Cannot show output after running cell in R notebook with trailing comment

[williamcplai]

Type: Bug

cannot show output after running cell in R notebook
how to configure ?

VS Code version: Positron 1.90.0 (d8da3ec9581aa7bcb9726babedacff4e3d528503, 2024-07-05T03:18:37.706Z)
OS version: Windows_NT x64 10.0.22631
Modes:

System Info

Item	Value
CPUs	12th Gen Intel(R) Core(TM) i7-12700H (20 x 2688)
GPU Status	2d_canvas: enabled canvas_oop_rasterization: enabled_on direct_rendering_display_compositor: disabled_off_ok gpu_compositing: enabled multiple_raster_threads: enabled_on opengl: enabled_on rasterization: enabled raw_draw: disabled_off_ok skia_graphite: disabled_off video_decode: enabled video_encode: enabled vulkan: disabled_off webgl: enabled webgl2: enabled webgpu: enabled
Load (avg)	undefined
Memory (System)	15.73GB (1.06GB free)
Process Argv
Screen Reader	no
VM	0%

Extensions: none

[petetronic]

Can you please share a little more information about the file you're running and the version of R you're using? Do you mean an R Markdown file? Or R cells in a Jupyter notebook?

[williamcplai]

After click the cells , it cannot show the outputs

[juliasilge]

Hmmm, we can't reproduce this problem on Windows or other OSes.

• Can you share what version of R you are running?
• Can you go to "Output" and choose the output channel for your notebook, then share the log file you find there? It will look something like this:

• Can you use the command "Toggle Developer Tools" and see if there are any errors or warnings relevant to notebook execution in those logs? It will look something like this:

[williamcplai]

R4.3.2

[R] *** Log started at Sun 14/07/2024 18:07:40.80
[R] *** Command line:
[R] "c:\Program Files\Positron\resources\app\extensions\positron-r\resources\ark\ark.exe" --connection_file C:\Users\William\AppData\Local\Temp\kernel-AX2jap\connection.json --log C:\Users\William\AppData\Local\Temp\kernel-AX2jap\kernel.log --startup-file "c:\Program Files\Positron\resources\app\extensions\positron-r\resources\scripts\startup.R" --session-mode notebook -- --interactive --no-restore-data
[Positron] Sending code to R: # The datasets package needs to be loaded to access our data

For a full list of these datasets, type library(help = "datasets")

