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Hemken / Statamarkdown

Functions to write Stata documentation with knitr
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Small improvement to `find_stata()` on Linux #26

Closed remlapmot closed 2 years ago

remlapmot commented 2 years ago

I started using Linux again and taking some of the discussion from #6 this hopefully improves find_stata() on Linux.

At the moment when I load the package it just finds the stata executable (which obvs I could change in the options).

Hemken commented 2 years ago

Thanks!

Hemken commented 2 years ago

Tom, thanks for the update!

I found that code did not work for me, so I have extended it to search a few likely directories in case Stata is not on the executable search PATH.

If you wouldn’t mind, could you install this latest tweak and verify that it still works for you? Your code is still intact, and runs first.

From: Tom Palmer @.> Sent: Sunday, February 20, 2022 12:40 PM To: Hemken/Statamarkdown @.> Cc: Subscribed @.***> Subject: [Hemken/Statamarkdown] Small improvement to find_stata() on Linux (PR #26)

I started using Linux again and taking some of the discussion from #6https://github.com/Hemken/Statamarkdown/pull/6 this hopefully improves find_stata() on Linux.

· tom:/usr/local/stata17$ ls -a

· . auto.dta installed.170 libstata-se.so stata stata.lic stata_pdf xstata

· .. docs isstata.170 libstata.so stata-mp stata17.png stinit xstata-mp

· ado inst2 libstata-mp.so setrwxp stata-se stata_br utilities xstata-se

At the moment when I load the package it just finds the stata executable (which obvs I could change in the options).

You can view, comment on, or merge this pull request online at:

https://github.com/Hemken/Statamarkdown/pull/26

Commit Summary

File Changes

(1 filehttps://github.com/Hemken/Statamarkdown/pull/26/files)

Patch Links:

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remlapmot commented 2 years ago

Hi Doug (sorry for long reply - and apologies if you already know all of this)

I have been bitten by PATH problems in R on Linux many times ... it took me a long time to discover the following.

This is because PATH is different depending upon whether R is launched as a user or superuser (as rstudio-server often is, e.g., it is when I run it under Windows Subsystem for Linux).

Initially, I added the /usr/local/stata-mp directory to my PATH in my .bashrc file. Then launching R as user from bash includes this directory in PATH and all is fine.

However, if I launched R as a superuser with sudo R (without adding to PATH in either the .Renviron or Renviron.site files), then PATH is only these few directories,

> Sys.getenv("PATH")
[1] "/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin"

My best solution is to add the /usr/local/stata17 directory to PATH in the Renviron.site file, which is in ${R_HOME}/etc (/usr/lib/R/etc in my Ubuntu), with the line

PATH=${PATH}:/usr/local/stata17

Then PATH in a sudo R session is

> Sys.getenv('PATH')
[1] "/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/usr/local/stata17"

And so calling Sys.which("stata-mp") in that finds stata-mp and all is well.

A slightly less good solution is to amend PATH in your .Renviron file, however, I think that means the sudo R/sudo rstudio-server session must be launched from the same directory that .Renviron file is in.

If I don't amend my PATH in Renviron.site/.Renviron both my code and your code don't find stata-mp under a sudo R or sudo rstudio-sever session because your additional directories don't include /usr/local/stata17 and that's not on PATH.

So you could add /usr/local/stata17 (and perhaps /usr/local/stata16 and /usr/local/stata15 as well) to the additional directories you added.

And perhaps we should add an explanation about PATH being different under R and sudo R/sudo rstudio-server sessions to the helpfiles?

All best, Tom

Hemken commented 2 years ago

I see! (You have discovered that I am recently using Statamarkdown in RStudio Server, nice detective work!) Thanks for the details. I am vaguely aware of some of these Linux configuration issues with other software, but had not investigated them with respect to Statamarkdown.

So I agree with you that:

From: Tom Palmer @.> Sent: Thursday, March 3, 2022 5:06 AM To: Hemken/Statamarkdown @.> Cc: Doug Hemken @.>; State change @.> Subject: Re: [Hemken/Statamarkdown] Small improvement to find_stata() on Linux (PR #26)

Hi Doug (sorry for long reply - and apologies if you already know all of this)

I have been bitten by PATH problems in R on Linux many times ... it took me a long time to discover the following.

This is because PATH is different depending upon whether R is launched as a user or superuser (as rstudio-server often is, e.g., it is when I run it under Windows Subsystem for Linux).

Initially, I added the /usr/local/stata-mp directory to my PATH in my .bashrc file. Then launching R as user from bash includes this directory in PATH and all is fine.

However, if I launched R as a superuser with sudo R (without adding to PATH in either the .Renviron or Renviron.site files), then PATH is only these few directories,

Sys.getenv("PATH")

[1] "/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin"

My best solution is to add the /usr/local/stata17 directory to PATH in the Renviron.site file, which is in ${R_HOME}/etc (/usr/lib/R/etc in my Ubuntu), with the line

PATH=${PATH}:/usr/local/stata17

Then PATH in a sudo R session is

Sys.getenv('PATH')

[1] "/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/usr/local/stata17"

And so calling Sys.which("stata-mp") in that finds stata-mp and all is well.

A slightly less good solution is to amend PATH in your .Renviron file, however, I think that means the sudo R/sudo rstudio-server session must be launched from the same directory that .Renviron file is in.

If I don't amend my PATH in Renviron.site/.Renviron both my code and your code don't find stata-mp under a sudo R or sudo rstudio-sever session because your additional directories don't include /usr/local/stata17 and that's not on PATH.

So you could add /usr/local/stata17 (and perhaps /usr/local/stata16 and /usr/local/stata15 as well) to the additional directories you added.

And perhaps we should add an explanation about PATH being different under R and sudo R/sudo rstudio-server sessions to the helpfiles?

All best, Tom

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