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  • Parsing line with delimiter in Python

    - by neversaint
    I have lines of data which I want to parse. The data looks like this: a score=216 expect=1.05e-06 a score=180 expect=0.0394 What I want to do is to have a subroutine that parse them and return 2 values (score and expect) for each line. However this function of mine doesn't seem to work: def scoreEvalFromMaf(mafLines): for word in mafLines[0]: if word.startswith("score="): theScore = word.split('=')[1] theEval = word.split('=')[2] return [theScore, theEval] raise Exception("encountered an alignment without a score") Please advice what's the right way to do it?

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  • What is the recommended way to package perl scripts for CPAN (and CorporatePAN)?

    - by szabgab
    Recently I looked at a module on CPAN that comes with a script to be installed which made me wonder. What is the recommended way to include a script in a package that should end up on the public CPAN and if there is any different recommendation for packages that would be released on an in-house CPAN server? The script starts like this: #!/usr/bin/perl eval 'exec /usr/bin/perl -S $0 ${1+"$@"}' if 0; # not running under some shell Two questions Do I understand correctly the eval part is unnecessary? That will be embedded by the CPAN client during installation and it will be very different when installing on Windows. What is the recommended sh-bang line? Would that be #!/usr/bin/env perl instead of the above?

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  • compare time using date command

    - by Andrei
    Say I want a certain block of bash script execute only if it is between 8 am (8:00) and 5 pm (17:00), and do nothing otherwise. The script is running continuously So far I am using date command. How to use it compare it current time within the range? Thanks

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  • How to grep lines having specific format.

    - by Nitin
    I have got a file with following format. 1234, 'US', 'IN',...... 324, 'US', 'IN',...... ... ... 53434, 'UK', 'XX', .... ... ... 253, 'IN', 'UP',.... 253, 'IN', 'MH',.... Here I want to extract only those lines having 'IN' as 2nd keyword. i.e. 253, 'IN', 'UP',.... 253, 'IN', 'MH',.... Can any one please tell me a command to grep it.

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  • Binding on a port with netpipes/netcat

    - by mindas
    I am trying to write a simple bash script that is listening on a port and responding with a trivial HTTP response. My specific issue is that I am not sure if the port is available and in case of bind failure I fall back to next port until bind succeeds. So far to me the easiest way to achieve this was something like: for (( i=$PORT_BASE; i < $(($PORT_BASE+$PORT_RANGE)); i++ )) do if [ $DEBUG -eq 1 ] ; then echo trying to bind on $i fi /usr/bin/faucet $i --out --daemon echo test 2>/dev/null if [ $? -eq 0 ] ; then #success? port=$i if [ $DEBUG -eq 1 ] ; then echo "bound on port $port" fi break fi done Here I am using faucet from netpipes Ubuntu package. The problem with this is that if I simply print "test" to the output, curl complains about non-standard HTTP response (error code 18). That's fair enough as I don't print HTTP-compatible response. If I replace echo test with echo -ne "HTTP/1.0 200 OK\r\n\r\ntest", curl still complains: user@server:$ faucet 10020 --out --daemon echo -ne "HTTP/1.0 200 OK\r\n\r\ntest" ... user@client:$ curl ip.of.the.server:10020 curl: (56) Failure when receiving data from the peer I think the problem lies in how faucet is printing the response and handling the connection. For example if I do the server side in netcat, curl works fine: user@server:$ echo -ne "HTTP/1.0 200 OK\r\n\r\ntest\r\n" | nc -l 10020 ... user@client:$ curl ip.of.the.server:10020 test user@client:$ I would be more than happy to replace faucet with netcat in my main script, but the problem is that I want to spawn independent server process to be able to run client from the same base shell. faucet has a very handy --daemon parameter as it forks to background and I can use $? (exit status code) to check if bind succeeded. If I was to use netcat for a similar purpose, I would have to fork it using & and $? would not work. Does anybody know why faucet isn't responding correctly in this particular case and/or can suggest a solution to this problem. I am not married neither to faucet nor netcat but would like the solution to be implemented using bash or it's utilities (as opposed to write something in yet another scripting language, such as Perl or Python).

