GLAD crashes when built with gcc-4.8
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@ramon-diaz-uriarte-2633
Last seen 5.3 years ago
Spain
Dear All, At least one function (daglad) from the GLAD package crashes with a segfault when compiled with gcc-4.8 but not with gcc-4.7. I am not sure if this is a problem with GLAD or, more unlikely, with R. (Details below) Has anybody seen something similar? Best, R. Details: ======== - How to reproduce the error ## make sure you are using gcc-4.8 and g++-4.8 biocLite("GLAD") library(GLAD) example(daglad) - Errors: there are several; these are some *** Error in `/home/ramon/Sources/R-3.1.0-64488/bin/exec/R': free(): invalid next size (fast): 0x0000000014144d70 *** ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x7aa16)[0x7f2ff0f04a16] /lib/x86_64-linux-gnu/libc.so.6(+0x7b793)[0x7f2ff0f05793] /home/ramon/Sources/R-3.1.0-64488/library/GLAD/libs/GLAD.so(mad_vector _double+0x184)[0x7f2fed753bc4] [1] "Optimization of the Breakpoints and DNA copy number calling" *** Error in `/usr/lib/R/bin/exec/R': corrupted double-linked list: 0x00000000010f24a0 *** *** caught segfault *** address 0x140000000a, cause 'memory not mapped' Traceback: 1: gc(FALSE) 2: system.time(BP <- merge(BP, profileCGH$SigmaC)) 3: BkpInfo.profileCGH(profileCGH) 4: BkpInfo(profileCGH) - OS: Debian GNU/Linux, a mixture of testing and unstable - version of gcc/g++: 4.8.2-1 and 4.7.3-9 (for Debian) - version of GLAD: 2.26.0 (for R-3.0.2) and 2.27.1 (for R-3.1.0) - versions of R: several from R-3.0.2 and R-3.1.0. For instance ## the current Debian version > version _ platform x86_64-pc-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 3 minor 0.2 year 2013 month 09 day 25 svn rev 63987 language R version.string R version 3.0.2 (2013-09-25) nickname Frisbee Sailing ## the R-devel that seems to be used in the testing of BioC packages > version _ platform x86_64-pc-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status Under development (unstable) major 3 minor 1.0 year 2013 month 12 day 19 svn rev 64488 language R version.string R Under development (unstable) (2013-12-19 r64488) nickname Unsuffered Consequences ## the latest R-devel > version _ platform x86_64-pc-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status Under development (unstable) major 3 minor 1.0 year 2013 month 12 day 27 svn rev 64562 language R version.string R Under development (unstable) (2013-12-27 r64562) nickname Unsuffered Consequences - version of GSL: crashes happen with the two available versions in Debian for libgsl0ldbl and libgsl0-dev: 1.16+dfsg-1 and 1.15+dfsg.2-2 -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Aut?noma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdiaz02 at gmail.com ramon.diaz at iib.uam.es http://ligarto.org/rdiaz
GLAD GLAD • 1.3k views
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@martin-morgan-1513
Last seen 2 days ago
United States
If possible run as. R -d valgrind -f script.R Where script.R is the minimal commands to produce the problem ( eg no need for biocLite). Compare the output with one less than the minimal script, looking in particular for 'invalid write' errors. -- Martin Morgan On Dec 28, 2013, at 8:32 AM, Ramon Diaz-Uriarte <rdiaz02 at="" gmail.com=""> wrote: > Dear All, > > At least one function (daglad) from the GLAD package crashes with a > segfault when compiled with gcc-4.8 but not with gcc-4.7. I am not sure if > this is a problem with GLAD or, more unlikely, with R. (Details below) > > > Has anybody seen something similar? > > Best, > > R. > > > Details: > ======== > > - How to reproduce the error > > ## make sure you are using gcc-4.8 and g++-4.8 > biocLite("GLAD") > library(GLAD) > example(daglad) > > > - Errors: there are several; these are some > > *** Error in `/home/ramon/Sources/R-3.1.0-64488/bin/exec/R': free(): invalid next size (fast): 0x0000000014144d70 *** > ======= Backtrace: ========= > /lib/x86_64-linux-gnu/libc.so.6(+0x7aa16)[0x7f2ff0f04a16] > /lib/x86_64-linux-gnu/libc.so.6(+0x7b793)[0x7f2ff0f05793] > /home/ramon/Sources/R-3.1.0-64488/library/GLAD/libs/GLAD.so(mad_vect or_double+0x184)[0x7f2fed753bc4] > > > [1] "Optimization of the Breakpoints and DNA copy number calling" > *** Error in `/usr/lib/R/bin/exec/R': corrupted double-linked list: 0x00000000010f24a0 *** > > > *** caught segfault *** > address 0x140000000a, cause 'memory not mapped' > > Traceback: > 1: gc(FALSE) > 2: system.time(BP <- merge(BP, profileCGH$SigmaC)) > 3: BkpInfo.profileCGH(profileCGH) > 4: BkpInfo(profileCGH) > > > - OS: Debian GNU/Linux, a mixture of testing and unstable > > - version of gcc/g++: 4.8.2-1 and 4.7.3-9 (for Debian) > > - version of GLAD: 2.26.0 (for R-3.0.2) and 2.27.1 (for R-3.1.0) > > - versions of R: several from R-3.0.2 and R-3.1.0. For instance > > ## the current Debian version >> version > _ > platform x86_64-pc-linux-gnu > arch x86_64 > os linux-gnu > system x86_64, linux-gnu > status > major 3 > minor 0.2 > year 2013 > month 09 > day 25 > svn rev 63987 > language R > version.string R version 3.0.2 (2013-09-25) > nickname Frisbee Sailing > > ## the R-devel that seems to be used in the testing of BioC packages >> version > _ > platform x86_64-pc-linux-gnu > arch x86_64 > os linux-gnu > system x86_64, linux-gnu > status Under development (unstable) > major 3 > minor 1.0 > year 2013 > month 12 > day 19 > svn rev 64488 > language R > version.string R Under development (unstable) (2013-12-19 r64488) > nickname Unsuffered Consequences > > ## the latest R-devel >> version > _ > platform x86_64-pc-linux-gnu > arch x86_64 > os linux-gnu > system x86_64, linux-gnu > status Under development (unstable) > major 3 > minor 1.0 > year 2013 > month 12 > day 27 > svn rev 64562 > language R > version.string R Under development (unstable) (2013-12-27 r64562) > nickname Unsuffered Consequences > > > - version of GSL: crashes happen with the two available versions in Debian > for libgsl0ldbl and libgsl0-dev: 1.16+dfsg-1 and 1.15+dfsg.2-2 > > > > > > > > > -- > Ramon Diaz-Uriarte > Department of Biochemistry, Lab B-25 > Facultad de Medicina > Universidad Aut?noma de Madrid > Arzobispo Morcillo, 4 > 28029 Madrid > Spain > > Phone: +34-91-497-2412 > > Email: rdiaz02 at gmail.com > ramon.diaz at iib.uam.es > > http://ligarto.org/rdiaz > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Martin, On Sat, 28-12-2013, at 23:07, mtmorgan at fhcrc.org wrote: > If possible run as. > > R -d valgrind -f script.R > > Where script.R is the minimal commands to produce the problem ( eg no > need for biocLite). Compare the output with one less than the minimal > script, looking in particular for 'invalid write' errors. This is a simple script: ################## library(GLAD) data(snijders) gm13330$Clone <- gm13330$BAC profileCGH <- as.profileCGH(gm13330) res <- daglad(profileCGH, mediancenter=FALSE, normalrefcenter=FALSE, genomestep=FALSE, smoothfunc="lawsglad", lkern="Exponential", model="Gaussian", qlambda=0.999, bandwidth=10, base=FALSE, round=1.5, lambdabreak=8, lambdaclusterGen=40, param=c(d=6), alpha=0.001, msize=2, method="centroid", nmin=1, nmax=8, amplicon=1, deletion=-5, deltaN=0.10, forceGL=c(-0.15,0.15), nbsigma=3, MinBkpWeight=0.35, CheckBkpPos=TRUE) ############# And, yes, running it through valgrind does show some "Invalid write" errors (and a bunch of "Invalid read"), all of which seem to be caused by C++ code in GLAD. Running the above script without the call to daglad does not