search for: do_internal

...ped' Traceback: 1: cbind(probe, gb) 2: makeBasefiles("Barley1.na22.annot.csv") aborting ... Segmentation fault valgrind says ==25398== Invalid read of size 8 ==25398== at 0x4E7BB2D: cbind (bind.c:1258) ==25398== by 0x4E7B430: do_bind (bind.c:1113) ==25398== by 0x4F42A1B: do_internal (names.c:1116) ==25398== by 0x4EF959B: Rf_eval (eval.c:463) ==25398== by 0x4EF9F91: Rf_applyClosure (eval.c:666) ==25398== by 0x4EF988D: Rf_eval (eval.c:507) ==25398== by 0x4EFC3E0: do_set (eval.c:1404) ==25398== by 0x4EF959B: Rf_eval (eval.c:463) ==25398== by 0x4EFB866: do_begin...

...ment 77D3CCD4 USER32.dll:77D3CCD4 DefRawInputProc 77D145BD USER32.dll:77D145BD TranslateMessageEx 77D147D4 USER32.dll:77D147D4 DefWindowProcA 77F65DA3 ntdll.dll:77F65DA3 KiUserCallbackDispatcher 005B602F R.dll:005B602F show 00477CD5 R.dll:00477CD5 do_selectlist 00509CB4 R.dll:00509CB4 do_internal 004DA9E8 R.dll:004DA9E8 Rf_eval 004DACD5 R.dll:004DACD5 Rf_applyClosure 004DA7F7 R.dll:004DA7F7 Rf_eval 004DA716 R.dll:004DA716 Rf_eval 004DA65E R.dll:004DA65E Rf_eval 004DCBBB R.dll:004DCBBB Rf_evalList 004DA910 R.dll:004DA910 Rf_eval 004DCBBB R.dll:004DCBBB Rf_evalList 004DA910 R...

...00 efl=00000246 Call stack: 7C911E58 ntdll.dll:7C911E58 RtlInitializeCriticalSection 7C910D5C ntdll.dll:7C910D5C wcsncpy 77C2C2DE msvcrt.dll:77C2C2DE free 1004BFB0 R.dll:1004BFB0 do_isseekable 1004C051 R.dll:1004C051 con_close 1004D33E R.dll:1004D33E do_close 100A8E41 R.dll:100A8E41 do_internal 1008494A R.dll:1008494A Rf_eval 10085595 R.dll:10085595 Rf_evalList 10084993 R.dll:10084993 Rf_eval 100875AB R.dll:100875AB Rf_applyClosure 100A9361 R.dll:100A9361 do_internal 100A99A5 R.dll:100A99A5 Rf_usemethod 100A9E1A R.dll:100A9E1A do_usemethod 1008494A R.dll:1008494A Rf_eval 1...

...1423== at 0x80F1390: SETCAR (memory.c:2626) ==11423== by 0x80C1617: R_HashSet (envir.c:219) ==11423== by 0x80C2CC1: Rf_defineVar (envir.c:1261) ==11423== by 0x814F6BE: RestoreToEnv (saveload.c:2043) ==11423== by 0x8150465: do_loadFromConn2 (saveload.c:2358) ==11423== by 0x80F95FF: do_internal (names.c:1097) ==11423== by 0x80CB320: Rf_eval (eval.c:431) ==11423== by 0x80CCAC1: do_begin (eval.c:1107) ==11423== by 0x80CB320: Rf_eval (eval.c:431) ==11423== by 0x80CB5E0: Rf_applyClosure (eval.c:614) ==11423== by 0x80CB1B7: Rf_eval (eval.c:455) ==11423== by 0x80CCAC1: do_begi...

...503== by 0x80A5F92: parse_expression (regex.c:5202) ==32503== by 0x80A614F: parse_branch (regex.c:4707) ==32503== by 0x80A621A: parse_reg_exp (regex.c:4666) ==32503== by 0x80A6618: Rf_regcomp (regex.c:4635) ==32503== by 0x8110CB4: do_gsub (character.c:1355) ==32503== by 0x80654A4: do_internal (names.c:1135) ==32503== by 0x815F0EB: Rf_eval (eval.c:461) ==32503== by 0x8160DA7: do_begin (eval.c:1174) ==32503== by 0x815F0EB: Rf_eval (eval.c:461) ==32503== by 0x8162210: Rf_applyClosure (eval.c:667) ==32503== ... ignore 85 byte/4 block leak in readline ... ==32503== 7,980 bytes in...

...0023 ds=0023 es=0023 fs=0038 gs=0000 efl=00000206 # # Call stack: # 004D2A04 R.dll:004D2A04 malloc # 0054FEFA R.dll:0054FEFA Rf_allocVector # 0051AA10 R.dll:0051AA10 call_S # 0051ABB7 R.dll:0051ABB7 call_S # 0051AF18 R.dll:0051AF18 do_int_unzip # 00559594 R.dll:00559594 do_internal # 0052A3C8 R.dll:0052A3C8 Rf_eval # 0052BA52 R.dll:0052BA52 do_begin # 0052A3C8 R.dll:0052A3C8 Rf_eval # 0052A3C8 R.dll:0052A3C8 Rf_eval # 0052BA52 R.dll:0052BA52 do_begin # 0052A3C8 R.dll:0052A3C8 Rf_eval # 0052A3C8 R.dll:0052A3C8 Rf_eval # 0052BA52 R.dll:0052BA52 do_begin # 0052A3...

