Cisortho install (install "à la main") ...

MMuy_Bien · 10 juil. 2009

Aie aie aie !!
alors ... tout supprimé tout detaré en user lol

Avec opt ça a l'air bon ...

[Elegans@localhost opt-3.19]$ ./configure --prefix=/var/www/html/
creating cache ./config.cache
checking for a BSD compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking whether make sets ${MAKE}... yes
checking for working aclocal... missing
checking for working autoconf... missing
checking for working automake... missing
checking for working autoheader... missing
checking for working makeinfo... missing
checking for gcc... gcc
checking whether the C compiler (gcc  ) works... yes
checking whether the C compiler (gcc  ) is a cross-compiler... no
checking whether we are using GNU C... yes
checking whether gcc accepts -g... yes
checking for c++... c++
checking whether the C++ compiler (c++  ) works... yes
checking whether the C++ compiler (c++  ) is a cross-compiler... no
checking whether we are using GNU C++... yes
checking whether c++ accepts -g... yes
checking for a BSD compatible install... /usr/bin/install -c
checking whether make sets ${MAKE}... (cached) yes
checking for ranlib... ranlib
checking for strdup... yes
checking for snprintf... yes
checking for longjmp... yes
checking how to run the C preprocessor... gcc -E
checking for signal.h... yes
checking return type of signal handlers... void
updating cache ./config.cache
creating ./config.status
creating test/Makefile
creating src/Makefile
creating ext/Makefile
creating Makefile
creating opt.spec
[Elegans@localhost opt-3.19]$ make
Making all in src
make[1]: Entering directory `/var/www/html/opt-3.19/src'
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.      -g -O2 -c opt_util.c
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.      -g -O2 -c opt_reg.c
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.      -g -O2 -c opt_regt.c
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.      -g -O2 -c opt_menu.c
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.      -g -O2 -c opt_proc.c
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.      -g -O2 -c ag.c
g++ -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.      -g -O2 -c opt_regcc.cc
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.      -g -O2 -c opt_num.c
rm -f libopt.a
ar cru libopt.a opt_util.o opt_reg.o opt_regt.o opt_menu.o opt_proc.o ag.o opt_regcc.o opt_num.o 
ranlib libopt.a
make[1]: Leaving directory `/var/www/html/opt-3.19/src'
Making all in test
make[1]: Entering directory `/var/www/html/opt-3.19/test'
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c t_num.c
gcc  -g -O2  -o t_num  t_num.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c testopt.c
gcc  -g -O2  -o testopt  testopt.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c birthday.c
gcc  -g -O2  -o birthday  birthday.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c hooktest.c
gcc  -g -O2  -o hooktest  hooktest.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c iloop.c
gcc  -g -O2  -o iloop  iloop.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c testmain.c
gcc  -g -O2  -o testmain  testmain.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c testtypes.c
gcc  -g -O2  -o testtypes  testtypes.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c tstring.c
gcc  -g -O2  -o tstring  tstring.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c tnull.c
gcc  -g -O2  -o tnull  tnull.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c manyopts.c
gcc  -g -O2  -o manyopts  manyopts.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c tarray.c
gcc  -g -O2  -o tarray  tarray.o ../src/libopt.a 
