes to the prompts
usethis::use_git()
## Create a file
writeLines("hola", "test.txt")
## Use git2r to add it (can also be done with the RStudio git panel)
git2r::add(path = "test.txt")
## Attempt to commit with the internal pkgdown code
pkgdown:::git("commit", "-m", "hola")
# Running git commit -m hola
#
# *** Please tell me who you are.
#
# Run
#
# git config --global user.email "you@example.com"
# git config --global user.name "Your Name"
#
# to set your account's default identity.
# Omit --global to set the identity only in this repository.
#
# fatal: unable to auto-detect email address (got 'fellg@DESKTOP-GB1AFPA.(none)')
# Error in processx::run("git", c(...), echo_cmd = echo_cmd, echo = echo, :
# System command 'git' failed, exit status: 128, stdout & stderr were printed
# Type .Last.error.trace to see where the error occured
traceback()
# 4: stop(cond)
# 3: throw(new_process_error(res, call = sys.call(), echo = echo,
# stderr_to_stdout, res$status, command = command, args = args))
# 2: processx::run("git", c(...), echo_cmd = echo_cmd, echo = echo,
# error_on_status = error_on_status)
# 1: pkgdown:::git("commit", "-m", "hola")
## pkgdown's internal code relies on processx::run("git", "commit"),
## unlike usethis::use_git() which relies on git2r::commit()
## git2r does work, used internally by usethis::use_git() earlier
git2r::commit(message = "hola")
# [d49a7de] 2020-05-21: hola
## From https://stackoverflow.com/a/2115116
## Find which config file(s) pkgdown/processx are using:
## indeed, it doesn't find my email and username since it doesn't
## find my C:/Users/fellg/.gitconfig git config file
# pkgdown:::git("config", "--list", "--show-origin")
processx::run("git", c("config", "--list", "--show-origin"), echo_cmd = TRUE, echo = TRUE, error_on_status = TRUE)
# Running git config --list --show-origin
# file:C:/Program Files/Git/etc/gitconfig http.sslbackend=openssl
# file:C:/Program Files/Git/etc/gitconfig http.sslcainfo=C:/Program Files/Git/mingw64/ssl/certs/ca-bundle.crt
# file:C:/Program Files/Git/etc/gitconfig credential.helper=manager
# file:C:/Program Files/Git/etc/gitconfig core.editor="C:\\Program Files\\Notepad++\\notepad++.exe" -multiInst -notabbar -nosession -noPlugin
# file:C:/Program Files/Git/etc/gitconfig core.autocrlf=input
# file:C:/Program Files/Git/etc/gitconfig core.fscache=true
# file:C:/Program Files/Git/etc/gitconfig core.symlinks=false
# file:C:/Program Files/Git/etc/gitconfig diff.astextplain.textconv=astextplain
# file:C:/Program Files/Git/etc/gitconfig filter.lfs.clean=git-lfs clean -- %f
# file:C:/Program Files/Git/etc/gitconfig filter.lfs.smudge=git-lfs smudge -- %f
# file:C:/Program Files/Git/etc/gitconfig filter.lfs.process=git-lfs filter-process
# file:C:/Program Files/Git/etc/gitconfig filter.lfs.required=true
# file:.git/config core.bare=false
# file:.git/config core.repositoryformatversion=0
# file:.git/config core.filemode=false
# file:.git/config core.symlinks=false
# file:.git/config core.ignorecase=true
# file:.git/config core.logallrefupdates=true
# $status
# [1] 0
#
# $stdout
# [1] "file:C:/Program Files/Git/etc/gitconfig\thttp.sslbackend=openssl\nfile:C:/Program Files/Git/etc/gitconfig\thttp.sslcainfo=C:/Program Files/Git/mingw64/ssl/certs/ca-bundle.crt\nfile:C:/Program