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RGLab / cytolib

c++ library for representing and interacting the gated cytometry data structure
GNU Affero General Public License v3.0
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misterious rstudio crash issue due to the inline member function #2

Closed mikejiang closed 6 years ago

mikejiang commented 6 years ago

The headeronly branch works fine for all the test cases at R console, but crashes R session within rstudio for several workspaces. e.g. the test case below will fail in rstudio

library(flowWorkspace)
path <- "~/rglab/workspace/flowWorkspace/wsTestSuite"
setLoglevel("Gate")
thisPath <- file.path(path, "combineNode/OrNode")
wsFile <- file.path(thisPath, "Test_EW.wsp")
ws <- openWorkspace(wsFile)
gs <- parseWorkspace(ws, name = 1, path = file.path(path))

I've spend the past two days trying to pinpoint the source of problem without success. Not sure if it has something to do with rstudio ( I am using Version 1.0.153).

To test it, the flowWorkspace/headeronly branch is required as well as RProtoBufLib/headeronly

mikejiang commented 6 years ago

The latest investigation shows the single line of libxml2 API call crashes rstudio after header-only version of flowWorkspace is loaded.

xmlDocPtr doc = xmlReadFile(sFileName.c_str(), NULL, 0);

which again, runs perfectly fine at R console. I will try the newer version of rstudio to see if it helps

mikejiang commented 6 years ago

by attaching gdb to rsession of rsutdio, I got backtrace info https://gist.github.com/mikejiang/f1218d22b0a34968958e89f861235dc3 which failed at some call of boost library. Not sure if it has to do with the discrepancy between BH used by us and boost used to compile rstudio

mikejiang commented 6 years ago

I've confirmed that rstudio 1.1.383 fixed the issue.