g++ -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c testcc.cc
testcc.cc: In function 'int main(int, char**)':
testcc.cc:71: warning: deprecated conversion from string constant to 'char*'
testcc.cc:74: warning: deprecated conversion from string constant to 'char*'
testcc.cc:74: warning: deprecated conversion from string constant to 'char*'
testcc.cc:75: warning: deprecated conversion from string constant to 'char*'
testcc.cc:77: warning: deprecated conversion from string constant to 'char*'
testcc.cc:78: warning: deprecated conversion from string constant to 'char*'
testcc.cc:81: warning: deprecated conversion from string constant to 'char*'
testcc.cc:83: warning: deprecated conversion from string constant to 'char*'
testcc.cc:83: warning: deprecated conversion from string constant to 'char*'
testcc.cc:85: warning: deprecated conversion from string constant to 'char*'
testcc.cc:85: warning: deprecated conversion from string constant to 'char*'
testcc.cc:87: warning: deprecated conversion from string constant to 'char*'
testcc.cc:88: warning: deprecated conversion from string constant to 'char*'
g++  -g -O2  -o testcc  testcc.o ../src/libopt.a 
gcc -DPACKAGE=\"opt\" -DVERSION=\"3.19\" -DHAVE_STRDUP=1 -DHAVE_SNPRINTF=1 -DHAVE_LONGJMP=1 -DHAVE_SIGNAL=1 -DRETSIGTYPE=void  -I. -I.  -I../src    -g -O2 -c testlong.c
gcc  -g -O2  -o testlong  testlong.o ../src/libopt.a 
make[1]: Leaving directory `/var/www/html/opt-3.19/test'
Making all in ext
make[1]: Entering directory `/var/www/html/opt-3.19/ext'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/var/www/html/opt-3.19/ext'
make[1]: Entering directory `/var/www/html/opt-3.19'
make[1]: Nothing to be done for `all-am'.
make[1]: Leaving directory `/var/www/html/opt-3.19'
[Elegans@localhost opt-3.19]$ make install
Making install in src
make[1]: Entering directory `/var/www/html/opt-3.19/src'
make[2]: Entering directory `/var/www/html/opt-3.19/src'
/bin/sh ../mkinstalldirs /var/www/html//lib
mkdir /var/www/html/lib
 /usr/bin/install -c -m 644 libopt.a /var/www/html//lib/libopt.a
 ranlib /var/www/html//lib/libopt.a
/bin/sh ../mkinstalldirs /var/www/html//include
mkdir /var/www/html/include
 /usr/bin/install -c -m 644 opt.h /var/www/html//include/opt.h
make[2]: Leaving directory `/var/www/html/opt-3.19/src'
make[1]: Leaving directory `/var/www/html/opt-3.19/src'
Making install in test
make[1]: Entering directory `/var/www/html/opt-3.19/test'
make[2]: Entering directory `/var/www/html/opt-3.19/test'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/var/www/html/opt-3.19/test'
make[1]: Leaving directory `/var/www/html/opt-3.19/test'
Making install in ext
make[1]: Entering directory `/var/www/html/opt-3.19/ext'
make[2]: Entering directory `/var/www/html/opt-3.19/ext'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/var/www/html/opt-3.19/ext'
make[1]: Leaving directory `/var/www/html/opt-3.19/ext'
make[1]: Entering directory `/var/www/html/opt-3.19'
make[2]: Entering directory `/var/www/html/opt-3.19'
make[2]: Nothing to be done for `install-exec-am'.
/bin/sh ./mkinstalldirs /var/www/html//info
mkdir /var/www/html/info
 /usr/bin/install -c -m 644 ./opt.info /var/www/html//info/opt.info
 /usr/bin/install -c -m 644 ./opt.info-1 /var/www/html//info/opt.info-1
 /usr/bin/install -c -m 644 ./opt.info-2 /var/www/html//info/opt.info-2
 install-info --info-dir=/var/www/html//info /var/www/html//info/opt.info
install-info: warning: no info dir entry in `/var/www/html//info/opt.info'
make[2]: Leaving directory `/var/www/html/opt-3.19'
make[1]: Leaving directory `/var/www/html/opt-3.19'
[Elegans@localhost opt-3.19]$ cd ..

