search for: rf_evallist

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

...4bb3c0) at objects.c:325 #12 0x5a114 in Rf_eval (e=0xb6a258, rho=0x4bb3c0) at eval.c:317 #13 0x5a730 in Rf_applyClosure (call=0xa21d14, op=0x907a14, arglist=0x4bb21c, rho=0x4bb078, suppliedenv=0x1b5300) at eval.c:501 #14 0x5a340 in Rf_eval (e=0xa21d14, rho=0x4bb078) at eval.c:352 #15 0x5bba4 in Rf_evalList (el=0xa21c50, rho=0x4bb078) at eval.c:1087 #16 0x5a244 in Rf_eval (e=0xa21c34, rho=0x4bb078) at eval.c:338 #17 0x5c58c in Rf_DispatchOrEval (call=0xa21ba8, generic=0x10cca0 "c", args=0xa21bc4, rho=0x4bb078, ans=0xefffc3c4, dropmissing=1) at eval.c:1386 #18 0x2f144 in do_c (call=0xa21b...

...eCriticalSection 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 100875AB R.dll:100875AB Rf_applyClosure 100846E0 R.dll:100846E0 Rf_ev...

...type=14, length=2000) at memory.c:1541 #6 0x808cb58 in Rf_duplicate (s=0x9548498) at duplicate.c:140 #7 0x80660fa in do_makelist (call=0x8a3f7c0, op=0x81a7c00, args=0x8239258, rho=0x824e510) at builtin.c:367 #8 0x809136f in Rf_eval (e=0x8a3f7c0, rho=0x824e510) at eval.c:424 #9 0x8092cf1 in Rf_evalList (el=0x8a3ee30, rho=0x824e510) at eval.c:1171 #10 0x80912f8 in Rf_eval (e=0x8a3f750, rho=0x824e510) at eval.c:422 #11 0x8091089 in Rf_eval (e=0x824037c, rho=0x8240670) at eval.c:368 #12 0x8090ff4 in Rf_eval (e=0x88211a0, rho=0x8240670) at eval.c:345 #13 0x8092cf1 in Rf_evalList (el=0x8821ddc, rho=0x...

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("

...ll: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.dll:004DA910 Rf_eval 004DB75C R.dll:004DB75C do_if 004DA9E8 R.dll:004DA9E8 Rf_eval 004DC0D2 R.dll:004DC0D2 do_begin 004DA9E8 R.dll:004DA9E8 Rf_eval 004DACD5 R.dll:004DACD5 Rf_applyClosure 004DA7F7 R.dll:...

...in "hdf5.c" [9] do_hdf5save(args = 0x9723284), line 1104 in "hdf5.c" [10] do_External(call = 0x86d62bc, op = 0x8371cd8, args = 0x972340c, env = 0x9723594), line 832 in "dotcode.c" [11] Rf_eval(e = 0x86d62bc, rho = 0x9723594), line 445 in "eval.c" [12] Rf_evalList(el = 0x86d6230, rho = 0x9723594, op = 0x837226c), line 1463 in "eval.c" [13] Rf_eval(e = 0x86d6214, rho = 0x9723594), line 438 in "eval.c" [14] do_begin(call = 0x86d56bc, op = 0x836709c, args = 0x86d61dc, rho = 0x9723594), line 1107 in "eval.c" [15] Rf_eval(e = 0...

...shing. code can be found at the end of the email. Much thanks for your time Regards Saptarshi BT OUTPUT: #0 0x00002b499ca40a6e in R_gc_internal (size_needed=0) at memory.c:1309 #1 0x00002b499ca42bc0 in Rf_cons (car=0x484ba98, cdr=0x484ba98) at memory.c:1766 #2 0x00002b499ca1e39d in Rf_evalList (el=0x4cd0f30, rho=0x488ca48, op=0x5077148) at eval.c:1489 #3 0x00002b499ca1de4d in Rf_eval (e=0x4cd1010, rho=0x488ca48) at eval.c:480 #4 0x00002b499ca1ea82 in do_begin (call=0x4cd1048, op=0x486a830, args=0x4cd1080, rho=0x488ca48) at eval.c:1174 #5 0x00002b499ca1dda6 in Rf_eval (e=0x4cd104...

...0x8954ae0, rho=0x9208338) at eval.c:453 ---Type <return> to continue, or q <return> to quit--- #16 0x080a5685 in do_set (call=0x8954a8c, op=0x9208338, args=0x8954aa8, rho=0x9208338) at eval.c:1283 #17 0x080a3b28 in Rf_eval (e=0x8954a8c, rho=0x9208338) at eval.c:418 #18 0x080a586b in Rf_evalList (el=0x8954a1c, rho=0x9208338) at eval.c:1372 #19 0x080a3a50 in Rf_eval (e=0x8954a00, rho=0x9208338) at eval.c:439 #20 0x080a5685 in do_set (call=0x89549ac, op=0x9208338, args=0x89549c8, rho=0x9208338) at eval.c:1283 #21 0x080a3b28 in Rf_eval (e=0x89549ac, rho=0x9208338) at eval.c:418 #22 0x080a...

