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Lots of invalid roxygen syntax puts R interpreter in looping crash/restart #6328

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JosiahParry opened this issue Feb 12, 2025 · 5 comments
Open

Lots of invalid roxygen syntax puts R interpreter in looping crash/restart #6328

JosiahParry opened this issue Feb 12, 2025 · 5 comments
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bug Something isn't working lang: r support

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@JosiahParry
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System details:

Positron and OS details:

Positron Version: 2025.02.0 (Universal) build 79
Code - OSS Version: 1.96.0
Commit: a268bc8
Date: 2025-01-21T02:44:54.581Z
Electron: 32.2.6
Chromium: 128.0.6613.186
Node.js: 20.18.1
V8: 12.8.374.38-electron.0
OS: Darwin arm64 24.0.0

Interpreter details:

R 4.4.0

Describe the issue:

Positron was stuck in a continual restart loop that i could not exit:

Image

Steps to reproduce the issue:

I cannot reproduce the issue. The issue occurred after I copied a very large character vector to the clipboard using clipr::write_clip() and pasted it to a new file.

Expected or desired behavior:

No editor issues.

Were there any error messages in the UI, Output panel, or Developer Tools console?

positron.log
@JosiahParry
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JosiahParry commented Feb 12, 2025 •
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This is actually reproduceable each and every time just by opening the 5.6k line file.

``` 2025-02-12 12:22:16.324 [info] ** Begin kernel log for session R 4.4.0 (r-ac5805c6) at 2/12/2025, 12:22:16 PM ** 2025-02-12 12:22:16.324 [info] Streaming kernel log file: /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/kernel-ilnOk0/kernel.log ** Begin kernel log for session R 4.4.0 (r-1346f678) at 2/12/2025, 12:22:18 PM ** Streaming kernel log file: /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/kernel-UDlqUj/kernel.log ** Begin kernel log for session R 4.4.0 (r-d69bb8df) at 2/12/2025, 12:22:21 PM ** Streaming kernel log file: /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/kernel-saYfEr/kernel.log [R] 2025-02-12T20:22:16.345132Z INFO Loaded connection information from frontend in /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/connection_r-ac5805c6.json [R] at crates/amalthea/src/kernel.rs:290 [R] [R] 2025-02-12T20:22:16.345148Z INFO Connection data: ConnectionFile { control_port: 22273, shell_port: 17987, stdin_port: 17088, iopub_port: 16552, hb_port: 22812, transport: "tcp", signature_scheme: "hmac-sha256", ip: "127.0.0.1", key: "b6d32341ce3e66a270fc3a9ead4fb04c" } [R] at crates/amalthea/src/kernel.rs:291 [R] [R] 2025-02-12T20:22:16.345364Z TRACE Binding to ZeroMQ 'Shell' socket at tcp://127.0.0.1:17987 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:16.350950Z TRACE Binding to ZeroMQ 'IOPub' socket at tcp://127.0.0.1:16552 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:16.351638Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:16.351736Z TRACE Binding to ZeroMQ 'Heartbeat' socket at tcp://127.0.0.1:22812 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:16.351768Z TRACE Entering kernel state: Starting [R] at crates/amalthea/src/socket/iopub.rs:386 [R] [R] 2025-02-12T20:22:16.351877Z TRACE Binding to ZeroMQ 'Stdin' socket at tcp://127.0.0.1:17088 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:16.352007Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:16.352073Z TRACE Binding to ZeroMQ 'Control' socket at tcp://127.0.0.1:22273 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:16.352438Z TRACE Binding to ZeroMQ 'OutboundNotifierTx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:115 [R] [R] 2025-02-12T20:22:16.352624Z TRACE Connecting to ZeroMQ 'OutboundNotifierRx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:120 [R] [R] 2025-02-12T20:22:16.353289Z TRACE Waiting for control messages [R] at crates/amalthea/src/socket/control.rs:58 [R] [R] 2025-02-12T20:22:16.357443Z TRACE Sending 'status/starting' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:16.536204Z INFO Successfully opened R shared library at '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib'. [R] at crates/harp/src/library.rs:30 [R] [R] 2025-02-12T20:22:16.536544Z TRACE R_HOME: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources" [R] at crates/ark/src/sys/unix/interface.rs:61 [R] [R] 2025-02-12T20:22:16.771423Z INFO Initializing global error handler [R] at crates/ark/src/errors.rs:54 [R] [R] 2025-02-12T20:22:16.772160Z DEBUG Setting default repositories to RStudio CRAN [R] at crates/ark/src/repos.rs:57 [R] [R] 2025-02-12T20:22:16.772169Z DEBUG Applying default repositories: {"CRAN": "https://cran.rstudio.com/"} [R] at crates/ark/src/repos.rs:146 [R] [R] 2025-02-12T20:22:16.772232Z INFO R has started and ark handlers have been registered, completing initialization. [R] at crates/ark/src/interface.rs:477 [R] [R] 2025-02-12T20:22:16.772235Z INFO Sending kernel info: R version 4.4.0 (2024-04-24) [R] at crates/ark/src/interface.rs:517 [R] [R] 2025-02-12T20:22:16.772295Z INFO Found R profile at '/Users/josiahparry/.Rprofile', sourcing now [R] at crates/ark/src/startup.rs:63 [R] [R] 2025-02-12T20:22:16.772604Z INFO Successfully sourced R profile at '/Users/josiahparry/.Rprofile' [R] at crates/ark/src/startup.rs:82 [R] [R] 2025-02-12T20:22:16.772618Z TRACE UI comm isn't connected, dropping `f`. [R] at crates/ark/src/interface.rs:1263 [R] [R] 2025-02-12T20:22:16.772632Z TRACE prompt_info(): n_frame = '0' [R] at crates/ark/src/interface.rs:847 [R] [R] 2025-02-12T20:22:16.772749Z TRACE R prompt: > [R] at crates/ark/src/interface.rs:689 [R] [R] 2025-02-12T20:22:16.835560Z TRACE Populated virtual namespace for datasets: 5 lines, 0 ok, 0 bad, 3 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:17.422254Z TRACE Populated virtual namespace for graphics: 5092 lines, 125 ok, 3 bad, 44 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:17.563372Z TRACE Populated virtual namespace for compiler: 2207 lines, 139 ok, 0 bad, 150 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:17.635145Z TRACE Populated virtual namespace for grDevices: 3973 lines, 212 ok, 0 bad, 75 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:17.738527Z INFO Received subscribe message on IOPub with subscription ''. [R] at crates/amalthea/src/socket/iopub.rs:260 [R] [R] 2025-02-12T20:22:17.738686Z TRACE Sending 'iopub_welcome' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:17.738829Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 97, 99, 53, 56, 48, 53, 99, 54], [114, 45, 97, 99, 53, 56, 48, 53, 99, 54]], header: JupyterHeader { msg_id: "49997438a0", session: "r-ac5805c6", username: "josiahparry", date: "2025-02-12T20:22:17.738Z", msg_type: "kernel_info_request", version: "5.3" }, parent_header: None, content: KernelInfoRequest } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:17.738838Z TRACE Got kernel info request; waiting for R to complete initialization [R] at crates/ark/src/shell.rs:121 [R] [R] 2025-02-12T20:22:17.738853Z TRACE Sending 'kernel_info_reply' message (reply to 'kernel_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.738890Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:17.739048Z TRACE Heartbeat message: [107, 97, 108, 108, 105, 99, 104, 111, 114, 101, 45, 104, 101, 97, 114, 116, 98, 101, 97, 116] [R] at crates/amalthea/src/socket/heartbeat.rs:41 [R] [R] 2025-02-12T20:22:17.739092Z TRACE Heartbeat message replied [R] at crates/amalthea/src/socket/heartbeat.rs:50 [R] [R] 2025-02-12T20:22:17.739095Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:17.743278Z TRACE Sending 'status/busy' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.743741Z TRACE Sending 'status/idle' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.747531Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 97, 99, 53, 56, 48, 53, 99, 54], [114, 45, 97, 99, 53, 56, 48, 53, 99, 54]], header: JupyterHeader { msg_id: "497d08fa6d", session: "r-ac5805c6", username: "josiahparry", date: "2025-02-12T20:22:17.746Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-lsp-r-11de8456", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:44851")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:17.747546Z INFO Received request to open comm: CommOpen { comm_id: "positron-lsp-r-11de8456", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:44851")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:17.747640Z INFO Comm channel opened; there are now 1 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:17.747658Z TRACE Connecting to LSP at '127.0.0.1:44851' [R] at crates/ark/src/lsp/backend.rs:372 [R] [R] 2025-02-12T20:22:17.747774Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.748402Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:17.748433Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 97, 99, 53, 56, 48, 53, 99, 54], [114, 45, 97, 99, 53, 56, 48, 53, 99, 54]], header: JupyterHeader { msg_id: "3dae0de019", session: "r-ac5805c6", username: "josiahparry", date: "2025-02-12T20:22:17.746Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-dap-r-84df89b8", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:45414")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:17.748438Z INFO Received request to open comm: CommOpen { comm_id: "positron-dap-r-84df89b8", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:45414")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:17.748443Z INFO DAP: Spawning thread [R] at crates/ark/src/dap/dap.rs:259 [R] [R] 2025-02-12T20:22:17.748499Z TRACE DAP: Thread starting at address 127.0.0.1:45414. [R] at crates/ark/src/dap/dap_server.rs:53 [R] [R] 2025-02-12T20:22:17.748524Z TRACE DAP: Waiting for client [R] at crates/ark/src/dap/dap_server.rs:62 [R] [R] 2025-02-12T20:22:17.748563Z INFO Comm channel opened; there are now 2 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:17.748577Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:17.748595Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 97, 99, 53, 56, 48, 53, 99, 54], [114, 45, 97, 99, 53, 56, 48, 53, 99, 54]], header: JupyterHeader { msg_id: "b827e9f6bf", session: "r-ac5805c6", username: "josiahparry", date: "2025-02-12T20:22:17.746Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-variables-r-0-7206b13b", target_name: "positron.variables", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:17.748598Z INFO Received request to open comm: CommOpen { comm_id: "positron-variables-r-0-7206b13b", target_name: "positron.variables", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:17.748628Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.748935Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.749227Z TRACE Sending 'comm_msg/LSP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:17.749363Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.749442Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.749508Z TRACE Sending 'comm_msg/DAP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:17.761207Z TRACE Connected to LSP at '127.0.0.1:44851' [R] at crates/ark/src/lsp/backend.rs:381 [R] [R] 2025-02-12T20:22:17.784004Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:17.784042Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 97, 99, 53, 56, 48, 53, 99, 54], [114, 45, 97, 99, 53, 56, 48, 53, 99, 54]], header: JupyterHeader { msg_id: "86bf00809d", session: "r-ac5805c6", username: "josiahparry", date: "2025-02-12T20:22:17.747Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-ui-r-1-79cb0d3c", target_name: "positron.ui", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:17.784047Z INFO Received request to open comm: CommOpen { comm_id: "positron-ui-r-1-79cb0d3c", target_name: "positron.ui", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:17.784078Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:17.784091Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 97, 99, 53, 56, 48, 53, 99, 54], [114, 45, 97, 99, 53, 56, 48, 53, 99, 54]], header: JupyterHeader { msg_id: "8f559f639a", session: "r-ac5805c6", username: "josiahparry", date: "2025-02-12T20:22:17.747Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.help" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:17.784093Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.help" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:17.784090Z INFO Comm channel opened; there are now 3 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:17.784105Z INFO Comm channel opened; there are now 4 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:17.784161Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.784527Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:17.784566Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 97, 99, 53, 56, 48, 53, 99, 54], [114, 45, 97, 99, 53, 56, 48, 53, 99, 54]], header: JupyterHeader { msg_id: "bd1d6769", session: "r-ac5805c6", username: "josiahparry", date: "2025-02-12T20:22:17.749Z", msg_type: "comm_msg", version: "5.3" }, parent_header: None, content: CommWireMsg { comm_id: "positron-ui-r-1-79cb0d3c", data: Object {"jsonrpc": String("2.0"), "method": String("call_method"), "params": Object {"method": String("setConsoleWidth"), "params": Array [Number(76)]}} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:17.784579Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:17.784591Z TRACE Comm manager: Sending message to comm 'positron.ui' [R] at crates/amalthea/src/comm/comm_manager.rs:140 [R] [R] 2025-02-12T20:22:17.784591Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 97, 99, 53, 56, 48, 53, 99, 54], [114, 45, 97, 99, 53, 56, 48, 53, 99, 54]], header: JupyterHeader { msg_id: "e744e448fd", session: "r-ac5805c6", username: "josiahparry", date: "2025-02-12T20:22:17.754Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.plot" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:17.784594Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.plot" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:17.784604Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.784616Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:17.784650Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 97, 99, 53, 56, 48, 53, 99, 54], [114, 45, 97, 99, 53, 56, 48, 53, 99, 54]], header: JupyterHeader { msg_id: "25f0b97926", session: "r-ac5805c6", username: "josiahparry", date: "2025-02-12T20:22:17.754Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:17.784652Z INFO Received request for open comms: CommInfoRequest { target_name: "" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:17.784663Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.784877Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.784984Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.785392Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.790541Z TRACE Handling 'setConsoleWidth' frontend RPC method [R] at crates/ark/src/ui/ui.rs:145 [R] in comm handler with name: "positron.ui", request: CallMethod(CallMethodParams { method: "setConsoleWidth", params: [Number(76)] }) [R] [R] 2025-02-12T20:22:17.792052Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.792462Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:17.792541Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 97, 99, 53, 56, 48, 53, 99, 54], [114, 45, 97, 99, 53, 56, 48, 53, 99, 54]], header: JupyterHeader { msg_id: "be6680f9", session: "r-ac5805c6", username: "josiahparry", date: "2025-02-12T20:22:17.761Z", msg_type: "comm_msg", version: "5.3" }, parent_header: None, content: CommWireMsg { comm_id: "positron-ui-r-1-79cb0d3c", data: Object {"jsonrpc": String("2.0"), "method": String("call_method"), "params": Object {"method": String("setConsoleWidth"), "params": Array [Number(76)]}} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:17.792565Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:17.792630Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 97, 99, 53, 56, 48, 53, 99, 54], [114, 45, 97, 99, 53, 56, 48, 53, 99, 54]], header: JupyterHeader { msg_id: "ff0b88c93b", session: "r-ac5805c6", username: "josiahparry", date: "2025-02-12T20:22:17.786Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-help-r-2-569e0cba", target_name: "positron.help", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:17.792638Z INFO Received request to open comm: CommOpen { comm_id: "positron-help-r-2-569e0cba", target_name: "positron.help", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:17.792763Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.792851Z TRACE Comm manager: Sending message to comm 'positron.ui' [R] at crates/amalthea/src/comm/comm_manager.rs:140 [R] [R] 2025-02-12T20:22:17.793435Z TRACE Received kernel request EstablishUiCommChannel(Sender { .. }) [R] at crates/ark/src/interface.rs:1216 [R] [R] 2025-02-12T20:22:17.793440Z INFO Sending message to UI comm: Event(PromptState(PromptStateParams { input_prompt: "> ", continuation_prompt: "+ " })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:17.793466Z INFO Sending message to UI comm: Event(WorkingDirectory(WorkingDirectoryParams { directory: "~/github/calcite" })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:17.793571Z TRACE Sending 'status/busy' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.793972Z TRACE Sending 'status/idle' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.794140Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.794628Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.794848Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.795067Z TRACE Sending 'comm_msg/variables/refresh' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:17.795470Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.796179Z TRACE Sending 'status/busy' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.796839Z TRACE Sending 'status/idle' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.797590Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.809564Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:17.809647Z INFO Comm channel opened; there are now 5 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:17.809956Z TRACE Handling 'setConsoleWidth' frontend RPC method [R] at crates/ark/src/ui/ui.rs:145 [R] in comm handler with name: "positron.ui", request: CallMethod(CallMethodParams { method: "setConsoleWidth", params: [Number(76)] }) [R] [R] 2025-02-12T20:22:17.810216Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.810764Z TRACE Sending 'comm_msg/positron-ui-r-1-79cb0d3c/CallMethodReply' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.811045Z TRACE Sending 'comm_msg/positron-ui-r-1-79cb0d3c/prompt_state' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:17.811254Z TRACE Sending 'comm_msg/positron-ui-r-1-79cb0d3c/CallMethodReply' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:17.811475Z TRACE Sending 'comm_msg/positron-ui-r-1-79cb0d3c/working_directory' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:18.099861Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 97, 99, 53, 56, 48, 53, 99, 54], [114, 45, 97, 99, 53, 56, 48, 53, 99, 54]], header: JupyterHeader { msg_id: "6ca297b6", session: "r-ac5805c6", username: "josiahparry", date: "2025-02-12T20:22:18.099Z", msg_type: "comm_msg", version: "5.3" }, parent_header: None, content: CommWireMsg { comm_id: "positron-ui-r-1-79cb0d3c", data: Object {"jsonrpc": String("2.0"), "method": String("call_method"), "params": Object {"method": String("packageVersion"), "params": Array [String("styler"), Null]}} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:18.099920Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:18.099946Z TRACE Comm manager: Sending message to comm 'positron.ui' [R] at crates/amalthea/src/comm/comm_manager.rs:140 [R] [R] 2025-02-12T20:22:18.100002Z TRACE Handling 'packageVersion' frontend RPC method [R] at crates/ark/src/ui/ui.rs:145 [R] in comm handler with name: "positron.ui", request: CallMethod(CallMethodParams { method: "packageVersion", params: [String("styler"), Null] }) [R] [R] 2025-02-12T20:22:18.100072Z TRACE Sending 'status/busy' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:18.101445Z TRACE Sending 'status/idle' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:18.119980Z TRACE Sending 'comm_msg/positron-ui-r-1-79cb0d3c/CallMethodReply' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:18.125333Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 97, 99, 53, 56, 48, 53, 99, 54], [114, 45, 97, 99, 53, 56, 48, 53, 99, 54]], header: JupyterHeader { msg_id: "99165851-81f5-432e-b190-a05d16c24df2", session: "r-ac5805c6", username: "josiahparry", date: "2025-02-12T20:22:18.123Z", msg_type: "execute_request", version: "5.3" }, parent_header: None, content: ExecuteRequest { code: "styler::style_file('/var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/styler-fb02df57-e30d-493f-920d-be035c92834f.R')", silent: true, store_history: false, user_expressions: Object {}, allow_stdin: true, stop_on_error: false } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:18.125351Z TRACE Code sent to R: styler::style_file('/var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/styler-fb02df57-e30d-493f-920d-be035c92834f.R') [R] at crates/ark/src/shell.rs:193 [R] [R] 2025-02-12T20:22:18.126200Z TRACE Sending 'status/busy' message (reply to 'execute_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:18.126801Z INFO Sending message to UI comm: Event(Busy(BusyParams { busy: true })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:18.127316Z TRACE Sending 'comm_msg/positron-ui-r-1-79cb0d3c/busy' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:18.442205Z INFO Sending message to UI comm: Event(Busy(BusyParams { busy: false })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:18.442227Z TRACE prompt_info(): n_frame = '0' [R] at crates/ark/src/interface.rs:847 [R] [R] 2025-02-12T20:22:18.442230Z TRACE R prompt: > [R] at crates/ark/src/interface.rs:689 [R] [R] 2025-02-12T20:22:18.442231Z INFO Sending message to UI comm: Event(PromptState(PromptStateParams { input_prompt: "> ", continuation_prompt: "+ " })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:18.442260Z TRACE Got R prompt '> ', completing execution [R] at crates/ark/src/interface.rs:1410 [R] [R] 2025-02-12T20:22:18.442331Z TRACE Sending `execute_reply`: Ok(ExecuteReply { status: Ok, execution_count: 0, user_expressions: Object {} }) [R] at crates/ark/src/interface.rs:1420 [R] [R] 2025-02-12T20:22:18.442420Z TRACE Sending 'execute_reply' message (reply to 'execute_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:18.442471Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:18.442564Z TRACE Sending 'comm_msg/positron-ui-r-1-79cb0d3c/busy' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:18.443279Z TRACE Sending 'comm_msg/positron-ui-r-1-79cb0d3c/prompt_state' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:18.443582Z TRACE Sending 'status/idle' message (reply to 'execute_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:18.448844Z INFO Got console prompt signal. [R] at crates/ark/src/variables/r_variables.rs:113 [R] [R] 2025-02-12T20:22:18.454638Z TRACE Populated virtual namespace for magrittr: 225 lines, 22 ok, 0 bad, 32 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in onload_hook with pkg: "magrittr" [R] [R] 2025-02-12T20:22:18.542859Z TRACE Populated virtual namespace for R.methodsS3: 680 lines, 35 ok, 0 bad, 4 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in onload_hook with pkg: "R.methodsS3" [R] ** Begin kernel log for session R 4.4.0 (r-f5bc7581) at 2/12/2025, 12:22:23 PM ** Streaming kernel log file: /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/kernel-q18mcP/kernel.log [R] 2025-02-12T20:22:18.824012Z INFO Loaded connection information from frontend in /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/connection_r-1346f678.json [R] at crates/amalthea/src/kernel.rs:290 [R] [R] 2025-02-12T20:22:18.824037Z INFO Connection data: ConnectionFile { control_port: 20562, shell_port: 23811, stdin_port: 23166, iopub_port: 16266, hb_port: 22841, transport: "tcp", signature_scheme: "hmac-sha256", ip: "127.0.0.1", key: "0122b16fda91f4b6efbe6113e308ad60" } [R] at crates/amalthea/src/kernel.rs:291 [R] [R] 2025-02-12T20:22:18.824347Z TRACE Binding to ZeroMQ 'Shell' socket at tcp://127.0.0.1:23811 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:18.825059Z TRACE Binding to ZeroMQ 'IOPub' socket at tcp://127.0.0.1:16266 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:18.825071Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:18.825125Z TRACE Binding to ZeroMQ 'Heartbeat' socket at tcp://127.0.0.1:22841 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:18.825147Z TRACE Entering kernel state: Starting [R] at crates/amalthea/src/socket/iopub.rs:386 [R] [R] 2025-02-12T20:22:18.825192Z TRACE Binding to ZeroMQ 'Stdin' socket at tcp://127.0.0.1:23166 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:18.825209Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:18.825308Z TRACE Binding to ZeroMQ 'Control' socket at tcp://127.0.0.1:20562 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:18.825365Z TRACE Binding to ZeroMQ 'OutboundNotifierTx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:115 [R] [R] 2025-02-12T20:22:18.825425Z TRACE Connecting to ZeroMQ 'OutboundNotifierRx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:120 [R] [R] 2025-02-12T20:22:18.825501Z TRACE Waiting for control messages [R] at crates/amalthea/src/socket/control.rs:58 [R] [R] 2025-02-12T20:22:18.825649Z TRACE Sending 'status/starting' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:18.930413Z INFO Successfully opened R shared library at '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib'. [R] at crates/harp/src/library.rs:30 [R] [R] 2025-02-12T20:22:18.930688Z TRACE R_HOME: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources" [R] at crates/ark/src/sys/unix/interface.rs:61 [R] [R] 2025-02-12T20:22:19.071068Z INFO Initializing global error handler [R] at crates/ark/src/errors.rs:54 [R] [R] 2025-02-12T20:22:19.071636Z DEBUG Setting default repositories to RStudio CRAN [R] at crates/ark/src/repos.rs:57 [R] [R] 2025-02-12T20:22:19.071642Z DEBUG Applying default repositories: {"CRAN": "https://cran.rstudio.com/"} [R] at crates/ark/src/repos.rs:146 [R] [R] 2025-02-12T20:22:19.071686Z INFO R has started and ark handlers have been registered, completing initialization. [R] at crates/ark/src/interface.rs:477 [R] [R] 2025-02-12T20:22:19.071692Z INFO Sending kernel info: R version 4.4.0 (2024-04-24) [R] at crates/ark/src/interface.rs:517 [R] [R] 2025-02-12T20:22:19.071726Z INFO Found R profile at '/Users/josiahparry/.Rprofile', sourcing now [R] at crates/ark/src/startup.rs:63 [R] [R] 2025-02-12T20:22:19.071928Z INFO Successfully sourced R profile at '/Users/josiahparry/.Rprofile' [R] at crates/ark/src/startup.rs:82 [R] [R] 2025-02-12T20:22:19.071941Z TRACE UI comm isn't connected, dropping `f`. [R] at crates/ark/src/interface.rs:1263 [R] [R] 2025-02-12T20:22:19.071951Z TRACE prompt_info(): n_frame = '0' [R] at crates/ark/src/interface.rs:847 [R] [R] 2025-02-12T20:22:19.072067Z TRACE R prompt: > [R] at crates/ark/src/interface.rs:689 [R] [R] 2025-02-12T20:22:19.129190Z TRACE Populated virtual namespace for datasets: 5 lines, 0 ok, 0 bad, 3 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:19.358073Z TRACE Populated virtual namespace for graphics: 5092 lines, 125 ok, 3 bad, 44 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:20.195936Z TRACE Populated virtual namespace for grDevices: 3973 lines, 212 ok, 0 bad, 75 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:20.276227Z INFO Received subscribe message on IOPub with subscription ''. [R] at crates/amalthea/src/socket/iopub.rs:260 [R] [R] 2025-02-12T20:22:20.276513Z TRACE Sending 'iopub_welcome' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:20.276752Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 49, 51, 52, 54, 102, 54, 55, 56], [114, 45, 49, 51, 52, 54, 102, 54, 55, 56]], header: JupyterHeader { msg_id: "725178a9a4", session: "r-1346f678", username: "josiahparry", date: "2025-02-12T20:22:20.276Z", msg_type: "kernel_info_request", version: "5.3" }, parent_header: None, content: KernelInfoRequest } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:20.276764Z TRACE Got kernel info request; waiting for R to complete initialization [R] at crates/ark/src/shell.rs:121 [R] [R] 2025-02-12T20:22:20.276787Z TRACE Sending 'kernel_info_reply' message (reply to 'kernel_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.276863Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:20.276886Z TRACE Sending 'status/busy' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.276956Z TRACE Heartbeat message: [107, 97, 108, 108, 105, 99, 104, 111, 114, 101, 45, 104, 101, 97, 114, 116, 98, 101, 97, 116] [R] at crates/amalthea/src/socket/heartbeat.rs:41 [R] [R] 2025-02-12T20:22:20.276993Z TRACE Heartbeat message replied [R] at crates/amalthea/src/socket/heartbeat.rs:50 [R] [R] 2025-02-12T20:22:20.276995Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:20.277034Z TRACE Sending 'status/idle' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.280239Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 49, 51, 52, 54, 102, 54, 55, 56], [114, 45, 49, 51, 52, 54, 102, 54, 55, 56]], header: JupyterHeader { msg_id: "da00fe9b54", session: "r-1346f678", username: "josiahparry", date: "2025-02-12T20:22:20.280Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-variables-r-3-271601f2", target_name: "positron.variables", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:20.280260Z INFO Received request to open comm: CommOpen { comm_id: "positron-variables-r-3-271601f2", target_name: "positron.variables", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:20.280517Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.313665Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:20.313675Z INFO Comm channel opened; there are now 1 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:20.313705Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 49, 51, 52, 54, 102, 54, 55, 56], [114, 45, 49, 51, 52, 54, 102, 54, 55, 56]], header: JupyterHeader { msg_id: "c405838d11", session: "r-1346f678", username: "josiahparry", date: "2025-02-12T20:22:20.280Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-ui-r-4-adeb03b7", target_name: "positron.ui", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:20.313711Z INFO Received request to open comm: CommOpen { comm_id: "positron-ui-r-4-adeb03b7", target_name: "positron.ui", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:20.313806Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:20.313824Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 49, 51, 52, 54, 102, 54, 55, 56], [114, 45, 49, 51, 52, 54, 102, 54, 55, 56]], header: JupyterHeader { msg_id: "9bcec6bb2f", session: "r-1346f678", username: "josiahparry", date: "2025-02-12T20:22:20.280Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-lsp-r-25cce38", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:49243")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:20.313827Z INFO Received request to open comm: CommOpen { comm_id: "positron-lsp-r-25cce38", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:49243")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:20.313875Z INFO Comm channel opened; there are now 2 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:20.313997Z INFO Comm channel opened; there are now 3 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:20.314045Z TRACE Connecting to LSP at '127.0.0.1:49243' [R] at crates/ark/src/lsp/backend.rs:372 [R] [R] 2025-02-12T20:22:20.314140Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.314201Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:20.314248Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 49, 51, 52, 54, 102, 54, 55, 56], [114, 45, 49, 51, 52, 54, 102, 54, 55, 56]], header: JupyterHeader { msg_id: "52421397a0", session: "r-1346f678", username: "josiahparry", date: "2025-02-12T20:22:20.280Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.help" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:20.314256Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.help" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:20.314515Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.314733Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.314783Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:20.314831Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 49, 51, 52, 54, 102, 54, 55, 56], [114, 45, 49, 51, 52, 54, 102, 54, 55, 56]], header: JupyterHeader { msg_id: "2b85f3c412", session: "r-1346f678", username: "josiahparry", date: "2025-02-12T20:22:20.282Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.plot" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:20.314837Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.plot" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:20.314856Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.314934Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.314952Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:20.315023Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 49, 51, 52, 54, 102, 54, 55, 56], [114, 45, 49, 51, 52, 54, 102, 54, 55, 56]], header: JupyterHeader { msg_id: "afa519acc5", session: "r-1346f678", username: "josiahparry", date: "2025-02-12T20:22:20.282Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:20.315030Z INFO Received request for open comms: CommInfoRequest { target_name: "" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:20.315178Z TRACE Received kernel request EstablishUiCommChannel(Sender { .. }) [R] at crates/ark/src/interface.rs:1216 [R] [R] 2025-02-12T20:22:20.315181Z INFO Sending message to UI comm: Event(PromptState(PromptStateParams { input_prompt: "> ", continuation_prompt: "+ " })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:20.315313Z INFO Sending message to UI comm: Event(WorkingDirectory(WorkingDirectoryParams { directory: "~/github/calcite" })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:20.315997Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.316056Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:20.316099Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 49, 51, 52, 54, 102, 54, 55, 56], [114, 45, 49, 51, 52, 54, 102, 54, 55, 56]], header: JupyterHeader { msg_id: "f90f993553", session: "r-1346f678", username: "josiahparry", date: "2025-02-12T20:22:20.282Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-dap-r-cc035890", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:61901")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:20.316107Z INFO Received request to open comm: CommOpen { comm_id: "positron-dap-r-cc035890", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:61901")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:20.316117Z INFO DAP: Spawning thread [R] at crates/ark/src/dap/dap.rs:259 [R] [R] 2025-02-12T20:22:20.316417Z INFO Comm channel opened; there are now 4 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:20.316434Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.316478Z TRACE DAP: Thread starting at address 127.0.0.1:61901. [R] at crates/ark/src/dap/dap_server.rs:53 [R] [R] 2025-02-12T20:22:20.316514Z TRACE DAP: Waiting for client [R] at crates/ark/src/dap/dap_server.rs:62 [R] [R] 2025-02-12T20:22:20.316535Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:20.316640Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.316826Z TRACE Sending 'comm_msg/LSP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:20.317022Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.317272Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.317644Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.317893Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.318006Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.318155Z TRACE Sending 'comm_msg/variables/refresh' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:20.318256Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.318480Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.318936Z TRACE Sending 'comm_msg/positron-ui-r-4-adeb03b7/prompt_state' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:20.319254Z TRACE Sending 'comm_msg/positron-ui-r-4-adeb03b7/working_directory' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:20.319492Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.320583Z TRACE Sending 'comm_msg/DAP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:20.323289Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 49, 51, 52, 54, 102, 54, 55, 56], [114, 45, 49, 51, 52, 54, 102, 54, 55, 56]], header: JupyterHeader { msg_id: "39b303b4", session: "r-1346f678", username: "josiahparry", date: "2025-02-12T20:22:20.321Z", msg_type: "comm_msg", version: "5.3" }, parent_header: None, content: CommWireMsg { comm_id: "positron-ui-r-4-adeb03b7", data: Object {"jsonrpc": String("2.0"), "method": String("call_method"), "params": Object {"method": String("packageVersion"), "params": Array [String("cli"), String("3.6.3.9002")]}} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:20.323383Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:20.323468Z TRACE Comm manager: Sending message to comm 'positron.ui' [R] at crates/amalthea/src/comm/comm_manager.rs:140 [R] [R] 2025-02-12T20:22:20.323625Z TRACE Handling 'packageVersion' frontend RPC method [R] at crates/ark/src/ui/ui.rs:145 [R] in comm handler with name: "positron.ui", request: CallMethod(CallMethodParams { method: "packageVersion", params: [String("cli"), String("3.6.3.9002")] }) [R] [R] 2025-02-12T20:22:20.324209Z TRACE Sending 'status/busy' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.324974Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 49, 51, 52, 54, 102, 54, 55, 56], [114, 45, 49, 51, 52, 54, 102, 54, 55, 56]], header: JupyterHeader { msg_id: "4744e6c834", session: "r-1346f678", username: "josiahparry", date: "2025-02-12T20:22:20.324Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-help-r-5-b3acd072", target_name: "positron.help", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:20.324979Z INFO Received request to open comm: CommOpen { comm_id: "positron-help-r-5-b3acd072", target_name: "positron.help", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:20.325131Z TRACE Sending 'status/idle' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.325573Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.325893Z TRACE Connected to LSP at '127.0.0.1:49243' [R] at crates/ark/src/lsp/backend.rs:381 [R] [R] 2025-02-12T20:22:20.326766Z TRACE Sending 'comm_msg/positron-ui-r-4-adeb03b7/CallMethodReply' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.327732Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:20.327746Z INFO Comm channel opened; there are now 5 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:20.327770Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 49, 51, 52, 54, 102, 54, 55, 56], [114, 45, 49, 51, 52, 54, 102, 54, 55, 56]], header: JupyterHeader { msg_id: "3c505ac5", session: "r-1346f678", username: "josiahparry", date: "2025-02-12T20:22:20.324Z", msg_type: "comm_msg", version: "5.3" }, parent_header: None, content: CommWireMsg { comm_id: "positron-ui-r-4-adeb03b7", data: Object {"jsonrpc": String("2.0"), "method": String("call_method"), "params": Object {"method": String("setConsoleWidth"), "params": Array [Number(76)]}} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:20.327781Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:20.327799Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 49, 51, 52, 54, 102, 54, 55, 56], [114, 45, 49, 51, 52, 54, 102, 54, 55, 56]], header: JupyterHeader { msg_id: "b73e2d25", session: "r-1346f678", username: "josiahparry", date: "2025-02-12T20:22:20.327Z", msg_type: "comm_msg", version: "5.3" }, parent_header: None, content: CommWireMsg { comm_id: "positron-ui-r-4-adeb03b7", data: Object {"jsonrpc": String("2.0"), "method": String("call_method"), "params": Object {"method": String("get_env_vars"), "params": Array [Array [String("TESTTHAT_MAX_FAILS")]]}} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:20.327806Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:20.327977Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.328505Z TRACE Comm manager: Sending message to comm 'positron.ui' [R] at crates/amalthea/src/comm/comm_manager.rs:140 [R] [R] 2025-02-12T20:22:20.328510Z TRACE Comm manager: Sending message to comm 'positron.ui' [R] at crates/amalthea/src/comm/comm_manager.rs:140 [R] [R] 2025-02-12T20:22:20.328530Z TRACE Handling 'setConsoleWidth' frontend RPC method [R] at crates/ark/src/ui/ui.rs:145 [R] in comm handler with name: "positron.ui", request: CallMethod(CallMethodParams { method: "setConsoleWidth", params: [Number(76)] }) [R] [R] 2025-02-12T20:22:20.328800Z TRACE Sending 'status/busy' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.328968Z TRACE Sending 'status/idle' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.329100Z TRACE Sending 'status/busy' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.329342Z TRACE Sending 'status/idle' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.335934Z TRACE Handling 'get_env_vars' frontend RPC method [R] at crates/ark/src/ui/ui.rs:145 [R] in comm handler with name: "positron.ui", request: CallMethod(CallMethodParams { method: "get_env_vars", params: [Array [String("TESTTHAT_MAX_FAILS")]] }) [R] [R] 2025-02-12T20:22:20.336143Z