Files/Git/etc/gitconfig\tcredential.helper=manager\nfile:C:/Program Files/Git/etc/gitconfig\tcore.editor=\"C:\\\\Program Files\\\\Notepad++\\\\notepad++.exe\" -multiInst -notabbar -nosession -noPlugin\nfile:C:/Program Files/Git/etc/gitconfig\tcore.autocrlf=input\nfile:C:/Program Files/Git/etc/gitconfig\tcore.fscache=true\nfile:C:/Program Files/Git/etc/gitconfig\tcore.symlinks=false\nfile:C:/Program Files/Git/etc/gitconfig\tdiff.astextplain.textconv=astextplain\nfile:C:/Program Files/Git/etc/gitconfig\tfilter.lfs.clean=git-lfs clean -- %f\nfile:C:/Program Files/Git/etc/gitconfig\tfilter.lfs.smudge=git-lfs smudge -- %f\nfile:C:/Program Files/Git/etc/gitconfig\tfilter.lfs.process=git-lfs filter-process\nfile:C:/Program Files/Git/etc/gitconfig\tfilter.lfs.required=true\nfile:.git/config\tcore.bare=false\nfile:.git/config\tcore.repositoryformatversion=0\nfile:.git/config\tcore.filemode=false\nfile:.git/config\tcore.symlinks=false\nfile:.git/config\tcore.ignorecase=true\nfile:.git/config\tcore.logallrefupdates=true\n"
#
# $stderr
# [1] ""
#
# $timeout
# [1] FALSE
processx::run("which", "git", echo_cmd = TRUE, echo = TRUE)
# Running which git
# /cmd/git
# $status
# [1] 0
#
# $stdout
# [1] "/cmd/git\n"
#
# $stderr
# [1] ""
#
# $timeout
# [1] FALSE
processx::run("git", "--version", echo_cmd = TRUE, echo = TRUE)
# Running git --version
# git version 2.26.2.windows.1
# $status
# [1] 0
#
# $stdout
# [1] "git version 2.26.2.windows.1\n"
#
# $stderr
# [1] ""
#
# $timeout
# [1] FALSE
git2r::git_config_files(repo = ".")
# file path
# 1 system C:/Program Files/Git/etc/gitconfig
# 2 xdg <NA>
# 3 global C:/Users/fellg/.gitconfig
# 4 local C:\\Users\\fellg\\Desktop\\testgit\\.git/config
################### git bash terminal output ###################################
## updated today with:
# $ git update-git-for-windows
## from https://stackoverflow.com/a/48924212
## It does find my username and email =)
# $ which git
# /mingw64/bin/git
#
# ## Related to https://github.com/jennybc/happy-git-with-r/issues/67#issuecomment-341849422
# $ echo $PATH | tr ':' '\n'
# /c/Users/fellg/bin
# /mingw64/bin
# /usr/local/bin
# /usr/bin
# /bin
# /mingw64/bin
# /usr/bin
# /c/Users/fellg/bin
# /d/Rtools/bin
# /d/MiKTeX2.9/miktex/bin/x64
# /c/Windows/system32
# /c/Windows
# /c/Windows/System32/Wbem
# /c/Windows/System32/WindowsPowerShell/v1.0
# /c/Windows/System32/OpenSSH
# /c/Program Files (x86)/Intel/Intel(R) Management Engine Components/DAL
# /c/Program Files/Intel/Intel(R) Management Engine Components/DAL
# /c/Program Files (x86)/NVIDIA Corporation/PhysX/Common
# /c/Program Files/NVIDIA Corporation/NVIDIA NvDLISR
# /c/Program Files/PuTTY
# /cmd
# /mingw64/bin
# /usr/bin
# /c/Users/fellg/AppData/Local/Microsoft/WindowsApps
# /usr/bin/vendor_perl
# /usr/bin/core_perl
#
# $ git config --list --show-origin
# file:C:/Program Files/Git/etc/gitconfig http.sslbackend=openssl
# file:C:/Program Files/Git/etc/gitconfig http.sslcainfo=C:/Program Files/Git/mingw64/ssl/certs/ca-bundle.crt
# file:C:/Program Files/Git/etc/gitconfig credential.helper=manager
# file:C:/Program Files/Git/etc/gitconfig core.editor="C:\\Program Files\\Notepad++\\notepad++.exe" -multiInst -notabbar -nosession -noPlugin
# file:C:/Program Files/Git/etc/gitconfig core.autocrlf=input
# file:C:/Program Files/Git/etc/gitconfig core.fscache=true
