Hi Christian,
I tried Installing root on cluster for xps. Installation is completed and xps starting working. But I'm getting a strange error which I dont know. Please find the following error.
when I run the function import.exon.scheme I get the following one
Creating new file </export/work/virpath/analyse.semaine1/schemes/Scheme.root>...
Importing </export/work/virpath/analyse.semaine1/library/HuGene-2_0-st.clf> as <HuGene-2_0-st.cxy>... Error in <TClass::LoadClassInfo>: no interpreter information for class XLayout is available eventhough it has a TClass initialization routine. Error in <TTree::Bronch>: Cannot find dictionary for class: XLayout <2598544> records imported...Finished Error in <TClass::LoadClassInfo>: no interpreter information for class XLayoutTreeInfo is available eventhough it has a TClass initialization routine. New dataset <HuGene-2_0-st> is added to Content... Importing </export/work/virpath/analyse.semaine1/Annotation/HuGene-2_0-st-v1.na35.hg19.probeset.csv> as <HuGene-2_0-st.anp>... Error in <TClass::LoadClassInfo>: no interpreter information for class XTreeSet is available eventhough it has a TClass initialization routine. Error in <TFile::mkdir>: An object with name HuGene-2_0-st exists already Error in <TClass::LoadClassInfo>: no interpreter information for class XExonAnnotation is available eventhough it has a TClass initialization routine. Error in <TTree::Bronch>: Cannot find dictionary for class: XExonAnnotation Error in <TClass::LoadClassInfo>: no interpreter information for class XProbesetAnnotation is available eventhough it has a TClass initialization routine. Error in <TTree::Bronch>: Cannot find dictionary for class: XProbesetAnnotation Number of probesets is <352859>. <352859> records read...Finishedcords read... <349239> records imported...Finished <257681> exon annotations imported. New dataset <HuGene-2_0-st> is added to Content... Importing </export/work/virpath/analyse.semaine1/library/HuGene-2_0-st.pgf> as <HuGene-2_0-st.scm>... Error in <TFile::mkdir>: An object with name HuGene-2_0-st exists already Error in <TTree::SetBranchAddress>: unknown branch -> AnnBranch Error in <TClass::LoadClassInfo>: no interpreter information for class XExonScheme is available eventhough it has a TClass initialization routine. Error in <TTree::Bronch>: Cannot find dictionary for class: XExonScheme Error in <TClass::LoadClassInfo>: no interpreter information for class XExonUnit is available eventhough it has a TClass initialization routine. Error in <TTree::Bronch>: Cannot find dictionary for class: XExonUnit Error in <TTree::Bronch>: Cannot find dictionary for class: XExonUnit Error in <TTree::Bronch>: Cannot find dictionary for class: XExonUnit Reading data from input file... Error in <TClass::LoadClassInfo>: no interpreter information for class XGCProbe is available eventhough it has a TClass initialization routine. Error in <TTree::Bronch>: Cannot find dictionary for class: XGCProbe Number of probesets is <352859>. Note: Number of annotated probesets <0> is not equal to number of probesets <352859>. <352859> records read...Finished Sorting data for probeset_type and position... Total number of controls is <23> Filling trees with data for probeset type: control->chip... Number of control->chip items is <0>. Filling trees with data for probeset type: control->bgp... *** Break *** floating point exception =========================================================== There was a crash. This is the entire stack trace of all threads: =========================================================== Thread 5 (Thread 0x7f8edd1a3700 (LWP 18596)): #0 0x00007f8ee04997ce in pthread_cond_timedwait GLIBC_2.3.2 () from /lib/x86_64-linux-gnu/libpthread.so.0 #1 0x0000000000b9e5f0 in rstudio::core::thread::ThreadsafeQueue<rstudio::core::system::file_monitor::(anonymous namespace)::RegistrationCommand>::wait(boost::posix_time::time_duration const&) [clone .isra.416] [clone .constprop.731] () #2 0x0000000000b9f79d in rstudio::core::system::file_monitor::(anonymous namespace)::checkForInput() () #3 0x0000000000be5bcc in rstudio::core::system::file_monitor::detail::run(boost::function<void ()> const&) () #4 0x0000000000b9eecc in rstudio::core::system::file_monitor::(anonymous namespace)::fileMonitorThreadMain() () #5 0x0000000000a6197e in boost::detail::thread_data<boost::function<void ()> >::run() () #6 0x0000000000d074a8 in thread_proxy () #7 0x00007f8ee0495182 in start_thread () from /lib/x86_64-linux-gnu/libpthread.so.0 #8 0x00007f8edef9c47d in clone () from /lib/x86_64-linux-gnu/libc.so.6 Thread 4 (Thread 0x7f8edc9a2700 (LWP 18597)): #0 0x00007f8edef9cb13 in epoll_wait () from /lib/x86_64-linux-gnu/libc.so.6 #1 0x0000000000a17490 in boost::asio::detail::task_io_service::run(boost::system::error_code&) () #2 0x0000000000a17e85 in boost::asio::io_service::run() () #3 0x0000000000d074a8 in thread_proxy () #4 0x00007f8ee0495182 in start_thread () from /lib/x86_64-linux-gnu/libpthread.so.0 #5 0x00007f8edef9c47d in clone () from /lib/x86_64-linux-gnu/libc.so.6 Thread 3 (Thread 0x7f8ed6900700 (LWP 18598)): #0 0x00007f8ee04997ce in pthread_cond_timedwait GLIBC_2.3.2 () from /lib/x86_64-linux-gnu/libpthread.so.0 #1 0x000000000068daa9 in bool boost::condition_variable_any::do_timed_wait<boost::unique_lock<boost::mutex> >(boost::unique_lock<boost::mutex>&, timespec const&) () #2 0x000000000068a151 in rstudio::session::ClientEventQueue::waitForEvent(boost::posix_time::time_duration const&) () #3 0x0000000000692157 in rstudio::session::ClientEventService::run() () #4 0x0000000000d074a8 in thread_proxy () #5 0x00007f8ee0495182 in start_thread () from /lib/x86_64-linux-gnu/libpthread.so.0 #6 0x00007f8edef9c47d in clone () from /lib/x86_64-linux-gnu/libc.so.6 Thread 2 (Thread 0x7f8ed60ff700 (LWP 18599)): #0 0x00007f8edef93da3 in select () from /lib/x86_64-linux-gnu/libc.so.6 #1 0x0000000000bc3336 in rstudio::core::system::(anonymous namespace)::standardStreamCaptureThread(int, boost::function<void (std::string const&)> const&, int, boost::function<void (std::string const&)> const&) () #2 0x0000000000d074a8 in thread_proxy () #3 0x00007f8ee0495182 in start_thread () from /lib/x86_64-linux-gnu/libpthread.so.0 #4 0x00007f8edef9c47d in clone () from /lib/x86_64-linux-gnu/libc.so.6 Thread 1 (Thread 0x7f8ee1060840 (LWP 18595)): #0 0x00007f8edef62b99 in waitpid () from /lib/x86_64-linux-gnu/libc.so.6 #1 0x00007f8edeee82e2 in ?? () from /lib/x86_64-linux-gnu/libc.so.6 #2 0x00007f8ecb5c6fd3 in TUnixSystem::StackTrace() () from /lib/libCore.so #3 0x00007f8ecb5c981c in TUnixSystem::DispatchSignals(ESignals) () from /lib/libCore.so #4 <signal handler called> #5 0x00007f8ecba67870 in XExonChip::ReadData(std::basic_ifstream<char, std::char_traits<char> >&, char const*, char const*, char, int) () from /export/lib/R/xps/libs/xps.so #6 0x00007f8ecba3e0a2 in XDNAChip::Import(std::basic_ifstream<char, std::char_traits<char> >&, char const*, char const*, char, int) () from /export/lib/R/xps/libs/xps.so #7 0x00007f8ecba1b5bc in XManager::Import(char const*, char const*, char const*, char const*, char const*, char, int) () from /export/lib/R/xps/libs/xps.so #8 0x00007f8ecba3cf23 in XSchemeManager::NewScheme(char const*, char const*, char const*, char const*, char, int) () from /export/lib/R/xps/libs/xps.so #9 0x00007f8ecbaf58e0 in ImportExonSchemes () from /export/lib/R/xps/libs/xps.so #10 0x00007f8ee098ae9c in ?? () from /usr/lib/R/lib/libR.so #11 0x00007f8ee09c2ccb in Rf_eval () from /usr/lib/R/lib/libR.so #12 0x00007f8ee0a53a15 in ?? () from /usr/lib/R/lib/libR.so #13 0x00007f8ee09c2ad3 in Rf_eval () from /usr/lib/R/lib/libR.so #14 0x00007f8ee09c5e9e in ?? () from /usr/lib/R/lib/libR.so #15 0x00007f8ee09c2ad3 in Rf_eval () from /usr/lib/R/lib/libR.so #16 0x00007f8ee09c4dc0 in ?? () from /usr/lib/R/lib/libR.so #17 0x00007f8ee09c2ad3 in Rf_eval () from /usr/lib/R/lib/libR.so #18 0x00007f8ee09c3e57 in Rf_applyClosure () from /usr/lib/R/lib/libR.so #19 0x00007f8ee09c28af in Rf_eval () from /usr/lib/R/lib/libR.so #20 0x00007f8ee09c5e9e in ?? () from /usr/lib/R/lib/libR.so #21 0x00007f8ee09c2ad3 in Rf_eval () from /usr/lib/R/lib/libR.so #22 0x00007f8ee09e9d62 in Rf_ReplIteration () from /usr/lib/R/lib/libR.so #23 0x00007f8ee09ea0b1 in ?? () from /usr/lib/R/lib/libR.so #24 0x00007f8ee09ea164 in run_Rmainloop () from /usr/lib/R/lib/libR.so #25 0x0000000000c7c0c2 in rstudio::r::session::runEmbeddedR(rstudio::core::FilePath const&, rstudio::core::FilePath const&, bool, bool, SA_TYPE, rstudio::r::session::Callbacks const&, rstudio::r::session::InternalCallbacks*) () #26 0x0000000000c5dcdd in rstudio::r::session::run(rstudio::r::session::ROptions const&, rstudio::r::session::RCallbacks const&) () #27 0x000000000066fc3f in main () import gdb =========================================================== 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 0x00007f8ecba67870 in XExonChip::ReadData(std::basic_ifstream<char, std::char_traits<char> >&, char const*, char const*, char, int) () from /export/lib/R/xps/libs/xps.so #6 0x00007f8ecba3e0a2 in XDNAChip::Import(std::basic_ifstream<char, std::char_traits<char> >&, char const*, char const*, char, int) () from /export/lib/R/xps/libs/xps.so #7 0x00007f8ecba1b5bc in XManager::Import(char const*, char const*, char const*, char const*, char const*, char, int) () from /export/lib/R/xps/libs/xps.so #8 0x00007f8ecba3cf23 in XSchemeManager::NewScheme(char const*, char const*, char const*, char const*, char, int) () from /export/lib/R/xps/libs/xps.so #9 0x00007f8ecbaf58e0 in ImportExonSchemes () from /export/lib/R/xps/libs/xps.so #10 0x00007f8ee098ae9c in ?? () from /usr/lib/R/lib/libR.so #11 0x00007f8ee09c2ccb in Rf_eval () from /usr/lib/R/lib/libR.so #12 0x00007f8ee0a53a15 in ?? () from /usr/lib/R/lib/libR.so #13 0x00007f8ee09c2ad3 in Rf_eval () from /usr/lib/R/lib/libR.so #14 0x00007f8ee09c5e9e in ?? () from /usr/lib/R/lib/libR.so #15 0x00007f8ee09c2ad3 in Rf_eval () from /usr/lib/R/lib/libR.so #16 0x00007f8ee09c4dc0 in ?? () from /usr/lib/R/lib/libR.so #17 0x00007f8ee09c2ad3 in Rf_eval () from /usr/lib/R/lib/libR.so #18 0x00007f8ee09c3e57 in Rf_applyClosure () from /usr/lib/R/lib/libR.so #19 0x00007f8ee09c28af in Rf_eval () from /usr/lib/R/lib/libR.so #20 0x00007f8ee09c5e9e in ?? () from /usr/lib/R/lib/libR.so #21 0x00007f8ee09c2ad3 in Rf_eval () from /usr/lib/R/lib/libR.so #22 0x00007f8ee09e9d62 in Rf_ReplIteration () from /usr/lib/R/lib/libR.so #23 0x00007f8ee09ea0b1 in ?? () from /usr/lib/R/lib/libR.so #24 0x00007f8ee09ea164 in run_Rmainloop () from /usr/lib/R/lib/libR.so #25 0x0000000000c7c0c2 in rstudio::r::session::runEmbeddedR(rstudio::core::FilePath const&, rstudio::core::FilePath const&, bool, bool, SA_TYPE, rstudio::r::session::Callbacks const&, rstudio::r::session::InternalCallbacks*) () #26 0x0000000000c5dcdd in rstudio::r::session::run(rstudio::r::session::ROptions const&, rstudio::r::session::RCallbacks const&) () #27 0x000000000066fc3f in main () import gdb ===========================================================