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  1. ROOT
  2. ROOT-9135

Get an error when working with the ROOT-related xps package in R

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    Details

    • Type: Bug
    • Status: Closed (View Workflow)
    • Priority: High
    • Resolution: Clarified
    • Affects Version/s: 5.34/36
    • Fix Version/s: None
    • Component/s: Core Libraries, Other
    • Labels:
      None
    • Environment:
    • Development:

      Description

      When I preprocessing the microarray data using the xps package(R programming language) at the end of the process, I encountered such an error.

       

      Converting raw data to expression levels...
      summarizing with <medianpolish>...

          • Break *** segmentation violation
            ===========================================================
            There was a crash.
            This is the entire stack trace of all threads:
            ===========================================================
            #0 0x00007f09df43907a in _GI__waitpid (pid=6123, stat_loc=stat_loc
            entry=0x7ffc8aa06300, options=options
            entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:29
            #1 0x00007f09df3b1fbb in do_system (line=<optimized out>) at ../sysdeps/posix/system.c:148
            #2 0x00007f09d637a034 in TUnixSystem::StackTrace() () from /usr/local/lib/root/libCore.so
            #3 0x00007f09d637c29c in TUnixSystem::DispatchSignals(ESignals) () from
            /usr/local/lib/root/libCore.so
            #4 <signal handler called>
            #5 0x00007f09d6c28797 in XExonProcesSet::UnitTree(XAlgorithm*, void*, int&) () from
            /home/parsa/R/x86_64-pc-linux-gnu-library/3.4/xps/libs/xps.so
            #6 0x00007f09d6c34d86 in XGCProcesSet::DoMultichipExpress(int, TTree*, int, TTree*,
            TFile*) () from /home/parsa/R/x86_64-pc-linux-gnu-library/3.4/xps/libs/xps.so
            #7 0x00007f09d6c212c1 in XGCProcesSet::Preprocess(char const*) () from
            /home/parsa/R/x86_64-pc-linux-gnu-library/3.4/xps/libs/xps.so
            #8 0x00007f09d6c0a325 in XPreProcessManager::Preprocess(char const*, char const*) () from
            /home/parsa/R/x86_64-pc-linux-gnu-library/3.4/xps/libs/xps.so
            #9 0x00007f09d6c597a4 in PreprocessRMA () from /home/parsa/R/x86_64-pc-linux-gnu-
            library/3.4/xps/libs/xps.so
            #10 0x00007f09dfa29dea in ?? () from /usr/lib/R/lib/libR.so
            #11 0x00007f09dfa640ad in Rf_eval () from /usr/lib/R/lib/libR.so
            #12 0x00007f09dfaff359 in ?? () from /usr/lib/R/lib/libR.so
            #13 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so
            #14 0x00007f09dfa67cb6 in ?? () from /usr/lib/R/lib/libR.so
            #15 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so
            #16 0x00007f09dfa66b4e in ?? () from /usr/lib/R/lib/libR.so
            #17 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so
            #18 0x00007f09dfa65eaf in ?? () from /usr/lib/R/lib/libR.so
            #19 0x00007f09dfa63c56 in Rf_eval () from /usr/lib/R/lib/libR.so
            #20 0x00007f09dfa66b4e in ?? () from /usr/lib/R/lib/libR.so
            #21 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so
            #22 0x00007f09dfa65eaf in ?? () from /usr/lib/R/lib/libR.so
            #23 0x00007f09dfa66476 in R_execMethod () from /usr/lib/R/lib/libR.so
            #24 0x00007f09dd047d09 in ?? () from /usr/lib/R/library/methods/libs/methods.so
            #25 0x00007f09dfa9cf1b in ?? () from /usr/lib/R/lib/libR.so
            #26 0x00007f09dfa63ff6 in Rf_eval () from /usr/lib/R/lib/libR.so
            #27 0x00007f09dfa65eaf in ?? () from /usr/lib/R/lib/libR.so
            #28 0x00007f09dfa63c56 in Rf_eval () from /usr/lib/R/lib/libR.so
            #29 0x00007f09dfa67cb6 in ?? () from /usr/lib/R/lib/libR.so
            #30 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so
            #31 0x00007f09dfa66b4e in ?? () from /usr/lib/R/lib/libR.so
            #32 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so#33 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so
            #34 0x00007f09dfa66b4e in ?? () from /usr/lib/R/lib/libR.so
            #35 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so
            #36 0x00007f09dfa65eaf in ?? () from /usr/lib/R/lib/libR.so
            #37 0x00007f09dfa63c56 in Rf_eval () from /usr/lib/R/lib/libR.so
            #38 0x00007f09dfa67cb6 in ?? () from /usr/lib/R/lib/libR.so
            #39 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so
            #40 0x00007f09dfa8d412 in Rf_ReplIteration () from /usr/lib/R/lib/libR.so
            #41 0x00007f09dfa8d811 in ?? () from /usr/lib/R/lib/libR.so
            #42 0x00007f09dfa8d8c8 in run_Rmainloop () from /usr/lib/R/lib/libR.so