# file:C:/Program Files/Git/etc/gitconfig core.symlinks=false
# file:C:/Program Files/Git/etc/gitconfig diff.astextplain.textconv=astextplain
# file:C:/Program Files/Git/etc/gitconfig filter.lfs.clean=git-lfs clean -- %f
# file:C:/Program Files/Git/etc/gitconfig filter.lfs.smudge=git-lfs smudge -- %f
# file:C:/Program Files/Git/etc/gitconfig filter.lfs.process=git-lfs filter-process
# file:C:/Program Files/Git/etc/gitconfig filter.lfs.required=true
# file:C:/Users/fellg/.gitconfig user.name=Leonardo Collado Torres
# file:C:/Users/fellg/.gitconfig user.email=lcolladotor@gmail.com
# ## More output
#
# $ git --version
# git version 2.26.2.windows.1
##################### RStudio terminal window output ##########################
## RStudio version: 1.2.5042
## Has "Git bash" selected under Global Options -> Terminal
# $ echo $SHELL
# /usr/bin/bash
#
# ## Different path to git than git bash
# ## though it's the xsame one used by
# $ which git
# /cmd/git
#
# ## It does find my config file though with my user name and email
# $ git config --global --list --show-origin
# file:C:/Users/fellg/.gitconfig user.name=Leonardo Collado Torres
# file:C:/Users/fellg/.gitconfig user.email=lcolladotor@gmail.com
# file:C:/Users/fellg/.gitconfig core.excludesfile=/Users/lcollado/.gitignore_global
# file:C:/Users/fellg/.gitconfig core.excludesfiles=/Users/lcollado/.gitignore_global
# file:C:/Users/fellg/.gitconfig core.editor=mate -w
# file:C:/Users/fellg/.gitconfig difftool.sourcetree.cmd=opendiff "$LOCAL" "$REMOTE"
# file:C:/Users/fellg/.gitconfig difftool.sourcetree.path=
# file:C:/Users/fellg/.gitconfig mergetool.sourcetree.cmd=/Applications/SourceTree.app/Contents/Resources
# /opendiff-w.sh "$LOCAL" "$REMOTE" -ancestor "$BASE" -merge "$MERGED"
# file:C:/Users/fellg/.gitconfig mergetool.sourcetree.trustexitcode=true
# file:C:/Users/fellg/.gitconfig alias.ci=commit
# file:C:/Users/fellg/.gitconfig alias.st=status
# file:C:/Users/fellg/.gitconfig alias.br=branch
# file:C:/Users/fellg/.gitconfig alias.co=checkout
# file:C:/Users/fellg/.gitconfig alias.last=log -1 HEAD
# file:C:/Users/fellg/.gitconfig alias.visual=gitk
# file:C:/Users/fellg/.gitconfig github.user=lcolladotor
# ## More output
#
# ## Related to https://github.com/jennybc/happy-git-with-r/issues/67#issuecomment-341849422
# $ echo $PATH | tr ':' '\n'
# /d/R/R-4.0.0/bin/x64
# /d/R/R-4.0.0/bin/x64
# /d/R/R-4.0.0/bin/x64
# /d/Rtools/bin
# /d/MiKTeX2.9/miktex/bin/x64
# /c/Windows/system32
# /c/Windows
# /c/Windows/System32/Wbem
# /c/Windows/System32/WindowsPowerShell/v1.0
# /c/Windows/System32/OpenSSH
# /c/Program Files (x86)/Intel/Intel(R) Management Engine Components/DAL
# /c/Program Files/Intel/Intel(R) Management Engine Components/DAL
# /c/Program Files (x86)/NVIDIA Corporation/PhysX/Common
# /c/Program Files/NVIDIA Corporation/NVIDIA NvDLISR
# /c/Program Files/PuTTY
# /cmd
# /mingw64/bin
# /usr/bin
# /c/Users/fellg/AppData/Local/Microsoft/WindowsApps
# /bin
# /c/Program Files/RStudio/bin/msys-ssh-1000-18
#
# $ git --version
# git version 2.26.2.windows.1
## git bash was installed as recommended at
## https://github.com/rstudio/rstudio/issues/2224#issuecomment-368260312
## which I see that it's not the same recommendation from
## https://github.com/jennybc/happy-git-with-r/issues/67#issuecomment-343800308
## (see the "Reinstalling, the only option I change is" section)
library("sessioninfo")