...usr/lib64/valgrind/vgpreload_memcheck-amd64-linux.so) ==14875== by 0x4EB0282: con_destroy (connections.c:3086) ==14875== by 0x4EB03B3: do_close (connections.c:3105) ==14875== by 0x4F795E4: do_internal (names.c:1236) ==14875== by 0x4F15F63: Rf_eval (eval.c:471) ==14875== by 0x4F19D7F: Rf_evalList (eval.c:1840) == A little more revealing, with two surprises noted, is > f <- tempdir() > a <- .A$new(con=file(f, "rb")) > close(a$con) > a <- .A$new(con=file(f, "rb")) > gc() ## run finalizer -- should complain about invalid connection!...

...5) ==13521== by 0x44A703: con_close1 (connections.c:2256) ==13521== by 0x44A742: con_close (connections.c:2283) ==13521== by 0x44D3A3: do_close (connections.c:2303) ==13521== by 0x4C43BB: do_internal (names.c:1089) ==13521== by 0x4978F5: Rf_eval (eval.c:398) ==13521== by 0x497F0D: Rf_evalList (eval.c:1400) > invisible(options(echo = TRUE)) > > foo <- 2 > save(foo, file = "foo.Rdata") > > > proc.time() [1] 22.509 0.216 21.774 0.004 0.004 > ==13521== ==13521== ERROR SUMMARY: 9 errors from 1 contexts (suppressed: 12 from 1) ==13521== malloc/fr...

...76e6c Rf_eval + 1020 2 libR.dylib 0x03677108 Rf_eval + 1688 3 libR.dylib 0x03676e6c Rf_eval + 1020 4 libR.dylib 0x03677108 Rf_eval + 1688 5 libR.dylib 0x03676e6c Rf_eval + 1020 6 libR.dylib 0x03677108 Rf_eval + 1688 7 libR.dylib 0x03678144 Rf_evalList + 148 8 libR.dylib 0x036bb5cc do_internal + 796 9 libR.dylib 0x03676fbc Rf_eval + 1356 10 libR.dylib 0x0367ad10 Rf_applyClosure + 1120 11 libR.dylib 0x03676e3c Rf_eval + 972 12 libR.dylib 0x0367ad10 Rf_applyClosure + 1120 13 libR.dylib 0x03676...

...76e6c Rf_eval + 1020 2 libR.dylib 0x03677108 Rf_eval + 1688 3 libR.dylib 0x03676e6c Rf_eval + 1020 4 libR.dylib 0x03677108 Rf_eval + 1688 5 libR.dylib 0x03676e6c Rf_eval + 1020 6 libR.dylib 0x03677108 Rf_eval + 1688 7 libR.dylib 0x03678144 Rf_evalList + 148 8 libR.dylib 0x036bb5cc do_internal + 796 9 libR.dylib 0x03676fbc Rf_eval + 1356 10 libR.dylib 0x0367ad10 Rf_applyClosure + 1120 11 libR.dylib 0x03676e3c Rf_eval + 972 12 libR.dylib 0x0367ad10 Rf_applyClosure + 1120 13 libR.dylib 0x03676...

...R.dll:0050C059 do_standardGeneric 004DA35F R.dll:004DA35F Rf_eval 004DA0F6 R.dll:004DA0F6 Rf_eval 004DA03E R.dll:004DA03E Rf_eval 004DA0F6 R.dll:004DA0F6 Rf_eval 004DA03E R.dll:004DA03E Rf_eval 004DA0F6 R.dll:004DA0F6 Rf_eval 004DA03E R.dll:004DA03E Rf_eval 004DC4BB R.dll:004DC4BB Rf_evalList 004DA2F0 R.dll:004DA2F0 Rf_eval 004DD2F3 R.dll:004DD2F3 Rf_DispatchOrEval 0056941B R.dll:0056941B do_subset2 004DA3C8 R.dll:004DA3C8 Rf_eval 004DA6B5 R.dll:004DA6B5 Rf_applyClosure 004DA1D7 R.dll:004DA1D7 Rf_eval 004DC2D5 R.dll:004DC2D5 do_set 004DA3C8 R.dll:004DA3C8 Rf_eval 004DBA5...