TRACE Sending 'comm_msg/positron-ui-r-4-adeb03b7/CallMethodReply' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.340174Z TRACE Sending 'comm_msg/positron-ui-r-4-adeb03b7/CallMethodReply' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:20.791274Z TRACE Populated virtual namespace for compiler: 2207 lines, 139 ok, 0 bad, 150 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] ** Begin kernel log for session R 4.4.0 (r-211f2d8e) at 2/12/2025, 12:22:25 PM ** Streaming kernel log file: /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/kernel-qhHHGA/kernel.log [R] 2025-02-12T20:22:21.139759Z INFO Loaded connection information from frontend in /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/connection_r-d69bb8df.json [R] at crates/amalthea/src/kernel.rs:290 [R] [R] 2025-02-12T20:22:21.139793Z INFO Connection data: ConnectionFile { control_port: 20695, shell_port: 17353, stdin_port: 18380, iopub_port: 22183, hb_port: 17088, transport: "tcp", signature_scheme: "hmac-sha256", ip: "127.0.0.1", key: "12b0cc1ca4d3116f65f1e58826cbdb4e" } [R] at crates/amalthea/src/kernel.rs:291 [R] [R] 2025-02-12T20:22:21.140265Z TRACE Binding to ZeroMQ 'Shell' socket at tcp://127.0.0.1:17353 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:21.141306Z TRACE Binding to ZeroMQ 'IOPub' socket at tcp://127.0.0.1:22183 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:21.141306Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:21.141372Z TRACE Binding to ZeroMQ 'Heartbeat' socket at tcp://127.0.0.1:17088 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:21.141389Z TRACE Entering kernel state: Starting [R] at crates/amalthea/src/socket/iopub.rs:386 [R] [R] 2025-02-12T20:22:21.141431Z TRACE Binding to ZeroMQ 'Stdin' socket at tcp://127.0.0.1:18380 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:21.141434Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:21.141516Z TRACE Binding to ZeroMQ 'Control' socket at tcp://127.0.0.1:20695 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:21.141571Z TRACE Binding to ZeroMQ 'OutboundNotifierTx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:115 [R] [R] 2025-02-12T20:22:21.141605Z TRACE Connecting to ZeroMQ 'OutboundNotifierRx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:120 [R] [R] 2025-02-12T20:22:21.141676Z TRACE Waiting for control messages [R] at crates/amalthea/src/socket/control.rs:58 [R] [R] 2025-02-12T20:22:21.141876Z TRACE Sending 'status/starting' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:21.249438Z INFO Successfully opened R shared library at '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib'. [R] at crates/harp/src/library.rs:30 [R] [R] 2025-02-12T20:22:21.249765Z TRACE R_HOME: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources" [R] at crates/ark/src/sys/unix/interface.rs:61 [R] [R] 2025-02-12T20:22:21.389054Z INFO Initializing global error handler [R] at crates/ark/src/errors.rs:54 [R] [R] 2025-02-12T20:22:21.389719Z DEBUG Setting default repositories to RStudio CRAN [R] at crates/ark/src/repos.rs:57 [R] [R] 2025-02-12T20:22:21.389730Z DEBUG Applying default repositories: {"CRAN": "https://cran.rstudio.com/"} [R] at crates/ark/src/repos.rs:146 [R] [R] 2025-02-12T20:22:21.389786Z INFO R has started and ark handlers have been registered, completing initialization. [R] at crates/ark/src/interface.rs:477 [R] [R] 2025-02-12T20:22:21.389792Z INFO Sending kernel info: R version 4.4.0 (2024-04-24) [R] at crates/ark/src/interface.rs:517 [R] [R] 2025-02-12T20:22:21.389828Z INFO Found R profile at '/Users/josiahparry/.Rprofile', sourcing now [R] at crates/ark/src/startup.rs:63 [R] [R] 2025-02-12T20:22:21.390012Z INFO Successfully sourced R profile at '/Users/josiahparry/.Rprofile' [R] at crates/ark/src/startup.rs:82 [R] [R] 2025-02-12T20:22:21.390022Z TRACE UI comm isn't connected, dropping `f`. [R] at crates/ark/src/interface.rs:1263 [R] [R] 2025-02-12T20:22:21.390033Z TRACE prompt_info(): n_frame = '0' [R] at crates/ark/src/interface.rs:847 [R] [R] 2025-02-12T20:22:21.390143Z TRACE R prompt: > [R] at crates/ark/src/interface.rs:689 [R] [R] 2025-02-12T20:22:21.447850Z TRACE Populated virtual namespace for datasets: 5 lines, 0 ok, 0 bad, 3 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:21.658304Z TRACE Populated virtual namespace for graphics: 5092 lines, 125 ok, 3 bad, 44 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:22.538276Z INFO Received subscribe message on IOPub with subscription ''. [R] at crates/amalthea/src/socket/iopub.rs:260 [R] [R] 2025-02-12T20:22:22.538462Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 100, 54, 57, 98, 98, 56, 100, 102], [114, 45, 100, 54, 57, 98, 98, 56, 100, 102]], header: JupyterHeader { msg_id: "f3150f1133", session: "r-d69bb8df", username: "josiahparry", date: "2025-02-12T20:22:22.538Z", msg_type: "kernel_info_request", version: "5.3" }, parent_header: None, content: KernelInfoRequest } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:22.538475Z TRACE Got kernel info request; waiting for R to complete initialization [R] at crates/ark/src/shell.rs:121 [R] [R] 2025-02-12T20:22:22.538491Z TRACE Sending 'iopub_welcome' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:22.538492Z TRACE Sending 'kernel_info_reply' message (reply to 'kernel_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.538552Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:22.538651Z TRACE Heartbeat message: [107, 97, 108, 108, 105, 99, 104, 111, 114, 101, 45, 104, 101, 97, 114, 116, 98, 101, 97, 116] [R] at crates/amalthea/src/socket/heartbeat.rs:41 [R] [R] 2025-02-12T20:22:22.538685Z TRACE Heartbeat message replied [R] at crates/amalthea/src/socket/heartbeat.rs:50 [R] [R] 2025-02-12T20:22:22.538687Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:22.538852Z TRACE Sending 'status/busy' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.539072Z TRACE Sending 'status/idle' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.550826Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 100, 54, 57, 98, 98, 56, 100, 102], [114, 45, 100, 54, 57, 98, 98, 56, 100, 102]], header: JupyterHeader { msg_id: "e264f64c20", session: "r-d69bb8df", username: "josiahparry", date: "2025-02-12T20:22:22.548Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-variables-r-6-17322f4a", target_name: "positron.variables", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:22.550844Z INFO Received request to open comm: CommOpen { comm_id: "positron-variables-r-6-17322f4a", target_name: "positron.variables", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:22.553170Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:22.553207Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 100, 54, 57, 98, 98, 56, 100, 102], [114, 45, 100, 54, 57, 98, 98, 56, 100, 102]], header: JupyterHeader { msg_id: "48fe25d432", session: "r-d69bb8df", username: "josiahparry", date: "2025-02-12T20:22:22.548Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-ui-r-7-ab1926d5", target_name: "positron.ui", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:22.553212Z INFO Received request to open comm: CommOpen { comm_id: "positron-ui-r-7-ab1926d5", target_name: "positron.ui", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:22.554526Z INFO Comm channel opened; there are now 1 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:22.554604Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:22.555411Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.556587Z INFO Comm channel opened; there are now 2 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:22.557070Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 100, 54, 57, 98, 98, 56, 100, 102], [114, 45, 100, 54, 57, 98, 98, 56, 100, 102]], header: JupyterHeader { msg_id: "218aef1620", session: "r-d69bb8df", username: "josiahparry", date: "2025-02-12T20:22:22.548Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.help" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:22.557078Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.help" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:22.559487Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.560851Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:22.563593Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 100, 54, 57, 98, 98, 56, 100, 102], [114, 45, 100, 54, 57, 98, 98, 56, 100, 102]], header: JupyterHeader { msg_id: "addd8d8952", session: "r-d69bb8df", username: "josiahparry", date: "2025-02-12T20:22:22.552Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.plot" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:22.563605Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.plot" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:22.565586Z TRACE Received kernel request EstablishUiCommChannel(Sender { .. }) [R] at crates/ark/src/interface.rs:1216 [R] [R] 2025-02-12T20:22:22.565596Z INFO Sending message to UI comm: Event(PromptState(PromptStateParams { input_prompt: "> ", continuation_prompt: "+ " })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:22.565684Z INFO Sending message to UI comm: Event(WorkingDirectory(WorkingDirectoryParams { directory: "~/github/calcite" })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:22.566524Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.566736Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.566946Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:22.566969Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 100, 54, 57, 98, 98, 56, 100, 102], [114, 45, 100, 54, 57, 98, 98, 56, 100, 102]], header: JupyterHeader { msg_id: "fde368e368", session: "r-d69bb8df", username: "josiahparry", date: "2025-02-12T20:22:22.553Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:22.566974Z INFO Received request for open comms: CommInfoRequest { target_name: "" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:22.567162Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.567189Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:22.567210Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 100, 54, 57, 98, 98, 56, 100, 102], [114, 45, 100, 54, 57, 98, 98, 56, 100, 102]], header: JupyterHeader { msg_id: "520b74a546", session: "r-d69bb8df", username: "josiahparry", date: "2025-02-12T20:22:22.553Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-lsp-r-fd4b4d5a", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:54201")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:22.567244Z INFO Received request to open comm: CommOpen { comm_id: "positron-lsp-r-fd4b4d5a", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:54201")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:22.569350Z TRACE Connecting to LSP at '127.0.0.1:54201' [R] at crates/ark/src/lsp/backend.rs:372 [R] [R] 2025-02-12T20:22:22.569354Z INFO Comm channel opened; there are now 3 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:22.569949Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:22.569981Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 100, 54, 57, 98, 98, 56, 100, 102], [114, 45, 100, 54, 57, 98, 98, 56, 100, 102]], header: JupyterHeader { msg_id: "11fc52a782", session: "r-d69bb8df", username: "josiahparry", date: "2025-02-12T20:22:22.565Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-dap-r-1036437e", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:47895")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:22.569987Z INFO Received request to open comm: CommOpen { comm_id: "positron-dap-r-1036437e", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:47895")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:22.569992Z INFO DAP: Spawning thread [R] at crates/ark/src/dap/dap.rs:259 [R] [R] 2025-02-12T20:22:22.570765Z INFO Comm channel opened; there are now 4 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:22.570837Z TRACE DAP: Thread starting at address 127.0.0.1:47895. [R] at crates/ark/src/dap/dap_server.rs:53 [R] [R] 2025-02-12T20:22:22.570872Z TRACE DAP: Waiting for client [R] at crates/ark/src/dap/dap_server.rs:62 [R] [R] 2025-02-12T20:22:22.570916Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:22.570971Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 100, 54, 57, 98, 98, 56, 100, 102], [114, 45, 100, 54, 57, 98, 98, 56, 100, 102]], header: JupyterHeader { msg_id: "6aed28cc53", session: "r-d69bb8df", username: "josiahparry", date: "2025-02-12T20:22:22.569Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-help-r-8-9e4a4044", target_name: "positron.help", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:22.570980Z INFO Received request to open comm: CommOpen { comm_id: "positron-help-r-8-9e4a4044", target_name: "positron.help", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:22.572062Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.573642Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.573994Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.575304Z TRACE Sending 'comm_msg/variables/refresh' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:22.579822Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.581906Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.583695Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:22.583826Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.583856Z INFO Comm channel opened; there are now 5 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:22.584588Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.586217Z TRACE Sending 'comm_msg/positron-ui-r-7-ab1926d5/prompt_state' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:22.586655Z TRACE Sending 'comm_msg/positron-ui-r-7-ab1926d5/working_directory' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:22.587179Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.587854Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.588509Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.589142Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.589592Z TRACE Sending 'comm_msg/LSP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:22.590143Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.592521Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.594976Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 100, 54, 57, 98, 98, 56, 100, 102], [114, 45, 100, 54, 57, 98, 98, 56, 100, 102]], header: JupyterHeader { msg_id: "1583064d", session: "r-d69bb8df", username: "josiahparry", date: "2025-02-12T20:22:22.592Z", msg_type: "comm_msg", version: "5.3" }, parent_header: None, content: CommWireMsg { comm_id: "positron-ui-r-7-ab1926d5", data: Object {"jsonrpc": String("2.0"), "method": String("call_method"), "params": Object {"method": String("setConsoleWidth"), "params": Array [Number(76)]}} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:22.594995Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:22.595164Z TRACE Comm manager: Sending message to comm 'positron.ui' [R] at crates/amalthea/src/comm/comm_manager.rs:140 [R] [R] 2025-02-12T20:22:22.595186Z TRACE Connected to LSP at '127.0.0.1:54201' [R] at crates/ark/src/lsp/backend.rs:381 [R] [R] 2025-02-12T20:22:22.596817Z TRACE Handling 'setConsoleWidth' frontend RPC method [R] at crates/ark/src/ui/ui.rs:145 [R] in comm handler with name: "positron.ui", request: CallMethod(CallMethodParams { method: "setConsoleWidth", params: [Number(76)] }) [R] [R] 2025-02-12T20:22:22.597124Z TRACE Sending 'comm_msg/DAP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:22.599837Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.600097Z TRACE Sending 'status/busy' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.600541Z TRACE Sending 'status/idle' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.613070Z TRACE Sending 'comm_msg/positron-ui-r-7-ab1926d5/CallMethodReply' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:22.623800Z TRACE Populated virtual namespace for compiler: 2207 lines, 139 ok, 0 bad, 150 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:22.787035Z TRACE Populated virtual namespace for tools: 35129 lines, 711 ok, 3 bad, 78 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in onload_hook with pkg: "tools" [R] [R] 2025-02-12T20:22:23.041832Z TRACE Populated virtual namespace for utils: 16143 lines, 502 ok, 1 bad, 73 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:23.060428Z TRACE Populated virtual namespace for grDevices: 3973 lines, 212 ok, 0 bad, 75 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:23.439581Z INFO Loaded connection information from frontend in /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/connection_r-f5bc7581.json [R] at crates/amalthea/src/kernel.rs:290 [R] [R] 2025-02-12T20:22:23.439601Z INFO Connection data: ConnectionFile { control_port: 21712, shell_port: 21632, stdin_port: 17759, iopub_port: 23364, hb_port: 24308, transport: "tcp", signature_scheme: "hmac-sha256", ip: "127.0.0.1", key: "4dc0ce1fc737b0688e5223accc9cf93a" } [R] at crates/amalthea/src/kernel.rs:291 [R] [R] 2025-02-12T20:22:23.439885Z TRACE Binding to ZeroMQ 'Shell' socket at tcp://127.0.0.1:21632 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:23.440485Z TRACE Binding to ZeroMQ 'IOPub' socket at tcp://127.0.0.1:23364 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:23.440498Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:23.440548Z TRACE Binding to ZeroMQ 'Heartbeat' socket at tcp://127.0.0.1:24308 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:23.440555Z TRACE Entering kernel state: Starting [R] at crates/amalthea/src/socket/iopub.rs:386 [R] [R] 2025-02-12T20:22:23.440595Z TRACE Binding to ZeroMQ 'Stdin' socket at tcp://127.0.0.1:17759 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:23.440598Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:23.440704Z TRACE Binding to ZeroMQ 'Control' socket at tcp://127.0.0.1:21712 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:23.440763Z TRACE Binding to ZeroMQ 'OutboundNotifierTx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:115 [R] [R] 2025-02-12T20:22:23.440807Z TRACE Connecting to ZeroMQ 'OutboundNotifierRx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:120 [R] [R] 2025-02-12T20:22:23.440892Z TRACE Waiting for control messages [R] at crates/amalthea/src/socket/control.rs:58 [R] [R] 2025-02-12T20:22:23.441021Z TRACE Sending 'status/starting' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:23.544347Z INFO Successfully opened R shared library at '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib'. [R] at crates/harp/src/library.rs:30 [R] [R] 2025-02-12T20:22:23.544704Z TRACE R_HOME: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources" [R] at crates/ark/src/sys/unix/interface.rs:61 [R] [R] 2025-02-12T20:22:23.687946Z INFO Initializing global error handler [R] at crates/ark/src/errors.rs:54 [R] [R] 2025-02-12T20:22:23.688563Z DEBUG Setting default repositories to RStudio CRAN [R] at crates/ark/src/repos.rs:57 [R] [R] 2025-02-12T20:22:23.688572Z DEBUG Applying default repositories: {"CRAN": "https://cran.rstudio.com/"} [R] at crates/ark/src/repos.rs:146 [R] [R] 2025-02-12T20:22:23.688623Z INFO R has started and ark handlers have been registered, completing initialization. [R] at crates/ark/src/interface.rs:477 [R] [R] 2025-02-12T20:22:23.688627Z INFO Sending kernel info: R version 4.4.0 (2024-04-24) [R] at crates/ark/src/interface.rs:517 [R] [R] 2025-02-12T20:22:23.688676Z INFO Found R profile at '/Users/josiahparry/.Rprofile', sourcing now [R] at crates/ark/src/startup.rs:63 [R] [R] 2025-02-12T20:22:23.688894Z INFO Successfully sourced R profile at '/Users/josiahparry/.Rprofile' [R] at crates/ark/src/startup.rs:82 [R] [R] 2025-02-12T20:22:23.688906Z TRACE UI comm isn't connected, dropping `f`. [R] at crates/ark/src/interface.rs:1263 [R] [R] 2025-02-12T20:22:23.688918Z TRACE prompt_info(): n_frame = '0' [R] at crates/ark/src/interface.rs:847 [R] [R] 2025-02-12T20:22:23.689042Z TRACE R prompt: > [R] at crates/ark/src/interface.rs:689 [R] [R] 2025-02-12T20:22:23.745554Z TRACE Populated virtual namespace for datasets: 5 lines, 0 ok, 0 bad, 3 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:23.925138Z TRACE Populated virtual namespace for graphics: 5092 lines, 125 ok, 3 bad, 44 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:24.738492Z TRACE Populated virtual namespace for grDevices: 3973 lines, 212 ok, 0 bad, 75 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:24.866521Z INFO Received subscribe message on IOPub with subscription ''. [R] at crates/amalthea/src/socket/iopub.rs:260 [R] [R] 2025-02-12T20:22:24.866742Z TRACE Sending 'iopub_welcome' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:24.866879Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 102, 53, 98, 99, 55, 53, 56, 49], [114, 45, 102, 53, 98, 99, 55, 53, 56, 49]], header: JupyterHeader { msg_id: "c7557eee70", session: "r-f5bc7581", username: "josiahparry", date: "2025-02-12T20:22:24.866Z", msg_type: "kernel_info_request", version: "5.3" }, parent_header: None, content: KernelInfoRequest } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:24.866890Z TRACE Got kernel info request; waiting for R to complete initialization [R] at crates/ark/src/shell.rs:121 [R] [R] 2025-02-12T20:22:24.866908Z TRACE Sending 'kernel_info_reply' message (reply to 'kernel_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.866952Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:24.867038Z TRACE Sending 'status/busy' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.867124Z TRACE Heartbeat message: [107, 97, 108, 108, 105, 99, 104, 111, 114, 101, 45, 104, 101, 97, 114, 116, 98, 101, 97, 116] [R] at crates/amalthea/src/socket/heartbeat.rs:41 [R] [R] 2025-02-12T20:22:24.867150Z TRACE Heartbeat message replied [R] at crates/amalthea/src/socket/heartbeat.rs:50 [R] [R] 2025-02-12T20:22:24.867153Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:24.867279Z TRACE Sending 'status/idle' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.870107Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 102, 53, 98, 99, 55, 53, 56, 49], [114, 45, 102, 53, 98, 99, 55, 53, 56, 49]], header: JupyterHeader { msg_id: "d1f66f987d", session: "r-f5bc7581", username: "josiahparry", date: "2025-02-12T20:22:24.869Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-dap-r-7b9afe0b", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:51378")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:24.870117Z INFO Received request to open comm: CommOpen { comm_id: "positron-dap-r-7b9afe0b", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:51378")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:24.870124Z INFO DAP: Spawning thread [R] at crates/ark/src/dap/dap.rs:259 [R] [R] 2025-02-12T20:22:24.870184Z TRACE DAP: Thread starting at address 127.0.0.1:51378. [R] at crates/ark/src/dap/dap_server.rs:53 [R] [R] 2025-02-12T20:22:24.870206Z TRACE DAP: Waiting for client [R] at crates/ark/src/dap/dap_server.rs:62 [R] [R] 2025-02-12T20:22:24.870225Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:24.870243Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 102, 53, 98, 99, 55, 53, 56, 49], [114, 45, 102, 53, 98, 99, 55, 53, 56, 49]], header: JupyterHeader { msg_id: "06ca34895e", session: "r-f5bc7581", username: "josiahparry", date: "2025-02-12T20:22:24.870Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-variables-r-9-6141d015", target_name: "positron.variables", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:24.870245Z INFO Received request to open comm: CommOpen { comm_id: "positron-variables-r-9-6141d015", target_name: "positron.variables", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:24.870278Z INFO Comm channel opened; there are now 1 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:24.870468Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.870625Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.870749Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.870875Z TRACE Sending 'comm_msg/DAP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:24.877597Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:24.877596Z INFO Comm channel opened; there are now 2 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:24.877666Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 102, 53, 98, 99, 55, 53, 56, 49], [114, 45, 102, 53, 98, 99, 55, 53, 56, 49]], header: JupyterHeader { msg_id: "4e42fdb637", session: "r-f5bc7581", username: "josiahparry", date: "2025-02-12T20:22:24.870Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-ui-r-10-ea4130fd", target_name: "positron.ui", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:24.877671Z INFO Received request to open comm: CommOpen { comm_id: "positron-ui-r-10-ea4130fd", target_name: "positron.ui", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:24.877699Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:24.877718Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 102, 53, 98, 99, 55, 53, 56, 49], [114, 45, 102, 53, 98, 99, 55, 53, 56, 49]], header: JupyterHeader { msg_id: "89b1e47644", session: "r-f5bc7581", username: "josiahparry", date: "2025-02-12T20:22:24.870Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-lsp-r-fcd15168", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:44201")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:24.877721Z INFO Received request to open comm: CommOpen { comm_id: "positron-lsp-r-fcd15168", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:44201")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:24.877720Z INFO Comm channel opened; there are now 3 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:24.877769Z INFO Comm channel opened; there are now 4 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:24.877783Z TRACE Connecting to LSP at '127.0.0.1:44201' [R] at crates/ark/src/lsp/backend.rs:372 [R] [R] 2025-02-12T20:22:24.877845Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:24.877861Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 102, 53, 98, 99, 55, 53, 56, 49], [114, 45, 102, 53, 98, 99, 55, 53, 56, 49]], header: JupyterHeader { msg_id: "80ef7deb1f", session: "r-f5bc7581", username: "josiahparry", date: "2025-02-12T20:22:24.870Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.help" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:24.877864Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.help" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:24.877865Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.877880Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.877921Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:24.877932Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 102, 53, 98, 99, 55, 53, 56, 49], [114, 45, 102, 53, 98, 99, 55, 53, 56, 49]], header: JupyterHeader { msg_id: "c7cc959d24", session: "r-f5bc7581", username: "josiahparry", date: "2025-02-12T20:22:24.873Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.plot" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:24.877936Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.plot" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:24.877962Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.877978Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:24.878005Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 102, 53, 98, 99, 55, 53, 56, 49], [114, 45, 102, 53, 98, 99, 55, 53, 56, 49]], header: JupyterHeader { msg_id: "442496060e", session: "r-f5bc7581", username: "josiahparry", date: "2025-02-12T20:22:24.873Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:24.878012Z INFO Received request for open comms: CommInfoRequest { target_name: "" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:24.878032Z TRACE Received kernel request EstablishUiCommChannel(Sender { .. }) [R] at crates/ark/src/interface.rs:1216 [R] [R] 2025-02-12T20:22:24.878035Z INFO Sending message to UI comm: Event(PromptState(PromptStateParams { input_prompt: "> ", continuation_prompt: "+ " })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:24.878054Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.878068Z INFO Sending message to UI comm: Event(WorkingDirectory(WorkingDirectoryParams { directory: "~/github/calcite" })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:24.878077Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:24.878238Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.878388Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.878536Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.878686Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.879067Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.879334Z TRACE Sending 'comm_msg/LSP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:24.879637Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.879923Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.880258Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.880449Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.880626Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.880844Z TRACE Connected to LSP at '127.0.0.1:44201' [R] at crates/ark/src/lsp/backend.rs:381 [R] [R] 2025-02-12T20:22:24.880900Z TRACE Sending 'comm_msg/positron-ui-r-10-ea4130fd/prompt_state' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:24.881066Z TRACE Sending 'comm_msg/positron-ui-r-10-ea4130fd/working_directory' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:24.881191Z TRACE Sending 'comm_msg/variables/refresh' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:24.884204Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 102, 53, 98, 99, 55, 53, 56, 49], [114, 45, 102, 53, 98, 99, 55, 53, 56, 49]], header: JupyterHeader { msg_id: "c0dce66f66", session: "r-f5bc7581", username: "josiahparry", date: "2025-02-12T20:22:24.883Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-help-r-11-fb9b98e1", target_name: "positron.help", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:24.884301Z INFO Received request to open comm: CommOpen { comm_id: "positron-help-r-11-fb9b98e1", target_name: "positron.help", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:24.884790Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.894949Z INFO Comm channel opened; there are now 5 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:24.894970Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:24.895147Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 102, 53, 98, 99, 55, 53, 56, 49], [114, 45, 102, 53, 98, 99, 55, 53, 56, 49]], header: JupyterHeader { msg_id: "9310adc1", session: "r-f5bc7581", username: "josiahparry", date: "2025-02-12T20:22:24.884Z", msg_type: "comm_msg", version: "5.3" }, parent_header: None, content: CommWireMsg { comm_id: "positron-ui-r-10-ea4130fd", data: Object {"jsonrpc": String("2.0"), "method": String("call_method"), "params": Object {"method": String("setConsoleWidth"), "params": Array [Number(76)]}} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:24.895173Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:24.895521Z TRACE Comm manager: Sending message to comm 'positron.ui' [R] at crates/amalthea/src/comm/comm_manager.rs:140 [R] [R] 2025-02-12T20:22:24.895669Z TRACE Handling 'setConsoleWidth' frontend RPC method [R] at crates/ark/src/ui/ui.rs:145 [R] in comm handler with name: "positron.ui", request: CallMethod(CallMethodParams { method: "setConsoleWidth", params: [Number(76)] }) [R] [R] 2025-02-12T20:22:24.896051Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.896765Z TRACE Sending 'status/busy' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.897081Z TRACE Sending 'status/idle' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:24.897919Z TRACE Sending 'comm_msg/positron-ui-r-10-ea4130fd/CallMethodReply' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:25.331326Z TRACE Populated virtual namespace for methods: 12044 lines, 512 ok, 0 bad, 249 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:25.337856Z TRACE Populated virtual namespace for compiler: 2207 lines, 139 ok, 0 bad, 150 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:25.748889Z INFO Loaded connection information from frontend in /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/connection_r-211f2d8e.json [R] at crates/amalthea/src/kernel.rs:290 [R] [R] 2025-02-12T20:22:25.748911Z INFO Connection data: ConnectionFile { control_port: 20274, shell_port: 15112, stdin_port: 21256, iopub_port: 22130, hb_port: 24969, transport: "tcp", signature_scheme: "hmac-sha256", ip: "127.0.0.1", key: "7fd3e63d4341b282a5e7437c593bd78e" } [R] at crates/amalthea/src/kernel.rs:291 [R] [R] 2025-02-12T20:22:25.749281Z TRACE Binding to ZeroMQ 'Shell' socket at tcp://127.0.0.1:15112 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:25.750126Z TRACE Binding to ZeroMQ 'IOPub' socket at tcp://127.0.0.1:22130 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:25.750134Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:25.750206Z TRACE Binding to ZeroMQ 'Heartbeat' socket at tcp://127.0.0.1:24969 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:25.750240Z TRACE Entering kernel state: Starting [R] at crates/amalthea/src/socket/iopub.rs:386 [R] [R] 2025-02-12T20:22:25.750358Z TRACE Binding to ZeroMQ 'Stdin' socket at tcp://127.0.0.1:21256 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:25.750371Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:25.750433Z TRACE Binding to ZeroMQ 'Control' socket at tcp://127.0.0.1:20274 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:25.750494Z TRACE Binding to ZeroMQ 'OutboundNotifierTx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:115 [R] [R] 2025-02-12T20:22:25.750639Z TRACE Connecting to ZeroMQ 'OutboundNotifierRx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:120 [R] [R] 2025-02-12T20:22:25.750789Z TRACE Waiting for control messages [R] at crates/amalthea/src/socket/control.rs:58 [R] [R] 2025-02-12T20:22:25.751127Z TRACE Sending 'status/starting' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:25.859003Z INFO Successfully opened R shared library at '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib'. [R] at crates/harp/src/library.rs:30 [R] [R] 2025-02-12T20:22:25.859336Z TRACE R_HOME: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources" [R] at crates/ark/src/sys/unix/interface.rs:61 [R] [R] 2025-02-12T20:22:25.998670Z INFO Initializing global error handler [R] at crates/ark/src/errors.rs:54 [R] [R] 2025-02-12T20:22:25.999213Z DEBUG Setting default repositories to RStudio CRAN [R] at crates/ark/src/repos.rs:57 [R] [R] 2025-02-12T20:22:25.999219Z DEBUG Applying default repositories: {"CRAN": "https://cran.rstudio.com/"} [R] at crates/ark/src/repos.rs:146 [R] [R] 2025-02-12T20:22:25.999261Z INFO R has started and ark handlers have been registered, completing initialization. [R] at crates/ark/src/interface.rs:477 [R] [R] 2025-02-12T20:22:25.999264Z INFO Sending kernel info: R version 4.4.0 (2024-04-24) [R] at crates/ark/src/interface.rs:517 [R] [R] 2025-02-12T20:22:25.999299Z INFO Found R profile at '/Users/josiahparry/.Rprofile', sourcing now [R] at crates/ark/src/startup.rs:63 [R] [R] 2025-02-12T20:22:25.999465Z INFO Successfully sourced R profile at '/Users/josiahparry/.Rprofile' [R] at crates/ark/src/startup.rs:82 [R] [R] 2025-02-12T20:22:25.999475Z TRACE UI comm isn't connected, dropping `f`. [R] at crates/ark/src/interface.rs:1263 [R] [R] 2025-02-12T20:22:25.999484Z TRACE prompt_info(): n_frame = '0' [R] at crates/ark/src/interface.rs:847 [R] [R] 2025-02-12T20:22:25.999590Z TRACE R prompt: > [R] at crates/ark/src/interface.rs:689 [R] [R] 2025-02-12T20:22:26.057755Z TRACE Populated virtual namespace for datasets: 5 lines, 0 ok, 0 bad, 3 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:26.265889Z TRACE Populated virtual namespace for graphics: 5092 lines, 125 ok, 3 bad, 44 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:26.931911Z TRACE Populated virtual namespace for tools: 35129 lines, 711 ok, 3 bad, 78 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in onload_hook with pkg: "tools" [R] [R] 2025-02-12T20:22:27.149967Z TRACE Populated virtual namespace for compiler: 2207 lines, 139 ok, 0 bad, 150 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:27.155636Z TRACE Populated virtual namespace for utils: 16143 lines, 502 ok, 1 bad, 73 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:27.169523Z TRACE Populated virtual namespace for grDevices: 3973 lines, 212 ok, 0 bad, 75 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:27.224790Z INFO Received subscribe message on IOPub with subscription ''. [R] at crates/amalthea/src/socket/iopub.rs:260 [R] [R] 2025-02-12T20:22:27.225010Z TRACE Sending 'iopub_welcome' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:27.225266Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 50, 49, 49, 102, 50, 100, 56, 101], [114, 45, 50, 49, 49, 102, 50, 100, 56, 101]], header: JupyterHeader { msg_id: "a155bb8076", session: "r-211f2d8e", username: "josiahparry", date: "2025-02-12T20:22:27.225Z", msg_type: "kernel_info_request", version: "5.3" }, parent_header: None, content: KernelInfoRequest } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:27.225276Z TRACE Got kernel info request; waiting for R to complete initialization [R] at crates/ark/src/shell.rs:121 [R] [R] 2025-02-12T20:22:27.225293Z TRACE Sending 'kernel_info_reply' message (reply to 'kernel_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.225338Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:27.225401Z TRACE Sending 'status/busy' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.225605Z TRACE Sending 'status/idle' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.225997Z TRACE Heartbeat message: [107, 97, 108, 108, 105, 99, 104, 111, 114, 101, 45, 104, 101, 97, 114, 116, 98, 101, 97, 116] [R] at crates/amalthea/src/socket/heartbeat.rs:41 [R] [R] 2025-02-12T20:22:27.226036Z TRACE Heartbeat message replied [R] at crates/amalthea/src/socket/heartbeat.rs:50 [R] [R] 2025-02-12T20:22:27.226038Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:27.228620Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 50, 49, 49, 102, 50, 100, 56, 101], [114, 45, 50, 49, 49, 102, 50, 100, 56, 101]], header: JupyterHeader { msg_id: "61fff81b2c", session: "r-211f2d8e", username: "josiahparry", date: "2025-02-12T20:22:27.228Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-lsp-r-cfd10d58", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:59644")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:27.228632Z INFO Received request to open comm: CommOpen { comm_id: "positron-lsp-r-cfd10d58", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:59644")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:27.228785Z INFO Comm channel opened; there are now 1 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:27.228821Z TRACE Connecting to LSP at '127.0.0.1:59644' [R] at crates/ark/src/lsp/backend.rs:372 [R] [R] 2025-02-12T20:22:27.228859Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.228892Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:27.228932Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 50, 49, 49, 102, 50, 100, 56, 101], [114, 45, 50, 49, 49, 102, 50, 100, 56, 101]], header: JupyterHeader { msg_id: "b883ac2d5a", session: "r-211f2d8e", username: "josiahparry", date: "2025-02-12T20:22:27.228Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-variables-r-12-edd6f642", target_name: "positron.variables", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:27.228940Z INFO Received request to open comm: CommOpen { comm_id: "positron-variables-r-12-edd6f642", target_name: "positron.variables", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:27.229062Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.229181Z TRACE Sending 'comm_msg/LSP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:27.229297Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.230557Z TRACE Connected to LSP at '127.0.0.1:59644' [R] at crates/ark/src/lsp/backend.rs:381 [R] [R] 2025-02-12T20:22:27.316034Z INFO 87 milliseconds wait before running task. [R] at crates/ark/src/interface.rs:1120 [R] in R task with thread: "ark-shell", interrupt: true [R] [R] 2025-02-12T20:22:27.316106Z INFO 85 milliseconds wait before running task. [R] at crates/ark/src/interface.rs:1120 [R] in R task with thread: "ark-lsp", interrupt: true [R] [R] 2025-02-12T20:22:27.316156Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:27.316156Z INFO Comm channel opened; there are now 2 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:27.316195Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 50, 49, 49, 102, 50, 100, 56, 101], [114, 45, 50, 49, 49, 102, 50, 100, 56, 101]], header: JupyterHeader { msg_id: "3e1dcc8fd5", session: "r-211f2d8e", username: "josiahparry", date: "2025-02-12T20:22:27.228Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-dap-r-c174f830", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:57034")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:27.316202Z INFO Received request to open comm: CommOpen { comm_id: "positron-dap-r-c174f830", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:57034")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:27.316208Z INFO DAP: Spawning thread [R] at crates/ark/src/dap/dap.rs:259 [R] [R] 2025-02-12T20:22:27.316242Z INFO Comm channel opened; there are now 3 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:27.316243Z TRACE DAP: Thread starting at address 127.0.0.1:57034. [R] at crates/ark/src/dap/dap_server.rs:53 [R] [R] 2025-02-12T20:22:27.316286Z TRACE DAP: Waiting for client [R] at crates/ark/src/dap/dap_server.rs:62 [R] [R] 2025-02-12T20:22:27.316309Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:27.316337Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 50, 49, 49, 102, 50, 100, 56, 101], [114, 45, 50, 49, 49, 102, 50, 100, 56, 101]], header: JupyterHeader { msg_id: "8a6873f587", session: "r-211f2d8e", username: "josiahparry", date: "2025-02-12T20:22:27.228Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-ui-r-13-721e9b7d", target_name: "positron.ui", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:27.316343Z INFO Received request to open comm: CommOpen { comm_id: "positron-ui-r-13-721e9b7d", target_name: "positron.ui", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:27.316373Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:27.316386Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 50, 49, 49, 102, 50, 100, 56, 101], [114, 45, 50, 49, 49, 102, 50, 100, 56, 101]], header: JupyterHeader { msg_id: "fe3f3275c2", session: "r-211f2d8e", username: "josiahparry", date: "2025-02-12T20:22:27.228Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.help" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:27.316389Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.help" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:27.316406Z INFO Comm channel opened; there are now 4 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:27.316445Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.316476Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.316499Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:27.316537Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 50, 49, 49, 102, 50, 100, 56, 101], [114, 45, 50, 49, 49, 102, 50, 100, 56, 101]], header: JupyterHeader { msg_id: "55ce018982", session: "r-211f2d8e", username: "josiahparry", date: "2025-02-12T20:22:27.231Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.plot" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:27.316558Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.plot" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:27.316602Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.316628Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:27.316643Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 50, 49, 49, 102, 50, 100, 56, 101], [114, 45, 50, 49, 49, 102, 50, 100, 56, 101]], header: JupyterHeader { msg_id: "9520f55fbd", session: "r-211f2d8e", username: "josiahparry", date: "2025-02-12T20:22:27.231Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:27.316647Z INFO Received request for open comms: CommInfoRequest { target_name: "" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:27.316696Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.316717Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:27.316740Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 50, 49, 49, 102, 50, 100, 56, 101], [114, 45, 50, 49, 49, 102, 50, 100, 56, 101]], header: JupyterHeader { msg_id: "3e9939fc", session: "r-211f2d8e", username: "josiahparry", date: "2025-02-12T20:22:27.235Z", msg_type: "comm_msg", version: "5.3" }, parent_header: None, content: CommWireMsg { comm_id: "positron-ui-r-13-721e9b7d", data: Object {"jsonrpc": String("2.0"), "method": String("call_method"), "params": Object {"method": String("setConsoleWidth"), "params": Array [Number(76)]}} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:27.316750Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:27.316755Z TRACE Comm manager: Sending message to comm 'positron.ui' [R] at crates/amalthea/src/comm/comm_manager.rs:140 [R] [R] 2025-02-12T20:22:27.316795Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.316811Z TRACE Handling 'setConsoleWidth' frontend RPC method [R] at crates/ark/src/ui/ui.rs:145 [R] in comm handler with name: "positron.ui", request: CallMethod(CallMethodParams { method: "setConsoleWidth", params: [Number(76)] }) [R] [R] 2025-02-12T20:22:27.317031Z TRACE Sending 'comm_msg/DAP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:27.317235Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.317552Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.317946Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.318259Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.318547Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.318834Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.319156Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.319398Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 50, 49, 49, 102, 50, 100, 56, 101], [114, 45, 50, 49, 49, 102, 50, 100, 56, 101]], header: JupyterHeader { msg_id: "f24bbab3e4", session: "r-211f2d8e", username: "josiahparry", date: "2025-02-12T20:22:27.319Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-help-r-14-91f7301c", target_name: "positron.help", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:27.319379Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.319407Z INFO Received request to open comm: CommOpen { comm_id: "positron-help-r-14-91f7301c", target_name: "positron.help", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:27.319763Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.320080Z TRACE Sending 'status/busy' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.320418Z TRACE Sending 'status/idle' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.320614Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.327142Z TRACE Received kernel request EstablishUiCommChannel(Sender { .. }) [R] at crates/ark/src/interface.rs:1216 [R] [R] 2025-02-12T20:22:27.327153Z INFO Sending message to UI comm: Event(PromptState(PromptStateParams { input_prompt: "> ", continuation_prompt: "+ " })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:27.327244Z INFO Sending message to UI comm: Event(WorkingDirectory(WorkingDirectoryParams { directory: "~/github/calcite" })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:27.327768Z TRACE Sending 'comm_msg/variables/refresh' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:27.330477Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:27.330643Z INFO Comm channel opened; there are now 5 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:27.335243Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.336710Z TRACE Sending 'comm_msg/positron-ui-r-13-721e9b7d/CallMethodReply' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:27.336978Z TRACE Sending 'comm_msg/positron-ui-r-13-721e9b7d/prompt_state' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:27.337199Z TRACE Sending 'comm_msg/positron-ui-r-13-721e9b7d/working_directory' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:27.738616Z TRACE Populated virtual namespace for stats: 24765 lines, 909 ok, 14 bad, 230 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:28.016105Z TRACE Populated virtual namespace for methods: 12044 lines, 512 ok, 0 bad, 249 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:28.108079Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 50, 49, 49, 102, 50, 100, 56, 101], [114, 45, 50, 49, 49, 102, 50, 100, 56, 101]], header: JupyterHeader { msg_id: "fd115a4f-4af1-4c1c-8366-d638ae7cd729", session: "r-211f2d8e", username: "josiahparry", date: "2025-02-12T20:22:28.107Z", msg_type: "comm_msg", version: "5.3" }, parent_header: None, content: CommWireMsg { comm_id: "positron-variables-r-12-edd6f642", data: Object {"jsonrpc": String("2.0"), "method": String("list")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:28.108134Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:28.108180Z TRACE Comm manager: Sending message to comm 'positron.variables' [R] at crates/amalthea/src/comm/comm_manager.rs:140 [R] [R] 2025-02-12T20:22:28.108207Z INFO Environment: Received message from frontend: Rpc("fd115a4f-4af1-4c1c-8366-d638ae7cd729", Object {"jsonrpc": String("2.0"), "method": String("list")}) [R] at crates/ark/src/variables/r_variables.rs:158 [R] [R] 2025-02-12T20:22:28.108377Z TRACE Sending 'status/busy' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:28.108829Z TRACE Sending 'status/idle' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:28.109298Z TRACE Sending 'comm_msg/variables/ListReply' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:28.341679Z TRACE Populated virtual namespace for base: 17506 lines, 1132 ok, 13 bad, 257 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:29.227144Z TRACE Heartbeat message: [107, 97, 108, 108, 105, 99, 104, 111, 114, 101, 45, 104, 101, 97, 114, 116, 98, 101, 97, 116] [R] at crates/amalthea/src/socket/heartbeat.rs:41 [R] [R] 2025-02-12T20:22:29.227179Z TRACE Heartbeat message replied [R] at crates/amalthea/src/socket/heartbeat.rs:50 [R] [R] 2025-02-12T20:22:29.227181Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:31.229451Z TRACE Heartbeat message: [107, 97, 108, 108, 105, 99, 104, 111, 114, 101, 45, 104, 101, 97, 114, 116, 98, 101, 97, 116] [R] at crates/amalthea/src/socket/heartbeat.rs:41 [R] [R] 2025-02-12T20:22:31.229497Z TRACE Heartbeat message replied [R] at crates/amalthea/src/socket/heartbeat.rs:50 [R] [R] 2025-02-12T20:22:31.229500Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:33.232625Z TRACE Heartbeat message: [107, 97, 108, 108, 105, 99, 104, 111, 114, 101, 45, 104, 101, 97, 114, 116, 98, 101, 97, 116] [R] at crates/amalthea/src/socket/heartbeat.rs:41 [R] [R] 2025-02-12T20:22:33.232671Z TRACE Heartbeat message replied [R] at crates/amalthea/src/socket/heartbeat.rs:50 [R] [R] 2025-02-12T20:22:33.232675Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:35.238276Z TRACE Heartbeat message: [107, 97, 108, 108, 105, 99, 104, 111, 114, 101, 45, 104, 101, 97, 114, 116, 98, 101, 97, 116] [R] at crates/amalthea/src/socket/heartbeat.rs:41 [R] [R] 2025-02-12T20:22:35.238373Z TRACE Heartbeat message replied [R] at crates/amalthea/src/socket/heartbeat.rs:50 [R] [R] 2025-02-12T20:22:35.238380Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:37.241789Z TRACE Heartbeat message: [107, 97, 108, 108, 105, 99, 104, 111, 114, 101, 45, 104, 101, 97, 114, 116, 98, 101, 97, 116] [R] at crates/amalthea/src/socket/heartbeat.rs:41 [R] [R] 2025-02-12T20:22:37.241887Z TRACE Heartbeat message replied [R] at crates/amalthea/src/socket/heartbeat.rs:50 [R] [R] 2025-02-12T20:22:37.241891Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:39.244330Z TRACE Heartbeat message: [107, 97, 108, 108, 105, 99, 104, 111, 114, 101, 45, 104, 101, 97, 114, 116, 98, 101, 97, 116] [R] at crates/amalthea/src/socket/heartbeat.rs:41 [R] [R] 2025-02-12T20:22:39.244374Z TRACE Heartbeat message replied [R] at crates/amalthea/src/socket/heartbeat.rs:50 [R] [R] 2025-02-12T20:22:39.244378Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] ** Begin kernel log for session R 4.4.0 (r-5eb1cd68) at 2/12/2025, 12:22:40 PM ** Streaming kernel log file: /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/kernel-rG6L1v/kernel.log ** Begin kernel log for session R 4.4.0 (r-bba39470) at 2/12/2025, 12:22:43 PM ** Streaming kernel log file: /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/kernel-ZVZ8br/kernel.log ** Begin kernel log for session R 4.4.0 (r-b1b3e933) at 2/12/2025, 12:22:45 PM ** Streaming kernel log file: /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/kernel-a0oqbT/kernel.log [R] 2025-02-12T20:22:40.832749Z INFO Loaded connection information from frontend in /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/connection_r-5eb1cd68.json [R] at crates/amalthea/src/kernel.rs:290 [R] [R] 2025-02-12T20:22:40.832769Z INFO Connection data: ConnectionFile { control_port: 15315, shell_port: 15809, stdin_port: 18912, iopub_port: 18603, hb_port: 15230, transport: "tcp", signature_scheme: "hmac-sha256", ip: "127.0.0.1", key: "bf0db15582e2714fdd96c2903f8ec91f" } [R] at crates/amalthea/src/kernel.rs:291 [R] [R] 2025-02-12T20:22:40.833051Z TRACE Binding to ZeroMQ 'Shell' socket at tcp://127.0.0.1:15809 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:40.833678Z TRACE Binding to ZeroMQ 'IOPub' socket at tcp://127.0.0.1:18603 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:40.833684Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:40.833807Z TRACE Binding to ZeroMQ 'Heartbeat' socket at tcp://127.0.0.1:15230 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:40.833840Z TRACE Entering kernel state: Starting [R] at crates/amalthea/src/socket/iopub.rs:386 [R] [R] 2025-02-12T20:22:40.833895Z TRACE Binding to ZeroMQ 'Stdin' socket at tcp://127.0.0.1:18912 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:40.833914Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:40.833967Z TRACE Binding to ZeroMQ 'Control' socket at tcp://127.0.0.1:15315 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:40.834015Z TRACE Binding to ZeroMQ 'OutboundNotifierTx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:115 [R] [R] 2025-02-12T20:22:40.834051Z TRACE Connecting to ZeroMQ 'OutboundNotifierRx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:120 [R] [R] 2025-02-12T20:22:40.834151Z TRACE Waiting for control messages [R] at crates/amalthea/src/socket/control.rs:58 [R] [R] 2025-02-12T20:22:40.834314Z TRACE Sending 'status/starting' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:40.938959Z INFO Successfully opened R shared library at '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib'. [R] at crates/harp/src/library.rs:30 [R] [R] 2025-02-12T20:22:40.939252Z TRACE R_HOME: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources" [R] at crates/ark/src/sys/unix/interface.rs:61 [R] [R] 2025-02-12T20:22:41.089094Z INFO Initializing global error handler [R] at crates/ark/src/errors.rs:54 [R] [R] 2025-02-12T20:22:41.089955Z DEBUG Setting default repositories to RStudio CRAN [R] at crates/ark/src/repos.rs:57 [R] [R] 2025-02-12T20:22:41.089968Z DEBUG Applying default repositories: {"CRAN": "https://cran.rstudio.com/"} [R] at crates/ark/src/repos.rs:146 [R] [R] 2025-02-12T20:22:41.090034Z INFO R has started and ark handlers have been registered, completing initialization. [R] at crates/ark/src/interface.rs:477 [R] [R] 2025-02-12T20:22:41.090039Z INFO Sending kernel info: R version 4.4.0 (2024-04-24) [R] at crates/ark/src/interface.rs:517 [R] [R] 2025-02-12T20:22:41.090095Z INFO Found R profile at '/Users/josiahparry/.Rprofile', sourcing now [R] at crates/ark/src/startup.rs:63 [R] [R] 2025-02-12T20:22:41.090307Z INFO Successfully sourced R profile at '/Users/josiahparry/.Rprofile' [R] at crates/ark/src/startup.rs:82 [R] [R] 2025-02-12T20:22:41.090318Z TRACE UI comm isn't connected, dropping `f`. [R] at crates/ark/src/interface.rs:1263 [R] [R] 2025-02-12T20:22:41.090329Z TRACE prompt_info(): n_frame = '0' [R] at crates/ark/src/interface.rs:847 [R] [R] 2025-02-12T20:22:41.090480Z TRACE R prompt: > [R] at crates/ark/src/interface.rs:689 [R] [R] 2025-02-12T20:22:41.150147Z TRACE Populated virtual namespace for datasets: 5 lines, 0 ok, 0 bad, 3 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:41.348902Z TRACE Populated virtual namespace for graphics: 5092 lines, 125 ok, 3 bad, 44 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:42.210386Z TRACE Populated virtual namespace for compiler: 2207 lines, 139 ok, 0 bad, 150 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:42.260914Z INFO Received subscribe message on IOPub with subscription ''. [R] at crates/amalthea/src/socket/iopub.rs:260 [R] [R] 2025-02-12T20:22:42.261124Z TRACE Sending 'iopub_welcome' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:42.261288Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 53, 101, 98, 49, 99, 100, 54, 56], [114, 45, 53, 101, 98, 49, 99, 100, 54, 56]], header: JupyterHeader { msg_id: "0a04c0a752", session: "r-5eb1cd68", username: "josiahparry", date: "2025-02-12T20:22:42.261Z", msg_type: "kernel_info_request", version: "5.3" }, parent_header: None, content: KernelInfoRequest } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:42.261300Z TRACE Got kernel info request; waiting for R to complete initialization [R] at crates/ark/src/shell.rs:121 [R] [R] 2025-02-12T20:22:42.261319Z TRACE Sending 'kernel_info_reply' message (reply to 'kernel_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.261367Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:42.261497Z TRACE Sending 'status/busy' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.261686Z TRACE Heartbeat message: [107, 97, 108, 108, 105, 99, 104, 111, 114, 101, 45, 104, 101, 97, 114, 116, 98, 101, 97, 116] [R] at crates/amalthea/src/socket/heartbeat.rs:41 [R] [R] 2025-02-12T20:22:42.261707Z TRACE Sending 'status/idle' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.261724Z TRACE Heartbeat message replied [R] at crates/amalthea/src/socket/heartbeat.rs:50 [R] [R] 2025-02-12T20:22:42.261743Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:42.264541Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 53, 101, 98, 49, 99, 100, 54, 56], [114, 45, 53, 101, 98, 49, 99, 100, 54, 56]], header: JupyterHeader { msg_id: "58a7761dcd", session: "r-5eb1cd68", username: "josiahparry", date: "2025-02-12T20:22:42.264Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-lsp-r-f355b5ed", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:56772")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:42.264554Z INFO Received request to open comm: CommOpen { comm_id: "positron-lsp-r-f355b5ed", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:56772")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:42.264631Z INFO Comm channel opened; there are now 1 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:42.264646Z TRACE Connecting to LSP at '127.0.0.1:56772' [R] at crates/ark/src/lsp/backend.rs:372 [R] [R] 2025-02-12T20:22:42.264751Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:42.264794Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 53, 101, 98, 49, 99, 100, 54, 56], [114, 45, 53, 101, 98, 49, 99, 100, 54, 56]], header: JupyterHeader { msg_id: "6f6cb27e35", session: "r-5eb1cd68", username: "josiahparry", date: "2025-02-12T20:22:42.264Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-variables-r-15-cce2d38", target_name: "positron.variables", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:42.264798Z INFO Received request to open comm: CommOpen { comm_id: "positron-variables-r-15-cce2d38", target_name: "positron.variables", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:42.264847Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.265043Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.265195Z TRACE Sending 'comm_msg/LSP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:42.265371Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.266575Z TRACE Connected to LSP at '127.0.0.1:56772' [R] at crates/ark/src/lsp/backend.rs:381 [R] [R] 2025-02-12T20:22:42.287792Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:42.287794Z INFO Comm channel opened; there are now 2 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:42.287836Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 53, 101, 98, 49, 99, 100, 54, 56], [114, 45, 53, 101, 98, 49, 99, 100, 54, 56]], header: JupyterHeader { msg_id: "5b6cb76433", session: "r-5eb1cd68", username: "josiahparry", date: "2025-02-12T20:22:42.264Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-dap-r-8619807b", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:57159")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:42.287842Z INFO Received request to open comm: CommOpen { comm_id: "positron-dap-r-8619807b", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:57159")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:42.287847Z INFO DAP: Spawning thread [R] at crates/ark/src/dap/dap.rs:259 [R] [R] 2025-02-12T20:22:42.287879Z INFO Comm channel opened; there are now 3 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:42.287891Z TRACE DAP: Thread starting at address 127.0.0.1:57159. [R] at crates/ark/src/dap/dap_server.rs:53 [R] [R] 2025-02-12T20:22:42.287930Z TRACE DAP: Waiting for client [R] at crates/ark/src/dap/dap_server.rs:62 [R] [R] 2025-02-12T20:22:42.287949Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:42.287974Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 53, 101, 98, 49, 99, 100, 54, 56], [114, 45, 53, 101, 98, 49, 99, 100, 54, 56]], header: JupyterHeader { msg_id: "8b55ab96fc", session: "r-5eb1cd68", username: "josiahparry", date: "2025-02-12T20:22:42.264Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-ui-r-16-2ce2ea52", target_name: "positron.ui", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:42.287980Z INFO Received request to open comm: CommOpen { comm_id: "positron-ui-r-16-2ce2ea52", target_name: "positron.ui", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:42.288012Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:42.288018Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.288029Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 53, 101, 98, 49, 99, 100, 54, 56], [114, 45, 53, 101, 98, 49, 99, 100, 54, 56]], header: JupyterHeader { msg_id: "ba466c54a9", session: "r-5eb1cd68", username: "josiahparry", date: "2025-02-12T20:22:42.265Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.help" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:42.288032Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.help" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:42.288025Z INFO Comm channel opened; there are now 4 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:42.288065Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.288123Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:42.288162Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 53, 101, 98, 49, 99, 100, 54, 56], [114, 45, 53, 101, 98, 49, 99, 100, 54, 56]], header: JupyterHeader { msg_id: "9b96688cce", session: "r-5eb1cd68", username: "josiahparry", date: "2025-02-12T20:22:42.269Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.plot" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:42.288165Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.plot" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:42.288196Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.288214Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:42.288226Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 53, 101, 98, 49, 99, 100, 54, 56], [114, 45, 53, 101, 98, 49, 99, 100, 54, 56]], header: JupyterHeader { msg_id: "2bb613af2e", session: "r-5eb1cd68", username: "josiahparry", date: "2025-02-12T20:22:42.269Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:42.288228Z INFO Received request for open comms: CommInfoRequest { target_name: "" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:42.288248Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.288283Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:42.288306Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 53, 101, 98, 49, 99, 100, 54, 56], [114, 45, 53, 101, 98, 49, 99, 100, 54, 56]], header: JupyterHeader { msg_id: "a386c027", session: "r-5eb1cd68", username: "josiahparry", date: "2025-02-12T20:22:42.271Z", msg_type: "comm_msg", version: "5.3" }, parent_header: None, content: CommWireMsg { comm_id: "positron-ui-r-16-2ce2ea52", data: Object {"jsonrpc": String("2.0"), "method": String("call_method"), "params": Object {"method": String("setConsoleWidth"), "params": Array [Number(76)]}} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:42.288318Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:42.288321Z TRACE Comm manager: Sending message to comm 'positron.ui' [R] at crates/amalthea/src/comm/comm_manager.rs:140 [R] [R] 2025-02-12T20:22:42.288351Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.288372Z TRACE Handling 'setConsoleWidth' frontend RPC method [R] at crates/ark/src/ui/ui.rs:145 [R] in comm handler with name: "positron.ui", request: CallMethod(CallMethodParams { method: "setConsoleWidth", params: [Number(76)] }) [R] [R] 2025-02-12T20:22:42.288449Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.288566Z TRACE Sending 'comm_msg/DAP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:42.288726Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.288953Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.289124Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.289301Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.289614Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.289818Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.290137Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.290367Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.290506Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 53, 101, 98, 49, 99, 100, 54, 56], [114, 45, 53, 101, 98, 49, 99, 100, 54, 56]], header: JupyterHeader { msg_id: "1c5fff28de", session: "r-5eb1cd68", username: "josiahparry", date: "2025-02-12T20:22:42.290Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-help-r-17-6d0e309a", target_name: "positron.help", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:42.290512Z INFO Received request to open comm: CommOpen { comm_id: "positron-help-r-17-6d0e309a", target_name: "positron.help", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:42.290635Z TRACE Sending 'status/busy' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.290890Z TRACE Sending 'status/idle' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.291454Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.293959Z TRACE Received kernel request EstablishUiCommChannel(Sender { .. }) [R] at crates/ark/src/interface.rs:1216 [R] [R] 2025-02-12T20:22:42.293966Z INFO Sending message to UI comm: Event(PromptState(PromptStateParams { input_prompt: "> ", continuation_prompt: "+ " })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:42.294007Z INFO Sending message to UI comm: Event(WorkingDirectory(WorkingDirectoryParams { directory: "~/github/calcite" })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:42.294194Z TRACE Sending 'comm_msg/variables/refresh' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:42.296632Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:42.297079Z INFO Comm channel opened; there are now 5 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:42.297445Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.297755Z TRACE Sending 'comm_msg/positron-ui-r-16-2ce2ea52/CallMethodReply' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:42.298007Z TRACE Sending 'comm_msg/positron-ui-r-16-2ce2ea52/prompt_state' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:42.298144Z TRACE Sending 'comm_msg/positron-ui-r-16-2ce2ea52/working_directory' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:42.318271Z TRACE Populated virtual namespace for utils: 16143 lines, 502 ok, 1 bad, 73 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:42.461383Z TRACE Populated virtual namespace for grDevices: 3973 lines, 212 ok, 0 bad, 75 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:42.821082Z TRACE Populated virtual namespace for tools: 35129 lines, 711 ok, 3 bad, 78 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in onload_hook with pkg: "tools" [R] ** Begin kernel log for session R 4.4.0 (r-9f3f86be) at 2/12/2025, 12:22:47 PM ** Streaming kernel log file: /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/kernel-RGmmnT/kernel.log [R] 2025-02-12T20:22:43.091115Z INFO Loaded connection information from frontend in /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/connection_r-bba39470.json [R] at crates/amalthea/src/kernel.rs:290 [R] [R] 2025-02-12T20:22:43.091133Z INFO Connection data: ConnectionFile { control_port: 15196, shell_port: 22522, stdin_port: 20440, iopub_port: 17232, hb_port: 23319, transport: "tcp", signature_scheme: "hmac-sha256", ip: "127.0.0.1", key: "4bdbbe980f8728d56ef770704a999771" } [R] at crates/amalthea/src/kernel.rs:291 [R] [R] 2025-02-12T20:22:43.091456Z TRACE Binding to ZeroMQ 'Shell' socket at tcp://127.0.0.1:22522 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:43.092141Z TRACE Binding to ZeroMQ 'IOPub' socket at tcp://127.0.0.1:17232 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:43.092148Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:43.092271Z TRACE Binding to ZeroMQ 'Heartbeat' socket at tcp://127.0.0.1:23319 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:43.092290Z TRACE Entering kernel state: Starting [R] at crates/amalthea/src/socket/iopub.rs:386 [R] [R] 2025-02-12T20:22:43.092376Z TRACE Binding to ZeroMQ 'Stdin' socket at tcp://127.0.0.1:20440 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:43.092385Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:43.092469Z TRACE Binding to ZeroMQ 'Control' socket at tcp://127.0.0.1:15196 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:43.092546Z TRACE Binding to ZeroMQ 'OutboundNotifierTx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:115 [R] [R] 2025-02-12T20:22:43.092610Z TRACE Connecting to ZeroMQ 'OutboundNotifierRx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:120 [R] [R] 2025-02-12T20:22:43.092685Z TRACE Waiting for control messages [R] at crates/amalthea/src/socket/control.rs:58 [R] [R] 2025-02-12T20:22:43.092853Z TRACE Sending 'status/starting' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:43.198754Z INFO Successfully opened R shared library at '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib'. [R] at crates/harp/src/library.rs:30 [R] [R] 2025-02-12T20:22:43.199059Z TRACE R_HOME: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources" [R] at crates/ark/src/sys/unix/interface.rs:61 [R] [R] 2025-02-12T20:22:43.336040Z INFO Initializing global error handler [R] at crates/ark/src/errors.rs:54 [R] [R] 2025-02-12T20:22:43.336572Z DEBUG Setting default repositories to RStudio CRAN [R] at crates/ark/src/repos.rs:57 [R] [R] 2025-02-12T20:22:43.336579Z DEBUG Applying default repositories: {"CRAN": "https://cran.rstudio.com/"} [R] at crates/ark/src/repos.rs:146 [R] [R] 2025-02-12T20:22:43.336618Z INFO R has started and ark handlers have been registered, completing initialization. [R] at crates/ark/src/interface.rs:477 [R] [R] 2025-02-12T20:22:43.336623Z INFO Sending kernel info: R version 4.4.0 (2024-04-24) [R] at crates/ark/src/interface.rs:517 [R] [R] 2025-02-12T20:22:43.336657Z INFO Found R profile at '/Users/josiahparry/.Rprofile', sourcing now [R] at crates/ark/src/startup.rs:63 [R] [R] 2025-02-12T20:22:43.336820Z INFO Successfully sourced R profile at '/Users/josiahparry/.Rprofile' [R] at crates/ark/src/startup.rs:82 [R] [R] 2025-02-12T20:22:43.336832Z TRACE UI comm isn't connected, dropping `f`. [R] at crates/ark/src/interface.rs:1263 [R] [R] 2025-02-12T20:22:43.336842Z TRACE prompt_info(): n_frame = '0' [R] at crates/ark/src/interface.rs:847 [R] [R] 2025-02-12T20:22:43.336955Z TRACE R prompt: > [R] at crates/ark/src/interface.rs:689 [R] [R] 2025-02-12T20:22:43.394582Z TRACE Populated virtual namespace for datasets: 5 lines, 0 ok, 0 bad, 3 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:43.661488Z TRACE Populated virtual namespace for graphics: 5092 lines, 125 ok, 3 bad, 44 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:43.717083Z TRACE Populated virtual namespace for grDevices: 3973 lines, 212 ok, 0 bad, 75 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:43.755397Z TRACE Populated virtual namespace for compiler: 2207 lines, 139 ok, 0 bad, 150 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:44.527679Z INFO Received subscribe message on IOPub with subscription ''. [R] at crates/amalthea/src/socket/iopub.rs:260 [R] [R] 2025-02-12T20:22:44.527911Z TRACE Sending 'iopub_welcome' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:44.528288Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 98, 98, 97, 51, 57, 52, 55, 48], [114, 45, 98, 98, 97, 51, 57, 52, 55, 48]], header: JupyterHeader { msg_id: "3dba565cf6", session: "r-bba39470", username: "josiahparry", date: "2025-02-12T20:22:44.528Z", msg_type: "kernel_info_request", version: "5.3" }, parent_header: None, content: KernelInfoRequest } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:44.528299Z TRACE Got kernel info request; waiting for R to complete initialization [R] at crates/ark/src/shell.rs:121 [R] [R] 2025-02-12T20:22:44.528315Z TRACE Sending 'kernel_info_reply' message (reply to 'kernel_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.528366Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:44.528457Z TRACE Sending 'status/busy' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.528542Z TRACE Heartbeat message: [107, 97, 108, 108, 105, 99, 104, 111, 114, 101, 45, 104, 101, 97, 114, 116, 98, 101, 97, 116] [R] at crates/amalthea/src/socket/heartbeat.rs:41 [R] [R] 2025-02-12T20:22:44.528587Z TRACE Heartbeat message replied [R] at crates/amalthea/src/socket/heartbeat.rs:50 [R] [R] 2025-02-12T20:22:44.528592Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:44.528681Z TRACE Sending 'status/idle' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.537395Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 98, 98, 97, 51, 57, 52, 55, 48], [114, 45, 98, 98, 97, 51, 57, 52, 55, 48]], header: JupyterHeader { msg_id: "d5016c0db6", session: "r-bba39470", username: "josiahparry", date: "2025-02-12T20:22:44.537Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-lsp-r-f21f8834", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:60537")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:44.537443Z INFO Received request to open comm: CommOpen { comm_id: "positron-lsp-r-f21f8834", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:60537")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:44.537531Z INFO Comm channel opened; there are now 1 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:44.537577Z TRACE Connecting to LSP at '127.0.0.1:60537' [R] at crates/ark/src/lsp/backend.rs:372 [R] [R] 2025-02-12T20:22:44.537666Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:44.537690Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 98, 98, 97, 51, 57, 52, 55, 48], [114, 45, 98, 98, 97, 51, 57, 52, 55, 48]], header: JupyterHeader { msg_id: "dd35c35f51", session: "r-bba39470", username: "josiahparry", date: "2025-02-12T20:22:44.537Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-dap-r-a79c5d01", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:45063")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:44.537693Z INFO Received request to open comm: CommOpen { comm_id: "positron-dap-r-a79c5d01", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:45063")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:44.537696Z INFO DAP: Spawning thread [R] at crates/ark/src/dap/dap.rs:259 [R] [R] 2025-02-12T20:22:44.537741Z INFO Comm channel opened; there are now 2 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:44.537780Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.537789Z TRACE DAP: Thread starting at address 127.0.0.1:45063. [R] at crates/ark/src/dap/dap_server.rs:53 [R] [R] 2025-02-12T20:22:44.537807Z TRACE DAP: Waiting for client [R] at crates/ark/src/dap/dap_server.rs:62 [R] [R] 2025-02-12T20:22:44.537820Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:44.537841Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 98, 98, 97, 51, 57, 52, 55, 48], [114, 45, 98, 98, 97, 51, 57, 52, 55, 48]], header: JupyterHeader { msg_id: "916457ff19", session: "r-bba39470", username: "josiahparry", date: "2025-02-12T20:22:44.537Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-variables-r-18-890b3b04", target_name: "positron.variables", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:44.537844Z INFO Received request to open comm: CommOpen { comm_id: "positron-variables-r-18-890b3b04", target_name: "positron.variables", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:44.537966Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.538234Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.538397Z TRACE Sending 'comm_msg/LSP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:44.538560Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.538782Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.538921Z TRACE Sending 'comm_msg/DAP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:44.539673Z TRACE Connected to LSP at '127.0.0.1:60537' [R] at crates/ark/src/lsp/backend.rs:381 [R] [R] 2025-02-12T20:22:44.559954Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:44.559990Z INFO Comm channel opened; there are now 3 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:44.559997Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 98, 98, 97, 51, 57, 52, 55, 48], [114, 45, 98, 98, 97, 51, 57, 52, 55, 48]], header: JupyterHeader { msg_id: "1358fc63c3", session: "r-bba39470", username: "josiahparry", date: "2025-02-12T20:22:44.537Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-ui-r-19-1b006053", target_name: "positron.ui", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:44.560003Z INFO Received request to open comm: CommOpen { comm_id: "positron-ui-r-19-1b006053", target_name: "positron.ui", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:44.560105Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:44.560118Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 98, 98, 97, 51, 57, 52, 55, 48], [114, 45, 98, 98, 97, 51, 57, 52, 55, 48]], header: JupyterHeader { msg_id: "46670d88b7", session: "r-bba39470", username: "josiahparry", date: "2025-02-12T20:22:44.537Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.help" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:44.560121Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.help" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:44.560125Z INFO Comm channel opened; there are now 4 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:44.560185Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.560189Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.560231Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:44.560253Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 98, 98, 97, 51, 57, 52, 55, 48], [114, 45, 98, 98, 97, 51, 57, 52, 55, 48]], header: JupyterHeader { msg_id: "f4be7023ee", session: "r-bba39470", username: "josiahparry", date: "2025-02-12T20:22:44.540Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.help" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:44.560257Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.help" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:44.560380Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.560392Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.560402Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:44.560418Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 98, 98, 97, 51, 57, 52, 55, 48], [114, 45, 98, 98, 97, 51, 57, 52, 55, 48]], header: JupyterHeader { msg_id: "349a84c615", session: "r-bba39470", username: "josiahparry", date: "2025-02-12T20:22:44.540Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.plot" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:44.560420Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.plot" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:44.560505Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.560523Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:44.560544Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 98, 98, 97, 51, 57, 52, 55, 48], [114, 45, 98, 98, 97, 51, 57, 52, 55, 48]], header: JupyterHeader { msg_id: "b80baaf05e", session: "r-bba39470", username: "josiahparry", date: "2025-02-12T20:22:44.540Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:44.560546Z INFO Received request for open comms: CommInfoRequest { target_name: "" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:44.560614Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.560664Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:44.560696Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 98, 98, 97, 51, 57, 52, 55, 48], [114, 45, 98, 98, 97, 51, 57, 52, 55, 48]], header: JupyterHeader { msg_id: "6f43a3c7", session: "r-bba39470", username: "josiahparry", date: "2025-02-12T20:22:44.544Z", msg_type: "comm_msg", version: "5.3" }, parent_header: None, content: CommWireMsg { comm_id: "positron-ui-r-19-1b006053", data: Object {"jsonrpc": String("2.0"), "method": String("call_method"), "params": Object {"method": String("setConsoleWidth"), "params": Array [Number(76)]}} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:44.560705Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:44.560720Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 98, 98, 97, 51, 57, 52, 55, 48], [114, 45, 98, 98, 97, 51, 57, 52, 55, 48]], header: JupyterHeader { msg_id: "4d0b34f0d5", session: "r-bba39470", username: "josiahparry", date: "2025-02-12T20:22:44.545Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-lsp-r-63fa5caf", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:51049")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:44.560722Z INFO Received request to open comm: CommOpen { comm_id: "positron-lsp-r-63fa5caf", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:51049")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:44.560757Z TRACE Comm manager: Sending message to comm 'positron.ui' [R] at crates/amalthea/src/comm/comm_manager.rs:140 [R] [R] 2025-02-12T20:22:44.560765Z INFO Comm channel opened; there are now 5 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:44.560796Z TRACE Connecting to LSP at '127.0.0.1:51049' [R] at crates/ark/src/lsp/backend.rs:372 [R] [R] 2025-02-12T20:22:44.560796Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.560915Z TRACE Handling 'setConsoleWidth' frontend RPC method [R] at crates/ark/src/ui/ui.rs:145 [R] in comm handler with name: "positron.ui", request: CallMethod(CallMethodParams { method: "setConsoleWidth", params: [Number(76)] }) [R] [R] 2025-02-12T20:22:44.561246Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.561336Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:44.561356Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 98, 98, 97, 51, 57, 52, 55, 48], [114, 45, 98, 98, 97, 51, 57, 52, 55, 48]], header: JupyterHeader { msg_id: "ce7d7ee003", session: "r-bba39470", username: "josiahparry", date: "2025-02-12T20:22:44.545Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-dap-r-f377e1bb", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:49930")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:44.561359Z INFO Received request to open comm: CommOpen { comm_id: "positron-dap-r-f377e1bb", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:49930")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:44.561363Z INFO DAP: Spawning thread [R] at crates/ark/src/dap/dap.rs:259 [R] [R] 2025-02-12T20:22:44.561417Z TRACE DAP: Thread starting at address 127.0.0.1:49930. [R] at crates/ark/src/dap/dap_server.rs:53 [R] [R] 2025-02-12T20:22:44.561468Z TRACE DAP: Waiting for client [R] at crates/ark/src/dap/dap_server.rs:62 [R] [R] 2025-02-12T20:22:44.561475Z INFO Comm channel opened; there are now 6 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:44.561493Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:44.561553Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.561813Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.563134Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.563528Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.563819Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.564167Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.564671Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 98, 98, 97, 51, 57, 52, 55, 48], [114, 45, 98, 98, 97, 51, 57, 52, 55, 48]], header: JupyterHeader { msg_id: "19b31eb6dc", session: "r-bba39470", username: "josiahparry", date: "2025-02-12T20:22:44.564Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-help-r-20-97c3ea0b", target_name: "positron.help", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:44.564682Z INFO Received request to open comm: CommOpen { comm_id: "positron-help-r-20-97c3ea0b", target_name: "positron.help", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:44.564728Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.564899Z TRACE Sending 'status/busy' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.565021Z TRACE Sending 'status/idle' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.565206Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.565397Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.565653Z TRACE Sending 'comm_msg/LSP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:44.565831Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.566039Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.566145Z TRACE Sending 'comm_msg/DAP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:44.566263Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.567245Z TRACE Connected to LSP at '127.0.0.1:51049' [R] at crates/ark/src/lsp/backend.rs:381 [R] [R] 2025-02-12T20:22:44.567624Z TRACE Received kernel request EstablishUiCommChannel(Sender { .. }) [R] at crates/ark/src/interface.rs:1216 [R] [R] 2025-02-12T20:22:44.567631Z INFO Sending message to UI comm: Event(PromptState(PromptStateParams { input_prompt: "> ", continuation_prompt: "+ " })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:44.567654Z INFO Sending message to UI comm: Event(WorkingDirectory(WorkingDirectoryParams { directory: "~/github/calcite" })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:44.568115Z TRACE Populated virtual namespace for tools: 35129 lines, 711 ok, 3 bad, 78 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in onload_hook with pkg: "tools" [R] [R] 2025-02-12T20:22:44.568357Z TRACE Sending 'comm_msg/variables/refresh' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:44.581879Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:44.582000Z INFO Comm channel opened; there are now 7 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:44.582155Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 98, 98, 97, 51, 57, 52, 55, 48], [114, 45, 98, 98, 97, 51, 57, 52, 55, 48]], header: JupyterHeader { msg_id: "e2009eee27", session: "r-bba39470", username: "josiahparry", date: "2025-02-12T20:22:44.564Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-help-r-21-bf85d866", target_name: "positron.help", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:44.582190Z INFO Received request to open comm: CommOpen { comm_id: "positron-help-r-21-bf85d866", target_name: "positron.help", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:44.582539Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.582908Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.596610Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:44.596649Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 98, 98, 97, 51, 57, 52, 55, 48], [114, 45, 98, 98, 97, 51, 57, 52, 55, 48]], header: JupyterHeader { msg_id: "a9e2caa9", session: "r-bba39470", username: "josiahparry", date: "2025-02-12T20:22:44.567Z", msg_type: "comm_msg", version: "5.3" }, parent_header: None, content: CommWireMsg { comm_id: "positron-ui-r-19-1b006053", data: Object {"jsonrpc": String("2.0"), "method": String("call_method"), "params": Object {"method": String("setConsoleWidth"), "params": Array [Number(76)]}} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:44.596658Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:44.596876Z INFO Comm channel opened; there are now 8 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:44.596891Z TRACE Comm manager: Sending message to comm 'positron.ui' [R] at crates/amalthea/src/comm/comm_manager.rs:140 [R] [R] 2025-02-12T20:22:44.599167Z ERROR Error receiving internal Help message: RecvError [R] at crates/ark/src/help/r_help.rs:127 [R] [R] 2025-02-12T20:22:44.599188Z TRACE Help comm positron-help-r-20-97c3ea0b closed. [R] at crates/ark/src/help/r_help.rs:134 [R] [R] 2025-02-12T20:22:44.599522Z TRACE Handling 'setConsoleWidth' frontend RPC method [R] at crates/ark/src/ui/ui.rs:145 [R] in comm handler with name: "positron.ui", request: CallMethod(CallMethodParams { method: "setConsoleWidth", params: [Number(76)] }) [R] [R] 2025-02-12T20:22:44.601147Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.601857Z TRACE Sending 'status/busy' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.602541Z TRACE Sending 'status/idle' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.603874Z TRACE Sending 'comm_msg/positron-ui-r-19-1b006053/CallMethodReply' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:44.604283Z TRACE Sending 'comm_msg/positron-ui-r-19-1b006053/prompt_state' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:44.605653Z TRACE Sending 'comm_msg/positron-ui-r-19-1b006053/working_directory' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:44.614184Z TRACE Sending 'comm_msg/positron-ui-r-19-1b006053/CallMethodReply' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:45.028128Z TRACE Populated virtual namespace for stats: 24765 lines, 909 ok, 14 bad, 230 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:45.214201Z TRACE Populated virtual namespace for utils: 16143 lines, 502 ok, 1 bad, 73 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] ** Begin kernel log for session R 4.4.0 (r-cecc87b5) at 2/12/2025, 12:22:50 PM ** Streaming kernel log file: /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/kernel-lLbhK4/kernel.log [R] 2025-02-12T20:22:45.686119Z INFO Loaded connection information from frontend in /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/connection_r-b1b3e933.json [R] at crates/amalthea/src/kernel.rs:290 [R] [R] 2025-02-12T20:22:45.686139Z INFO Connection data: ConnectionFile { control_port: 22565, shell_port: 16525, stdin_port: 15472, iopub_port: 20249, hb_port: 23608, transport: "tcp", signature_scheme: "hmac-sha256", ip: "127.0.0.1", key: "c5845d387d1cd1172a16fb37467f44fb" } [R] at crates/amalthea/src/kernel.rs:291 [R] [R] 2025-02-12T20:22:45.686413Z TRACE Binding to ZeroMQ 'Shell' socket at tcp://127.0.0.1:16525 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:45.687066Z TRACE Binding to ZeroMQ 'IOPub' socket at tcp://127.0.0.1:20249 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:45.687081Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:45.687169Z TRACE Binding to ZeroMQ 'Heartbeat' socket at tcp://127.0.0.1:23608 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:45.687190Z TRACE Entering kernel state: Starting [R] at crates/amalthea/src/socket/iopub.rs:386 [R] [R] 2025-02-12T20:22:45.687273Z TRACE Binding to ZeroMQ 'Stdin' socket at tcp://127.0.0.1:15472 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:45.687295Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:45.687370Z TRACE Binding to ZeroMQ 'Control' socket at tcp://127.0.0.1:22565 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:45.687448Z TRACE Binding to ZeroMQ 'OutboundNotifierTx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:115 [R] [R] 2025-02-12T20:22:45.687505Z TRACE Connecting to ZeroMQ 'OutboundNotifierRx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:120 [R] [R] 2025-02-12T20:22:45.687610Z TRACE Waiting for control messages [R] at crates/amalthea/src/socket/control.rs:58 [R] [R] 2025-02-12T20:22:45.687775Z TRACE Sending 'status/starting' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:45.793876Z INFO Successfully opened R shared library at '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib'. [R] at crates/harp/src/library.rs:30 [R] [R] 2025-02-12T20:22:45.794184Z TRACE R_HOME: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources" [R] at crates/ark/src/sys/unix/interface.rs:61 [R] [R] 2025-02-12T20:22:45.927222Z INFO Initializing global error handler [R] at crates/ark/src/errors.rs:54 [R] [R] 2025-02-12T20:22:45.927797Z DEBUG Setting default repositories to RStudio CRAN [R] at crates/ark/src/repos.rs:57 [R] [R] 2025-02-12T20:22:45.927809Z DEBUG Applying default repositories: {"CRAN": "https://cran.rstudio.com/"} [R] at crates/ark/src/repos.rs:146 [R] [R] 2025-02-12T20:22:45.927852Z INFO R has started and ark handlers have been registered, completing initialization. [R] at crates/ark/src/interface.rs:477 [R] [R] 2025-02-12T20:22:45.927857Z INFO Sending kernel info: R version 4.4.0 (2024-04-24) [R] at crates/ark/src/interface.rs:517 [R] [R] 2025-02-12T20:22:45.927900Z INFO Found R profile at '/Users/josiahparry/.Rprofile', sourcing now [R] at crates/ark/src/startup.rs:63 [R] [R] 2025-02-12T20:22:45.928089Z INFO Successfully sourced R profile at '/Users/josiahparry/.Rprofile' [R] at crates/ark/src/startup.rs:82 [R] [R] 2025-02-12T20:22:45.928103Z TRACE UI comm isn't connected, dropping `f`. [R] at crates/ark/src/interface.rs:1263 [R] [R] 2025-02-12T20:22:45.928113Z TRACE prompt_info(): n_frame = '0' [R] at crates/ark/src/interface.rs:847 [R] [R] 2025-02-12T20:22:45.928206Z TRACE R prompt: > [R] at crates/ark/src/interface.rs:689 [R] [R] 2025-02-12T20:22:45.985011Z TRACE Populated virtual namespace for datasets: 5 lines, 0 ok, 0 bad, 3 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:46.160131Z TRACE Populated virtual namespace for graphics: 5092 lines, 125 ok, 3 bad, 44 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:46.950567Z TRACE Populated virtual namespace for utils: 16143 lines, 502 ok, 1 bad, 73 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:47.079017Z INFO Received subscribe message on IOPub with subscription ''. [R] at crates/amalthea/src/socket/iopub.rs:260 [R] [R] 2025-02-12T20:22:47.079206Z TRACE Sending 'iopub_welcome' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:47.079337Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 98, 49, 98, 51, 101, 57, 51, 51], [114, 45, 98, 49, 98, 51, 101, 57, 51, 51]], header: JupyterHeader { msg_id: "8eb8766f7f", session: "r-b1b3e933", username: "josiahparry", date: "2025-02-12T20:22:47.079Z", msg_type: "kernel_info_request", version: "5.3" }, parent_header: None, content: KernelInfoRequest } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:47.079347Z TRACE Got kernel info request; waiting for R to complete initialization [R] at crates/ark/src/shell.rs:121 [R] [R] 2025-02-12T20:22:47.079363Z TRACE Sending 'kernel_info_reply' message (reply to 'kernel_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.079403Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:47.079487Z TRACE Heartbeat message: [107, 97, 108, 108, 105, 99, 104, 111, 114, 101, 45, 104, 101, 97, 114, 116, 98, 101, 97, 116] [R] at crates/amalthea/src/socket/heartbeat.rs:41 [R] [R] 2025-02-12T20:22:47.079507Z TRACE Heartbeat message replied [R] at crates/amalthea/src/socket/heartbeat.rs:50 [R] [R] 2025-02-12T20:22:47.079509Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:47.079537Z TRACE Sending 'status/busy' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.079673Z TRACE Sending 'status/idle' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.084232Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 98, 49, 98, 51, 101, 57, 51, 51], [114, 45, 98, 49, 98, 51, 101, 57, 51, 51]], header: JupyterHeader { msg_id: "8f84e30c10", session: "r-b1b3e933", username: "josiahparry", date: "2025-02-12T20:22:47.083Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-variables-r-22-3a8072f9", target_name: "positron.variables", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:47.084276Z INFO Received request to open comm: CommOpen { comm_id: "positron-variables-r-22-3a8072f9", target_name: "positron.variables", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:47.084756Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.102666Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:47.102686Z INFO Comm channel opened; there are now 1 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:47.102701Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 98, 49, 98, 51, 101, 57, 51, 51], [114, 45, 98, 49, 98, 51, 101, 57, 51, 51]], header: JupyterHeader { msg_id: "6eb01c4beb", session: "r-b1b3e933", username: "josiahparry", date: "2025-02-12T20:22:47.083Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-ui-r-23-891f8c1b", target_name: "positron.ui", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:47.102706Z INFO Received request to open comm: CommOpen { comm_id: "positron-ui-r-23-891f8c1b", target_name: "positron.ui", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:47.102743Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:47.102761Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 98, 49, 98, 51, 101, 57, 51, 51], [114, 45, 98, 49, 98, 51, 101, 57, 51, 51]], header: JupyterHeader { msg_id: "5a069723aa", session: "r-b1b3e933", username: "josiahparry", date: "2025-02-12T20:22:47.083Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-lsp-r-a563ac88", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:60865")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:47.102764Z INFO Received request to open comm: CommOpen { comm_id: "positron-lsp-r-a563ac88", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:60865")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:47.102766Z INFO Comm channel opened; there are now 2 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:47.102794Z INFO Comm channel opened; there are now 3 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:47.102806Z TRACE Connecting to LSP at '127.0.0.1:60865' [R] at crates/ark/src/lsp/backend.rs:372 [R] [R] 2025-02-12T20:22:47.102866Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:47.102883Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.102885Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 98, 49, 98, 51, 101, 57, 51, 51], [114, 45, 98, 49, 98, 51, 101, 57, 51, 51]], header: JupyterHeader { msg_id: "d951f44c69", session: "r-b1b3e933", username: "josiahparry", date: "2025-02-12T20:22:47.083Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.help" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:47.102888Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.help" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:47.102915Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.102947Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:47.102974Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 98, 49, 98, 51, 101, 57, 51, 51], [114, 45, 98, 49, 98, 51, 101, 57, 51, 51]], header: JupyterHeader { msg_id: "4415e4a506", session: "r-b1b3e933", username: "josiahparry", date: "2025-02-12T20:22:47.084Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-dap-r-cfc71299", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:60078")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:47.102979Z INFO Received request to open comm: CommOpen { comm_id: "positron-dap-r-cfc71299", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:60078")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:47.102983Z INFO DAP: Spawning thread [R] at crates/ark/src/dap/dap.rs:259 [R] [R] 2025-02-12T20:22:47.103020Z TRACE DAP: Thread starting at address 127.0.0.1:60078. [R] at crates/ark/src/dap/dap_server.rs:53 [R] [R] 2025-02-12T20:22:47.103025Z INFO Comm channel opened; there are now 4 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:47.103049Z TRACE DAP: Waiting for client [R] at crates/ark/src/dap/dap_server.rs:62 [R] [R] 2025-02-12T20:22:47.103059Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:47.103072Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 98, 49, 98, 51, 101, 57, 51, 51], [114, 45, 98, 49, 98, 51, 101, 57, 51, 51]], header: JupyterHeader { msg_id: "a5e249f9c4", session: "r-b1b3e933", username: "josiahparry", date: "2025-02-12T20:22:47.085Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.plot" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:47.103075Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.plot" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:47.103099Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.103103Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.103115Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:47.103126Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 98, 49, 98, 51, 101, 57, 51, 51], [114, 45, 98, 49, 98, 51, 101, 57, 51, 51]], header: JupyterHeader { msg_id: "b08d8810f4", session: "r-b1b3e933", username: "josiahparry", date: "2025-02-12T20:22:47.085Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:47.103129Z INFO Received request for open comms: CommInfoRequest { target_name: "" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:47.103180Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.103186Z TRACE Received kernel request EstablishUiCommChannel(Sender { .. }) [R] at crates/ark/src/interface.rs:1216 [R] [R] 2025-02-12T20:22:47.103190Z INFO Sending message to UI comm: Event(PromptState(PromptStateParams { input_prompt: "> ", continuation_prompt: "+ " })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:47.103208Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:47.103219Z INFO Sending message to UI comm: Event(WorkingDirectory(WorkingDirectoryParams { directory: "~/github/calcite" })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:47.103253Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.103377Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.103461Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.103624Z TRACE Sending 'comm_msg/LSP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:47.103960Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.104149Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.104526Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.105131Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.105377Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 98, 49, 98, 51, 101, 57, 51, 51], [114, 45, 98, 49, 98, 51, 101, 57, 51, 51]], header: JupyterHeader { msg_id: "7bf20f1151", session: "r-b1b3e933", username: "josiahparry", date: "2025-02-12T20:22:47.105Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-help-r-24-4926e9f5", target_name: "positron.help", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:47.105381Z INFO Received request to open comm: CommOpen { comm_id: "positron-help-r-24-4926e9f5", target_name: "positron.help", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:47.105548Z TRACE Sending 'comm_msg/DAP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:47.105694Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.106153Z TRACE Connected to LSP at '127.0.0.1:60865' [R] at crates/ark/src/lsp/backend.rs:381 [R] [R] 2025-02-12T20:22:47.106280Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.106579Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.106993Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.107198Z TRACE Sending 