library(datasets)
data(iris)
summary(iris)
[Positron] SEND execute_request to Shell: {"buffers":[],"content":{"code":"# The datasets package needs to be loaded to access our data \n# For a full list of these datasets, type library(help = "datasets")\nlibrary(datasets)\ndata(iris)\nsummary(iris)","allow_stdin":true,"silent":false,"store_history":true,"user_expressions":{},"stop_on_error":true},"header":{"msg_id":"positron-notebook-cell-34","msg_type":"execute_request","version":"5.0","date":"2024-07-14T10:07:57.314Z","session":"57cab38faca1b653054ad9edb568b074","username":"William"},"metadata":{},"parent_header":{}}
[Positron] SEND execute_request: OK
[Positron] R kernel status changed: idle => busy
[Positron] RECV status/busy from iopub: {"header":{"msg_id":"467c404b-1030-4714-94ca-30ce60b73f0a","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:07:57.315305600+00:00","msg_type":"status","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-34","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:07:57.314Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"execution_state":"busy"},"buffers":[]}
[Positron] RECV execute_input from iopub: {"header":{"msg_id":"ab911983-544f-417e-af18-2516090560ab","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:07:57.315526600+00:00","msg_type":"execute_input","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-34","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:07:57.314Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"code":"# The datasets package needs to be loaded to access our data \n# For a full list of these datasets, type library(help = "datasets")\nlibrary(datasets)\ndata(iris)\nsummary(iris)","execution_count":1},"buffers":[]}
[Positron] RECV comm_msg/positron-ui-r-9-c9099c32/undefined from iopub: {"header":{"msg_id":"04dfcfd7-a75d-4d4b-9a93-e031e80927f8","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:07:57.315679100+00:00","msg_type":"comm_msg","version":"5.3"},"parent_header":{},"metadata":{},"content":{"comm_id":"positron-ui-r-9-c9099c32","data":{"method":"busy","params":{"busy":true}}},"buffers":[]}
[Positron] RECV comm_msg/positron-ui-r-9-c9099c32/undefined from iopub: {"header":{"msg_id":"9c2dc0d4-dc0d-4b4d-99f0-7d80c0f0600f","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:07:57.323966+00:00","msg_type":"comm_msg","version":"5.3"},"parent_header":{},"metadata":{},"content":{"comm_id":"positron-ui-r-9-c9099c32","data":{"method":"busy","params":{"busy":false}}},"buffers":[]}
[Positron] RECV comm_msg/positron-ui-r-9-c9099c32/undefined from iopub: {"header":{"msg_id":"b7e3555b-f19f-4cbb-9b17-34f8f195dbb7","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:07:57.324019500+00:00","msg_type":"comm_msg","version":"5.3"},"parent_header":{},"metadata":{},"content":{"comm_id":"positron-ui-r-9-c9099c32","data":{"method":"prompt_state","params":{"input_prompt":"> ","continuation_prompt":"+ "}}},"buffers":[]}
[Positron] RECV execute_result from iopub: {"header":{"msg_id":"2fe5be71-b6ad-43d0-9c27-701f6a08bb47","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:07:57.324031800+00:00","msg_type":"execute_result","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-34","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:07:57.314Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"data":{"text/plain":" Sepal.Length Sepal.Width Petal.Length Petal.Width Species \n Min. :4.300 Min. :2.000 Min. :1.000 Min. :0.100 setosa :50 \n 1st Qu.:5.100 1st Qu.:2.800 1st Qu.:1.600 1st Qu.:0.300 versicolor:50 \n Median :5.800 Median :3.000 Median :4.350 Median :1.300 virginica :50 \n Mean :5.843 Mean :3.057 Mean :3.758 Mean :1.199 \n 3rd Qu.:6.400 3rd Qu.:3.300 3rd Qu.:5.100 3rd Qu.:1.800 \n Max. :7.900 Max. :4.400 Max. :6.900 Max. :2.500 "},"execution_count":1,"metadata":{}},"buffers":[]}
[Positron] R kernel status changed: busy => idle
[Positron] RECV status/idle from iopub: {"header":{"msg_id":"efc254c5-372d-4d82-86cd-3638a66a4a90","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:07:57.324092300+00:00","msg_type":"status","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-34","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:07:57.314Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"execution_state":"idle"},"buffers":[]}
[Positron] RECV execute_reply from shell: {"header":{"msg_id":"b4e1fc7f-0dcf-4fc1-98a1-1c57db6db8d2","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:07:57.324044700+00:00","msg_type":"execute_reply","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-34","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:07:57.314Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"status":"ok","execution_count":1,"user_expressions":{}},"buffers":[]}
[Positron] RECV comm_msg/positron-variables-r-10-ba2b1da1/undefined from iopub: {"header":{"msg_id":"bd56de09-9eb7-4824-8e5d-405f7b35b05f","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:07:57.333867800+00:00","msg_type":"comm_msg","version":"5.3"},"parent_header":{},"metadata":{},"content":{"comm_id":"positron-variables-r-10-ba2b1da1","data":{"method":"update","params":{"assigned":[{"access_key":"iris","display_name":"iris","display_value":"[150 rows x 5 columns] <data.frame>","display_type":"data.frame [150, 5]","type_info":"","size":7256,"kind":"table","length":5,"has_children":true,"has_viewer":true,"is_truncated":false,"updated_time":1720951677333}],"unevaluated":[],"removed":[],"version":2}}},"buffers":[]}