Hi all, I'm preparing a package which uses .Fortran to interface a Fortran 95 function. This F95 function simply receives the name of a file from R, opens this file and forwards its content to a F95 module, which, in turn, makes the real computation. The F95 module is a pre-existing one and I'm trying to use it in its actual state. Thus, data transfer between R and this F95 module is

...")) close(a$con) a <- .A$new(con=file(f, "rb")) bin <- readBin(a$con, raw(), as.integer(1e8)) crashes (hangs, usually) at the last line, with valgrind saying ==14875== Invalid read of size 8 ==14875== at 0x4EB23DA: do_readbin (connections.c:3678) ==14875== by 0x4F795E4: do_internal (names.c:1236) ==14875== by 0x4F15F63: Rf_eval (eval.c:471) ==14875== by 0x4F18BA7: do_begin (eval.c:1422) ==14875== by 0x4F15F63: Rf_eval (eval.c:471) ==14875== by 0x4F16F0C: Rf_applyClosure (eval.c:840) ==14875== by 0x4F16276: Rf_eval (eval.c:515) ==14875== by 0x4F19939: do_set...

Full_Name: Juho Vuori Version: 2.7.0 (2008-04-22) OS: Linux poseidon.fimr.fi 2.6.23.17-88.fc7PAE #1 SMP Thu May 15 00:22:53 EDT 2008 i686 i686 i386 GNU/Linux Submission from: (NULL) (193.166.188.194) Calling read.table() twice the following way causes a segmentation fault in R. Run R and type the following commands: > read.table(stdin()) 0: 1 2 3 1: 3 2: Error in scan(file, what, nmax, sep,

...) bt #0 0x00007f735647f4fd in fgets () from /lib/libc.so.6 #1 0x00007f7356b39fe3 in do_system (call=<value optimized out>, op=<value optimized out>, args=<value optimized out>, rho=<value optimized out>) at ../../../src/unix/sys-unix.c:273 #2 0x00007f7356aa1c09 in do_internal (call=<value optimized out>, op=<value optimized out>, args=0xace1d220, env=0xa90e3820) at ../../../src/main/names.c:1150 #3 0x00007f7356a6ec11 in Rf_eval (e=0x872638, rho=0xa90e3820) at ../../../src/main/eval.c:461 [...] #90 0x00007f7356a92950 in run_Rmainloop () at ../../...

...0023 ds=0023 es=0023 fs=0038 gs=0000 efl=00000206 # # Call stack: # 004D2A04 R.dll:004D2A04 malloc # 0054FEFA R.dll:0054FEFA Rf_allocVector # 0051AA10 R.dll:0051AA10 call_S # 0051ABB7 R.dll:0051ABB7 call_S # 0051AF18 R.dll:0051AF18 do_int_unzip # 00559594 R.dll:00559594 do_internal # 0052A3C8 R.dll:0052A3C8 Rf_eval # 0052BA52 R.dll:0052BA52 do_begin # 0052A3C8 R.dll:0052A3C8 Rf_eval # 0052A3C8 R.dll:0052A3C8 Rf_eval # 0052BA52 R.dll:0052BA52 do_begin # 0052A3C8 R.dll:0052A3C8 Rf_eval # 0052A3C8 R.dll:0052A3C8 Rf_eval # 0052BA52 R.dll:0052BA52 do_begin # 0052A3...

...0023 ds=0023 es=0023 fs=0038 gs=0000 efl=00000206 # # Call stack: # 004D2A04 R.dll:004D2A04 malloc # 0054FEFA R.dll:0054FEFA Rf_allocVector # 0051AA10 R.dll:0051AA10 call_S # 0051ABB7 R.dll:0051ABB7 call_S # 0051AF18 R.dll:0051AF18 do_int_unzip # 00559594 R.dll:00559594 do_internal # 0052A3C8 R.dll:0052A3C8 Rf_eval # 0052BA52 R.dll:0052BA52 do_begin # 0052A3C8 R.dll:0052A3C8 Rf_eval # 0052A3C8 R.dll:0052A3C8 Rf_eval # 0052BA52 R.dll:0052BA52 do_begin # 0052A3C8 R.dll:0052A3C8 Rf_eval # 0052A3C8 R.dll:0052A3C8 Rf_eval # 0052BA52 R.dll:0052BA52 do_begin # 0052A3...