mais pour le cisortho ...

[Elegans@localhost cisortho-0.9.0]$ ./configure --prefix=/var/www/html/
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
/var/www/html/cisortho-0.9.0/missing: Unknown `--run' option
Try `/var/www/html/cisortho-0.9.0/missing --help' for more information
configure: WARNING: `missing' script is too old or missing
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for a BSD-compatible install... /usr/bin/install -c
checking whether ln -s works... yes
checking whether make sets $(MAKE)... (cached) yes
Using CPPFLAGS = 
checking for --enable-debug... no
checking for --enable-profile... no
checking for --enable-stldebug... no
checking for optMain in -lopt... yes
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking opt.h usability... yes
checking opt.h presence... yes
checking for opt.h... yes
checking for an ANSI C-conforming const... yes
configure: creating ./config.status
config.status: creating src/Makefile
config.status: creating Makefile
config.status: executing depfiles commands
[Elegans@localhost cisortho-0.9.0]$ make
Making all in src
make[1]: Entering directory `/var/www/html/cisortho-0.9.0/src'
if g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"cisortho\" -DVERSION=\"0.9.0\" -DHAVE_LIBOPT=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1  -I. -I.     -Wall -Wno-parentheses -O3 -DNDEBUG -MT genome_index.o -MD -MP -MF ".deps/genome_index.Tpo" -c -o genome_index.o genome_index.cpp; \
    then mv -f ".deps/genome_index.Tpo" ".deps/genome_index.Po"; else rm -f ".deps/genome_index.Tpo"; exit 1; fi
genome_index.cpp: In function 'int main(int, const char**)':
genome_index.cpp:278: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:278: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:279: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:279: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:280: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:280: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:281: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:281: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:282: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:282: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:283: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:283: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:284: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:284: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:285: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:285: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:286: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:286: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:287: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:287: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:288: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:288: warning: deprecated conversion from string constant to 'char*'
genome_index.cpp:290: error: invalid conversion from 'int (*)(int, const char**)' to 'int (*)(int, char**)'
genome_index.cpp:290: error:   initializing argument 1 of 'void optMain(int (*)(int, char**))'
genome_index.cpp:303: error: invalid conversion from 'const char***' to 'char***'
genome_index.cpp:303: error:   initializing argument 2 of 'void opt(int*, char***)'
genome_index.cpp:306: error: invalid conversion from 'const char***' to 'char***'
genome_index.cpp:306: error:   initializing argument 2 of 'void opt(int*, char***)'
make[1]: *** [genome_index.o] Error 1
make[1]: Leaving directory `/var/www/html/cisortho-0.9.0/src'
make: *** [all-recursive] Error 1
[Elegans@localhost cisortho-0.9.0]$

Alors est ce que c'est l'install de opt qui n'a pas marché ? Je ne pense pas parceque ce n'est pas le meme message d'erreur qu'au début.
... pffff il peuvent pas le mettre dans un dépot et puis yum install cisortho lol

[Elegans@localhost cisortho-0.9.0]$ ls
acinclude.m4  AUTHORS    config.log     configure     COPYING  INSTALL     Makefile     Makefile.in  mkinstalldirs  perl    src
aclocal.m4    ChangeLog  config.status  configure.in  depcomp  install-sh  Makefile.am  missing      NEWS           README
[Elegans@localhost cisortho-0.9.0]$

Ne me laisse pas tomber Pikachu ... j'aurais jamais pensé dire ça dans ma vie lol

Pikachu_2014 · 10 juil. 2009

Tu n'avais pas besoin de relancer une compilation d'opt, d'autant plus que tu n'as pas relancé de make install après. opt a été bien installé plus haut, on n'y touche plus.

Reste à s'occuper de cisortho. Peux-tu poster le contenu du fichier src/genome_index.cpp ?

MMuy_Bien · 10 juil. 2009

mer... j'ai oublié le make install ... c'est pas la peine ? J'ai supprimé tous les dossiers de cisortho et opt et retelechargé opt pour reprendre a 0. Il est quand meme resté installé ?

#include <iostream>
#include <sstream>

#include "opt.h"
#include "index_trie.h"
#include "dnacol.h"
#include "dna_scanning.h"
#include "dnastats.h"
#include "dna.h"
#include "litestream.h"