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  • CVS in cmd/gui works only the third time I run a command.

    - by Somebody still uses you MS-DOS
    I'm using CVS in the command line. I'm in my repository folder. When I call a CVS command, I get... cvs [log aborted]: unrecognized auth response from localhost: -f [pserver aborted]: /opt/cvs/XXXXXX: no such repository ...2 times. The third time I run the command, it works with no problems. I tried to use a GUI client (CrossVC) and the same problem occurs. I tried inside gVim and Vim using VCSCommand and I'm having the same issues as well. I've tested with different times between each command, but I still have the same problems. I'm using a CVS configuration with stunnel. Why am I having problem with this setup? Why every time just the third time that I try to run the command that actually works?

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  • objdump -S - source code listing

    - by anon
    How does objdump manage to display source code? Is there a reference to the source file in the binary? I tried running strings on the binary and couldn't find any reference to the source file listed... Thanks.

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  • Is there a way to find a specific file and then change into the directory containing it in one go?

    - by bergyman
    I'm looking for a way to find what I know will be a unique file, and then change into the directory containing that file. Something along the lines of: find . -name 'Subscription.java' | xargs cd Or: find . -name 'Subscription.java' -exec cd {} \; I know this won't work because it's both trying to cd supplying the entire absolute path, which contains the file, and also because xargs can't do any built in shell commands...but you get the point of what I want to accomplish.

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  • How to implement/debug a sensor driver in ANDROID

    - by CVS-2600Hertz-wordpress-com
    Does anyone know of a walk-through or any examples of any code to setup sensors in android. I have the drivers available to me. Also i have implemented the sensors library as instructed in the Android-Reference along the sensors.h template. I am still unable to get any response at the apps level. How do i trace this issue? what might be the problem? Thanks in advance UPDATE: Jorgesys's link below points to a great APP to test if the sensor drivers are functioning properly or not. Not that i know they are not functioning, Any ideas of on where to dig??...

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  • Getting error that the database is locked when refreshing the page

    - by acidzombie24
    The title is a joke. However it is serious as far as my app is concerned. I am running apache with mod mono and my asp.net app is using mono sqlite as its db. When i refresh the page twice i get the DB is locked error. The folder it is in is chmod 777. The webapp is creating sqlite.db and sqlite.db-journal but it doesnt seem to be able to delete the journal. i'm confused. What permissions do i need to set these? i tried precreating the files using 777 and had no luck.

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  • inode_operations , warning: initialization from incompatible pointer type

    - by djTeller
    Hi everyone, I'm trying to compile a simple Kernel program that read and write from a proc file. I'm trying to set permission to that file by overriding the permission fp in inode_operations struct (.permission) static int module_permission(struct inode *inode, int op, struct nameidata *foo) { . . . } static struct inode_operations Inode_Ops_4_Our_Proc_File = { .permission = module_permission, /* check for permissions */ }; Our_Proc_File->proc_iops = &Inode_Ops_4_Our_Proc_File; For some reason, when I compile this i get - warning: initialization from incompatible pointer type on the following line: .permission = module_permission, /* check for permissions */ Any idea how to solve this? Thanks!

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  • How can I quickly sum all numbers in a file?

    - by Mark Roberts
    I have a file which contains several thousand numbers, each on it's own line: 34 42 11 6 2 99 ... I'm looking to write a script which will print the sum of all numbers in the file. I've got a solution, but it's not very efficient. (It takes several minutes to run.) I'm looking for a more efficient solution. Any suggestions?

