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Biologist
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@biologist-9801
Last seen 4.8 years ago
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
===========================================================
