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

MMuy_Bien · 9 juil. 2009

Bonjour,

je me tourne vers vous car je dois installer une série de programme "à la main" et maintenant que j'ai compris le fonctionnement de yum, j'aimerais comprendre cette méthode qui à l'air plus compliqué (yum install cisortho .. ne marche pas ! Je précise que je ne le fais pas pour le plaisir mais parceque je suis obligé.).

Alors infos complementaires :
Le logiciel que je cherche à installer à la base est MaqGene. Dans le tar il y a les dossiers
bin/
bin32/
bin64/
cgi/
src/
web/

les fichiers :
install
install.sh

et le fichier texte README qui donne la marche à suivre .. step1, 2, 3, 4, ...
Cisortho est le 1er des logiciels complementaires à installer pour faire tourner MaqGene (sans compter Apache et PHP) et necessite une install à la main ...

Dans le readme il donne les commandes à executer :

STEP 1.  Install Apache2 (httpd version 2.x.x)
STEP 2.  Install PHP 5.x.x
STEP 3.  Configure httpd for use with PHP, and for use with MAQGene

Tout ça je l'ai fait avec YUM il y a un moment donc pas la peine de le faire à la main ...

STEP 4.  Download and install cisortho-0.9.0.tar.gz from Sourceforge
# This will install the necessary cisortho executables for use with MAQGene
$ tar zxvf cisortho-0.9.0.tar.gz
$ cd cisortho-0.9.0
$ ./configure --prefix=/path/to/maqgene/bin
$ make
$ make install

et là c'est le drame !
si je lui dit

[root@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++... no
checking for c++... no
checking for gpp... no
checking for aCC... no
checking for CC... no
checking for cxx... no
checking for cc++... no
checking for cl... no
checking for FCC... no
checking for KCC... no
checking for RCC... no
checking for xlC_r... no
checking for xlC... no
checking whether we are using the GNU C++ compiler... no
checking whether g++ accepts -g... no
checking dependency style of g++... none
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... no
configure: error: Please use --with-build-path so we can find the library.
[root@localhost cisortho-0.9.0]#

Comment utilise-t-on cette option --with-build-path ?
Qu'est ce que le build-path ?

Un petit coup de pouce serait le bienvenu ...🙁:-?
Merci d'avance

Pikachu_2014 · 9 juil. 2009

Bonjour,

peux-tu poster le fichier config.log généré dans les sources de cisortho ?

MMuy_Bien · 9 juil. 2009

Salut Pikapika !

alors le fichier config.log (je l'avais meme pa vu lui ! oo')

This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by configure, which was
generated by GNU Autoconf 2.59.  Invocation command line was

  $ ./configure --prefix=/var/www/html/

## --------- ##
## Platform. ##
## --------- ##

hostname = localhost.localdomain
uname -m = i686
uname -r = 2.6.27.25-170.2.72.fc10.i686
uname -s = Linux
uname -v = #1 SMP Sun Jun 21 19:03:24 EDT 2009

/usr/bin/uname -p = unknown
/bin/uname -X     = unknown

/bin/arch              = i686
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
hostinfo               = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /usr/kerberos/sbin
PATH: /usr/kerberos/bin
PATH: /usr/local/sbin
PATH: /usr/local/bin
PATH: /sbin
PATH: /bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /root/bin