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  • Kernel dealing with the section headers in an ELF

    - by uki
    I recently read that the kernel and the dynamic loader mostly deal with the program header tables in an ELF file and that assemblers, compilers and linkers deal with the section header tables. The number of program header tables and section header tables are mentioned in the ELF header in fields named e_phnum and e_shnum respectively. e_phnum is two bytes in size, so if the number of program headers is 65535, we use a scheme known as extended numbering where, e_phnum is set to 0xffff and sh_link field of the zeroth section header table holds the actual count. My doubt is : If the count of program headers exceeds 65535, does that mean the kernel and/or the dynamic loader end up having to read the section table?

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  • Simple POSIX threads question

    - by Andy
    Hi, I have this POSIX thread: void subthread(void) { while(!quit_thread) { // do something ... // don't waste cpu cycles if(!quit_thread) usleep(500); } // free resources ... // tell main thread we're done quit_thread = FALSE; } Now I want to terminate subthread() from my main thread. I've tried the following: quit_thread = TRUE; // wait until subthread() has cleaned its resources while(quit_thread); But it does not work! The while() clause does never exit although my subthread clearly sets quit_thread to FALSE after having freed its resources! If I modify my shutdown code like this: quit_thread = TRUE; // wait until subthread() has cleaned its resources while(quit_thread) usleep(10); Then everything is working fine! Could someone explain to me why the first solution does not work and why the version with usleep(10) suddenly works? I know that this is not a pretty solution. I could use semaphores/signals for this but I'd like to learn something about multithreading, so I'd like to know why my first solution doesn't work. Thanks!

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  • Perl standard input with argument inside Bash

    - by neversaint
    I want to have such pipe in bash #! /usr/bin/bash cut -f1,2 file1.txt | myperl.pl foo | sort -u Now in myperl.pl it has content like this my $argv = $ARG[0] || "foo"; while (<>) { chomp; if ($argv eq "foo") { # do something with $_ } else { # do another } } But why the Perl script can't recognize the parameter passed through bash? Namely the code break with this message: Can't open foo: No such file or directory at myperl.pl line 15. What the right way to do it so that my Perl script can receive standard input and parameter at the same time?

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  • symlink and sudo executable

    - by CodeMedic
    If I have the below sudoers entry usera ALL=(userb) NOPASSWD: /home/userc/bin/executable-file usera ALL=(userb) NOPASSWD: /home/userc/bin/link-to-another-executable-file When I log-on as usera and try running the below commands, it works sudo -u userb /home/userc/bin/executable-file but NOT the one below. sudo -u userb /home/userc/bin/link-to-another-executable-file Sorry, user usera is not allowed to execute '/home/userc/bin/link-to-another-executable-file' as userb on hostname. Any ideas?

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  • Are there any platforms where using structure copy on an fd_set (for select() or pselect()) causes p

    - by Jonathan Leffler
    The select() and pselect() system calls modify their arguments (the 'struct fd_set *' arguments), so the input value tells the system which file descriptors to check and the return values tell the programmer which file descriptors are currently usable. If you are going to call them repeatedly for the same set of file descriptors, you need to ensure that you have a fresh copy of the descriptors for each call. The obvious way to do that is to use a structure copy: struct fd_set ref_set_rd; struct fd_set ref_set_wr; struct fd_set ref_set_er; ... ...code to set the reference fd_set_xx values... ... while (!done) { struct fd_set act_set_rd = ref_set_rd; struct fd_set act_set_wr = ref_set_wr; struct fd_set act_set_er = ref_set_er; int bits_set = select(max_fd, &act_set_rd, &act_set_wr, &act_set_er, &timeout); if (bits_set > 0) { ...process the output values of act_set_xx... } } My question: Are there any platforms where it is not safe to do a structure copy of the struct fd_set values as shown? I'm concerned lest there be hidden memory allocation or anything unexpected like that. (There are macros/functions FD_SET(), FD_CLR(), FD_ZERO() and FD_ISSET() to mask the internals from the application.) I can see that MacOS X (Darwin) is safe; other BSD-based systems are likely to be safe, therefore. You can help by documenting other systems that you know are safe in your answers. (I do have minor concerns about how well the struct fd_set would work with more than 8192 open file descriptors - the default maximum number of open files is only 256, but the maximum number is 'unlimited'. Also, since the structures are 1 KB, the copying code is not dreadfully efficient, but then running through a list of file descriptors to recreate the input mask on each cycle is not necessarily efficient either. Maybe you can't do select() when you have that many file descriptors open, though that is when you are most likely to need the functionality.) There's a related SO question - asking about 'poll() vs select()' which addresses a different set of issues from this question.

