So, we're actually changing the code submission requirement for the mid-term to a requirement that you fill out a survey instead - we haven't had the resources to implement the infrastructure we wanted to have in place before you submitted your code to us.
I'll also make a post about this to the announcement list, but:
1) No student mid-term code submission.
2) Students need to take a survey instead.
3) Instructions for completing the survey will be sent to the program
announcement list.
4) You will be able to complete the survey between July 9 - July 16th.
I'll also update the FAQ in the next few days.
Cheers,
LH
execve("/usr/local/bin/perl", ["perl", "-le", "phylotest.pl"], [/* 41 vars */]) = 0
uname({sys="Linux", node="JamieHidThis", ...}) = 0
brk(0) = 0x9643000
open("/etc/ld.so.preload", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/tls/i686/mmx/libperl.so", O_RDONLY) = -1 ENOENT (No such file or directory)
stat64("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/tls/i686/mmx", 0xbfffa1a0) = -1 ENOENT (No such file or directory)
open("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/tls/i686/libperl.so", O_RDONLY) = -1 ENOENT (No such file or directory)
stat64("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/tls/i686", 0xbfffa1a0) = -1 ENOENT (No such file or directory)
open("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/tls/mmx/libperl.so", O_RDONLY) = -1 ENOENT (No such file or directory)
stat64("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/tls/mmx", 0xbfffa1a0) = -1 ENOENT (No such file or directory)
open("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/tls/libperl.so", O_RDONLY) = -1 ENOENT (No such file or directory)
stat64("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/tls", 0xbfffa1a0) = -1 ENOENT (No such file or directory)
open("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/i686/mmx/libperl.so", O_RDONLY) = -1 ENOENT (No such file or directory)
stat64("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/i686/mmx", 0xbfffa1a0) = -1 ENOENT (No such file or directory)
open("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/i686/libperl.so", O_RDONLY) = -1 ENOENT (No such file or directory)
stat64("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/i686", 0xbfffa1a0) = -1 ENOENT (No such file or directory)
open("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/mmx/libperl.so", O_RDONLY) = -1 ENOENT (No such file or directory)
stat64("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/mmx", 0xbfffa1a0) = -1 ENOENT (No such file or directory)
open("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/libperl.so", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0@\10\2\000"..., 512) = 512
fstat64(3, {st_mode=S_IFREG|0555, st_size=1194580, ...}) = 0
old_mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xb75f8000
old_mmap(NULL, 1205760, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) = 0x944000
old_mmap(0xa5e000, 45056, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED, 3, 0x119000) = 0xa5e000
old_mmap(0xa69000, 5632, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0xa69000
close(3) = 0
open("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/libnsl.so.1", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/etc/ld.so.cache", O_RDONLY) = 3
fstat64(3, {st_mode=S_IFREG|0644, st_size=80436, ...}) = 0
old_mmap(NULL, 80436, PROT_READ, MAP_PRIVATE, 3, 0) = 0xb75e4000
close(3) = 0
open("/lib/libnsl.so.1", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0 <\0\000"..., 512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=87563, ...}) = 0
old_mmap(NULL, 80480, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) = 0xc5b000
old_mmap(0xc6c000, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED, 3, 0x11000) = 0xc6c000
old_mmap(0xc6d000, 6752, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0xc6d000
close(3) = 0
open("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/libdl.so.2", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/lib/libdl.so.2", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0\260\32"..., 512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=13601, ...}) = 0