...do_begin () #13 0x080b70b7 in Rf_eval () #14 0x080b80b1 in do_for () #15 0x080b70b7 in Rf_eval () #16 0x080b87a5 in do_begin () #17 0x080b70b7 in Rf_eval () #18 0x080b70b7 in Rf_eval () #19 0x080b87a5 in do_begin () #20 0x080b70b7 in Rf_eval () #21 0x080b73c3 in Rf_applyClosure () #22 0x080e03b4 in do_internal () #23 0x080e0b37 in Rf_usemethod () #24 0x080b9f34 in Rf_DispatchOrEval () #25 0x0813b48b in do_subset () #26 0x09fe39f0 in ?? () #27 0x081d620b in _length_code () #28 0x0be7aa5c in ?? () #29 0x0c05a050 in ?? () #30 0xbff046a8 in ?? ()

Full_Name: Juan Gea Version: R version 2.6.2 OS: Fedora Core 6 Submission from: (NULL) (79.153.48.49) Abort: objeS <- matrix("AAA",1000000) class(objeS) outTxt <- textConnection("vaClob", open = "w", local = FALSE) dput(objeS,outTxt) close(outTxt) R version 2.6.2 (2008-02-08) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN

...00007ffff78d84bc in R_forceAndCall (e=e at entry=0x17f3da88, n=n at entry=1, rho=rho at entry=0x17f3e0c0) at eval.c:1676 #23 0x00007ffff782cd92 in do_lapply (call=<optimized out>, op=<optimized out>, args=<optimized out>, rho=0x17f3e0c0) at apply.c:70 #24 0x00007ffff79092e9 in do_internal (call=<optimized out>, op=<optimized out>, args=<optimized out>, env=0x17f3e0c0) at names.c:1360 #25 0x00007ffff78c462a in bcEval (body=body at entry=0x74abd8, rho=rho at entry=0x17f3e0c0, useCache=useCache at entry=TRUE) at eval.c:6449 #26 0x00007ffff78d4138 in Rf_eval (e...

...50c "/home/sonne/Documents/work/fml/repositories/shogun/trunk/src/features/Features.so", asLocal=1, now=1, DLLsearchpath=0x9a81f20 "") at Rdynload.c:543 #10 0xb7d6f657 in do_dynload (call=0x9e23998, op=0x9a91e44, args=0xa60d5e0, env=0xa60d650) at Rdynload.c:904 #11 0xb7e43dba in do_internal (call=0x9e239d0, op=0x9a8798c, args=0xa60d5e0, env=0xa60d650) at names.c:1129 #12 0xb7e0df21 in Rf_eval (e=0x9e239d0, rho=0xa60d650) at eval.c:463 #13 0xb7e11a3c in Rf_applyClosure (call=0xa60d74c, op=0x9e23a94, arglist=0xa60d6dc, rho=0x9a9a720, suppliedenv=0x9a9a73c) at eval.c:669 #14 0xb7e0de19 i...

If anyone has a few extra CPU cycles to spare, I'd appreciate it if you could verify a problem that I have encountered. Run the code below and tell me if it crashes your R before completion. library(lme4) data(bdf) dump<-sapply( 1:50000, function(i) { fm <- lme(langPOST ~ IQ.ver.cen + avg.IQ.ver.cen, data = bdf, random = ~ IQ.ver.cen | schoolNR); cat("

...... ==8058== Address 0x5EFDA80 is 0 bytes after a block of size 232,024 alloc'd ==8058== at 0x401A6EE: malloc (vg_replace_malloc.c:149) ==8058== by 0x80EFBC9: Rf_allocVector (memory.c:1952) ==8058== by 0x807B6CB: do_makevector (builtin.c:558) ==8058== by 0x80F9946: do_internal (names.c:1091) ==8058== by 0x80C9478: Rf_eval (eval.c:424) Note that it computes x(j) and then, if j is out of bounds, resets j to be at the end of the x array and recomputes x(j). It should not compute x(j) if j is out of bounds. A fix that keeps this looking like Fortran IV is to put ...

I have an R script that I run using nohup R CMD BATCH r.in r.out & The code loops through data from the database and takes hours. The problem is, in about an hour and a half after I start the script the program stops and I get /usr/lib/R/bin/BATCH: line 55: 14067 Done ( echo "invisible(options(echo = TRUE))"; cat ${in}; echo "proc.time()" ) 14068

...643== by 0x80A5E22: parse_expression (regex.c:5202) ==28643== by 0x80A5FDF: parse_branch (regex.c:4707) ==28643== by 0x80A60AA: parse_reg_exp (regex.c:4666) ==28643== by 0x80A64A8: Rf_regcomp (regex.c:4635) ==28643== by 0x8110AE0: do_gsub (character.c:1355) ==28643== by 0x80653BC: do_internal (names.c:1129) ==28643== by 0x815EF17: Rf_eval (eval.c:461) ==28643== by 0x8160BD3: do_begin (eval.c:1174) ==28643== by 0x815EF17: Rf_eval (eval.c:461) ==28643== by 0x816203C: Rf_applyClosure (eval.c:667) ==28643== ==28643== LEAK SUMMARY: ==28643== definitely lost: 8,078 bytes in 2,0...