[Positron] SEND heartbeat with timeout of 30 seconds
[Positron] Sending code to R: names(iris) <- tolower(names(iris))
library(dplyr)
[Positron] SEND execute_request to Shell: {"buffers":[],"content":{"code":"names(iris) <- tolower(names(iris))\nlibrary(dplyr)","allow_stdin":true,"silent":false,"store_history":true,"user_expressions":{},"stop_on_error":true},"header":{"msg_id":"positron-notebook-cell-35","msg_type":"execute_request","version":"5.0","date":"2024-07-14T10:08:12.995Z","session":"57cab38faca1b653054ad9edb568b074","username":"William"},"metadata":{},"parent_header":{}}
[Positron] SEND execute_request: OK
[Positron] R kernel status changed: idle => busy
[Positron] RECV status/busy from iopub: {"header":{"msg_id":"bb0e1d66-21d8-4136-a55f-7a5ea3357f94","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:12.996067100+00:00","msg_type":"status","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-35","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:08:12.995Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"execution_state":"busy"},"buffers":[]}
[Positron] RECV execute_input from iopub: {"header":{"msg_id":"c9d0bead-6cf6-433e-939f-e92757ddce1f","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:12.996124700+00:00","msg_type":"execute_input","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-35","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:08:12.995Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"code":"names(iris) <- tolower(names(iris))\nlibrary(dplyr)","execution_count":2},"buffers":[]}
[Positron] RECV comm_msg/positron-ui-r-9-c9099c32/undefined from iopub: {"header":{"msg_id":"34bc18dc-ec0e-4155-9718-4fff680dd4c0","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:12.996310800+00:00","msg_type":"comm_msg","version":"5.3"},"parent_header":{},"metadata":{},"content":{"comm_id":"positron-ui-r-9-c9099c32","data":{"method":"busy","params":{"busy":true}}},"buffers":[]}
[Positron] RECV comm_msg/positron-ui-r-9-c9099c32/undefined from iopub: {"header":{"msg_id":"4e3a5675-ef2e-494c-b21a-22a1ecd3cb0d","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:13.305744100+00:00","msg_type":"comm_msg","version":"5.3"},"parent_header":{},"metadata":{},"content":{"comm_id":"positron-ui-r-9-c9099c32","data":{"method":"busy","params":{"busy":false}}},"buffers":[]}
[Positron] RECV comm_msg/positron-ui-r-9-c9099c32/undefined from iopub: {"header":{"msg_id":"aae60f94-9232-4bd9-9163-62fb3c061ed5","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:13.305772800+00:00","msg_type":"comm_msg","version":"5.3"},"parent_header":{},"metadata":{},"content":{"comm_id":"positron-ui-r-9-c9099c32","data":{"method":"prompt_state","params":{"input_prompt":"> ","continuation_prompt":"+ "}}},"buffers":[]}
[Positron] RECV stream from iopub: {"header":{"msg_id":"db7778d3-9d6a-44b4-a938-0cd2a3c122b8","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:13.305782100+00:00","msg_type":"stream","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-35","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:08:12.995Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"name":"stdout","text":"\nAttaching package: ‘dplyr’\n\nThe following objects are masked from ‘package:stats’:\n\n filter, lag\n\nThe following objects are masked from ‘package:base’:\n\n intersect, setdiff, setequal, union\n\n"},"buffers":[]}
[Positron] R kernel status changed: busy => idle
[Positron] RECV status/idle from iopub: {"header":{"msg_id":"9814e41f-d6a1-4d01-96c7-87dbf6d97e46","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:13.305803200+00:00","msg_type":"status","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-35","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:08:12.995Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"execution_state":"idle"},"buffers":[]}
[Positron] RECV execute_reply from shell: {"header":{"msg_id":"9b7dcfbc-37e8-42df-8346-85550e9a93b1","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:13.305677+00:00","msg_type":"execute_reply","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-35","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:08:12.995Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"status":"ok","execution_count":2,"user_expressions":{}},"buffers":[]}
[Positron] RECV comm_msg/positron-variables-r-10-ba2b1da1/undefined from iopub: {"header":{"msg_id":"2fc99dc4-760c-44e2-83b0-1ff0414a1f3c","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:13.390118600+00:00","msg_type":"comm_msg","version":"5.3"},"parent_header":{},"metadata":{},"content":{"comm_id":"positron-variables-r-10-ba2b1da1","data":{"method":"update","params":{"assigned":[{"access_key":"iris","display_name":"iris","display_value":"[150 rows x 5 columns] <data.frame>","display_type":"data.frame [150, 5]","type_info":"","size":7256,"kind":"table","length":5,"has_children":true,"has_viewer":true,"is_truncated":false,"updated_time":1720951693389}],"unevaluated":[],"removed":[],"version":3}}},"buffers":[]}
[Positron] Sending code to R: # filter() the data for species virginica
virginica <- filter(iris, species == "virginica")
head(virginica) # This dispalys the first six rows
