WARNING: the argument --multi-file is deprecated. This is not fatal, as GenProg can handle certain deprecated options as of the March 2012 refactor.
However, you may want to consult the GenProg documentation to avoid using 
deprecated options in the future, and verify that your config is doing what you
think it is doing.WARNING: the argument --suffix-extension is deprecated. This is not fatal, as GenProg can handle certain deprecated options as of the March 2012 refactor.
However, you may want to consult the GenProg documentation to avoid using 
deprecated options in the future, and verify that your config is doing what you
think it is doing.--allow-coverage-fail false
--appp 0.5
--asm-code-only false
--best-edit-rule "1 * fault_loc_weight ; 1 * max_test_fail_prob ; -1 * num_tests"
--best-test-rule "1 * test_fail_prob ; 1 * test_fail_count ; -1 * test_pass_count"
--compiler "gcc"
--compiler-command "perl compile.pl __EXE_NAME__ > /dev/null"
--compiler-opts ""
--continue false
--coverage-info ""
--coverage-per-test false
--crossover "one"
--crossp 0.5
--delp 0.85
--describe-machine true
--diversity-selection 0
--edit-script false
--elf-risc false
--exclude-edits ""
--exp-diff false
--fault-file ""
--fault-path "coverage.path.neg"
--fault-scheme "path"
--fitness-in-parallel 1
--fix-file ""
--fix-oracle ""
--fix-path "coverage.path.pos"
--fix-scheme "default"
--flatten-path ""
--format "txt"
--gen-per-exchange 1
--generations 10
--gui false
--hostname "127.0.0.1"
--ignore-dead-code false
--ignore-equiv-appends false
--ignore-standard-headers false
--ignore-string-equiv-fixes false
--ignore-untyped-returns false
--incoming-pop ""
--keep-source false
--label-repair false
--max-evals 0
--minimization false
--mt-cov false
--multiopt-minimize false
--multiopt-no-inf false
--neg-tests 3
--neg-weight 0.35
--negative-test-weight 2
--neutral-walk-max-size 0
--neutral-walk-weight ""
--nht-id "global"
--nht-port 51000
--nht-server ""
--no-rep-cache false
--no-test-cache false
--num-comps 2
--num-objectives 2
--oracle-genome ""
--popsize 40
--port 60000
--pos-tests 7805
--pos-weight 0.65
--prefix "preprocessed"
--preprocessor ""
--print-incremental-evals false
--print-source-name false
--program "bugged-program.txt"
--promut 1
--quiet false
--regen-paths false
--rep "cilpatch"
--rep-cache "default.cache"
--repp 0.75
--samp-strat "variant"
--sample 0.1
--sample-runs 100
--sanity "no"
--search "ga"
--seed 2
--semantic-check "scope"
--single-fitness false
--skip-failed-sanity-tests false
--skip-tests ""
--split-search 0
--sport 65000
--subatom-constp 0.5
--subatom-mutp 0
--super-mutant false
--super-mutant-size 50
--swap-bug false
--swapp 0
--template-cache ""
--templates ""
--test-command "__TEST_SCRIPT__ __TEST_NAME__ __EXE_NAME__ >& /dev/null"
--test-script "./test.sh"
--tournament-size 2
--tweet false
--uniq false
--valgrind false
--variants-exchanged 50
uname -a: Linux ip-172-31-47-240 2.6.34.7-61.fc13.i686.PAE #1 SMP Tue Oct 19 04:24:06 UTC 2010 i686 i686 i386 GNU/Linux
date: Tue Jun 21 10:27:42 EDT 2016
id: uid=0(root) gid=0(root) groups=0(root),1(bin),2(daemon),3(sys),4(adm),6(disk),10(wheel) context=system_u:system_r:kernel_t:s0
cat /etc/redhat-release: Fedora release 13 (Goddard)
grep 'model name' /proc/cpuinfo: model name	: Intel(R) Xeon(R) CPU E5-2651 v2 @ 1.80GHz
grep 'MemTotal' /proc/meminfo: MemTotal:        1747596 kB
grep 'SwapTotal' /proc/meminfo: SwapTotal:             0 kB
cilRep: preprocessing IO function signatures: /tmp/tmpacc102.c /tmp/tmpb7ad21.c
cilRep: done preprocessing IO function signatures
faultLocRep: compute_localization: fault_scheme: path, fix_scheme: default
cachingRep: default.cache: loaded
faultlocRep: default.cache: loaded
cilRep: default.cache: loaded
cilRep: default.cache: saved
cachingRep: default.cache: saved
faultlocRep: default.cache: saved
cilrep done serialize
cilRep: stmt_count = 3226
cilRep: stmts in weighted_path = 243
cilRep: total weight = 157.95
cilRep: stmts in weighted_path with weight >= 1.0 = 0
cilRep: Zend/zend_builtin_functions.c (code bank/base file; atoms [1,3226])
cilRep: 1 file(s) total in representation
search: genetic algorithm begins (|original| = 0.0201931 MB)
search: initial population (sizeof one variant = 0.0207396 MB)
	779 d(1507) 
	780 d(1675) 
	780 d(2331) 
	777 r(1534,1527) 
	780 d(1354) 
	752 r(1654,1605) 
	766 d(1594) 
	/root/genprog-many-bugs/php-bug-2011-11-08-c3e56a152c-3598185a74/000007/Zend/zend_builtin_functions.c  r(2334,2835)  fails to compile
	  0 r(2334,2835) 
	757 d(1595) 
	749 d(1595) 
	778 d(1508) 
	780 r(2328,2325) 
	780 a(2321,1820) 
	23415 r(3179,3176) 

Repair Found: r(3179,3176)
Repair Name: r(3179,3176) 
Test Condition: 0
Test Cases Skipped: ""
Current Time: 1466521578.359659
Rep: saving test cache

Variant Test Case Queries: 17916
"Test Suite Evaluations": 2.29457

Compile Failures: 1
Wall-Clock Seconds Elapsed: 2315.99
  Activity Name                     Count Seconds = Percent of Total Time
  compile                              13 324.951 = 14.8375%
  test                               9325 1865.104 = 85.162%
  TOTAL                                   2190.065 = 94.5626% (avg CPU usage)
php-bug-2011-11-08-c3e56a152c-3598185a74.tar.gz
Tue Jun 21 11:06:19 EDT 2016
shutting down