old_mmap(NULL, 12244, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) = 0x907000
old_mmap(0x909000, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED, 3, 0x1000) = 0x909000
close(3) = 0
open("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/libm.so.6", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/lib/tls/libm.so.6", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0\3604\0"..., 512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=185942, ...}) = 0
old_mmap(NULL, 135616, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) = 0xee2000
old_mmap(0xf03000, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED, 3, 0x21000) = 0xf03000
close(3) = 0
open("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/libpthread.so.0", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/lib/tls/libpthread.so.0", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0\0G\0\000"..., 512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=86486, ...}) = 0
old_mmap(NULL, 65140, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) = 0x33d000
old_mmap(0x34a000, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED, 3, 0xc000) = 0x34a000
old_mmap(0x34b000, 7796, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x34b000
close(3) = 0
open("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/libc.so.6", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/lib/tls/libc.so.6", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0\200X\1"..., 512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=1516255, ...}) = 0
old_mmap(NULL, 1279980, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) = 0x15c000
old_mmap(0x28f000, 12288, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED, 3, 0x132000) = 0x28f000
old_mmap(0x292000, 10220, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x292000
close(3) = 0
open("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/libcrypt.so.1", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/lib/libcrypt.so.1", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0\220\t\0"..., 512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=22242, ...}) = 0
old_mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xb75e3000
old_mmap(NULL, 181308, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) = 0x111000
old_mmap(0x116000, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED, 3, 0x4000) = 0x116000
old_mmap(0x117000, 156732, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x117000
close(3) = 0
open("/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE/libutil.so.1", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/lib/libutil.so.1", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0000\16\0"..., 512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=11375, ...}) = 0
old_mmap(NULL, 11012, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) = 0xabf000
old_mmap(0xac1000, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED, 3, 0x1000) = 0xac1000
close(3) = 0
old_mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xb75e2000
set_thread_area({entry_number:-1 -> 6, base_addr:0xb75e2080, limit:1048575, seg_32bit:1, contents:0, read_exec_only:0, limit_in_pages:1, seg_not_present:0, useable:1}) = 0
munmap(0xb75e4000, 80436) = 0
set_tid_address(0xb75e20c8) = 20752
rt_sigaction(SIGRTMIN, {0x341660, [], SA_RESTORER|SA_SIGINFO, 0x347f80}, NULL, 8) = 0rt_sigprocmask(SIG_UNBLOCK, [RTMIN], NULL, 8) = 0
getrlimit(RLIMIT_STACK, {rlim_cur=10240*1024, rlim_max=RLIM_INFINITY}) = 0
rt_sigaction(SIGFPE, {SIG_IGN}, {SIG_DFL}, 8) = 0
brk(0) = 0x9643000
brk(0x9664000) = 0x9664000
brk(0) = 0x9664000
getuid32() = 507
geteuid32() = 507
getgid32() = 507
getegid32() = 507
open("/usr/lib/locale/locale-archive", O_RDONLY|O_LARGEFILE) = 3
fstat64(3, {st_mode=S_IFREG|0644, st_size=32148976, ...}) = 0
mmap2(NULL, 2097152, PROT_READ, MAP_PRIVATE, 3, 0) = 0xb73e2000
close(3) = 0
mmap2(NULL, 135168, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xb73c1000
time([1182268075]) = 1182268075