#include <unistd.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <dirent.h>


using std::cerr;
using std::cout;
using std::endl;
using std::string;

int MinTreeDepth = 6;
int MaxTreeDepth = 50;
int MaxSuffixLoad = 2;
int PrefixLength = 2;
int ChunkSize = 100000;
char *OutfilePrefix = NULL;
char *SinglePrefix = NULL;
char *FolderPrefix = NULL;

char * DataDirectory = const_cast<char *>(".");

int n_DNA, n_Species;
char **DNA, **Species;

int GenomeIndex(int argc, char const** argv){

  if (OutfilePrefix == NULL){
    cerr<<"Please provide an output file prefix (option -o)"<<endl;
    exit(53);
  }

    
  std::ostringstream TreeTempDir; 
  std::ostringstream PosTempDir; 

  if (FolderPrefix == NULL){
    PosTempDir<<getpid()<<"_gpos";
    TreeTempDir<<getpid()<<"_itrie";
  }
  else {
    PosTempDir<<FolderPrefix<<"_gpos";
    TreeTempDir<<FolderPrefix<<"_itrie";
  }
    
  //parse dna from SequenceFile, build a dna_collection from it
  if (n_Species != n_DNA) {
    cerr<<"You must have the same number of species names as genomic sequence files."<<endl;
    exit(53);
  }

  std::vector<string> sSpecies(n_Species);
  std::string sDataDirectory(DataDirectory);

  for (int g=0; g < n_Species; g++) sSpecies[g] = Species[g];

  cis::dna_collection dnac;
  for (int g=0; g < n_DNA; g++){
    try {
      std::cout<<"Parsing "<<DNA[g]<<" genomic sequence file..."<<std::endl;
      dnac.add(sSpecies[g], sDataDirectory, DNA[g]);
    }
    catch (string &msg){ cerr<<msg<<endl; return 2; }
}

  dnac.calc_offsets();
  dnac.open_dnas();

  mkdir(TreeTempDir.str().c_str(), 0755);
  mkdir(PosTempDir.str().c_str(), 0755);
  DIR * treedir = opendir(TreeTempDir.str().c_str());
  DIR * posdir = opendir(PosTempDir.str().c_str());

  std::ofstream treefile, posfile;
  std::ifstream tree_bufbase;
  litestream tree_bufstream(tree_bufbase, ChunkSize);

//   bfs::path treedir(TreeTempDir.str());
//   bfs::path posdir(PosTempDir.str());
//   bfs::create_directory(treedir);
//   bfs::create_directory(posdir);

  index_trie::set_max_suffix_load(MaxSuffixLoad);
  index_trie * root = new index_trie();
  
  cout<<"Scanning all dna for prefixes...";
  cout.flush();

  std::set<cis::dnastring> Prefixes, ptmp;
  std::set<cis::dnastring>::iterator prefix_iter;

  if (FolderPrefix != NULL){

    dirent * current_file;
    while ((current_file = readdir(treedir)) != NULL){

//     bfs::directory_iterator end_itr; // default construction yields past-the-end
//     for (bfs::directory_iterator itr(treedir); itr != end_itr; ++itr){

      string prefix = current_file->d_name;
      //string prefix = itr->leaf();
      cis::dnastring dprefix = cis::ToDNAString(prefix);
      Prefixes.insert(dprefix);
    }


    cis::dnastring pfx;
    for (prefix_iter = Prefixes.begin();
         prefix_iter != Prefixes.end(); ++prefix_iter){

      pfx = *prefix_iter;

      string spfx = cis::FromDNAString(pfx);

      string treepath = TreeTempDir.str() + spfx;
      string pospath = PosTempDir.str() + spfx;

      tree_bufstream.open(treepath.c_str());

      if (! tree_bufstream.good()){
        cerr<<"Couldn't open "<<spfx<<" in "<<treepath<<endl;
        exit(50);
      }

      node_info subroot = readNode(tree_bufstream);

      root->insertfile(pfx.c_str(), pfx.size(),
                       treepath, subroot.subtree_size,
                       pospath, subroot.suffix_count);

      tree_bufstream.close();
    }
  }

  else {

    for (cis::DNAS::iterator dna_it = dnac.begin(); 
         dna_it != dnac.end(); ++dna_it){
      
      ptmp = dnastats::Spectrum(*(*dna_it), PrefixLength, ChunkSize);
      Prefixes.insert(ptmp.begin(), ptmp.end());
    }
    
    cout<<"found "<<Prefixes.size()<<" prefixes."<<endl;
    