options(width = 120)
session_info()
# - Session info -------------------------------------------------------------------------------------------------------
# setting value
# version R version 4.0.0 (2020-04-24)
# os Windows 10 x64
# system x86_64, mingw32
# ui RStudio
# language (EN)
# collate English_United States.1252
# ctype English_United States.1252
# tz America/New_York
# date 2020-05-21
#
# - Packages -----------------------------------------------------------------------------------------------------------
# package * version date lib source
# assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
# cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
# crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
# digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
# fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
# fs 1.4.1 2020-04-04 [1] CRAN (R 4.0.0)
# git2r 0.27.1 2020-05-03 [1] CRAN (R 4.0.0)
# glue 1.4.1 2020-05-13 [1] CRAN (R 4.0.0)
# magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
# MASS 7.3-51.5 2019-12-20 [1] CRAN (R 4.0.0)
# memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
# packrat 0.5.0 2018-11-14 [1] CRAN (R 4.0.0)
# pkgdown 1.5.1 2020-04-09 [1] CRAN (R 4.0.0)
# processx 3.4.2 2020-02-09 [1] CRAN (R 4.0.0)
# ps 1.3.3 2020-05-08 [1] CRAN (R 4.0.0)
# R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
# rlang 0.4.6 2020-05-02 [1] CRAN (R 4.0.0)
# rsconnect 0.8.16 2019-12-13 [1] CRAN (R 4.0.0)
# rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0)
# sessioninfo * 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
# usethis 1.6.1 2020-04-29 [1] CRAN (R 4.0.0)
# withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)
#
# [1] D:/R/R-4.0.0/library
############# re-install git for windows https://gitforwindows.org/ ############
## Use the same options as recommended at
## https://github.com/jennybc/happy-git-with-r/issues/67#issuecomment-343800308
## (see the "Reinstalling, the only option I change is" section)
## Create a file
setwd("testgit")
writeLines("hola", "test2.txt")
## Use git2r to add it (can also be done with the RStudio git panel)
git2r::add(path = "test2.txt")
## Attempt to commit with the internal pkgdown code
pkgdown:::git("commit", "-m", "hola2")
# Running git commit -m hola2
#
# *** Please tell me who you are.
#
# Run
#
# git config --global user.email "you@example.com"
# git config --global user.name "Your Name"
#
# to set your account's default identity.
# Omit --global to set the identity only in this repository.
#
# fatal: unable to auto-detect email address (got 'fellg@DESKTOP-GB1AFPA.(none)')
# Error in processx::run("git", c(...), echo_cmd = echo_cmd, echo = echo, :
# System command 'git' failed, exit status: 128, stdout & stderr were printed
# Type .Last.error.trace to see where the error occured
traceback()
# 4: stop(cond)
# 3: throw(new_process_error(res, call = sys.call(), echo = echo,
# stderr_to_stdout, res$status, command = command, args = args))
# 2: processx::run("git", c(...), echo_cmd = echo_cmd, echo = echo,
# error_on_status = error_on_status)
# 1: pkgdown:::git("commit", "-m", "hola2")
processx::run("git", c("commit", "-m", "hola2"), echo_cmd = TRUE, echo = TRUE)