stat64("/home/jestill/src/bioperl/bioperl-live/5.8.0/i386-linux-thread-multi", 0xbfffa800) = -1 ENOENT (No such file or directory)
stat64("/home/jestill/src/bioperl/bioperl-live/5.8.0", 0xbfffa800) = -1 ENOENT (No such file or directory)
stat64("/home/jestill/src/bioperl/bioperl-live/i386-linux-thread-multi", 0xbfffa800) = -1 ENOENT (No such file or directory)
stat64("/usr/lib/perl5/5.8.0/5.8.0/i386-linux-thread-multi", 0xbfffa800) = -1 ENOENT (No such file or directory)
stat64("/usr/lib/perl5/5.8.0/5.8.0", 0xbfffa800) = -1 ENOENT (No such file or directory)
stat64("/usr/lib/perl5/5.8.0/i386-linux-thread-multi", {st_mode=S_IFDIR|0755, st_size=8192, ...}) = 0
ioctl(0, SNDCTL_TMR_TIMEBASE or TCGETS, {B38400 opost isig icanon echo ...}) = 0
_llseek(0, 0, 0xbfffa5f0, SEEK_CUR) = -1 ESPIPE (Illegal seek)
ioctl(1, SNDCTL_TMR_TIMEBASE or TCGETS, {B38400 opost isig icanon echo ...}) = 0
_llseek(1, 0, 0xbfffa5f0, SEEK_CUR) = -1 ESPIPE (Illegal seek)
ioctl(2, SNDCTL_TMR_TIMEBASE or TCGETS, {B38400 opost isig icanon echo ...}) = 0
_llseek(2, 0, 0xbfffa5f0, SEEK_CUR) = -1 ESPIPE (Illegal seek)
open("/dev/null", O_RDONLY|O_LARGEFILE) = 3
ioctl(3, SNDCTL_TMR_TIMEBASE or TCGETS, 0xbfffa688) = -1 ENOTTY (Inappropriate ioctl for device)
_llseek(3, 0, [0], SEEK_CUR) = 0
fcntl64(3, F_SETFD, FD_CLOEXEC) = 0
fstat64(3, {st_mode=S_IFCHR|0666, st_rdev=makedev(1, 3), ...}) = 0
rt_sigaction(SIGCHLD, NULL, {SIG_DFL}, 8) = 0
readlink("/proc/self/exe", "/usr/bin/perl", 4095) = 13
getpid() = 20752
getppid() = 20751
close(3) = 0
exit_group(0) = ?
Process 20752 detached
$ perl -MBio::Perl -le 'print Bio::Perl->VERSION;'
$dbh->do("SET FOREIGN_KEY_CHECKS=0");
#UPDATE tree TABLE HERE
$dbh->do("SET FOREIGN_KEY_CHECKS=1");to deal with this in MySQL.I am now trying to see if this will fix the problem without introducing new errors.
unless ($dbh->{AutoCommit}) {
$dbh->commit;
}
is_rooted ENUM ('FALSE', 'TRUE') DEFAULT 'TRUE'in the tree table.ALTER TABLE tree ADD CONSTRAINT FKNode
FOREIGN KEY (node_id) REFERENCES node (node_id);is giving the error:Both tables must be InnoDB tables and they must not be TEMPORARY tables.
All of my tables are now InnoDB tables so this is not the problem.
Corresponding columns in the foreign key and the referenced key must have similar internal data types inside InnoDB so that they can be compared without a type conversion. The size and sign of integer types must be the same. The length of string types need not be the same. For non-binary (character) string columns, the character set and collation must be the same.
Both columns in the broken SQL are INT(11) so this is probably not the problem.
In the referencing table, there must be an index where the foreign key columns are listed as the first columns in the same order. Such an index is created on the referencing table automatically if it does not exist.
This is it, adding indexes to the tables fixed the problem.
In the referenced table, there must be an index where the referenced columns are listed as the first columns in the same order.
This is it, adding indexes to the tables fixed the problem.
Index prefixes on foreign key columns are not supported. One consequence of this is that BLOB and TEXT columns cannot be included in a foreign key, because indexes on those columns must always include a prefix length.
This is not the problem since the columns are INT(11).
If the CONSTRAINT symbol clause is given, the symbol value must be unique in the database. If the clause is not given, InnoDB creates the name automatically.
This is not the problem since FKnode is a unique value in the database. As a test, I ran the SQL without specifying the symbol, and I still have the error.
$dbh->commit();is currently causing fatal errors with the message
commit ineffective with AutoCommit enabled at ./parseTreesPG.pl line 736According to the documentation, this error message occurs when AutoCommit is off, or when transactions are not supported by the system you are using.
CREATE TABLE tree (
tree_id INTEGER NOT NULL auto_increment,
name VARCHAR(32) NOT NULL,
identifier VARCHAR(16),
node_id INTEGER NOT NULL
, PRIMARY KEY (tree_id)
, UNIQUE (name)
,
)TYPE=INNODB;