## ----------- ##
## Core tests. ##
## ----------- ##

configure:1356: checking for a BSD-compatible install
configure:1411: result: /usr/bin/install -c
configure:1422: checking whether build environment is sane
configure:1465: result: yes
configure:1489: WARNING: `missing' script is too old or missing
configure:1530: checking for gawk
configure:1546: found /bin/gawk
configure:1556: result: gawk
configure:1566: checking whether make sets $(MAKE)
configure:1586: result: yes
configure:1767: checking for style of include used by make
configure:1795: result: GNU
configure:1866: checking for gcc
configure:1882: found /usr/bin/gcc
configure:1892: result: gcc
configure:2136: checking for C compiler version
configure:2139: gcc --version </dev/null >&5
gcc (GCC) 4.3.2 20081105 (Red Hat 4.3.2-7)
Copyright (C) 2008 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:2142: $? = 0
configure:2144: gcc -v </dev/null >&5
Using built-in specs.
Target: i386-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-cpu=generic --build=i386-redhat-linux
Thread model: posix
gcc version 4.3.2 20081105 (Red Hat 4.3.2-7) (GCC) 
configure:2147: $? = 0
configure:2149: gcc -V </dev/null >&5
gcc: '-V' option must have argument
configure:2152: $? = 1
configure:2175: checking for C compiler default output file name
configure:2178: gcc    conftest.c  >&5
configure:2181: $? = 0
configure:2227: result: a.out
configure:2232: checking whether the C compiler works
configure:2238: ./a.out
configure:2241: $? = 0
configure:2258: result: yes
configure:2265: checking whether we are cross compiling
configure:2267: result: no
configure:2270: checking for suffix of executables
configure:2272: gcc -o conftest    conftest.c  >&5
configure:2275: $? = 0
configure:2300: result: 
configure:2306: checking for suffix of object files
configure:2327: gcc -c   conftest.c >&5
configure:2330: $? = 0
configure:2352: result: o
configure:2356: checking whether we are using the GNU C compiler
configure:2380: gcc -c   conftest.c >&5
configure:2386: $? = 0
configure:2390: test -z 
             || test ! -s conftest.err
configure:2393: $? = 0
configure:2396: test -s conftest.o
configure:2399: $? = 0
configure:2412: result: yes
configure:2418: checking whether gcc accepts -g
configure:2439: gcc -c -g  conftest.c >&5
configure:2445: $? = 0
configure:2449: test -z 
             || test ! -s conftest.err
configure:2452: $? = 0
configure:2455: test -s conftest.o
configure:2458: $? = 0
configure:2469: result: yes
configure:2486: checking for gcc option to accept ANSI C
configure:2556: gcc  -c -g -O2  conftest.c >&5
configure:2562: $? = 0
configure:2566: test -z 
             || test ! -s conftest.err
configure:2569: $? = 0
configure:2572: test -s conftest.o
configure:2575: $? = 0
configure:2593: result: none needed
configure:2611: gcc -c -g -O2  conftest.c >&5
conftest.c:2: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'me'
configure:2617: $? = 1
configure: failed program was:
| #ifndef __cplusplus
|   choke me
| #endif
configure:2752: checking dependency style of gcc
configure:2842: result: gcc3
configure:2864: checking how to run the C preprocessor
configure:2899: gcc -E  conftest.c
configure:2905: $? = 0
configure:2937: gcc -E  conftest.c
conftest.c:11:28: error: ac_nonexistent.h: No such file or directory
configure:2943: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "cisortho"
| #define VERSION "0.9.0"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:2982: result: gcc -E
configure:3006: gcc -E  conftest.c
configure:3012: $? = 0
configure:3044: gcc -E  conftest.c
conftest.c:11:28: error: ac_nonexistent.h: No such file or directory
configure:3050: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "cisortho"
| #define VERSION "0.9.0"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:3145: checking for g++
configure:3174: result: no
configure:3145: checking for c++
configure:3174: result: no
configure:3145: checking for gpp
configure:3174: result: no
configure:3145: checking for aCC
configure:3174: result: no
configure:3145: checking for CC
configure:3174: result: no
configure:3145: checking for cxx
configure:3174: result: no
configure:3145: checking for cc++
configure:3174: result: no
configure:3145: checking for cl
configure:3174: result: no
configure:3145: checking for FCC
configure:3174: result: no
configure:3145: checking for KCC
configure:3174: result: no
configure:3145: checking for RCC
configure:3174: result: no
configure:3145: checking for xlC_r
configure:3174: result: no
configure:3145: checking for xlC
configure:3174: result: no
configure:3187: checking for C++ compiler version
configure:3190: g++ --version </dev/null >&5