lead to any problems (no invalid writes or reads). What version of gcc are you guys using in the zin2 and zin1 machines? (googling around I get the impression that the default for Ubuntu 12.04 is 4.6.3) Best, R. [1] "Smoothing for each Chromosome" ==28614== Invalid read of size 8 ==28614== at 0xC9DA1B9: awsBkp (chrBreakpoints.cpp:214) ==28614== by 0x4EE9B6B: do_dotCode (dotcode.c:1722) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F286D6: do_for (eval.c:1509) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0x95d5280 is 0 bytes after a block of size 576 alloc'd ==28614== at 0x4C2935B: malloc (vg_replace_malloc.c:270) ==28614== by 0x4F58E54: Rf_allocVector (memory.c:2465) ==28614== by 0x4EE31C0: do_dotCode (dotcode.c:1563) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F286D6: do_for (eval.c:1509) ==28614== ==28614== Invalid read of size 8 ==28614== at 0xC9E1E6F: void std::__introselect<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long) (stl_algo.h:2242) ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) ==28614== by 0xC9DB618: putLevel (chrBreakpoints.cpp:360) ==28614== by 0xC9DB9E8: putLevel_awsBkp (chrBreakpoints.cpp:168) ==28614== by 0x4EE9B6B: do_dotCode (dotcode.c:1722) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== Address 0xa196fd0 is 0 bytes after a block of size 32 alloc'd ==28614== at 0x4C298F9: operator new(unsigned long) (vg_replace_malloc.c:298) ==28614== by 0xC9DB8CD: putLevel (new_allocator.h:104) ==28614== by 0xC9DB9E8: putLevel_awsBkp (chrBreakpoints.cpp:168) ==28614== by 0x4EE9B6B: do_dotCode (dotcode.c:1722) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== [1] "Optimization of the Breakpoints and DNA copy number calling" ==28614== Invalid read of size 8 ==28614== at 0xC9E1E6F: void std::__introselect<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long) (stl_algo.h:2242) ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) ==28614== by 0xC9E389D: detectOutliers (glad-utils.cpp:242) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== Address 0xb412da0 is 0 bytes after a block of size 32 alloc'd ==28614== at 0x4C298F9: operator new(unsigned long) (vg_replace_malloc.c:298) ==28614== by 0xC9E3ACA: detectOutliers (new_allocator.h:104) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== ==28614== Invalid read of size 8 ==28614== at 0xC9E1E6F: void std::__introselect<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long) (stl_algo.h:2242) ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) ==28614== by 0xC9E2AEC: mad_vector_double (glad-utils.cpp:626) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0xbb08750 is 0 bytes after a block of size 32 alloc'd ==28614== at 0x4C298F9: operator new(unsigned long) (vg_replace_malloc.c:298) ==28614== by 0xC9E2C42: mad_vector_double (new_allocator.h:104) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== ==28614== Invalid read of size 8 ==28614== at 0xC9E1E6F: void std::__introselect<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long) (stl_algo.h:2242) ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0xbb087b0 is 0 bytes after a block of size 32 alloc'd ==28614== at 0x4C298F9: operator new(unsigned long) (vg_replace_malloc.c:298) ==28614== by 0xC9E2C1A: mad_vector_double (new_allocator.h:104) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== ==28614== Conditional jump or move depends on uninitialised value(s) ==28614== at 0xC9E1E78: void std::__introselect<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long) (stl_algo.h:2242) ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== ==28614== Invalid read of size 8 ==28614== at 0xC9E1E14: void std::__introselect<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long) (stl_algo.h:87) ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0xbb0b218 is 312 bytes inside a block of size 512 free'd ==28614== at 0x4C2AB5C: operator delete(void*) (vg_replace_malloc.c:480) ==28614== by 0xC9E5208: std::_Rb_tree<int, std::pair<int="" const,="" std::vector<int,="" std::allocator<int=""> > >, std::_Select1st<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > >, std::less<int>, std::allocator<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > > >::_M_erase(std::_Rb_tree_node<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > >*) (new_allocator.h:110) ==28614== by 0xC9E51F6: std::_Rb_tree<int, std::pair<int="" const,="" std::vector<int,="" std::allocator<int=""> > >, std::_Select1st<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > >, std::less<int>, std::allocator<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > > >::_M_erase(std::_Rb_tree_node<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > >*) (stl_tree.h:1125) ==28614== by 0xC9E6084: loopRemove (stl_tree.h:860) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== ==28614== Invalid read of size 8 ==28614== at 0xC9E1E7A: void std::__introselect<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long) (stl_algo.h:2245) ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0xbb0b220 is 320 bytes inside a block of size 512 free'd ==28614== at 0x4C2AB5C: operator delete(void*) (vg_replace_malloc.c:480) ==28614== by 0xC9E5208: std::_Rb_tree<int, std::pair<int="" const,="" std::vector<int,="" std::allocator<int=""> > >, std::_Select1st<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > >, std::less<int>, std::allocator<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > > >::_M_erase(std::_Rb_tree_node<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > >*) (new_allocator.h:110) ==28614== by 0xC9E51F6: std::_Rb_tree<int, std::pair<int="" const,="" std::vector<int,="" std::allocator<int=""> > >, std::_Select1st<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > >, std::less<int>, std::allocator<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > > >::_M_erase(std::_Rb_tree_node<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > >*) (stl_tree.h:1125) ==28614== by 0xC9E6084: loopRemove (stl_tree.h:860) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== ==28614== Invalid write of size 8 ==28614== at 0xC9E1EB0: void std::__introselect<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long) (move.h:177) ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0xbb0b220 is 320 bytes inside a block of size 512 free'd ==28614== at 0x4C2AB5C: operator delete(void*) (vg_replace_malloc.c:480) ==28614== by 0xC9E5208: std::_Rb_tree<int, std::pair<int="" const,="" std::vector<int,="" std::allocator<int=""> > >, std::_Select1st<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > >, std::less<int>, std::allocator<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > > >::_M_erase(std::_Rb_tree_node<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > >*) (new_allocator.h:110) ==28614== by 0xC9E51F6: std::_Rb_tree<int, std::pair<int="" const,="" std::vector<int,="" std::allocator<int=""> > >, std::_Select1st<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > >, std::less<int>, std::allocator<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > > >::_M_erase(std::_Rb_tree_node<std::pair<int const,="" std::vector<int,="" std::allocator<int=""> > > >*) (stl_tree.h:1125) ==28614== by 0xC9E6084: loopRemove (stl_tree.h:860) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== ==28614== Invalid read of size 8 ==28614== at 0xC9E1EB8: void std::__introselect<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long) (move.h:177) ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0xbb087b0 