[Positron] SEND execute_request to Shell: {"buffers":[],"content":{"code":"# filter() the data for species virginica\nvirginica <- filter(iris, species == "virginica")\nhead(virginica) # This dispalys the first six rows","allow_stdin":true,"silent":false,"store_history":true,"user_expressions":{},"stop_on_error":true},"header":{"msg_id":"positron-notebook-cell-36","msg_type":"execute_request","version":"5.0","date":"2024-07-14T10:08:16.939Z","session":"57cab38faca1b653054ad9edb568b074","username":"William"},"metadata":{},"parent_header":{}}
[Positron] SEND execute_request: OK
[Positron] R kernel status changed: idle => busy
[Positron] RECV status/busy from iopub: {"header":{"msg_id":"5c3ff9b5-86dc-4c13-a9ab-7808b1e10748","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:16.940888400+00:00","msg_type":"status","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-36","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:08:16.939Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"execution_state":"busy"},"buffers":[]}
[Positron] RECV execute_input from iopub: {"header":{"msg_id":"5d9c17b9-a320-4d34-9c15-07faec9276be","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:16.940949400+00:00","msg_type":"execute_input","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-36","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:08:16.939Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"code":"# filter() the data for species virginica\nvirginica <- filter(iris, species == "virginica")\nhead(virginica) # This dispalys the first six rows","execution_count":3},"buffers":[]}
[Positron] RECV comm_msg/positron-ui-r-9-c9099c32/undefined from iopub: {"header":{"msg_id":"60796f6b-f557-40c8-99b7-b7f07a70f1c7","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:16.941151300+00:00","msg_type":"comm_msg","version":"5.3"},"parent_header":{},"metadata":{},"content":{"comm_id":"positron-ui-r-9-c9099c32","data":{"method":"busy","params":{"busy":false}}},"buffers":[]}
[Positron] RECV comm_msg/positron-ui-r-9-c9099c32/undefined from iopub: {"header":{"msg_id":"f21b8175-0a1e-4617-841c-b2f14ae1a1b3","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:16.941210200+00:00","msg_type":"comm_msg","version":"5.3"},"parent_header":{},"metadata":{},"content":{"comm_id":"positron-ui-r-9-c9099c32","data":{"method":"prompt_state","params":{"input_prompt":"+ ","continuation_prompt":"+ "}}},"buffers":[]}
[Positron] R kernel status changed: busy => idle
[Positron] RECV status/idle from iopub: {"header":{"msg_id":"bede5ccc-1b70-401b-a451-ff1507d8606f","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:16.941234200+00:00","msg_type":"status","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-36","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:08:16.939Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"execution_state":"idle"},"buffers":[]}
[Positron] RECV execute_reply from shell: {"header":{"msg_id":"e396b705-3d86-42d0-ad89-5fe49d023118","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:16.941140+00:00","msg_type":"execute_reply","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-36","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:08:16.939Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"status":"error","execution_count":3,"ename":"IncompleteInput","evalue":"Code fragment is not complete: # filter() the data for species virginica\nvirginica <- filter(iris, species == "virginica")\nhead(virginica) # This dispalys the first six rows","traceback":[]},"buffers":[]}
[Positron] Sending code to R: ginica <- filter(iris, species == "virginica")
head(virginica) # This dispalys the first six rows
[Positron] SEND execute_request to Shell: {"buffers":[],"content":{"code":"ginica <- filter(iris, species == "virginica")\nhead(virginica) # This dispalys the first six rows","allow_stdin":true,"silent":false,"store_history":true,"user_expressions":{},"stop_on_error":true},"header":{"msg_id":"positron-notebook-cell-37","msg_type":"execute_request","version":"5.0","date":"2024-07-14T10:08:19.089Z","session":"57cab38faca1b653054ad9edb568b074","username":"William"},"metadata":{},"parent_header":{}}
[Positron] SEND execute_request: OK
[Positron] R kernel status changed: idle => busy
[Positron] RECV status/busy from iopub: {"header":{"msg_id":"c13d0599-e08e-49a4-9f07-ae3d07ec3818","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:19.091191400+00:00","msg_type":"status","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-37","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:08:19.089Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"execution_state":"busy"},"buffers":[]}
[Positron] RECV execute_input from iopub: {"header":{"msg_id":"05b01bbe-4283-43c3-b9e0-3349b2e6f14a","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:19.091258+00:00","msg_type":"execute_input","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-37","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:08:19.089Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"code":"ginica <- filter(iris, species == "virginica")\nhead(virginica) # This dispalys the first six rows","execution_count":4},"buffers":[]}
[Positron] RECV comm_msg/positron-ui-r-9-c9099c32/undefined from iopub: {"header":{"msg_id":"571aee23-4bb6-4a94-bb31-3c40bddc70db","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:19.091462600+00:00","msg_type":"comm_msg","version":"5.3"},"parent_header":{},"metadata":{},"content":{"comm_id":"positron-ui-r-9-c9099c32","data":{"method":"busy","params":{"busy":false}}},"buffers":[]}