./configure: line 3191: g++: command not found
configure:3193: $? = 127
configure:3195: g++ -v </dev/null >&5
./configure: line 3196: g++: command not found
configure:3198: $? = 127
configure:3200: g++ -V </dev/null >&5
./configure: line 3201: g++: command not found
configure:3203: $? = 127
configure:3206: checking whether we are using the GNU C++ compiler
configure:3230: g++ -c   conftest.cc >&5
./configure: line 3231: g++: command not found
configure:3236: $? = 127
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "cisortho"
| #define VERSION "0.9.0"
| /* end confdefs.h.  */
| 
| int
| main ()
| {
| #ifndef __GNUC__
|        choke me
| #endif
| 
|   ;
|   return 0;
| }
configure:3262: result: no
configure:3268: checking whether g++ accepts -g
configure:3289: g++ -c -g  conftest.cc >&5
./configure: line 3290: g++: command not found
configure:3295: $? = 127
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "cisortho"
| #define VERSION "0.9.0"
| /* end confdefs.h.  */
| 
| int
| main ()
| {
| 
|   ;
|   return 0;
| }
configure:3319: result: no
configure:3361: g++ -c   conftest.cc >&5
./configure: line 3362: g++: command not found
configure:3367: $? = 127
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "cisortho"
| #define VERSION "0.9.0"
| /* end confdefs.h.  */
| 
| #include <stdlib.h>
| int
| main ()
| {
| exit (42);
|   ;
|   return 0;
| }
configure:3361: g++ -c   conftest.cc >&5
./configure: line 3362: g++: command not found
configure:3367: $? = 127
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "cisortho"
| #define VERSION "0.9.0"
| /* end confdefs.h.  */
| extern "C" void std::exit (int) throw (); using std::exit;
| #include <stdlib.h>
| int
| main ()
| {
| exit (42);
|   ;
|   return 0;
| }
configure:3361: g++ -c   conftest.cc >&5
./configure: line 3362: g++: command not found
configure:3367: $? = 127
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "cisortho"
| #define VERSION "0.9.0"
| /* end confdefs.h.  */
| extern "C" void std::exit (int); using std::exit;
| #include <stdlib.h>
| int
| main ()
| {
| exit (42);
|   ;
|   return 0;
| }
configure:3361: g++ -c   conftest.cc >&5
./configure: line 3362: g++: command not found
configure:3367: $? = 127
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "cisortho"
| #define VERSION "0.9.0"
| /* end confdefs.h.  */
| extern "C" void exit (int) throw ();
| #include <stdlib.h>
| int
| main ()
| {
| exit (42);
|   ;
|   return 0;
| }
configure:3361: g++ -c   conftest.cc >&5
./configure: line 3362: g++: command not found
configure:3367: $? = 127
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "cisortho"
| #define VERSION "0.9.0"
| /* end confdefs.h.  */
| extern "C" void exit (int);
| #include <stdlib.h>
| int
| main ()
| {
| exit (42);
|   ;
|   return 0;
| }
configure:3361: g++ -c   conftest.cc >&5
./configure: line 3362: g++: command not found
configure:3367: $? = 127
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "cisortho"
| #define VERSION "0.9.0"
| /* end confdefs.h.  */
| void exit (int);
| #include <stdlib.h>
| int
| main ()
| {
| exit (42);
|   ;
|   return 0;
| }
configure:3450: checking dependency style of g++
configure:3540: result: none
configure:3570: checking for a BSD-compatible install
configure:3625: result: /usr/bin/install -c
configure:3636: checking whether ln -s works
configure:3640: result: yes
configure:3647: checking whether make sets $(MAKE)
configure:3667: result: yes
configure:3682: result: Using CPPFLAGS = 
configure:3699: checking for --enable-debug
configure:3708: result: no
configure:3711: checking for --enable-profile
configure:3720: result: no
configure:3723: checking for --enable-stldebug
configure:3732: result: no
configure:3759: checking for optMain in -lopt
configure:3789: gcc -o conftest -g -O2   -L/razor/5/users/bigelow/gaia/usr/lib64 -L/razor/5/users/bigelow/gaia/usr/local/lib64 conftest.c -lopt   >&5
/usr/bin/ld: cannot find -lopt
collect2: ld returned 1 exit status
configure:3795: $? = 1
configure: failed program was:
| /* confdefs.h.  */
| 
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "cisortho"
| #define VERSION "0.9.0"
| #ifdef __cplusplus
| void exit (int);
| #endif
| /* end confdefs.h.  */
| 
| /* Override any gcc2 internal prototype to avoid an error.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| /* We use char because int might match the return type of a gcc2
|    builtin and then its argument prototype would still apply.  */
| char optMain ();
| int
| main ()
| {
| optMain ();
|   ;
|   return 0;
| }
configure:3821: result: no
configure:3831: error: Please use --with-build-path so we can find the library.