...inue, or q <return> to quit--- #16 0x080a3b27 in Rf_eval (e=0x8955188, rho=0x94f57b0) at eval.c:453 #17 0x080a5895 in do_set (call=0x8955134, op=0x94f57b0, args=0x8955150, rho=0x94f57b0) at eval.c:1283 #18 0x080a3d18 in Rf_eval (e=0x8955134, rho=0x94f57b0) at eval.c:418 #19 0x080a5a7b in Rf_evalList (el=0x89550c4, rho=0x94f57b0) at eval.c:1372 #20 0x080a3c40 in Rf_eval (e=0x89550a8, rho=0x94f57b0) at eval.c:439 #21 0x080a5895 in do_set (call=0x8955054, op=0x94f57b0, args=0x8955070, rho=0x94f57b0) at eval.c:1283 #22 0x080a3d18 in Rf_eval (e=0x8955054, rho=0x94f57b0) at eval.c:418 #23 0x080...

...401 #6 0x080a3b28 in Rf_eval (e=0x82c5d28, rho=0x8f1ecd4) at eval.c:418 #7 0x080a3db2 in Rf_applyClosure (call=0x8324ff0, op=0x82c5c48, arglist=0x8d05e80, rho=0x8f385f0, suppliedenv=0x81f65a0) at eval.c:609 #8 0x080a3937 in Rf_eval (e=0x8324ff0, rho=0x8f385f0) at eval.c:453 #9 0x080a586b in Rf_evalList (el=0x8324f9c, rho=0x8f385f0) at eval.c:1372 #10 0x080c9a3c in do_internal (call=0x8324ef4, op=0x81fb5c8, args=0x832515c, env=0x8f385f0) at names.c:1053 #11 0x080a3b28 in Rf_eval (e=0x8324ef4, rho=0x8f385f0) at eval.c:418 #12 0x080a3db2 in Rf_applyClosure (call=0x878ef30, op=0x8324e14, argl...

...b75aac) at objects.c:325 #17 0x56aa0 in Rf_eval (e=0x430e4c, rho=0xb75aac) at eval.c:317 #18 0x570bc in Rf_applyClosure (call=0x3db454, op=0x31df48, arglist=0xb750c0, rho=0xb792e4, suppliedenv=0x1b2868) at eval.c:501 #19 0x56ccc in Rf_eval (e=0x3db454, rho=0xb792e4) at eval.c:352 #20 0x58530 in Rf_evalList (el=0x3db4e0, rho=0xb792e4) at eval.c:1087 #21 0x56bd0 in Rf_eval (e=0x3db550, rho=0xb792e4) at eval.c:338 ---Type <return> to continue, or q <return> to quit--- #22 0x57c8c in do_begin (call=0x3db56c, op=0x1c37c4, args=0x3db588, rho=0xb792e4) at eval.c:803 #23 0x56aa0 in Rf_eval (e...

...nal # 0047F494 R.DLL:0047F494 Rf_eval # 00480808 R.DLL:00480808 do_begin # 0047F494 R.DLL:0047F494 Rf_eval # 0047FAA6 R.DLL:0047FAA6 Rf_applyClosure # 0047F6DD R.DLL:0047F6DD Rf_eval # 00481065 R.DLL:00481065 do_set # 0047F494 R.DLL:0047F494 Rf_eval # 004812D9 R.DLL:004812D9 Rf_evalList # 0047F5E2 R.DLL:0047F5E2 Rf_eval # 00481065 R.DLL:00481065 do_set # 0047F494 R.DLL:0047F494 Rf_eval # 00480808 R.DLL:00480808 do_begin # 0047F494 R.DLL:0047F494 Rf_eval # 0047FAA6 R.DLL:0047FAA6 Rf_applyClosure # 0047F6DD R.DLL:0047F6DD Rf_eval # 0049D325 R.DLL:0049D325 R_P...

...a62c8 forcePromise + 184 29 libR.dylib 0x003a12c8 Rf_eval + 712 30 libR.dylib 0x003a1650 Rf_eval + 1616 31 libR.dylib 0x003a62c8 forcePromise + 184 32 libR.dylib 0x003a12c8 Rf_eval + 712 33 libR.dylib 0x003a1650 Rf_eval + 1616 34 libR.dylib 0x003a2488 Rf_evalList + 168 35 libR.dylib 0x003a15a8 Rf_eval + 1448 36 libR.dylib 0x003a45f4 do_set + 980 37 libR.dylib 0x003a14dc Rf_eval + 1244 38 libR.dylib 0x003a2b08 do_begin + 104 39 libR.dylib 0x003a14dc Rf_eval + 1244 40 libR.dylib 0x003a4f58 Rf_applyClosure + 728...