    cis::dnastring pfx;
    for (prefix_iter = Prefixes.begin();
         prefix_iter != Prefixes.end(); ++prefix_iter){
      
      pfx = *prefix_iter;
      
      index_trie * subroot = new index_trie();
      subroot->build_subtree(pfx, dnac, MinTreeDepth, MaxTreeDepth, ChunkSize);
      subroot->push();
      
      cis::NUC lastNuc = *pfx.rbegin();
      
      if (! subroot->empty()){
        
        subroot->count();
        
        string spfx = cis::FromDNAString(pfx);
        string treepath = TreeTempDir.str() + string("/") + spfx;
        string pospath = PosTempDir.str() + string("/") + spfx;
        
        treefile.open(treepath.c_str(), std::ios::out | std::ios::binary);
        //treefile.open(treedir / spfx, std::ios::out | std::ios::binary);
        if (! treefile){
          cerr<<"Couldn't open "<<spfx<<" in "<<treepath<<endl;
          exit(50);
        }
        
        posfile.open(pospath.c_str(), std::ios::out | std::ios::binary);
        //posfile.open(posdir / spfx, std::ios::out | std::ios::binary);
        if (! posfile){
          cerr<<"Couldn't open "<<spfx<<" in "<<treepath<<endl;
          exit(50);
        }

        cout<<"Writing subtree with prefix "<<spfx<<", "
            <<subroot->nbytes<<" bytes, "
            <<subroot->nsuffixes<<" patterns...";
        cout.flush();
        
        subroot->write(lastNuc, treefile, posfile);
        treefile.close();
        posfile.close();

        root->insertfile(pfx.c_str(), pfx.size(), 
                         treepath, subroot->nbytes,
                         pospath, subroot->nsuffixes);
//         root->insertfile(pfx.c_str(), pfx.size(), 
//                          treedir / spfx, subroot->nbytes,
//                          posdir / spfx, subroot->nsuffixes);

        cout<<"done."<<endl;

        //return 0;

      } 
        
      delete subroot; //memory
    }

  }



  string tree(OutfilePrefix); tree += ".itrie";
  treefile.open(tree.c_str(), std::ios::out | std::ios::binary);

  string pos(OutfilePrefix); pos += ".gpos";
  posfile.open(pos.c_str(), std::ios::out | std::ios::binary);

  //return 0;

  root->push();
  root->count();
  root->write(cis::X, treefile, posfile);

  cout<<"Wrote "<<root->nbytes<<" bytes and "
      <<root->nsuffixes<<" patterns."<<endl;

  delete root;

  treefile.close();
  posfile.close();

  string dnasrc(OutfilePrefix); dnasrc += ".dnas";
  std::ofstream dnafile;
  dnafile.open(dnasrc.c_str());

  for (cis::DNAS::iterator dna_it = dnac.begin(); 
       dna_it != dnac.end(); ++dna_it) 
    dnafile<<*(*dna_it)<<endl;

  dnafile.close();


  //delete all files in treedir, posdir
  cout<<"Removing all files in "
      <<TreeTempDir.str().c_str()
      <<" and "<<PosTempDir.str().c_str()<<"."<<endl;

  dirent * current_file;
  while ((current_file = readdir(treedir)) != NULL) {
    cout<<"Would be unlinking "<<current_file->d_name<<endl;
    //unlink(current_file->d_name);
  }
  rmdir(TreeTempDir.str().c_str());

  while ((current_file = readdir(posdir)) != NULL) {
    cout<<"Would be unlinking "<<current_file->d_name<<endl;
    //unlink(current_file->d_name);
  }
  rmdir(PosTempDir.str().c_str());
  