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_c_compiler_gnu=yes
ac_cv_cxx_compiler_gnu=no
ac_cv_env_CC_set=
ac_cv_env_CC_value=
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=
ac_cv_env_CXX_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_exeext=
ac_cv_lib_opt_optMain=no
ac_cv_objext=o
ac_cv_path_install='/usr/bin/install -c'
ac_cv_prog_AWK=gawk
ac_cv_prog_CPP='gcc -E'
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_cc_g=yes
ac_cv_prog_cc_stdc=
ac_cv_prog_cxx_g=no
ac_cv_prog_make_make_set=yes
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_CXX_dependencies_compiler_type=none

## ----------------- ##
## Output variables. ##
## ----------------- ##

ACLOCAL='aclocal-1.9'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='tar'
AUTOCONF='autoconf'
AUTOHEADER='autoheader'
AUTOMAKE='automake-1.9'
AWK='gawk'
CC='gcc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2'
CPP='gcc -E'
CPPFLAGS=''
CXX='g++'
CXXDEPMODE='depmode=none'
CXXFLAGS='-Wall -Wno-parentheses -O3 -DNDEBUG'
CYGPATH_W='echo'
DEFS=''
DEPDIR='.deps'
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP=''
EXEEXT=''
INCLUDES=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s'
LDFLAGS=' -L/razor/5/users/bigelow/gaia/usr/lib64 -L/razor/5/users/bigelow/gaia/usr/local/lib64'
LIBOBJS=''
LIBS=''
LN_S='ln -s'
LTLIBOBJS=''
MAKEINFO='makeinfo'
OBJEXT='o'
PACKAGE='cisortho'
PACKAGE_BUGREPORT=''
PACKAGE_NAME=''
PACKAGE_STRING=''
PACKAGE_TARNAME=''
PACKAGE_VERSION=''
PATH_SEPARATOR=':'
SET_MAKE=''
SHELL='/bin/sh'
STRIP=''
VERSION='0.9.0'
ac_ct_CC='gcc'
ac_ct_CXX='g++'
ac_ct_STRIP=''
am__fastdepCC_FALSE='#'
am__fastdepCC_TRUE=''
am__fastdepCXX_FALSE=''
am__fastdepCXX_TRUE='#'
am__include='include'
am__leading_dot='.'
am__quote=''
am__tar='${AMTAR} chof - "$$tardir"'
am__untar='${AMTAR} xf -'
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${prefix}/share'
exec_prefix='NONE'
host_alias=''
includedir='${prefix}/include'
infodir='${prefix}/info'
install_sh='/var/www/html/cisortho-0.9.0/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localstatedir='${prefix}/var'
mandir='${prefix}/man'
mkdir_p='mkdir -p --'
oldincludedir='/usr/include'
prefix='/var/www/html/'
program_transform_name='s,x,x,'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

#define PACKAGE "cisortho"
#define PACKAGE_BUGREPORT ""
#define PACKAGE_NAME ""
#define PACKAGE_STRING ""
#define PACKAGE_TARNAME ""
#define PACKAGE_VERSION ""
#define VERSION "0.9.0"
#endif
#ifdef __cplusplus
void exit (int);

configure: exit 1

:-?

Pikachu_2014 · 9 juil. 2009

Il manquerait une bibliothèque "opt" ou "libopt" qui à dire vrai ne me dit rien. Et un nom aussi vague n'est guère propice aux recherches google.
Peux-tu jeter un oeil à la doc. livrée dans les sources de cisortho pour voir une référence particulière à cette dépendance (qui n'est pas dans les dépôts, ce qui est sûr) ?

MMuy_Bien · 9 juil. 2009

Nan rien dans la doc qui fait reference a opt ou libopt (ou lopt) ...

ça te servirai le INSTALL.txt ou c'est pas la peine ?

Pikachu_2014 · 9 juil. 2009

Oui, c'est toujours ça de pris. Peux-tu le poster ?