'comm_msg/positron-ui-r-23-891f8c1b/prompt_state' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:47.107467Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:47.107493Z INFO Comm channel opened; there are now 5 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:47.107500Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 98, 49, 98, 51, 101, 57, 51, 51], [114, 45, 98, 49, 98, 51, 101, 57, 51, 51]], header: JupyterHeader { msg_id: "fb73f186", session: "r-b1b3e933", username: "josiahparry", date: "2025-02-12T20:22:47.105Z", msg_type: "comm_msg", version: "5.3" }, parent_header: None, content: CommWireMsg { comm_id: "positron-ui-r-23-891f8c1b", data: Object {"jsonrpc": String("2.0"), "method": String("call_method"), "params": Object {"method": String("setConsoleWidth"), "params": Array [Number(76)]}} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:47.107513Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:47.107579Z TRACE Sending 'comm_msg/positron-ui-r-23-891f8c1b/working_directory' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:47.107586Z TRACE Comm manager: Sending message to comm 'positron.ui' [R] at crates/amalthea/src/comm/comm_manager.rs:140 [R] [R] 2025-02-12T20:22:47.107673Z TRACE Handling 'setConsoleWidth' frontend RPC method [R] at crates/ark/src/ui/ui.rs:145 [R] in comm handler with name: "positron.ui", request: CallMethod(CallMethodParams { method: "setConsoleWidth", params: [Number(76)] }) [R] [R] 2025-02-12T20:22:47.107952Z TRACE Sending 'comm_msg/variables/refresh' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:47.108128Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.108395Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.108602Z TRACE Sending 'status/busy' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.108779Z TRACE Sending 'status/idle' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.118035Z TRACE Sending 'comm_msg/positron-ui-r-23-891f8c1b/CallMethodReply' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:47.396781Z TRACE Populated virtual namespace for tools: 35129 lines, 711 ok, 3 bad, 78 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in onload_hook with pkg: "tools" [R] [R] 2025-02-12T20:22:47.401447Z TRACE Populated virtual namespace for grDevices: 3973 lines, 212 ok, 0 bad, 75 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] ** Begin kernel log for session R 4.4.0 (r-7060276c) at 2/12/2025, 12:22:52 PM ** Streaming kernel log file: /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/kernel-FUG7Cl/kernel.log [R] 2025-02-12T20:22:47.869171Z INFO Loaded connection information from frontend in /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/connection_r-9f3f86be.json [R] at crates/amalthea/src/kernel.rs:290 [R] [R] 2025-02-12T20:22:47.869195Z INFO Connection data: ConnectionFile { control_port: 21122, shell_port: 16944, stdin_port: 16640, iopub_port: 17443, hb_port: 17357, transport: "tcp", signature_scheme: "hmac-sha256", ip: "127.0.0.1", key: "716afc106f152699f0c5294e99b91190" } [R] at crates/amalthea/src/kernel.rs:291 [R] [R] 2025-02-12T20:22:47.869552Z TRACE Binding to ZeroMQ 'Shell' socket at tcp://127.0.0.1:16944 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:47.870218Z TRACE Binding to ZeroMQ 'IOPub' socket at tcp://127.0.0.1:17443 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:47.870234Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:47.870292Z TRACE Binding to ZeroMQ 'Heartbeat' socket at tcp://127.0.0.1:17357 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:47.870304Z TRACE Entering kernel state: Starting [R] at crates/amalthea/src/socket/iopub.rs:386 [R] [R] 2025-02-12T20:22:47.870377Z TRACE Binding to ZeroMQ 'Stdin' socket at tcp://127.0.0.1:16640 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:47.870384Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:47.870458Z TRACE Binding to ZeroMQ 'Control' socket at tcp://127.0.0.1:21122 [R] at crates/amalthea/src/socket/socket.rs:82 [R] [R] 2025-02-12T20:22:47.870496Z TRACE Binding to ZeroMQ 'OutboundNotifierTx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:115 [R] [R] 2025-02-12T20:22:47.870524Z TRACE Connecting to ZeroMQ 'OutboundNotifierRx' socket at inproc://outbound_notif [R] at crates/amalthea/src/socket/socket.rs:120 [R] [R] 2025-02-12T20:22:47.870609Z TRACE Waiting for control messages [R] at crates/amalthea/src/socket/control.rs:58 [R] [R] 2025-02-12T20:22:47.870748Z TRACE Sending 'status/starting' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:47.971241Z INFO Successfully opened R shared library at '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib'. [R] at crates/harp/src/library.rs:30 [R] [R] 2025-02-12T20:22:47.971515Z TRACE R_HOME: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources" [R] at crates/ark/src/sys/unix/interface.rs:61 [R] [R] 2025-02-12T20:22:48.102205Z INFO Initializing global error handler [R] at crates/ark/src/errors.rs:54 [R] [R] 2025-02-12T20:22:48.102782Z DEBUG Setting default repositories to RStudio CRAN [R] at crates/ark/src/repos.rs:57 [R] [R] 2025-02-12T20:22:48.102787Z DEBUG Applying default repositories: {"CRAN": "https://cran.rstudio.com/"} [R] at crates/ark/src/repos.rs:146 [R] [R] 2025-02-12T20:22:48.102831Z INFO R has started and ark handlers have been registered, completing initialization. [R] at crates/ark/src/interface.rs:477 [R] [R] 2025-02-12T20:22:48.102837Z INFO Sending kernel info: R version 4.4.0 (2024-04-24) [R] at crates/ark/src/interface.rs:517 [R] [R] 2025-02-12T20:22:48.102875Z INFO Found R profile at '/Users/josiahparry/.Rprofile', sourcing now [R] at crates/ark/src/startup.rs:63 [R] [R] 2025-02-12T20:22:48.103050Z INFO Successfully sourced R profile at '/Users/josiahparry/.Rprofile' [R] at crates/ark/src/startup.rs:82 [R] [R] 2025-02-12T20:22:48.103060Z TRACE UI comm isn't connected, dropping `f`. [R] at crates/ark/src/interface.rs:1263 [R] [R] 2025-02-12T20:22:48.103069Z TRACE prompt_info(): n_frame = '0' [R] at crates/ark/src/interface.rs:847 [R] [R] 2025-02-12T20:22:48.103193Z TRACE R prompt: > [R] at crates/ark/src/interface.rs:689 [R] [R] 2025-02-12T20:22:48.162072Z TRACE Populated virtual namespace for datasets: 5 lines, 0 ok, 0 bad, 3 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:48.332911Z TRACE Populated virtual namespace for graphics: 5092 lines, 125 ok, 3 bad, 44 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:49.035925Z TRACE Populated virtual namespace for tools: 35129 lines, 711 ok, 3 bad, 78 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in onload_hook with pkg: "tools" [R] [R] 2025-02-12T20:22:49.320930Z INFO Received subscribe message on IOPub with subscription ''. [R] at crates/amalthea/src/socket/iopub.rs:260 [R] [R] 2025-02-12T20:22:49.321096Z TRACE Sending 'iopub_welcome' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:49.321290Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 57, 102, 51, 102, 56, 54, 98, 101], [114, 45, 57, 102, 51, 102, 56, 54, 98, 101]], header: JupyterHeader { msg_id: "fca891cfce", session: "r-9f3f86be", username: "josiahparry", date: "2025-02-12T20:22:49.321Z", msg_type: "kernel_info_request", version: "5.3" }, parent_header: None, content: KernelInfoRequest } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:49.321306Z TRACE Got kernel info request; waiting for R to complete initialization [R] at crates/ark/src/shell.rs:121 [R] [R] 2025-02-12T20:22:49.321323Z TRACE Sending 'kernel_info_reply' message (reply to 'kernel_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.321380Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:49.321445Z TRACE Sending 'status/busy' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.321604Z TRACE Sending 'status/idle' message (reply to 'kernel_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.321604Z TRACE Heartbeat message: [107, 97, 108, 108, 105, 99, 104, 111, 114, 101, 45, 104, 101, 97, 114, 116, 98, 101, 97, 116] [R] at crates/amalthea/src/socket/heartbeat.rs:41 [R] [R] 2025-02-12T20:22:49.321628Z TRACE Heartbeat message replied [R] at crates/amalthea/src/socket/heartbeat.rs:50 [R] [R] 2025-02-12T20:22:49.321629Z TRACE Listening for heartbeats [R] at crates/amalthea/src/socket/heartbeat.rs:28 [R] [R] 2025-02-12T20:22:49.325170Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 57, 102, 51, 102, 56, 54, 98, 101], [114, 45, 57, 102, 51, 102, 56, 54, 98, 101]], header: JupyterHeader { msg_id: "baed0b9855", session: "r-9f3f86be", username: "josiahparry", date: "2025-02-12T20:22:49.324Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-variables-r-25-59bb611f", target_name: "positron.variables", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:49.325199Z INFO Received request to open comm: CommOpen { comm_id: "positron-variables-r-25-59bb611f", target_name: "positron.variables", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:49.325355Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.342155Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:49.342181Z INFO Comm channel opened; there are now 1 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:49.342197Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 57, 102, 51, 102, 56, 54, 98, 101], [114, 45, 57, 102, 51, 102, 56, 54, 98, 101]], header: JupyterHeader { msg_id: "b432ddcb74", session: "r-9f3f86be", username: "josiahparry", date: "2025-02-12T20:22:49.325Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-lsp-r-eb65c9f6", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:62230")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:49.342204Z INFO Received request to open comm: CommOpen { comm_id: "positron-lsp-r-eb65c9f6", target_name: "positron.lsp", data: Object {"client_address": String("127.0.0.1:62230")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:49.342248Z INFO Comm channel opened; there are now 2 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:49.342281Z TRACE Connecting to LSP at '127.0.0.1:62230' [R] at crates/ark/src/lsp/backend.rs:372 [R] [R] 2025-02-12T20:22:49.342347Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:49.342370Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 57, 102, 51, 102, 56, 54, 98, 101], [114, 45, 57, 102, 51, 102, 56, 54, 98, 101]], header: JupyterHeader { msg_id: "b761f7d06d", session: "r-9f3f86be", username: "josiahparry", date: "2025-02-12T20:22:49.325Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-ui-r-26-11f233ae", target_name: "positron.ui", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:49.342374Z INFO Received request to open comm: CommOpen { comm_id: "positron-ui-r-26-11f233ae", target_name: "positron.ui", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:49.342391Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.342402Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:49.342420Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 57, 102, 51, 102, 56, 54, 98, 101], [114, 45, 57, 102, 51, 102, 56, 54, 98, 101]], header: JupyterHeader { msg_id: "b894019900", session: "r-9f3f86be", username: "josiahparry", date: "2025-02-12T20:22:49.325Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-dap-r-c3758980", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:57691")} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:49.342422Z INFO Received request to open comm: CommOpen { comm_id: "positron-dap-r-c3758980", target_name: "positron.dap", data: Object {"client_address": String("127.0.0.1:57691")} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:49.342426Z INFO DAP: Spawning thread [R] at crates/ark/src/dap/dap.rs:259 [R] [R] 2025-02-12T20:22:49.342456Z INFO Comm channel opened; there are now 3 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:49.342458Z INFO Comm channel opened; there are now 4 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:49.342466Z TRACE DAP: Thread starting at address 127.0.0.1:57691. [R] at crates/ark/src/dap/dap_server.rs:53 [R] [R] 2025-02-12T20:22:49.342479Z TRACE Received kernel request EstablishUiCommChannel(Sender { .. }) [R] at crates/ark/src/interface.rs:1216 [R] [R] 2025-02-12T20:22:49.342483Z TRACE DAP: Waiting for client [R] at crates/ark/src/dap/dap_server.rs:62 [R] [R] 2025-02-12T20:22:49.342490Z INFO Sending message to UI comm: Event(PromptState(PromptStateParams { input_prompt: "> ", continuation_prompt: "+ " })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:49.342501Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:49.342517Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 57, 102, 51, 102, 56, 54, 98, 101], [114, 45, 57, 102, 51, 102, 56, 54, 98, 101]], header: JupyterHeader { msg_id: "9236995659", session: "r-9f3f86be", username: "josiahparry", date: "2025-02-12T20:22:49.325Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.help" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:49.342520Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.help" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:49.342521Z INFO Sending message to UI comm: Event(WorkingDirectory(WorkingDirectoryParams { directory: "~/github/calcite" })) [R] at crates/ark/src/ui/sender.rs:50 [R] [R] 2025-02-12T20:22:49.342549Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.342587Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:49.342613Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 57, 102, 51, 102, 56, 54, 98, 101], [114, 45, 57, 102, 51, 102, 56, 54, 98, 101]], header: JupyterHeader { msg_id: "b372874194", session: "r-9f3f86be", username: "josiahparry", date: "2025-02-12T20:22:49.326Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "positron.plot" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:49.342618Z INFO Received request for open comms: CommInfoRequest { target_name: "positron.plot" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:49.342644Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.342658Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:49.342670Z INFO Received shell request: JupyterMessage { zmq_identities: [[114, 45, 57, 102, 51, 102, 56, 54, 98, 101], [114, 45, 57, 102, 51, 102, 56, 54, 98, 101]], header: JupyterHeader { msg_id: "fd916bb9aa", session: "r-9f3f86be", username: "josiahparry", date: "2025-02-12T20:22:49.326Z", msg_type: "comm_info_request", version: "5.3" }, parent_header: None, content: CommInfoRequest { target_name: "" } } [R] at crates/amalthea/src/socket/shell.rs:185 [R] [R] 2025-02-12T20:22:49.342673Z INFO Received request for open comms: CommInfoRequest { target_name: "" } [R] at crates/amalthea/src/socket/shell.rs:247 [R] [R] 2025-02-12T20:22:49.342727Z TRACE Sending 'comm_info_reply' message (reply to 'comm_info_request') via Shell socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.342747Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:49.342752Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.342866Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.343003Z TRACE Sending 'comm_msg/LSP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:49.343149Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.343342Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.343483Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.343675Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.343996Z TRACE Sending 'comm_msg/DAP/unknown' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:49.344704Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.344978Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 57, 102, 51, 102, 56, 54, 98, 101], [114, 45, 57, 102, 51, 102, 56, 54, 98, 101]], header: JupyterHeader { msg_id: "8628ba3f8c", session: "r-9f3f86be", username: "josiahparry", date: "2025-02-12T20:22:49.344Z", msg_type: "comm_open", version: "5.3" }, parent_header: None, content: CommOpen { comm_id: "positron-help-r-27-5a3c69b", target_name: "positron.help", data: Object {} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:49.344986Z INFO Received request to open comm: CommOpen { comm_id: "positron-help-r-27-5a3c69b", target_name: "positron.help", data: Object {} } [R] at crates/amalthea/src/socket/shell.rs:286 [R] [R] 2025-02-12T20:22:49.345106Z TRACE Sending 'comm_msg/variables/refresh' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:49.345215Z TRACE Connected to LSP at '127.0.0.1:62230' [R] at crates/ark/src/lsp/backend.rs:381 [R] [R] 2025-02-12T20:22:49.345356Z TRACE Sending 'comm_msg/positron-ui-r-26-11f233ae/prompt_state' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:49.345581Z TRACE Sending 'comm_msg/positron-ui-r-26-11f233ae/working_directory' message via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:204 [R] [R] 2025-02-12T20:22:49.345865Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.346152Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.346440Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.346978Z TRACE Sending 'status/busy' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.347186Z TRACE Sending 'status/idle' message (reply to 'comm_info_request') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.347393Z TRACE Sending 'status/busy' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.355822Z INFO Comm channel opened; there are now 5 open comms [R] at crates/amalthea/src/comm/comm_manager.rs:118 [R] [R] 2025-02-12T20:22:49.355846Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:49.355891Z INFO Received shell notification: JupyterMessage { zmq_identities: [[114, 45, 57, 102, 51, 102, 56, 54, 98, 101], [114, 45, 57, 102, 51, 102, 56, 54, 98, 101]], header: JupyterHeader { msg_id: "8c4e88dc", session: "r-9f3f86be", username: "josiahparry", date: "2025-02-12T20:22:49.344Z", msg_type: "comm_msg", version: "5.3" }, parent_header: None, content: CommWireMsg { comm_id: "positron-ui-r-26-11f233ae", data: Object {"jsonrpc": String("2.0"), "method": String("call_method"), "params": Object {"method": String("setConsoleWidth"), "params": Array [Number(76)]}} } } [R] at crates/amalthea/src/socket/shell.rs:232 [R] [R] 2025-02-12T20:22:49.356004Z TRACE Waiting for shell messages [R] at crates/amalthea/src/socket/shell.rs:106 [R] [R] 2025-02-12T20:22:49.356013Z TRACE Comm manager: Sending message to comm 'positron.ui' [R] at crates/amalthea/src/comm/comm_manager.rs:140 [R] [R] 2025-02-12T20:22:49.356080Z TRACE Handling 'setConsoleWidth' frontend RPC method [R] at crates/ark/src/ui/ui.rs:145 [R] in comm handler with name: "positron.ui", request: CallMethod(CallMethodParams { method: "setConsoleWidth", params: [Number(76)] }) [R] [R] 2025-02-12T20:22:49.356146Z TRACE Sending 'status/idle' message (reply to 'comm_open') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.356292Z TRACE Sending 'status/busy' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.356510Z TRACE Sending 'status/idle' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.367638Z TRACE Sending 'comm_msg/positron-ui-r-26-11f233ae/CallMethodReply' message (reply to 'comm_msg') via IOPub socket [R] at crates/amalthea/src/wire/wire_message.rs:196 [R] [R] 2025-02-12T20:22:49.375556Z TRACE Populated virtual namespace for compiler: 2207 lines, 139 ok, 0 bad, 150 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:49.545379Z TRACE Populated virtual namespace for utils: 16143 lines, 502 ok, 1 bad, 73 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] [R] 2025-02-12T20:22:49.554421Z TRACE Populated virtual namespace for grDevices: 3973 lines, 212 ok, 0 bad, 75 skipped [R] at crates/ark/src/srcref.rs:93 [R] in R task with thread: "main", interrupt: false [R] in resource_loaded_namespaces [R] ** Begin kernel log for session R 4.4.0 (r-3826c745) at 2/12/2025, 12:22:54 PM ** Streaming kernel log file: /var/folders/wd/xq999jjj3bx2w8cpg7lkfxlm0000gn/T/kernel-RvlRF6/kernel.log 

</details>

@juliasilge
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I've got this project open:

Image

Can you tell me what I should do from here to generate the looping crash?

@juliasilge juliasilge added lang: r info needed Waiting on information labels Feb 12, 2025
@JosiahParry
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The file wasn't committed yet. The issue is a massive amount of invalid roxygen syntax. I've been able to fix the syntax and thus avoid the issue. I've attached the file (as a zip b/c 5k lines inline is a weee bit too much).

Having this file open break positron

components-generated.R.zip

@juliasilge juliasilge changed the title Positron in continuous restart cycle Lots of invalid roxygen syntax puts R interpreter in looping crash/restart Feb 12, 2025
@juliasilge juliasilge added bug Something isn't working support and removed info needed Waiting on information labels Feb 12, 2025
@juliasilge
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Well, I can definitely reproduce. 😳

@JosiahParry
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Godspeed 🫡

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@juliasilge @JosiahParry