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  • measure the response time of a link

    - by Ahoura Ghotbi
    I am trying to create a simple load balance script and I was wondering if it is possible to find the response time of a server live? By that I mean is it possible to measure how long it takes for a server to respond after the request has been sent out? What I am trying to do is fairly simple, I want to send a request to a link/server and do a count down, if the server took more than 5 seconds to reply, I would like to fall on the backup server. Note that it doesnt have to be in pure php, I wouldnt mind using other languages such as javascript, C/C++, asp, but I prefer to do it in PHP. if it is possible to do the task, could you just point me to the right direction so I can read up on it. Clarification What I want to do is not to download a file and see how long it took, my servers have high load and it takes a while for them to respond when you click on a file to download, what I want to do is to measure the time it takes the server to respond (in this situation, its the time it takes the server to respond and allow the user to download the file), and if it takes longer than x seconds, it should fall back on a backup server.

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  • What to do if exec() fails?

    - by Grigory
    Let's suppose we have a code doing something like this: int pipes[2]; pipe(pipes); pid_t p = fork(); if(0 == p) { dup2(pipes[1], STDOUT_FILENO); execv("/path/to/my/program", NULL); ... } else { //... parent process stuff } As you can see, it's creating a pipe, forking and using the pipe to read the child's output (I can't use popen here, because I also need the PID of the child process for other purposes). Question is, what should happen if in the above code, execv fails? Should I call exit() or abort()? As far as I know, those functions close the open file descriptors. Since fork-ed process inherits the parent's file descriptors, does it mean that the file descriptors used by the parent process will become unusable?

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  • Create File Speedily From Individual Column

    - by neversaint
    I have a data that looks like this: -1 1:-0.394668 2:-0.794872 3:-1 4:-0.871341 5:0.9365 6:0.75597 1 1:-0.463641 2:-0.897436 3:-1 4:-0.871341 5:0.44378 6:0.121824 1 1:-0.469432 2:-0.897436 3:-1 4:-0.871341 5:0.32668 6:0.302529 -1 1:-0.241547 2:-0.538462 3:-1 4:-0.871341 5:0.9994 6:0.987166 1 1:-0.757233 2:-0.948718 3:-1 4:-0.871341 5:-0.33904 6:0.915401 1 1:-0.167147 2:-0.589744 3:-1 4:-0.871341 5:0.95078 6:0.991566 The first column is class, and next 6 columns are features. I want to create 6 files for individual features. For example feat1_file.txt will contain -1 1:-0.394668 1 1:-0.463641 ... 1 1:-0.757233 1 1:-0.167147 feat2_file.txt will contain -1 2:-0.794872 ... 1 2:-0.589744 and so on. I have a Perl code that does this but it is horribly slow. Is there a way to do it faster? Typically the input files will contain 100K lines. use strict; use Data::Dumper; use Carp; my $input = $ARGV[0] || "myinput.txt"; my $INFILE_file_name = $input; # input file name open ( INFILE, '<', $INFILE_file_name ) or croak "$0 : failed to open input file $INFILE_file_name : $!\n"; my $out1 = $input."_feat_1.txt"; my $out2 = $input."_feat_2.txt"; my $out3 = $input."_feat_3.txt"; my $out4 = $input."_feat_4.txt"; my $out5 = $input."_feat_5.txt"; my $out6 = $input."_feat_6.txt"; unlink($out1); unlink($out2); unlink($out3); unlink($out4); unlink($out5); unlink($out6); print "$out1\n"; while ( <INFILE> ) { chomp; my @els = split(/\s+/,$_); my $lbl = $els[0]; my $OUTFILE1_file_name = $out1; # output file name open ( OUTFILE1, '>>', $OUTFILE1_file_name ) or croak "$0 : failed to open output file $OUTFILE1_file_name : $!\n"; print OUTFILE1 "$lbl $els[1]\n"; close ( OUTFILE1 ); # close output file my $OUTFILE2_file_name = $out2; # output file name open ( OUTFILE2, '>>', $OUTFILE2_file_name ) or croak "$0 : failed to open output file $OUTFILE2_file_name : $!\n"; print OUTFILE2 "$lbl $els[2]\n"; close ( OUTFILE2 ); # close output file # Etc.. until OUTFILE 6 } close (INFILE);