is 0 bytes after a block of size 32 alloc'd ==28614== at 0x4C298F9: operator new(unsigned long) (vg_replace_malloc.c:298) ==28614== by 0xC9E2C1A: mad_vector_double (new_allocator.h:104) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== ==28614== Conditional jump or move depends on uninitialised value(s) ==28614== at 0xC9E1E8B: void std::__introselect<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long) (stl_algo.h:2245) ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== ==28614== Conditional jump or move depends on uninitialised value(s) ==28614== at 0xC9E1EA0: void std::__introselect<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long) (stl_algo.h:2245) ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== ==28614== Invalid write of size 8 ==28614== at 0xC9E1EA7: void std::__introselect<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long) (move.h:176) ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0xbb087b0 is 0 bytes after a block of size 32 alloc'd ==28614== at 0x4C298F9: operator new(unsigned long) (vg_replace_malloc.c:298) ==28614== by 0xC9E2C1A: mad_vector_double (new_allocator.h:104) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== ==28614== Conditional jump or move depends on uninitialised value(s) ==28614== at 0xC9E1EC6: void std::__introselect<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long) (stl_algo.h:2242) ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== ==28614== Invalid read of size 8 ==28614== at 0xC9E1E97: void std::__introselect<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long) (stl_algo.h:2245) ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0xbb08ff8 is 8 bytes before a block of size 8,352 alloc'd ==28614== at 0x4C2935B: malloc (vg_replace_malloc.c:270) ==28614== by 0x4F58E54: Rf_allocVector (memory.c:2465) ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) ==28614== by 0x4F2514E: evalseq (eval.c:1693) ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) ==28614== ==28614== Invalid read of size 8 ==28614== at 0xC9E1F5E: void std::__introselect<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long) (stl_algo.h:1935) ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0xbb087b0 is 0 bytes after a block of size 32 alloc'd ==28614== at 0x4C298F9: operator new(unsigned long) (vg_replace_malloc.c:298) ==28614== by 0xC9E2C1A: mad_vector_double (new_allocator.h:104) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== ==28614== Invalid write of size 8 ==28614== at 0xC9E1F6A: void std::__introselect<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long) (stl_heap.h:262) ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0xbb087b0 is 0 bytes after a block of size 32 alloc'd ==28614== at 0x4C298F9: operator new(unsigned long) (vg_replace_malloc.c:298) ==28614== by 0xC9E2C1A: mad_vector_double (new_allocator.h:104) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== ==28614== Conditional jump or move depends on uninitialised value(s) ==28614== at 0xC9E1F68: void std::__introselect<__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, __gnu_cxx::__normal_iterator<double*, std::vector<double,="" std::allocator<double=""> > >, long) (stl_algo.h:1935) ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) ==28614== by 0xC9E7423: loop_chromosome_removeLevel (loopRemove.cpp:252) ==28614== by 0xC9E75B2: OptmisationBreakpointsStep (loopRemove.cpp:322) ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster (daglad.cpp:79) ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) ==28614== by 0x4F25F9D: do_set (eval.c:1991) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== ==28614== Invalid read of size 1 ==28614== at 0x4F55D3F: R_gc_internal (memory.c:1575) ==28614== by 0x4F58BDA: Rf_allocVector (memory.c:2434) ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) ==28614== by 0x4F2514E: evalseq (eval.c:1693) ==28614== by 0x4F25020: evalseq (eval.c:1703) ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0xa8e0943 is 3 bytes inside a block of size 216 free'd ==28614== at 0x4C2A68C: free (vg_replace_malloc.c:446) ==28614== by 0x4F5688E: R_gc_internal (memory.c:1011) ==28614== by 0x4F58A69: Rf_allocVector (memory.c:2284) ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) ==28614== by 0x4F19176: bcEval (eval.c:4446) ==28614== by 0x4F22787: Rf_eval (eval.c:554) ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) ==28614== by 0x4F1A928: bcEval (eval.c:4670) ==28614== by 0x4F22787: Rf_eval (eval.c:554) ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) ==28614== by 0x4F22730: Rf_eval (eval.c:670) ==28614== by 0x4F22EE9: forcePromise (eval.c:458) ==28614== ==28614== Invalid read of size 8 ==28614== at 0x4F55D4B: R_gc_internal (memory.c:1575) ==28614== by 0x4F58BDA: Rf_allocVector (memory.c:2434) ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) ==28614== by 0x4F2514E: evalseq (eval.c:1693) ==28614== by 0x4F25020: evalseq (eval.c:1703) ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0xa8e0958 is 24 bytes inside a block of size 216 free'd ==28614== at 0x4C2A68C: free (vg_replace_malloc.c:446) ==28614== by 0x4F5688E: R_gc_internal (memory.c:1011) ==28614== by 0x4F58A69: Rf_allocVector (memory.c:2284) ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) ==28614== by 0x4F19176: bcEval (eval.c:4446) ==28614== by 0x4F22787: Rf_eval (eval.c:554) ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) ==28614== by 0x4F1A928: bcEval (eval.c:4670) ==28614== by 0x4F22787: Rf_eval (eval.c:554) ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) ==28614== by 0x4F22730: Rf_eval (eval.c:670) ==28614== by 0x4F22EE9: forcePromise (eval.c:458) ==28614== ==28614== Invalid write of size 1 ==28614== at 0x4F55D4F: R_gc_internal (memory.c:1575) ==28614== by 0x4F58BDA: Rf_allocVector (memory.c:2434) ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) ==28614== by 0x4F2514E: evalseq (eval.c:1693) ==28614== by 0x4F25020: evalseq (eval.c:1703) ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0xa8e0943 is 3 bytes inside a block of size 216 free'd ==28614== at 0x4C2A68C: free (vg_replace_malloc.c:446) ==28614== by 0x4F5688E: R_gc_internal (memory.c:1011) ==28614== by 0x4F58A69: Rf_allocVector (memory.c:2284) ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) ==28614== by 0x4F19176: bcEval (eval.c:4446) ==28614== by 0x4F22787: Rf_eval (eval.c:554) ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) ==28614== by 0x4F1A928: bcEval (eval.c:4670) ==28614== by 0x4F22787: Rf_eval (eval.c:554) ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) ==28614== by 0x4F22730: Rf_eval (eval.c:670) ==28614== by 0x4F22EE9: forcePromise (eval.c:458) ==28614== ==28614== Invalid read of size 8 ==28614== at 0x4F55D52: R_gc_internal (memory.c:1575) ==28614== by 0x4F58BDA: Rf_allocVector (memory.c:2434) ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) ==28614== by 0x4F2514E: evalseq (eval.c:1693) ==28614== by 0x4F25020: evalseq (eval.c:1703) ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0xa8e0950 is 16 bytes inside a block of size 216 free'd ==28614== at 0x4C2A68C: free (vg_replace_malloc.c:446) ==28614== by 0x4F5688E: R_gc_internal (memory.c:1011) ==28614== by 0x4F58A69: Rf_allocVector (memory.c:2284) ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) ==28614== by 0x4F19176: bcEval (eval.c:4446) ==28614== by 0x4F22787: Rf_eval (eval.c:554) ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) ==28614== by 