            #43 0x00000000004007cb in main ()
            #44 0x00007f09df38d830 in __libc_start_main (main=0x4007b0 <main>, argc=1,
            argv=0x7ffc8aa0d538, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>,
            stack_end=0x7ffc8aa0d528) at ../csu/libc-start.c:291
            #45 0x0000000000400809 in _start ()
            ===========================================================
            The lines below might hint at the cause of the crash.
            If they do not help you then please submit a bug report at
            http://root.cern.ch/bugs. Please post the ENTIRE stack trace
            from above as an attachment in addition to anything else
            that might help us fixing this issue.
            ===========================================================
            #5 0x00007f09d6c28797 in XExonProcesSet::UnitTree(XAlgorithm*, void*, int&) () from
            /home/parsa/R/x86_64-pc-linux-gnu-library/3.4/xps/libs/xps.so
            #6 0x00007f09d6c34d86 in XGCProcesSet::DoMultichipExpress(int, TTree*, int, TTree*,
            TFile*) () from /home/parsa/R/x86_64-pc-linux-gnu-library/3.4/xps/libs/xps.so
            #7 0x00007f09d6c212c1 in XGCProcesSet::Preprocess(char const*) () from
            /home/parsa/R/x86_64-pc-linux-gnu-library/3.4/xps/libs/xps.so
            #8 0x00007f09d6c0a325 in XPreProcessManager::Preprocess(char const*, char const*) () from
            /home/parsa/R/x86_64-pc-linux-gnu-library/3.4/xps/libs/xps.so
            #9 0x00007f09d6c597a4 in PreprocessRMA () from /home/parsa/R/x86_64-pc-linux-gnu-
            library/3.4/xps/libs/xps.so
            #10 0x00007f09dfa29dea in ?? () from /usr/lib/R/lib/libR.so
            #11 0x00007f09dfa640ad in Rf_eval () from /usr/lib/R/lib/libR.so
            #12 0x00007f09dfaff359 in ?? () from /usr/lib/R/lib/libR.so
            #13 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so
            #14 0x00007f09dfa67cb6 in ?? () from /usr/lib/R/lib/libR.so
            #15 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so
            #16 0x00007f09dfa66b4e in ?? () from /usr/lib/R/lib/libR.so
            #17 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so
            #18 0x00007f09dfa65eaf in ?? () from /usr/lib/R/lib/libR.so
            #19 0x00007f09dfa63c56 in Rf_eval () from /usr/lib/R/lib/libR.so
            #20 0x00007f09dfa66b4e in ?? () from /usr/lib/R/lib/libR.so
            #21 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so
            #22 0x00007f09dfa65eaf in ?? () from /usr/lib/R/lib/libR.so
            #23 0x00007f09dfa66476 in R_execMethod () from /usr/lib/R/lib/libR.so
            #24 0x00007f09dd047d09 in ?? () from /usr/lib/R/library/methods/libs/methods.so
            #25 0x00007f09dfa9cf1b in ?? () from /usr/lib/R/lib/libR.so
            #26 0x00007f09dfa63ff6 in Rf_eval () from /usr/lib/R/lib/libR.so
            #27 0x00007f09dfa65eaf in ?? () from /usr/lib/R/lib/libR.so#28 0x00007f09dfa63c56 in Rf_eval () from /usr/lib/R/lib/libR.so
            #29 0x00007f09dfa67cb6 in ?? () from /usr/lib/R/lib/libR.so
            #30 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so
            #31 0x00007f09dfa66b4e in ?? () from /usr/lib/R/lib/libR.so
            #32 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so
            #33 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so
            #34 0x00007f09dfa66b4e in ?? () from /usr/lib/R/lib/libR.so
            #35 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so
            #36 0x00007f09dfa65eaf in ?? () from /usr/lib/R/lib/libR.so
            #37 0x00007f09dfa63c56 in Rf_eval () from /usr/lib/R/lib/libR.so
            #38 0x00007f09dfa67cb6 in ?? () from /usr/lib/R/lib/libR.so
            #39 0x00007f09dfa63e8c in Rf_eval () from /usr/lib/R/lib/libR.so
            #40 0x00007f09dfa8d412 in Rf_ReplIteration () from /usr/lib/R/lib/libR.so
            #41 0x00007f09dfa8d811 in ?? () from /usr/lib/R/lib/libR.so
            #42 0x00007f09dfa8d8c8 in run_Rmainloop () from /usr/lib/R/lib/libR.so
            #43 0x00000000004007cb in main ()
            #44 0x00007f09df38d830 in __libc_start_main (main=0x4007b0 <main>, argc=1,
            argv=0x7ffc8aa0d538, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>,
            stack_end=0x7ffc8aa0d528) at ../csu/libc-start.c:291
            #45 0x0000000000400809 in _start ()
            ===========================================================
            Segmentation fault (core dumped)

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            • Assignee:
              axel Axel Naumann
              Reporter:
              4f6c7d2ab14c6531c008 Ehsan Parsa (Inactive)
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              • Created:
                Updated:
                Resolved: