Output Not Captured

[terrytangyuan]

See this part of the code: https://github.com/rstudio/tflearn/blob/master/tests/testthat/test-hooks.R#L17
where the output doesn't seem to be captured using py_capture_stdout. Is this the correct way to use it? The capture.output from R only captures the output for the return value of linear_dnn_combined_regression. Is py_capture_stdout able to capture loggings from TF?

[terrytangyuan]

Seems like probably an issue regarding how TF tells whether RStudio is an interactive environment. https://github.com/tensorflow/tensorflow/blob/master/tensorflow/python/platform/tf_logging.py#L55
Perhaps we can also have a function for capturing standard error which is where logs in non-interactive environment go to.

[jjallaire]

Yes, py_capture_output only captures output. We do however already have some hooks to interact with the TF logging system (we use them in py_suppress_warnings. If you let me know exactly the behavior you want here (perhaps with a simple repro) I can make some combination of py_capture_output and py_suppress_warnings make it happen.

[terrytangyuan]

Oh I see. Yea I am expecting the following as part of the output:

INFO:tensorflow:Create CheckpointSaverHook.
INFO:tensorflow:Saving checkpoints for 2 into /var/folders/ln/c7r_x26x46b7vzpftbfh64zc0000gp/T//RtmpbD66eR/tflearn_a32c5e4d2404/model.ckpt.
INFO:tensorflow:loss = 438.822, step = 2
INFO:tensorflow:global_step = 2
INFO:tensorflow:global_step = 6 (0.016 sec)
INFO:tensorflow:global_step = 10 (0.002 sec)

[jjallaire]

I think the problem may be here:

https://github.com/tensorflow/tensorflow/blob/master/tensorflow/python/platform/tf_logging.py#L39-L56

You can that TF is trying to determine whether the session is interactive. In the case that it is it will pipe output to stdout (which we could then capture) however in the case where it's not it sends it to stderr. That relies on the state of sys.flags.interactive which we maybe able to set by passing the correct command line flag to startup.

[jjallaire]

Okay, the function is now renamed py_capture_output. By default it captures both stdout and stderr but it can be configured to capture just one or the other:

2071de8

This should get you what you are looking for, let me know if it doesn't.

[terrytangyuan]

Thanks, will try!

[jjallaire]

Closing this. Feel free to re-open if you have additional issues.

[terrytangyuan]

Just gave it a try. Still looks like not able to capture those output. Not a blocker though.

[jjallaire]

I'd really like to get this resolved. Can you provide me the smallest possible snippet of R code that exhibits the problem and I'll dig in further?

…

On Sun, Feb 12, 2017 at 12:55 PM, Yuan (Terry) Tang < ***@***.***> wrote: Oh I see. Yea I am expecting the following as part of the output: INFO:tensorflow:Create CheckpointSaverHook. INFO:tensorflow:Saving checkpoints for 2 into /var/folders/ln/c7r_x26x46b7vzpftbfh64zc0000gp/T//RtmpbD66eR/tflearn_a32c5e4d2404/model.ckpt. INFO:tensorflow:loss = 438.822, step = 2 INFO:tensorflow:global_step = 2 INFO:tensorflow:global_step = 6 (0.016 sec) INFO:tensorflow:global_step = 10 (0.002 sec) — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#7 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAGXx_RHe-siWXcluMnCsXCExmM3uy5xks5rb0eogaJpZM4L-TQY> .

[terrytangyuan]

Here it is:

> output <- reticulate::py_capture_output(tf$logging$warn("asdf"))
WARNING:tensorflow:asdf
> output
[1] ""

[jjallaire]

Interesting, for me this actually successfully captures the output! Here's my exact code as executed (I think it's the same):

library(tensorflow)
output <- reticulate::py_capture_output(tf$logging$warn("asdf"))

Are you certain you've upgraded to the latest versions of tensorflow and reticulate?

[terrytangyuan]

Yes, I've removed all packages and reinstalled everything. Otherwise py_capture_output won't be available in old versions.

[jjallaire]

What platform are you on?

…

On Thu, Feb 16, 2017 at 7:01 PM Yuan (Terry) Tang ***@***.***> wrote: Yes, I've removed all packages and reinstalled everything. Otherwise py_capture_output won't be available in old versions. — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#7 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAGXx_bU8pU96XOCVHWN27EOiC4D9BTXks5rdONAgaJpZM4L-TQY> .

[terrytangyuan]

Okay apologize that I didn't clean up my environment properly. That one worked as expected. However, here's what's weird:

> library(tensorflow)
> tf$logging$get_verbosity()
[1] 30
> tf$logging$WARN
[1] 30
> tf$logging$set_verbosity(tf$logging$INFO)
> tf$logging$get_verbosity()
[1] 20
> output <- reticulate::py_capture_output(tf$logging$info("asdf"))
INFO:tensorflow:asdf
> output
[1] ""

Verbosity is set to info correctly but the output is not captured.

Could you try if you can reproduce it?

[jjallaire]

It looks to me like the INFO stream is bypassing stderr. If I write this then the output is correctly captured:

output <- reticulate::py_capture_output({
  sys <- import("sys")
  sys$stderr$write("foo")  
})

Are you just trying to prevent INFO messages from being printed at all? If so we could do something like we do for py_suppress_warnings:

https://github.com/rstudio/tensorflow/blob/master/R/package.R#L35-L45

[terrytangyuan]

I am trying to capture a regex in the output. But it's not super important. I think this is an issue on the Python API end. I'll reopen if this turns out to be very critical.