0x4F1A928: bcEval (eval.c:4670) ==28614== by 0x4F22787: Rf_eval (eval.c:554) ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) ==28614== by 0x4F22730: Rf_eval (eval.c:670) ==28614== by 0x4F22EE9: forcePromise (eval.c:458) ==28614== ==28614== Invalid write of size 8 ==28614== at 0x4F55D5A: R_gc_internal (memory.c:1575) ==28614== by 0x4F58BDA: Rf_allocVector (memory.c:2434) ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) ==28614== by 0x4F2514E: evalseq (eval.c:1693) ==28614== by 0x4F25020: evalseq (eval.c:1703) ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0xa927af8 is 24 bytes inside a block of size 256 free'd ==28614== at 0x4C2A68C: free (vg_replace_malloc.c:446) ==28614== by 0x4F5688E: R_gc_internal (memory.c:1011) ==28614== by 0x4F58A69: Rf_allocVector (memory.c:2284) ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) ==28614== by 0x4F19176: bcEval (eval.c:4446) ==28614== by 0x4F22787: Rf_eval (eval.c:554) ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) ==28614== by 0x4F1A928: bcEval (eval.c:4670) ==28614== by 0x4F22787: Rf_eval (eval.c:554) ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) ==28614== by 0x4F22730: Rf_eval (eval.c:670) ==28614== by 0x4F22EE9: forcePromise (eval.c:458) ==28614== ==28614== Invalid write of size 8 ==28614== at 0x4F55D5E: R_gc_internal (memory.c:1575) ==28614== by 0x4F58BDA: Rf_allocVector (memory.c:2434) ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) ==28614== by 0x4F2514E: evalseq (eval.c:1693) ==28614== by 0x4F25020: evalseq (eval.c:1703) ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0xa8e0950 is 16 bytes inside a block of size 216 free'd ==28614== at 0x4C2A68C: free (vg_replace_malloc.c:446) ==28614== by 0x4F5688E: R_gc_internal (memory.c:1011) ==28614== by 0x4F58A69: Rf_allocVector (memory.c:2284) ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) ==28614== by 0x4F19176: bcEval (eval.c:4446) ==28614== by 0x4F22787: Rf_eval (eval.c:554) ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) ==28614== by 0x4F1A928: bcEval (eval.c:4670) ==28614== by 0x4F22787: Rf_eval (eval.c:554) ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) ==28614== by 0x4F22730: Rf_eval (eval.c:670) ==28614== by 0x4F22EE9: forcePromise (eval.c:458) ==28614== ==28614== Use of uninitialised value of size 8 ==28614== at 0x4F55BA4: R_gc_internal (memory.c:1575) ==28614== by 0x4F58BDA: Rf_allocVector (memory.c:2434) ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) ==28614== by 0x4F2514E: evalseq (eval.c:1693) ==28614== by 0x4F25020: evalseq (eval.c:1703) ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== ==28614== Invalid write of size 8 ==28614== at 0x4F55BA4: R_gc_internal (memory.c:1575) ==28614== by 0x4F58BDA: Rf_allocVector (memory.c:2434) ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) ==28614== by 0x4F2514E: evalseq (eval.c:1693) ==28614== by 0x4F25020: evalseq (eval.c:1703) ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== by 0x4F24D36: do_begin (eval.c:1620) ==28614== by 0x4F2298F: Rf_eval (eval.c:623) ==28614== Address 0x1a is not stack'd, malloc'd or (recently) free'd ==28614== *** caught segfault *** address 0x1a, cause 'memory not mapped' ==28614== ==28614== Process terminating with default action of signal 11 (SIGSEGV) ==28614== General Protection Fault ==28614== at 0x5817F7A: snprintf (snprintf.c:29) ==28614== by 0x4F8BEDD: Rf_EncodeReal (printutils.c:200) ==28614== by 0x4F8D4EF: Rf_EncodeElement (printutils.c:691) ==28614== by 0x4ED1CD0: vector2buff (deparse.c:1387) ==28614== by 0x4ED47BB: deparse2buff (deparse.c:1184) ==28614== by 0x4ED600A: args2buff.isra.5 (deparse.c:1511) ==28614== by 0x4ED42F9: deparse2buff (deparse.c:1169) ==28614== by 0x4ED675B: Rf_deparse1 (deparse.c:495) ==28614== by 0x4F0B7BD: R_GetTraceback (errors.c:1344) ==28614== by 0x4F4DFCF: sigactionSegv (main.c:563) ==28614== by 0x55BA20F: ??? (in /lib/x86_64-linux- gnu/libpthread-2.17.so) ==28614== by 0x4F55BA3: R_gc_internal (memory.c:1575) ==28614== ==28614== HEAP SUMMARY: ==28614== in use at exit: 30,524,124 bytes in 12,208 blocks ==28614== total heap usage: 53,083 allocs, 40,875 frees, 260,247,507 bytes allocated ==28614== ==28614== LEAK SUMMARY: ==28614== definitely lost: 0 bytes in 0 blocks ==28614== indirectly lost: 0 bytes in 0 blocks ==28614== possibly lost: 0 bytes in 0 blocks ==28614== still reachable: 30,524,124 bytes in 12,208 blocks ==28614== suppressed: 0 bytes in 0 blocks ==28614== Rerun with --leak-check=full to see details of leaked memory ==28614== ==28614== For counts of detected and suppressed errors, rerun with: -v ==28614== Use --track-origins=yes to see where uninitialised values come from ==28614== ERROR SUMMARY: 447 errors from 26 contexts (suppressed: 2 from 2) Segmentation fault > -- > Martin Morgan > > On Dec 28, 2013, at 8:32 AM, Ramon Diaz-Uriarte <rdiaz02 at="" gmail.com=""> wrote: > > > Dear All, > > > > At least one function (daglad) from the GLAD package crashes with a > > segfault when compiled with gcc-4.8 but not with gcc-4.7. I am not sure if > > this is a problem with GLAD or, more unlikely, with R. (Details below) > > > > > > Has anybody seen something similar? > > > > Best, > > > > R. > > > > > > Details: > > ======== > > > > - How to reproduce the error > > > > ## make sure you are using gcc-4.8 and g++-4.8 > > biocLite("GLAD") > > library(GLAD) > > example(daglad) > > > > > > - Errors: there are several; these are some > > > > *** Error in `/home/ramon/Sources/R-3.1.0-64488/bin/exec/R': free(): invalid next size (fast): 0x0000000014144d70 *** > > ======= Backtrace: ========= > > /lib/x86_64-linux-gnu/libc.so.6(+0x7aa16)[0x7f2ff0f04a16] > > /lib/x86_64-linux-gnu/libc.so.6(+0x7b793)[0x7f2ff0f05793] > > /home/ramon/Sources/R-3.1.0-64488/library/GLAD/libs/GLAD.so(mad_ve ctor_double+0x184)[0x7f2fed753bc4] > > > > > > [1] "Optimization of the Breakpoints and DNA copy number calling" > > *** Error in `/usr/lib/R/bin/exec/R': corrupted double-linked list: 0x00000000010f24a0 *** > > > > > > *** caught segfault *** > > address 0x140000000a, cause 'memory not mapped' > > > > Traceback: > > 1: gc(FALSE) > > 2: system.time(BP <- merge(BP, profileCGH$SigmaC)) > > 3: BkpInfo.profileCGH(profileCGH) > > 4: BkpInfo(profileCGH) > > > > > > - OS: Debian GNU/Linux, a mixture of testing and unstable > > > > - version of gcc/g++: 4.8.2-1 and 4.7.3-9 (for Debian) > > > > - version of GLAD: 2.26.0 (for R-3.0.2) and 2.27.1 (for R-3.1.0) > > > > - versions of R: several from R-3.0.2 and R-3.1.0. For instance > > > > ## the current Debian version > >> version > > _ > > platform x86_64-pc-linux-gnu > > arch x86_64 > > os linux-gnu > > system x86_64, linux-gnu > > status > > major 3 > > minor 0.2 > > year 2013 > > month 09 > > day 25 > > svn rev 63987 > > language R > > version.string R version 3.0.2 (2013-09-25) > > nickname Frisbee Sailing > > > > ## the R-devel that seems to be used in the testing of BioC packages > >> version > > _ > > platform x86_64-pc-linux-gnu > > arch x86_64 > > os linux-gnu > > system x86_64, linux-gnu > > status Under development (unstable) > > major 3 > > minor 1.0 > > year 2013 > > month 12 > > day 19 > > svn rev 64488 > > language R > > version.string R Under development (unstable) (2013-12-19 r64488) > > nickname Unsuffered Consequences > > > > ## the latest R-devel > >> version > > _ > > platform x86_64-pc-linux-gnu > > arch x86_64 > > os linux-gnu > > system x86_64, linux-gnu > > status Under development (unstable) > > major 3 > > minor 1.0 > > year 2013 > > month 12 > > day 27 > > svn rev 64562 > > language R > > version.string R Under development (unstable) (2013-12-27 r64562) > > nickname Unsuffered Consequences > > > > > > - version of GSL: crashes happen with the two available versions in Debian > > for libgsl0ldbl and libgsl0-dev: 1.16+dfsg-1 and 1.15+dfsg.2-2 > > > > > > > > > -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Aut?noma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdiaz02 at gmail.com ramon.diaz at iib.uam.es http://ligarto.org/rdiaz
