Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-10-07

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All times shown according to UTC.

Time Nick Message
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09:06 kai whoa
09:07 kai there's also hmmer3 files _with_ a secondary structure predicion?
09:07 kai damn
09:08 kai ah, and it's possible to have them or not have them, in the same file
09:08 kai bliss
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10:53 CIA-95 bioperl-live: Kai Blin master * r7a0b851 / (3 files in 3 dirs):
10:53 CIA-95 bioperl-live: Bio::SearchIO::hmmer3: Deal with possible model track
10:53 CIA-95 bioperl-live: Some hmmer3 result files have a line giving a secondary structure model.
10:53 CIA-95 bioperl-live: Deal with these results while not breaking the existing files. - http://bit.ly/b6IO3L
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11:33 kai man
11:33 kai yet another one
11:33 kai production use sucks
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12:12 CIA-95 bioperl-live: Kai Blin master * rf642bfa / (3 files in 3 dirs):
12:12 CIA-95 bioperl-live: Bio::SearchIO::hmmer3: Model file indicator is at end of line
12:12 CIA-95 bioperl-live: Forgot a $ in the regext for the secondary structure mode line detection
12:12 CIA-95 bioperl-live: regex, so that regex misdetected alignments containing Cys-Ser AAs.
12:12 CIA-95 bioperl-live: Add a test case, fix the bug. - http://bit.ly/cLWUX2
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14:00 qwebirc490160 Hi
14:01 qwebirc490160 New to BioPerl, got a few question regarding the filehandling of Seq::IO
14:02 kai sure
14:03 qwebirc490160 thanks, I been getting the error Too many open files. which i assume that seqio opens the file handle during parsing and are not closing them
14:03 qwebirc490160 i could really find any doc on how to close those filehandles that are opened
14:03 qwebirc490160 couldn't
14:04 kai uhm
14:04 kai good question.. :)
14:05 qwebirc490160 i read on cpan man page on seqio, and it says Other operations, such as read(), sysread(), write(), close(), and printf() are not supported.
14:06 kai that's just for the newFh constructor for all I can see
14:12 kai Bio::SeqIO->close() should close the stream
14:12 kai try using that
14:13 kai do you know the deobfuscator at http://bioperl.org/cgi-bin/deob_interface.cgi
14:15 Guest24220 anyone installed Bio::DB::BigWig on x86_64?
14:17 Guest24220 its giveing me pain
14:17 Guest24220 http://bioperl.pastebin.com/y2htHzCq
14:18 Guest24220 gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -o blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o /homes/www-potato/build/src/​kent/src/lib/x86_64/jkweb.a -lz
14:18 Guest24220 /usr/bin/ld: /homes/www-potato/build/src/kent/s​rc/lib/x86_64/jkweb.a(bbiRead.o): relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC
14:21 qwebirc490160 thanks kai, i am gona try it out, maybe this should be added to the doc
14:22 Guest24220 qwebirc490160: what are you doing that opens so many files in the same scope?
14:23 kai Guest24220: some systems have ridiculously low limits
14:23 Guest24220 ic
14:24 Guest24220 I'm trying to get GBrowse running off a Bio::DB::BigWig adaptor, but I can't install Bio::DB::BigWig!
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14:30 kai hey pyrimidine
14:31 Guest24220 yello
14:32 kai pyrimidine: I rolled out my hmmer3 parser in our production system and my stupid users went and found bugs
14:32 kai sorry for the churn
14:38 Guest24220 in Bio::BigFile, what is the correct way to "recompile with -fPIC"?
14:38 Guest24220 I should edit Build.PL right?
14:39 Guest24220 I can't see the appropriate place for CFLaGS
14:47 Guest24220 [www-potato@ge-002 Bio-BigFile-1.03-9Q6V9I]$ diff Build.PL~ Build.PL
14:47 Guest24220 19c19
14:47 Guest24220 <     extra_linker_flags => ["$jk_lib/$LibFile",'-lz'],
14:47 Guest24220 ---
14:47 Guest24220 >     extra_linker_flags => ["$jk_lib/$LibFile",'-lz','--cflags=-fPIC'],
14:48 Guest24220 gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -o blib/arch/auto/Bio/DB/BigFile/BigFile.so lib/Bio/DB/BigFile.o /homes/www-potato/build/src/​kent/src/lib/x86_64/jkweb.a -lz --cflags=-fPIC
14:48 Guest24220 recompile with -fPIC
14:49 Guest24220 does this mean that the jk stuff need -fPIC?
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15:03 Guest24220 yes it does
15:03 Guest24220 now I just need to get this bigwig workign!
15:07 kai qwebirc490160: on SearchIO, close seems to close the writing filehandle
15:09 kai qwebirc490160: you could try and instead of passing a filename to Bio::SearchIO, do the open yourself, pass the filehandle, and once you're done do the close yourself as well
15:12 kai qwebirc490160: ah, my bad, I think SearchIO->close() is calling Root::IO->close()
15:12 kai which closes the filehandle, for all I can see
15:12 kai so simply calling close() on your searchio object should be sufficient
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17:47 rbuels pyrimidine: want to go to the Google-sponsored giant party, um, i mean the mentor summit?
17:53 pyrimidine rbuels: wish I could, but I'm already going to the GMOD Hackathon, and it's hard to go anywhere at the moment with a wife and newborn at home
17:53 pyrimidine I think she might kill me if I raise it
17:54 rbuels haha
17:54 pyrimidine :)
17:55 pyrimidine did anyone else from OBF want to go?
17:55 rbuels pyrimidine: haven't heard from anybody
17:55 rbuels pyrimidine: you saw the email to the mentors list right?
17:55 pyrimidine rbuels: yes
17:55 rbuels good, i'm glad it actually went out
17:57 pyrimidine might be worth asking some specific mentors directly, or even someone from OBF not with GSoC (if google allows it)
17:58 rbuels hmmm
17:59 rbuels pyrimidine: can you think of anybody i should ask directly?
17:59 pyrimidine ask deafferret, he'd be a lot of fun
17:59 pyrimidine :)
18:00 pyrimidine mode #bioperl +o rbuels
18:00 pyrimidine gah
18:00 pyrimidine mode #bioperl +o deafferret
18:00 pyrimidine heh
18:01 * pyrimidine having problems with forward slashes today...
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18:01 rbuels wasn't deafferret a backup mentor for something?
18:02 pyrimidine I think that was mark jensen
18:02 * rbuels bets google will actually check that people were mentors
18:03 pyrimidine just make sure we pick someone who represents OBF well (eg no mouthbreathers)
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18:04 pyrimidine jesus, Ubuntu 10.10 is 3 days away ?!?  I just upgraded to 10.4...
18:05 * rbuels is still on ... something old
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18:06 rbuels jaunty ... what's that
18:06 pyrimidine 10.10 will be maverick meerkat
18:06 pyrimidine looks like 11.04 will be natty narwhal
18:09 pyrimidine at least 10.04 is LTS, so I won't upgrade for a while
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18:18 kblin so, am I going to meet one of you crazy people on the mentor summit? :)
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18:43 rbuels kblin: i'll be there
18:43 rbuels kblin: and andreas prlic looks like he will be there too
18:48 kblin great, looking forward to that then :)
18:50 kblin I've stumbled over andreas' name before..
18:50 kblin probably on last year's summit
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