[Positron] RECV comm_msg/positron-ui-r-9-c9099c32/undefined from iopub: {"header":{"msg_id":"f1b24198-1b7e-454d-a7fd-2c8604785d7f","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:19.091507500+00:00","msg_type":"comm_msg","version":"5.3"},"parent_header":{},"metadata":{},"content":{"comm_id":"positron-ui-r-9-c9099c32","data":{"method":"prompt_state","params":{"input_prompt":"+ ","continuation_prompt":"+ "}}},"buffers":[]}
[Positron] R kernel status changed: busy => idle
[Positron] RECV status/idle from iopub: {"header":{"msg_id":"a5d0eb12-09a7-4d7b-b2e5-d9c214336c61","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:19.091552200+00:00","msg_type":"status","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-37","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:08:19.089Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"execution_state":"idle"},"buffers":[]}
[Positron] RECV execute_reply from shell: {"header":{"msg_id":"56b4f5b1-e4ac-4725-b140-61248033b0b7","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:19.091498600+00:00","msg_type":"execute_reply","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-37","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:08:19.089Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"status":"error","execution_count":4,"ename":"IncompleteInput","evalue":"Code fragment is not complete: ginica <- filter(iris, species == "virginica")\nhead(virginica) # This dispalys the first six rows","traceback":[]},"buffers":[]}
[Positron] Sending code to R: sepalLength6 <- filter(iris, species == "virginica", sepal.length > 6)
tail(sepalLength6) # compare this to head()
[Positron] SEND execute_request to Shell: {"buffers":[],"content":{"code":"sepalLength6 <- filter(iris, species == "virginica", sepal.length > 6)\ntail(sepalLength6) # compare this to head()","allow_stdin":true,"silent":false,"store_history":true,"user_expressions":{},"stop_on_error":true},"header":{"msg_id":"positron-notebook-cell-38","msg_type":"execute_request","version":"5.0","date":"2024-07-14T10:08:21.082Z","session":"57cab38faca1b653054ad9edb568b074","username":"William"},"metadata":{},"parent_header":{}}
[Positron] SEND execute_request: OK
[Positron] R kernel status changed: idle => busy
[Positron] RECV status/busy from iopub: {"header":{"msg_id":"b0e16d96-3688-4693-8a6a-4307b976437a","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:21.083027100+00:00","msg_type":"status","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-38","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:08:21.082Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"execution_state":"busy"},"buffers":[]}
[Positron] RECV execute_input from iopub: {"header":{"msg_id":"204635f2-63a3-45f1-b0fe-ca8ca7ec0927","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:21.083074500+00:00","msg_type":"execute_input","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-38","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:08:21.082Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"code":"sepalLength6 <- filter(iris, species == "virginica", sepal.length > 6)\ntail(sepalLength6) # compare this to head()","execution_count":5},"buffers":[]}
[Positron] RECV execute_reply from shell: {"header":{"msg_id":"cca46ef0-a32e-4384-9e27-1e1774cd5565","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:21.083315400+00:00","msg_type":"execute_reply","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-38","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:08:21.082Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"status":"error","execution_count":5,"ename":"IncompleteInput","evalue":"Code fragment is not complete: sepalLength6 <- filter(iris, species == "virginica", sepal.length > 6)\ntail(sepalLength6) # compare this to head()","traceback":[]},"buffers":[]}
[Positron] RECV comm_msg/positron-ui-r-9-c9099c32/undefined from iopub: {"header":{"msg_id":"cd0e9ef4-dff0-4d3d-af4a-ff6387ef4115","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:21.083346600+00:00","msg_type":"comm_msg","version":"5.3"},"parent_header":{},"metadata":{},"content":{"comm_id":"positron-ui-r-9-c9099c32","data":{"method":"busy","params":{"busy":false}}},"buffers":[]}
[Positron] RECV comm_msg/positron-ui-r-9-c9099c32/undefined from iopub: {"header":{"msg_id":"1ebfea6d-ea89-4fc6-8e27-4802b47e51c5","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:21.083374600+00:00","msg_type":"comm_msg","version":"5.3"},"parent_header":{},"metadata":{},"content":{"comm_id":"positron-ui-r-9-c9099c32","data":{"method":"prompt_state","params":{"input_prompt":"+ ","continuation_prompt":"+ "}}},"buffers":[]}
[Positron] R kernel status changed: busy => idle
[Positron] RECV status/idle from iopub: {"header":{"msg_id":"ac165976-77dc-4112-a822-1ec7b0ed116f","session":"15316e9f-2b4f-4bd9-8c78-35bd410127ce","username":"kernel","date":"2024-07-14T10:08:21.083384+00:00","msg_type":"status","version":"5.3"},"parent_header":{"msg_id":"positron-notebook-cell-38","session":"57cab38faca1b653054ad9edb568b074","username":"William","date":"2024-07-14T10:08:21.082Z","msg_type":"execute_request","version":"5.0"},"metadata":{},"content":{"execution_state":"idle"},"buffers":[]}