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Entering edit mode
----- Original Message ----- > From: "Ramon Diaz-Uriarte" <rdiaz02 at="" gmail.com=""> > To: "Martin Morgan" <mtmorgan at="" fhcrc.org=""> > Cc: bioconductor at r-project.org, "ramon diaz" <ramon.diaz at="" iib.uam.es=""> > Sent: Saturday, December 28, 2013 2:46:17 PM > Subject: Re: [BioC] GLAD crashes when built with gcc-4.8 > > > Hi Martin, > > On Sat, 28-12-2013, at 23:07, mtmorgan at fhcrc.org wrote: > > If possible run as. > > > > R -d valgrind -f script.R > > > > Where script.R is the minimal commands to produce the problem ( eg > > no > > need for biocLite). Compare the output with one less than the > > minimal > > script, looking in particular for 'invalid write' errors. > > > This is a simple script: > > ################## > library(GLAD) > data(snijders) > gm13330$Clone <- gm13330$BAC > profileCGH <- as.profileCGH(gm13330) > > res <- daglad(profileCGH, mediancenter=FALSE, normalrefcenter=FALSE, > genomestep=FALSE, > smoothfunc="lawsglad", lkern="Exponential", > model="Gaussian", > qlambda=0.999, bandwidth=10, base=FALSE, round=1.5, > lambdabreak=8, lambdaclusterGen=40, param=c(d=6), > alpha=0.001, msize=2, > method="centroid", nmin=1, nmax=8, > amplicon=1, deletion=-5, deltaN=0.10, > forceGL=c(-0.15,0.15), nbsigma=3, > MinBkpWeight=0.35, CheckBkpPos=TRUE) > ############# > > > And, yes, running it through valgrind does show some "Invalid write" > errors > (and a bunch of "Invalid read"), all of which seem to be caused by > C++ code > in GLAD. Running the above script without the call to daglad does > not lead > to any problems (no invalid writes or reads). > > > What version of gcc are you guys using in the zin2 and zin1 machines? > (googling around I get the impression that the default for Ubuntu > 12.04 is > 4.6.3) > Yes, 4.6.3 on both, see: http://bioconductor.org/checkResults/release/bioc- LATEST/zin1-NodeInfo.html http://bioconductor.org/checkResults/devel/bioc- LATEST/zin2-NodeInfo.html Dan > > > Best, > > > R. > > > > > > > [1] "Smoothing for each Chromosome" > ==28614== Invalid read of size 8 > ==28614== at 0xC9DA1B9: awsBkp (chrBreakpoints.cpp:214) > ==28614== by 0x4EE9B6B: do_dotCode (dotcode.c:1722) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F286D6: do_for (eval.c:1509) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0x95d5280 is 0 bytes after a block of size 576 > alloc'd > ==28614== at 0x4C2935B: malloc (vg_replace_malloc.c:270) > ==28614== by 0x4F58E54: Rf_allocVector (memory.c:2465) > ==28614== by 0x4EE31C0: do_dotCode (dotcode.c:1563) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F286D6: do_for (eval.c:1509) > ==28614== > ==28614== Invalid read of size 8 > ==28614== at 0xC9E1E6F: void > std::__introselect<__gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, __gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > __gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, long) (stl_algo.h:2242) > ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) > ==28614== by 0xC9DB618: putLevel (chrBreakpoints.cpp:360) > ==28614== by 0xC9DB9E8: putLevel_awsBkp (chrBreakpoints.cpp:168) > ==28614== by 0x4EE9B6B: do_dotCode (dotcode.c:1722) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== Address 0xa196fd0 is 0 bytes after a block of size 32 > alloc'd > ==28614== at 0x4C298F9: operator new(unsigned long) > (vg_replace_malloc.c:298) > ==28614== by 0xC9DB8CD: putLevel (new_allocator.h:104) > ==28614== by 0xC9DB9E8: putLevel_awsBkp (chrBreakpoints.cpp:168) > ==28614== by 0x4EE9B6B: do_dotCode (dotcode.c:1722) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== > [1] "Optimization of the Breakpoints and DNA copy number calling" > ==28614== Invalid read of size 8 > ==28614== at 0xC9E1E6F: void > std::__introselect<__gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, __gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > __gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, long) (stl_algo.h:2242) > ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) > ==28614== by 0xC9E389D: detectOutliers (glad-utils.cpp:242) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== Address 0xb412da0 is 0 bytes after a block of size 32 > alloc'd > ==28614== at 0x4C298F9: operator new(unsigned long) > (vg_replace_malloc.c:298) > ==28614== by 0xC9E3ACA: detectOutliers (new_allocator.h:104) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== > ==28614== Invalid read of size 8 > ==28614== at 0xC9E1E6F: void > std::__introselect<__gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, __gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > __gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, long) (stl_algo.h:2242) > ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) > ==28614== by 0xC9E2AEC: mad_vector_double (glad-utils.cpp:626) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0xbb08750 is 0 bytes after a block of size 32 > alloc'd > ==28614== at 0x4C298F9: operator new(unsigned long) > (vg_replace_malloc.c:298) > ==28614== by 0xC9E2C42: mad_vector_double (new_allocator.h:104) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== > ==28614== Invalid read of size 8 > ==28614== at 0xC9E1E6F: void > std::__introselect<__gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, __gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > __gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, long) (stl_algo.h:2242) > ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) > ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0xbb087b0 is 0 bytes after a block of size 32 > alloc'd > ==28614== at 0x4C298F9: operator new(unsigned long) > (vg_replace_malloc.c:298) > ==28614== by 0xC9E2C1A: mad_vector_double (new_allocator.h:104) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== > ==28614== Conditional jump or move depends on uninitialised value(s) > ==28614== at 0xC9E1E78: void > std::__introselect<__gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, __gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > __gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, long) (stl_algo.h:2242) > ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) > ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== > ==28614== Invalid read of size 8 > ==28614== at 0xC9E1E14: void > std::__introselect<__gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, __gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > __gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, long) (stl_algo.h:87) > ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) > ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0xbb0b218 is 312 bytes inside a block of size 512 > free'd > ==28614== at 0x4C2AB5C: operator delete(void*) > (vg_replace_malloc.c:480) > ==28614== by 0xC9E5208: std::_Rb_tree<int, std::pair<int="" const,=""> std::vector<int, std::allocator<int=""> > >, > std::_Select1st<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > >, std::less<int>, > std::allocator<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > > > >::_M_erase(std::_Rb_tree_node<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > >*) (new_allocator.h:110) > ==28614== by 0xC9E51F6: std::_Rb_tree<int, std::pair<int="" const,=""> std::vector<int, std::allocator<int=""> > >, > std::_Select1st<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > >, std::less<int>, > std::allocator<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > > > >::_M_erase(std::_Rb_tree_node<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > >*) (stl_tree.h:1125) > ==28614== by 0xC9E6084: loopRemove (stl_tree.h:860) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== > ==28614== Invalid read of size 8 > ==28614== at 0xC9E1E7A: void > std::__introselect<__gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, __gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > __gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, long) (stl_algo.h:2245) > ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) > ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0xbb0b220 is 320 bytes inside a block of size 512 > free'd > ==28614== at 0x4C2AB5C: operator delete(void*) > (vg_replace_malloc.c:480) > ==28614== by 0xC9E5208: std::_Rb_tree<int, std::pair<int="" const,=""> std::vector<int, std::allocator<int=""> > >, > std::_Select1st<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > >, std::less<int>, > std::allocator<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > > > >::_M_erase(std::_Rb_tree_node<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > >*) (new_allocator.h:110) > ==28614== by 0xC9E51F6: std::_Rb_tree<int, std::pair<int="" const,=""> std::vector<int, std::allocator<int=""> > >, > std::_Select1st<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > >, std::less<int>, > std::allocator<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > > > >::_M_erase(std::_Rb_tree_node<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > >*) (stl_tree.h:1125) > ==28614== by 0xC9E6084: loopRemove (stl_tree.h:860) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== > ==28614== Invalid write of size 8 > ==28614== at 0xC9E1EB0: void > std::__introselect<__gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, __gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > __gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, long) (move.h:177) > ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) > ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0xbb0b220 is 320 bytes inside a block of size 512 > free'd > ==28614== at 0x4C2AB5C: operator delete(void*) > (vg_replace_malloc.c:480) > ==28614== by 0xC9E5208: std::_Rb_tree<int, std::pair<int="" const,=""> std::vector<int, std::allocator<int=""> > >, > std::_Select1st<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > >, std::less<int>, > std::allocator<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > > > >::_M_erase(std::_Rb_tree_node<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > >*) (new_allocator.h:110) > ==28614== by 0xC9E51F6: std::_Rb_tree<int, std::pair<int="" const,=""> std::vector<int, std::allocator<int=""> > >, > std::_Select1st<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > >, std::less<int>, > std::allocator<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > > > >::_M_erase(std::_Rb_tree_node<std::pair<int const,="" std::vector<int,=""> std::allocator<int> > > >*) (stl_tree.h:1125) > ==28614== by 0xC9E6084: loopRemove (stl_tree.h:860) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== > ==28614== Invalid read of size 8 > ==28614== at 0xC9E1EB8: void > std::__introselect<__gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, __gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > __gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, long) (move.h:177) > ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) > ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0xbb087b0 is 0 bytes after a block of size 32 > alloc'd > ==28614== at 0x4C298F9: operator new(unsigned long) > (vg_replace_malloc.c:298) > ==28614== by 0xC9E2C1A: mad_vector_double (new_allocator.h:104) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== > ==28614== Conditional jump or move depends on uninitialised value(s) > ==28614== at 0xC9E1E8B: void > std::__introselect<__gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, __gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > __gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, long) (stl_algo.h:2245) > ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) > ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== > ==28614== Conditional jump or move depends on uninitialised value(s) > ==28614== at 0xC9E1EA0: void > std::__introselect<__gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, __gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > __gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, long) (stl_algo.h:2245) > ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) > ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== > ==28614== Invalid write of size 8 > ==28614== at 0xC9E1EA7: void > std::__introselect<__gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, __gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > __gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, long) (move.h:176) > ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) > ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0xbb087b0 is 0 bytes after a block of size 32 > alloc'd > ==28614== at 0x4C298F9: operator new(unsigned long) > (vg_replace_malloc.c:298) > ==28614== by 0xC9E2C1A: mad_vector_double (new_allocator.h:104) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== > ==28614== Conditional jump or move depends on uninitialised value(s) > ==28614== at 0xC9E1EC6: void > std::__introselect<__gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, __gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > __gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, long) (stl_algo.h:2242) > ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) > ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== > ==28614== Invalid read of size 8 > ==28614== at 0xC9E1E97: void > std::__introselect<__gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, __gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > __gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, long) (stl_algo.h:2245) > ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) > ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0xbb08ff8 is 8 bytes before a block of size 8,352 > alloc'd > ==28614== at 0x4C2935B: malloc (vg_replace_malloc.c:270) > ==28614== by 0x4F58E54: Rf_allocVector (memory.c:2465) > ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) > ==28614== by 0x4F2514E: evalseq (eval.c:1693) > ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) > ==28614== > ==28614== Invalid read of size 8 > ==28614== at 0xC9E1F5E: void > std::__introselect<__gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, __gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > __gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, long) (stl_algo.h:1935) > ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) > ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0xbb087b0 is 0 bytes after a block of size 32 > alloc'd > ==28614== at 0x4C298F9: operator new(unsigned long) > (vg_replace_malloc.c:298) > ==28614== by 0xC9E2C1A: mad_vector_double (new_allocator.h:104) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== > ==28614== Invalid write of size 8 > ==28614== at 0xC9E1F6A: void > std::__introselect<__gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, __gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > __gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, long) (stl_heap.h:262) > ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) > ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0xbb087b0 is 0 bytes after a block of size 32 > alloc'd > ==28614== at 0x4C298F9: operator new(unsigned long) > (vg_replace_malloc.c:298) > ==28614== by 0xC9E2C1A: mad_vector_double (new_allocator.h:104) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== > ==28614== Conditional jump or move depends on uninitialised value(s) > ==28614== at 0xC9E1F68: void > std::__introselect<__gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > long>(__gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, __gnu_cxx::__normal_iterator<double*,> std::vector<double, std::allocator<double=""> > >, > __gnu_cxx::__normal_iterator<double*, std::vector<double,=""> std::allocator<double> > >, long) (stl_algo.h:1935) > ==28614== by 0xC9E21E3: quantile_vector_double (stl_algo.h:5377) > ==28614== by 0xC9E2BA6: mad_vector_double (glad-utils.cpp:634) > ==28614== by 0xC9E394F: detectOutliers (glad-utils.cpp:243) > ==28614== by 0xC9E6074: loopRemove (loopRemove.cpp:63) > ==28614== by 0xC9E7423: loop_chromosome_removeLevel > (loopRemove.cpp:252) > ==28614== by 0xC9E75B2: OptmisationBreakpointsStep > (loopRemove.cpp:322) > ==28614== by 0xC9DC4A4: daglad_OptmisationBreakpoints_findCluster > (daglad.cpp:79) > ==28614== by 0x4EE84FB: do_dotCode (dotcode.c:1901) > ==28614== by 0x4F22BA3: Rf_eval (eval.c:651) > ==28614== by 0x4F25F9D: do_set (eval.c:1991) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== > ==28614== Invalid read of size 1 > ==28614== at 0x4F55D3F: R_gc_internal (memory.c:1575) > ==28614== by 0x4F58BDA: Rf_allocVector (memory.c:2434) > ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) > ==28614== by 0x4F2514E: evalseq (eval.c:1693) > ==28614== by 0x4F25020: evalseq (eval.c:1703) > ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0xa8e0943 is 3 bytes inside a block of size 216 > free'd > ==28614== at 0x4C2A68C: free (vg_replace_malloc.c:446) > ==28614== by 0x4F5688E: R_gc_internal (memory.c:1011) > ==28614== by 0x4F58A69: Rf_allocVector (memory.c:2284) > ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) > ==28614== by 0x4F19176: bcEval (eval.c:4446) > ==28614== by 0x4F22787: Rf_eval (eval.c:554) > ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) > ==28614== by 0x4F1A928: bcEval (eval.c:4670) > ==28614== by 0x4F22787: Rf_eval (eval.c:554) > ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) > ==28614== by 0x4F22730: Rf_eval (eval.c:670) > ==28614== by 0x4F22EE9: forcePromise (eval.c:458) > ==28614== > ==28614== Invalid read of size 8 > ==28614== at 0x4F55D4B: R_gc_internal (memory.c:1575) > ==28614== by 0x4F58BDA: Rf_allocVector (memory.c:2434) > ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) > ==28614== by 0x4F2514E: evalseq (eval.c:1693) > ==28614== by 0x4F25020: evalseq (eval.c:1703) > ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0xa8e0958 is 24 bytes inside a block of size 216 > free'd > ==28614== at 0x4C2A68C: free (vg_replace_malloc.c:446) > ==28614== by 0x4F5688E: R_gc_internal (memory.c:1011) > ==28614== by 0x4F58A69: Rf_allocVector (memory.c:2284) > ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) > ==28614== by 0x4F19176: bcEval (eval.c:4446) > ==28614== by 0x4F22787: Rf_eval (eval.c:554) > ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) > ==28614== by 0x4F1A928: bcEval (eval.c:4670) > ==28614== by 0x4F22787: Rf_eval (eval.c:554) > ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) > ==28614== by 0x4F22730: Rf_eval (eval.c:670) > ==28614== by 0x4F22EE9: forcePromise (eval.c:458) > ==28614== > ==28614== Invalid write of size 1 > ==28614== at 0x4F55D4F: R_gc_internal (memory.c:1575) > ==28614== by 0x4F58BDA: Rf_allocVector (memory.c:2434) > ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) > ==28614== by 0x4F2514E: evalseq (eval.c:1693) > ==28614== by 0x4F25020: evalseq (eval.c:1703) > ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0xa8e0943 is 3 bytes inside a block of size 216 > free'd > ==28614== at 0x4C2A68C: free (vg_replace_malloc.c:446) > ==28614== by 0x4F5688E: R_gc_internal (memory.c:1011) > ==28614== by 0x4F58A69: Rf_allocVector (memory.c:2284) > ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) > ==28614== by 0x4F19176: bcEval (eval.c:4446) > ==28614== by 0x4F22787: Rf_eval (eval.c:554) > ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) > ==28614== by 0x4F1A928: bcEval (eval.c:4670) > ==28614== by 0x4F22787: Rf_eval (eval.c:554) > ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) > ==28614== by 0x4F22730: Rf_eval (eval.c:670) > ==28614== by 0x4F22EE9: forcePromise (eval.c:458) > ==28614== > ==28614== Invalid read of size 8 > ==28614== at 0x4F55D52: R_gc_internal (memory.c:1575) > ==28614== by 0x4F58BDA: Rf_allocVector (memory.c:2434) > ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) > ==28614== by 0x4F2514E: evalseq (eval.c:1693) > ==28614== by 0x4F25020: evalseq (eval.c:1703) > ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0xa8e0950 is 16 bytes inside a block of size 216 > free'd > ==28614== at 0x4C2A68C: free (vg_replace_malloc.c:446) > ==28614== by 0x4F5688E: R_gc_internal (memory.c:1011) > ==28614== by 0x4F58A69: Rf_allocVector (memory.c:2284) > ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) > ==28614== by 0x4F19176: bcEval (eval.c:4446) > ==28614== by 0x4F22787: Rf_eval (eval.c:554) > ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) > ==28614== by 0x4F1A928: bcEval (eval.c:4670) > ==28614== by 0x4F22787: Rf_eval (eval.c:554) > ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) > ==28614== by 0x4F22730: Rf_eval (eval.c:670) > ==28614== by 0x4F22EE9: forcePromise (eval.c:458) > ==28614== > ==28614== Invalid write of size 8 > ==28614== at 0x4F55D5A: R_gc_internal (memory.c:1575) > ==28614== by 0x4F58BDA: Rf_allocVector (memory.c:2434) > ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) > ==28614== by 0x4F2514E: evalseq (eval.c:1693) > ==28614== by 0x4F25020: evalseq (eval.c:1703) > ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0xa927af8 is 24 bytes inside a block of size 256 > free'd > ==28614== at 0x4C2A68C: free (vg_replace_malloc.c:446) > ==28614== by 0x4F5688E: R_gc_internal (memory.c:1011) > ==28614== by 0x4F58A69: Rf_allocVector (memory.c:2284) > ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) > ==28614== by 0x4F19176: bcEval (eval.c:4446) > ==28614== by 0x4F22787: Rf_eval (eval.c:554) > ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) > ==28614== by 0x4F1A928: bcEval (eval.c:4670) > ==28614== by 0x4F22787: Rf_eval (eval.c:554) > ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) > ==28614== by 0x4F22730: Rf_eval (eval.c:670) > ==28614== by 0x4F22EE9: forcePromise (eval.c:458) > ==28614== > ==28614== Invalid write of size 8 > ==28614== at 0x4F55D5E: R_gc_internal (memory.c:1575) > ==28614== by 0x4F58BDA: Rf_allocVector (memory.c:2434) > ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) > ==28614== by 