# Running git commit -m hola2
#
# *** Please tell me who you are.
#
# Run
#
# git config --global user.email "you@example.com"
# git config --global user.name "Your Name"
#
# to set your account's default identity.
# Omit --global to set the identity only in this repository.
#
# fatal: unable to auto-detect email address (got 'fellg@DESKTOP-GB1AFPA.(none)')
# Error in processx::run("git", c("commit", "-m", "hola2"), echo_cmd = TRUE, :
# System command 'git' failed, exit status: 128, stdout & stderr were printed
# Type .Last.error.trace to see where the error occured
## The git re-install (1 setting changed) removed unix tools like which
## as expected given the text describing the settings
processx::run("which", "git", echo_cmd = TRUE, echo = TRUE)
# Running which git
# Error in rethrow_call(c_processx_exec, command, c(command, args), stdin, :
# Command 'which' not found @win/processx.c:983 (processx_exec)
# Type .Last.error.trace to see where the error occured
## The git re-install did affect the PATH as seen from the RStudio terminal
# $ echo $PATH | tr ':' '\n'
# /d/R/R-4.0.0/bin/x64
# /d/Rtools/bin
# /d/MiKTeX2.9/miktex/bin/x64
# /c/Windows/system32
# /c/Windows
# /c/Windows/System32/Wbem
# /c/Windows/System32/WindowsPowerShell/v1.0
# /c/Windows/System32/OpenSSH
# /c/Program Files (x86)/Intel/Intel(R) Management Engine Components/DAL
# /c/Program Files/Intel/Intel(R) Management Engine Components/DAL
# /c/Program Files (x86)/NVIDIA Corporation/PhysX/Common
# /c/Program Files/NVIDIA Corporation/NVIDIA NvDLISR
# /c/Program Files/PuTTY
# /cmd
# /c/Users/fellg/AppData/Local/Microsoft/WindowsApps
# /bin
# /c/Program Files/RStudio/bin/msys-ssh-1000-18
## On the git bash terminal, it only removed the second "/mingw64/bin" from
## $ echo $PATH | tr ':' '\n'
############ Reinstalling git bash with the "use git from git bash only"
## As expected, processx::run() and the RStudio terminal can't find git now
setwd("testgit")
pkgdown:::git("commit", "-m", "hola2")
# Running git commit -m hola2
# Error in rethrow_call(c_processx_exec, command, c(command, args), stdin, :
# Command 'git' not found @win/processx.c:983 (processx_exec)
# Type .Last.error.trace to see where the error occured
processx::run("git", c("commit", "-m", "hola2"), echo_cmd = TRUE, echo = TRUE)
# Running git commit -m hola2
# Error in rethrow_call(c_processx_exec, command, c(command, args), stdin, :
# Command 'git' not found @win/processx.c:983 (processx_exec)
# Type .Last.error.trace to see where the error occured
traceback()