//   bfs::remove_all(treedir);
//   bfs::remove_all(posdir);

  return 0;
}


int main(int argc, char const**argv){

  OptRegister(&MinTreeDepth,OPT_INT,               'x', "min-tree-depth","minimum pattern length to search.");
  OptRegister(&MaxTreeDepth,OPT_INT,               'y', "max-tree-depth","maximum depth of the index tree.");
  OptRegister(&PrefixLength,OPT_INT,               'p', "prefix-length","length of prefix (3 is good) for splitting the subtree building.");
  OptRegister(&MaxSuffixLoad,OPT_INT,               'l', "max-suffix-load","maximum number of suffixes at a leaf before pushing further");
  OptRegister(&ChunkSize,OPT_INT,                  'c', "chunk-size","size of reading a chunk of DNA sequence for scanning");
  optrega_array(&n_Species, &Species, OPT_STRING,'n', "species-names","species names (comma-separated)");
  optrega_array(&n_DNA, &DNA, OPT_STRING,        's', "sequence-files","sequence files (comma-separated)");
  OptRegister(&DataDirectory, OPT_STRING,        't', "dna-directory", "directory containing 'sequence-files'");
  OptRegister(&OutfilePrefix,OPT_STRING,         'o', "outfile-prefix","prefix on output files with extensions 'gpos', 'itree', and 'dnas'");
  OptRegister(&SinglePrefix,OPT_STRING,          'f', "single-prefix","for testing");
  OptRegister(&FolderPrefix,OPT_STRING,          'd', "folder-prefix","for partial runs");

  optMain(GenomeIndex);

  if (argc==1){
    char const** myargv;
    char const* mybuf[2];
    mybuf[0]=argv[0];
    mybuf[1]="$";
    myargv=mybuf;
    int myargc=2;
    cout<<endl<<endl
        <<"Build a tree and genome position index file from a sequence file"<<endl
        <<"for fast, ungapped pattern searching."<<endl;

    opt(&myargc,&myargv);
  }
    
  else opt(&argc,&argv);
  return GenomeIndex(argc,argv);
}

uummmm à quoi ça sert de faire tout plein d'include au début si ils sont commentés ... a moins que # ne commente pas mais bon ...

Pikachu_2014 · 10 juil. 2009

Le temps de me pencher dessus, je répondrai à quelques-unes des questions en suspens :
* pourquoi opt et cisortho ne sont pas dans les dépôts ? Plusieurs raisons :
- des logiciels très spécialisés, de toute évidence, donc peu communs et surtout peu utilisés par le commun des mortels dont ton humble serviteur, et donc moins prioritaires,
- Fedora est une distribution communautaire, chacun est libre de suggérer des programmes à empaqueter, et surtout de contribuer aux dépôts en packagant et en proposant à la communauté lesdits programmes ; on n'attend que toi sur ce coup ^^ ;
* il est quand même installé opt ? Oui, il est quand même installé ; le fait de supprimer les sources ne supprime évidemment pas l'application déployée, celle-ci l'étant dans /usr/local ;
* des includes commentés ? Que nenni, en C++, les commentaires sont précédés de "//" ou bien encadrés par "/* ... */" ; le "#" indique une directive destinée au préprocesseur, et nullement un caractère de commentaire.

MMuy_Bien · 10 juil. 2009

... hummmm pour ce qui est de creer les paquetages je verrai :-D , creer un dépot Bionformatique.noarch.rpm lol et mettre tout ça et mon programme aussi lol.

Pour opt oui c'est logique mais je sais pas je pensais que l'install etait dans le dossier /opt/ (oui c'est completement co..) mais alors du coup le probléme de droit (vu que je l'ai fait la 1ere fois en root) ?

Pour les comm, donc en python
#coucou n'est pas important
en C
#coucou est trés important ! :hammer:

MMuy_Bien · 15 juil. 2009

Salut tout le monde ! Je up le probléme si pikachu passe par là ou d'autres :-D

Le probléme : compiler cisortho ...

make: *** [all-recursive] Error 1

lors de la compilation de cisortho ...

Pikachu_2014 · 15 juil. 2009

Je vois que tu essaies de compiler la version 0.9 de cisortho... Or une version 1.1 est disponible. Avec cette dernière, les erreurs d'appel d'opt() sont corrigées.

MMuy_Bien · 15 juil. 2009

Salut Pikachu !