0x4F2514E: evalseq (eval.c:1693) > ==28614== by 0x4F25020: evalseq (eval.c:1703) > ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0xa8e0950 is 16 bytes inside a block of size 216 > free'd > ==28614== at 0x4C2A68C: free (vg_replace_malloc.c:446) > ==28614== by 0x4F5688E: R_gc_internal (memory.c:1011) > ==28614== by 0x4F58A69: Rf_allocVector (memory.c:2284) > ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) > ==28614== by 0x4F19176: bcEval (eval.c:4446) > ==28614== by 0x4F22787: Rf_eval (eval.c:554) > ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) > ==28614== by 0x4F1A928: bcEval (eval.c:4670) > ==28614== by 0x4F22787: Rf_eval (eval.c:554) > ==28614== by 0x4F23CEC: Rf_applyClosure (eval.c:1033) > ==28614== by 0x4F22730: Rf_eval (eval.c:670) > ==28614== by 0x4F22EE9: forcePromise (eval.c:458) > ==28614== > ==28614== Use of uninitialised value of size 8 > ==28614== at 0x4F55BA4: R_gc_internal (memory.c:1575) > ==28614== by 0x4F58BDA: Rf_allocVector (memory.c:2434) > ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) > ==28614== by 0x4F2514E: evalseq (eval.c:1693) > ==28614== by 0x4F25020: evalseq (eval.c:1703) > ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== > ==28614== Invalid write of size 8 > ==28614== at 0x4F55BA4: R_gc_internal (memory.c:1575) > ==28614== by 0x4F58BDA: Rf_allocVector (memory.c:2434) > ==28614== by 0x4EEF81F: duplicate1 (duplicate.c:236) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4EEFA99: duplicate1 (duplicate.c:230) > ==28614== by 0x4F22DB1: EnsureLocal (eval.c:1243) > ==28614== by 0x4F2514E: evalseq (eval.c:1693) > ==28614== by 0x4F25020: evalseq (eval.c:1703) > ==28614== by 0x4F2535E: applydefine.isra.16 (eval.c:1893) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== by 0x4F24D36: do_begin (eval.c:1620) > ==28614== by 0x4F2298F: Rf_eval (eval.c:623) > ==28614== Address 0x1a is not stack'd, malloc'd or (recently) free'd > ==28614== > > *** caught segfault *** > address 0x1a, cause 'memory not mapped' > ==28614== > ==28614== Process terminating with default action of signal 11 > (SIGSEGV) > ==28614== General Protection Fault > ==28614== at 0x5817F7A: snprintf (snprintf.c:29) > ==28614== by 0x4F8BEDD: Rf_EncodeReal (printutils.c:200) > ==28614== by 0x4F8D4EF: Rf_EncodeElement (printutils.c:691) > ==28614== by 0x4ED1CD0: vector2buff (deparse.c:1387) > ==28614== by 0x4ED47BB: deparse2buff (deparse.c:1184) > ==28614== by 0x4ED600A: args2buff.isra.5 (deparse.c:1511) > ==28614== by 0x4ED42F9: deparse2buff (deparse.c:1169) > ==28614== by 0x4ED675B: Rf_deparse1 (deparse.c:495) > ==28614== by 0x4F0B7BD: R_GetTraceback (errors.c:1344) > ==28614== by 0x4F4DFCF: sigactionSegv (main.c:563) > ==28614== by 0x55BA20F: ??? (in > /lib/x86_64-linux-gnu/libpthread-2.17.so) > ==28614== by 0x4F55BA3: R_gc_internal (memory.c:1575) > ==28614== > ==28614== HEAP SUMMARY: > ==28614== in use at exit: 30,524,124 bytes in 12,208 blocks > ==28614== total heap usage: 53,083 allocs, 40,875 frees, > 260,247,507 bytes allocated > ==28614== > ==28614== LEAK SUMMARY: > ==28614== definitely lost: 0 bytes in 0 blocks > ==28614== indirectly lost: 0 bytes in 0 blocks > ==28614== possibly lost: 0 bytes in 0 blocks > ==28614== still reachable: 30,524,124 bytes in 12,208 blocks > ==28614== suppressed: 0 bytes in 0 blocks > ==28614== Rerun with --leak-check=full to see details of leaked > memory > ==28614== > ==28614== For counts of detected and suppressed errors, rerun with: > -v > ==28614== Use --track-origins=yes to see where uninitialised values > come from > ==28614== ERROR SUMMARY: 447 errors from 26 contexts (suppressed: 2 > from 2) > Segmentation fault > > > > > > > > > > > > > > > > > > -- > > Martin Morgan > > > > On Dec 28, 2013, at 8:32 AM, Ramon Diaz-Uriarte <rdiaz02 at="" gmail.com=""> > > wrote: > > > > > Dear All, > > > > > > At least one function (daglad) from the GLAD package crashes with > > > a > > > segfault when compiled with gcc-4.8 but not with gcc-4.7. I am > > > not sure if > > > this is a problem with GLAD or, more unlikely, with R. (Details > > > below) > > > > > > > > > Has anybody seen something similar? > > > > > > Best, > > > > > > R. > > > > > > > > > Details: > > > ======== > > > > > > - How to reproduce the error > > > > > > ## make sure you are using gcc-4.8 and g++-4.8 > > > biocLite("GLAD") > > > library(GLAD) > > > example(daglad) > > > > > > > > > - Errors: there are several; these are some > > > > > > *** Error in `/home/ramon/Sources/R-3.1.0-64488/bin/exec/R': > > > free(): invalid next size (fast): 0x0000000014144d70 *** > > > ======= Backtrace: ========= > > > /lib/x86_64-linux-gnu/libc.so.6(+0x7aa16)[0x7f2ff0f04a16] > > > /lib/x86_64-linux-gnu/libc.so.6(+0x7b793)[0x7f2ff0f05793] > > > /home/ramon/Sources/R-3.1.0-64488/library/GLAD/libs/GLAD.so(mad_ vector_double+0x184)[0x7f2fed753bc4] > > > > > > > > > [1] "Optimization of the Breakpoints and DNA copy number calling" > > > *** Error in `/usr/lib/R/bin/exec/R': corrupted double-linked > > > list: 0x00000000010f24a0 *** > > > > > > > > > *** caught segfault *** > > > address 0x140000000a, cause 'memory not mapped' > > > > > > Traceback: > > > 1: gc(FALSE) > > > 2: system.time(BP <- merge(BP, profileCGH$SigmaC)) > > > 3: BkpInfo.profileCGH(profileCGH) > > > 4: BkpInfo(profileCGH) > > > > > > > > > - OS: Debian GNU/Linux, a mixture of testing and unstable > > > > > > - version of gcc/g++: 4.8.2-1 and 4.7.3-9 (for Debian) > > > > > > - version of GLAD: 2.26.0 (for R-3.0.2) and 2.27.1 (for R-3.1.0) > > > > > > - versions of R: several from R-3.0.2 and R-3.1.0. For instance > > > > > > ## the current Debian version > > >> version > > > _ > > > platform x86_64-pc-linux-gnu > > > arch x86_64 > > > os linux-gnu > > > system x86_64, linux-gnu > > > status > > > major 3 > > > minor 0.2 > > > year 2013 > > > month 09 > > > day 25 > > > svn rev 63987 > > > language R > > > version.string R version 3.0.2 (2013-09-25) > > > nickname Frisbee Sailing > > > > > > ## the R-devel that seems to be used in the testing of BioC > > > packages > > >> version > > > _ > > > platform x86_64-pc-linux-gnu > > > arch x86_64 > > > os linux-gnu > > > system x86_64, linux-gnu > > > status Under development (unstable) > > > major 3 > > > minor 1.0 > > > year 2013 > > > month 12 > > > day 19 > > > svn rev 64488 > > > language R > > > version.string R Under development (unstable) (2013-12-19 r64488) > > > nickname Unsuffered Consequences > > > > > > ## the latest R-devel > > >> version > > > _ > > > platform x86_64-pc-linux-gnu > > > arch x86_64 > > > os linux-gnu > > > system x86_64, linux-gnu > > > status Under development (unstable) > > > major 3 > > > minor 1.0 > > > year 2013 > > > month 12 > > > day 27 > > > svn rev 64562 > > > language R > > > version.string R Under development (unstable) (2013-12-27 r64562) > > > nickname Unsuffered Consequences > > > > > > > > > - version of GSL: crashes happen with the two available versions > > > in Debian > > > for libgsl0ldbl and libgsl0-dev: 1.16+dfsg-1 and 1.15+dfsg.2-2 > > > > > > > > > > > > > > > > -- > Ramon Diaz-Uriarte > Department of Biochemistry, Lab B-25 > Facultad de Medicina > Universidad Aut?noma de Madrid > Arzobispo Morcillo, 4 > 28029 Madrid > Spain > > Phone: +34-91-497-2412 > > Email: rdiaz02 at gmail.com > ramon.diaz at iib.uam.es > > http://ligarto.org/rdiaz > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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