Root installation for xps on cluster
2
0
Entering edit mode
Biologist ▴ 110
@biologist-9801
Last seen 4.0 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
===========================================================

 

 

xps root • 1.5k views
ADD COMMENT
0
Entering edit mode
cstrato ★ 3.9k
@cstrato-908
Last seen 5.5 years ago
Austria

Which version of ROOT did you install on the cluster?
Did you compile 'xps'?

The following error:
Error in <TTree::Bronch>: Cannot find dictionary for class: XLayout
means that the Dictionary for xps was not built or is not recognized.

Please have a look at the 'CHECK report for xps on zin1' on the Bioconductor server 'zin1', see:
http://bioconductor.org/checkResults/release/bioc-LATEST/xps/zin1-checksrc.html

There you will find the lines:
Generating dictionary xpsDict.cxx...
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c xpsDict.cxx

Furthermore, from the stack trace I see that you are using RStudio, which I am not sure can be
used with the cluster.

Since I have neither experience with Linux clusters nor with RStudio I am afraid that I am the
wrong person to ask. Maybe someone else can help you in this case.

Regards,
Christian

ADD COMMENT

Login before adding your answer.

Traffic: 526 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6