J'ai telechargé cisortho 1.1, décompréssé dans /var/www/html. Je me suis placé dans le dossier fraichement décompréssé et dans une console en user j'ai tapé :

[Elegans@localhost cisortho-1.1]$ ./configure --prefix=/var/www/html/

ça se passe bien mais en root je fais le make et toujours les meme rerreurs

cisortho.cpp: In function 'int Cutoff(int, char**)':
cisortho.cpp:164: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:164: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:164: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp: In function 'int main(int, char**)':
cisortho.cpp:223: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:223: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:224: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:224: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:225: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:225: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:226: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:226: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:227: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:227: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:228: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:228: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:229: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:229: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:230: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:230: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:231: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:231: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:232: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:232: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:233: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:233: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:234: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:234: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:235: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:235: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:236: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:236: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:237: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:237: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:238: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:238: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:239: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:239: warning: deprecated conversion from string constant to 'char*'
cisortho.cpp:246: warning: deprecated conversion from string constant to 'char*'

[...]

make[1]: *** [load.o] Error 1
make[1]: Leaving directory `/var/www/html/cisortho-1.1/src'
make: *** [all-recursive] Error 1

Donc ça n'a pas l'air d'avoir un lien avec opt. Mais question. le prefix de la 1ere commande c'est l'endroit ou il va s'installer c'est ça ? Il ne faudrai pas que je mette une path genre /home/share ... ?

Pikachu_2014 · 15 juil. 2009

Pour faire les choses simplement, le configure et le make devront être faits en tant que simple utilisateur. Seul le make install, pour lequel de tels droits seront nécessaires vu ton préfixe, sera fait en root.
Supprime les sources, redécompresse l'archive de cisortho dans ton répertoire personnel avec ton compte à toi, et relance la compilation, toujours en tant que simple utilisateur.

Au passage, la racine "/var/www/html/" pour ton installation est-elle vraiment justifiée ? Cela ne me semble guère standard...

pingou · 15 juil. 2009

Pikachu_2014 wrote:Pour faire les choses simplement, le configure et le make devront être faits en tant que simple utilisateur. Seul le make install, pour lequel de tels droits seront nécessaires vu ton préfixe, sera fait en root.

Comme déjà dis dans le commentaire 12...

MMuy_Bien · 15 juil. 2009

Salut !

Pikachu_2014 wrote:Au passage, la racine "/var/www/html/" pour ton installation est-elle vraiment justifiée ? Cela ne me semble guère standard...

Euuuuh non pas du tout ... j'ai lu que c'etait le path d'installation donc j'ai mis le dossier à partir duquel je vais l'utiliser mais l'installation peut se faire autre part en fait ... que me conseille tu ?/usr/local/share ? ......

J'ai lu aussi qu'aprés une compilation qui n'a pas marché il faut faire un

make clean

...

proxy · 15 juil. 2009

En général, lorsqu'on ne précise pas le prefix, la valeur par défaut est /usr/local

MMuy_Bien · 15 juil. 2009

Salut !!

Alors j'ai contacté le developeur de Cisortho et il m'a dit que le fichier dispo sur sourceforge n'etait pas bon et qu'il va le changer.
Il me contactera quand cela sera fait. Je reviendrai alors poster si tout va bien ou (je ne l'espere pas) si j'ai un probléme.

Voila
Merci beaucoup Pikachu !! J'ai quand meme appris pas mal de choses !!

Pikachu_2014 · 15 juil. 2009

Euh... Ca m'a pas empêché de le compiler ceci dit, je teste toujours ce que je fais avant de donner les indications ^^.

Le retour auprès du développeur est une excellente initiative 🙂.

MMuy_Bien · 15 juil. 2009

:-o
Tu dois avoir une librairie que je n'ai pas !
Tu avais mis quoi comme prefix ??

Oui le developpeur m'a dit qu'il allait faire une installation plus rapide et facile ...
On va voir ...:roll:

Pikachu_2014 · 15 juil. 2009

J'attends toujours que tu recompiles le programme selon la procédure décrite au commentaire #27.
Là on pourra peut-être jouer à comparer...