Loading shared library error, libpng, Stata, Hydrogen

[mateokhan]

When using Hydrogen in Atom, I don't see the expected output when using Stata code; instead, I receive an error, the error in the log:

/usr/local/stata15/stata-se: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory

I originally had difficulty getting Stata to work on Linux Mint 19.3. Used a workaround utilizing https://github.com/dirtyhawk/stata-integration.git ; due to there being a difficulty getting that libpng12 to come in. The workaround created a folder named: /usr/local/stata15/libpngworkaround/lib

This is where the libpng12.so.0 is, is there a simple way of directing to it? Or might I need to retry the Stata install and figure out how to avoid the workaround? My bad if I'm way off here.

• Operating System: Linux Mint 19.3
• Stata version 15-se
• Package version 1.11.1

[kylebarron]

Are you able to run Stata outside Atom? If so, then you probably just need to open Atom with your LD_LIBRARY_PATH set to include that library location. Something like

LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/path/to/libraries" atom /path/to/code/dir

Then I think Atom will be opened with that LD_LIBRARY_PATH in its process.env, and that will be passed on to the kernel when it's created.

Also, I haven't used Stata for a while, but you should check out my previous solution for getting it to work with libpng on linux: https://github.com/kylebarron/stata-png-fix

[mateokhan]

I am able to run Stata outside of Atom. I did try and set the LD_LIBRARY_PATH, and looked at the link you provided for https://github.com/kylebarron/stata-png-fix to see if that might improve anything. Still receiving the same error after.

Just to make sure I'm not introducing operator error: I used LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/Stata15"

Just to make sure, I did see that hydrogen works with other kernels (python), and the problem was reproducible using JupyterLab (i.e. same error for Stata, works with python).

[kylebarron]

Oh the issue there is that you're providing the path to the wrong place. You need to find wherever libpng is, not where the stata executable is

[mateokhan]

Alright! Got it pointed to the right location, I assume, but now getting a very different error. The console_debug is now just my Stata welcome screen.

[?1h= _ (R) / / __/ / ___/ / / // / // 15.1 Copyright 1985-2017 StataCorp LLC Statistics/Data Analysis StataCorp 4905 Lakeway Drive Special Edition College Station, Texas 77845 USA 800-STATA-PC http://www.stata.com 979-696-4600 stata@stata.com 979-696-4601 (fax)

Single-user Stata perpetual license: Serial number: #### Licensed to: X X

Notes:

1. Unicode is supported; see help unicode_advice.
2. Maximum number of variables is set to 5000; see help set_maxvar.

running /usr/local/bin/profile.do ...

.

If this is a different "issue" I can close this and continue to try and make it work. The LD path just needed the command to be pointed in the right direction.

[kylebarron]

What's the error? That looks normal on the console debug script

[mateokhan]

When I attempt to run a line in hydrogen, I get a very long red error pane in hydrogen with Stata as the header, that has a lot of TIMEOUT errors (this looked similar to before when I wasn't locating libpng library), but at the end it's confusing. The last line states,

<pexpect.pty_spawn.spawn object at 0x7f5d10440ac8> command: /usr/local/stata15/stata-se args: [b'/usr/local/stata15/stata-se'] buffer (last 100 chars): 'riables is set to 5000; see help set_maxvar.\r\n\r\nrunning /usr/local/bin/profile.do ...\r\n\r\n\x1b[0m\x1b[37m. ' before (last 100 chars): 'riables is set to 5000; see help set_maxvar.\r\n\r\nrunning /usr/local/bin/profile.do ...\r\n\r\n\x1b[0m\x1b[37m. ' after: match: None match_index: None exitstatus: None flag_eof: False pid: 2237 child_fd: 80 closed: False timeout: 30 delimiter: logfile: <_io.TextIOWrapper name='/home/user/.stata_kernel_cache/console_debug.log' mode='w' encoding='utf-8'> logfile_read: None logfile_send: None maxread: 2000 ignorecase: False searchwindowsize: None delaybeforesend: None delayafterclose: 0.1 delayafterterminate: 0.1 searcher: searcher_re: 0: re.compile('\r\n. ')

When I try to run this with Jupyter console in terminal, there's quite a bit more error lines that look similar, but the very end says File "/home/user/anaconda3/lib/python3.7/site-packages/jupyter_console/ptshell.py", line 326, in init_kernel_info raise RuntimeError("Kernel didn't respond to kernel_info_request") RuntimeError: Kernel didn't respond to kernel_info_request

I don't know if this latter information helps, just trying to give a full picture.