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  • Dynamic loaded libraries and shared global symbols

    - by phlipsy
    Since I observed some strange behavior of global variables in my dynamically loaded libraries, I wrote the following test. At first we need a statically linked library: The header test.hpp #ifndef __BASE_HPP #define __BASE_HPP #include <iostream> class test { private: int value; public: test(int value) : value(value) { std::cout << "test::test(int) : value = " << value << std::endl; } ~test() { std::cout << "test::~test() : value = " << value << std::endl; } int get_value() const { return value; } void set_value(int new_value) { value = new_value; } }; extern test global_test; #endif // __BASE_HPP and the source test.cpp #include "base.hpp" test global_test = test(1); Then I wrote a dynamically loaded library: library.cpp #include "base.hpp" extern "C" { test* get_global_test() { return &global_test; } } and a client program loading this library: client.cpp #include <iostream> #include <dlfcn.h> #include "base.hpp" typedef test* get_global_test_t(); int main() { global_test.set_value(2); // global_test from libbase.a std::cout << "client: " << global_test.get_value() << std::endl; void* handle = dlopen("./liblibrary.so", RTLD_LAZY); if (handle == NULL) { std::cout << dlerror() << std::endl; return 1; } get_global_test_t* get_global_test = NULL; void* func = dlsym(handle, "get_global_test"); if (func == NULL) { std::cout << dlerror() << std::endl; return 1; } else get_global_test = reinterpret_cast<get_global_test_t*>(func); test* t = get_global_test(); // global_test from liblibrary.so std::cout << "liblibrary.so: " << t->get_value() << std::endl; std::cout << "client: " << global_test.get_value() << std::endl; dlclose(handle); return 0; } Now I compile the statically loaded library with g++ -Wall -g -c base.cpp ar rcs libbase.a base.o the dynamically loaded library g++ -Wall -g -fPIC -shared library.cpp libbase.a -o liblibrary.so and the client g++ -Wall -g -ldl client.cpp libbase.a -o client Now I observe: The client and the dynamically loaded library possess a different version of the variable global_test. But in my project I'm using cmake. The build script looks like this: CMAKE_MINIMUM_REQUIRED(VERSION 2.6) PROJECT(globaltest) ADD_LIBRARY(base STATIC base.cpp) ADD_LIBRARY(library MODULE library.cpp) TARGET_LINK_LIBRARIES(library base) ADD_EXECUTABLE(client client.cpp) TARGET_LINK_LIBRARIES(client base dl) analyzing the created makefiles I found that cmake builds the client with g++ -Wall -g -ldl -rdynamic client.cpp libbase.a -o client This ends up in a slightly different but fatal behavior: The global_test of the client and the dynamically loaded library are the same but will be destroyed two times at the end of the program. Am I using cmake in a wrong way? Is it possible that the client and the dynamically loaded library use the same global_test but without this double destruction problem?

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