# 12: stop(cond)
# 11: throw(e)
# 10: h(simpleError(msg, call))
# 9: .handleSimpleError(function (e)
# {
# e$`_nframe` <- nframe
# e$call <- call
# if (inherits(e, "simpleError")) {
# class(e) <- c("c_error", "rlib_error", "error", "condition")
# }
# e$`_ignore` <- list(c(nframe + 1L, sys.nframe() + 1L))
# throw(e)
# }, "Command 'git' not found @win/processx.c:983 (processx_exec)",
# base::quote(do.call(".Call", list(.NAME, ...))))
# 8: .Call(structure(list(name = "processx_exec", address = <pointer: 0x000001a8b0f1f5f0>,
# dll = structure(list(name = "processx", path = "D:/R/R-4.0.0/library/processx/libs/x64/processx.dll",
# dynamicLookup = FALSE, handle = <pointer: 0x0000000068080000>,
# info = <pointer: 0x000001a8b0ea4510>), class = "DLLInfo"),
# numParameters = 16L), class = c("CallRoutine", "NativeSymbolInfo"
# )), "git", c("git", "commit", "-m", "hola2"), NULL, "|", "|",
# FALSE, list(echo = FALSE), list(), NULL, FALSE, FALSE, <environment>,
# TRUE, NULL, "", "PROCESSX_PSUPG0B88ZG2_1590103219=YES")
# 7: do.call(".Call", list(.NAME, ...))
# 6: withCallingHandlers(do.call(".Call", list(.NAME, ...)), error = function(e) {
# e$`_nframe` <- nframe
# e$call <- call
# if (inherits(e, "simpleError")) {
# class(e) <- c("c_error", "rlib_error", "error", "condition")
# }
# e$`_ignore` <- list(c(nframe + 1L, sys.nframe() + 1L))
# throw(e)
# })
# 5: rethrow_call(c_processx_exec, command, c(command, args), stdin,
# stdout, stderr, pty, pty_options, connections, env, windows_verbatim_args,
# windows_hide_window, private, cleanup, wd, encoding, paste0("PROCESSX_",
# private$tree_id, "=YES"))
# 4: process_initialize(self, private, command, args, stdin, stdout,
# stderr, pty, pty_options, connections, poll_connection, env,
# cleanup, cleanup_tree, wd, echo_cmd, supervise, windows_verbatim_args,
# windows_hide_window, encoding, post_process)
# 3: .subset2(public_bind_env, "initialize")(...)
# 2: process$new(command, args, echo_cmd = echo_cmd, wd = wd, windows_verbatim_args = windows_verbatim_args,
# windows_hide_window = windows_hide_window, stdout = "|",
# stderr = stderr, env = env, encoding = encoding, cleanup_tree = cleanup_tree,
# ...)
# 1: processx::run("git", c("commit", "-m", "hola2"), echo_cmd = TRUE,
# echo = TRUE)
## From the RStudio terminal:
# $ which git
# which: no git in (/d/R/R-4.0.0/bin/x64:/d/Rtools/bin:/d/MiKTeX2.9/miktex/bin/x64:/c/Windows/system32:/c/Windows:/c/Windows/Syste
# m32/Wbem:/c/Windows/System32/WindowsPowerShell/v1.0:/c/Windows/System32/OpenSSH:/c/Program Files (x86)/Intel/Intel(R) Management
# Engine Components/DAL:/c/Program Files/Intel/Intel(R) Management Engine Components/DAL:/c/Program Files (x86)/NVIDIA Corporatio
# n/PhysX/Common:/c/Program Files/NVIDIA Corporation/NVIDIA NvDLISR:/c/Program Files/PuTTY:/c/Users/fellg/AppData/Local/Microsoft/
# WindowsApps:/bin:/c/Program Files/RStudio/bin/msys-ssh-1000-18)
## git2r still works though, so it's not affected by git bash installation steps
git2r::commit(message = "hola2 - 'use git from git bash only' scenario")
# [d69d79b] 2020-05-21: hola2 - 'use git from git bash only' scenario
## The RStudio git panel also worked (I thought that it wouldn't since
## we told git to only be available from git bash)
writeLines("hola", "test3.txt")
## I was able to commit that file from the RStudio git panel, it showed
## the following info:
# >>> C:/Program Files/Git/bin/git.exe commit -F C:/Users/fellg/AppData/Local/Temp/RtmpWQJO82/git-commit-message-3ba832ed5222.txt
# [master e4785c1] prueba
# 1 file changed, 1 insertion(+)
# create mode 100644 test3.txt
writeLines("hola", "test4.txt")
git2r::add(path = "test4.txt")
## Try using processx with the full git path I saw Rstudio use
processx::run("C:\\Program Files\\Git\\bin\\git.exe", c("commit", "-m", "test4"), echo_cmd = TRUE, echo = TRUE)
# Running "C:\Program Files\Git\bin\git.exe" commit -m test4
#
# *** Please tell me who you are.
#
# Run
#
# git config --global user.email "you@example.com"
# git config --global user.name "Your Name"
#
# to set your account's default identity.
# Omit --global to set the identity only in this repository.
#
# fatal: unable to auto-detect email address (got 'fellg@DESKTOP-GB1AFPA.(none)')
# Error in processx::run("C:\\Program Files\\Git\\bin\\git.exe", c("commit", :
# System command 'git.exe' failed, exit status: 128, stdout & stderr were printed
# Type .Last.error.trace to see where the error occured
traceback()
# 3: stop(cond)
# 2: throw(new_process_error(res, call = sys.call(), echo = echo,
# stderr_to_stdout, res$status, command = command, args = args))
# 1: processx::run("C:\\Program Files\\Git\\bin\\git.exe", c("commit",
# "-m", "test4"), echo_cmd = TRUE, echo = TRUE)
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