[juliasilge]

For me locally, where something like head(iris) works correctly, I see:

1. SEND execute_request: OK
2. R kernel status changed: idle => busy
3. RECV status/busy from iopub
4. RECV execute_input from iopub
5. RECV comm_msg/positron-ui-r-3-ae6ecc73/undefined from iopub
6. RECV execute_result from iopub that has the content in it that needs to be displayed

In these logs from @williamcplai where it is not working correctly, we see steps 1 through 5 that look correct, but then there is no execute_result that comes through. Looks like the info is not getting sent over.

[seeM]

I think this is an ARK bug. Executing code that has a trailing comment when using 'stop' runtime behavior stops the execute_result message from coming through.

If I then shutdown the kernel, I see this backtrace:

[R] Process exit code 134
[R] 
[R] Backtrace:
[R]    0: std::backtrace::Backtrace::create
[R]    1: ark::main::{{closure}}::{{closure}}
[R]    2: ark::main::{{closure}}
[R]    3: std::panicking::rust_panic_with_hook
[R]    4: std::panicking::begin_panic_handler::{{closure}}
[R]    5: std::sys_common::backtrace::__rust_end_short_backtrace
[R]    6: _rust_begin_unwind
[R]    7: core::panicking::panic_fmt
[R]    8: core::result::unwrap_failed
[R]    9: ark::interface::RMain::refresh_lsp
[R]   10: ark::interface::RMain::read_console
[R]   11: harp::exec::try_catch::callback
[R]   12: R_withCallingErrorHandler
[R]              at /Volumes/Builds/R4/R-4.3.2/src/main/errors.c:2613:16
[R]   13: harp::exec::top_level_exec::callback
[R]   14: R_ToplevelExec
[R]              at /Volumes/Builds/R4/R-4.3.2/src/main/context.c:799:2
[R]   15: harp::exec::r_sandbox
[R]   16: _r_read_console
[R]   17: Rf_ReplIteration
[R]              at /Volumes/Builds/R4/R-4.3.2/src/main/main.c:210:10
[R]   18: R_ReplConsole
[R]              at /Volumes/Builds/R4/R-4.3.2/src/main/main.c:314:11
[R]   19: run_Rmainloop
[R]              at /Volumes/Builds/R4/R-4.3.2/src/main/main.c:1200:5
[R]   20: ark::interface::start_r
[R]   21: ark::main
[R]   22: std::sys_common::backtrace::__rust_begin_short_backtrace
[R]   23: std::rt::lang_start::{{closure}}
[R]   24: std::rt::lang_start_internal
[R]   25: _main
[R] 
[R]     at crates/ark/src/main.rs:488
[R] 
[R] 

Details

If I run an R notebook cell with code 1, the output shows as expected.

But if I add a trailing comment, the output doesn't show: 1 #. As Julia pointed out, the execute_result is missing for some reason.

The console handles the trailing comment fine. The only difference that I see between console and notebook is that the notebook uses 'stop' runtime behavior and the console uses 'continue'.

I'm not sure why the console uses 'continue', I would've thought that 'stop' is more intuitive – maybe it's a Python vs R thing?

[juliasilge]

Ah thank you so much @seeM! We'll get this planned for fixes in ark.

@williamcplai for a short term workaround, you could avoid trailing comments, so remove # This dispalys the first six rows or put it on the previous line.

[jmcphers]

Also reported in posit-dev/positron#4789.

[DavisVaughan]

We have a guess that we are doing autobracing like {1 # } when really it needs to be like {\n1 # \n}