MMuy_Bien · 9 juil. 2009

mais bien sur ...

OVERVIEW of CisOrtho:

The CisOrtho website runs on two machines, which I'll call WEB and
BACKEND.  WEB runs a perl-CGI script that accepts the user query and
writes the input in a scan directory monitored by a crontab-driven
shell script running on BACKEND, called 'launch.bash'.  When
launch.bash finds a file there, it calls cisortho through a perl
wrapper called 'results'.  Finally, cisortho runs and produces html
results files to the directory out/, that the user can browse for a
limited time.

This process accumulates files in scan/ and out/ that are monitored by
another crontab-driven shell script, 'cleanup.bash' that deletes them
when they are more than a few weeks old.

Soon, this crude file-based, crontab-dependent communication between
two machines will be replaced by SOAP communication.  Thus, the
'listening ears' will be a CGI server running on BACKEND rather than a
crontab job.  Also, there will be no need for temporary files that
must be mounted on both machines.  Instead, the user input data will
be sent directly from WEB to BACKEND as a SOAP message.

Please let me know if there is a better way to achieve this.  


The entire set of software consists of the following:

in WEBROOT:

index.html
methods.html
download.html

per/              #directory of permanent cisortho input files
per/CElegans      #elegans non-exonic genomic sequences in RDB format
per/CBriggsae     #briggsae non-exonic genomic sequences in RDB format
per/eb_geneinfo   #contains gene name, chromosome, start, end, strand
per/eb.null       #HMMER 'null' stats file, containing nucleotide freq. in
                  #elegans and briggsae genomes combined
per/eb.pri        #HMMER priors stats file
per/options       #file containing input options for the cisortho binary
scan/               #directory that the CGI script '$CGIROOT/query' deposits user submitted
                    #input data.  This directory is scanned by a bash script called 'launch.bash'
                    #that is controlled by 'cisortho.cron', a crontab job
out/                #directory where cisortho writes output html search results files.
download/
graphics/           #contain extra html files for the cisortho website
log/                #log files for cisortho

launch.bash         #bash script, scans 'scan/' for the presence of new input files and if found,
                    #calls '$CGIROOT/results', a perl script that launches cisortho
cleanup.bash        #scans 'scan/' and 'out/', deleting old files and directories periodically
cisortho.cron       #launches 'launch.bash', and 'cleanup.bash'
cisortho            #the actual c++ binary.                


in CGIROOT:

CGIsubs.pm        #perl module with helper CGI subroutines
query             #perl CGI script for accepting user input submission, writes the input to 'scan/'
results           #perl script for parsing the user input and calling cisortho


Other notes:

* launch.bash implements a primitive lock-file based mechanism for
  limiting to 2 concurrently running instances of CisOrtho.

* launch.bash is run once per minute by cisortho.cron.  During that minute,
  launch.bash itself checks the presence of new files once per second.  This way,
  there is no delay for the user to see that the input is being processed.  This
  is essentially a poor-man's implementation of SOAP or other
  message-based response system.

* upon clicking 'submit', the input is evaluated by the query script,
  and there is no deposit to 'scan/' if the input contains errors.

Bouska · 9 juil. 2009

Merci Google 🙂 : http://nis-www.lanl.gov/~jt/Software/opt/opt-3.19.tar.gz (cf. : http://dev.wormbase.org/cisortho/download.html). De plus, il me semble que "gcc-c++" ne soit pas installé ("g++ not found") : là, c'est merci yum 🙂

MMuy_Bien · 9 juil. 2009

salut !

merci bouska !
ah ouais !! donc je fais un wget de ce lien un yum install gcc et normalement le configure devrait marcher ?
et cette histoire de --with-build-path ? il ne me redemandera pas cette option ?

Je peux pas tester je suis plus au boulot. Verditct demain 9h.

Bouska · 9 juil. 2009

Muy_Bien wrote:ah ouais !! donc je fais un wget de ce lien un yum install gcc et normalement le configure devrait marcher ?
et cette histoire de --with-build-path ? il ne me redemandera pas cette option ?

Pour le "yum install gcc-c++ gcc" (les deux au cas où), y'a effectivement que ça à faire. Par contre, pour le "opt", c'est plus compliqué puisqu'il faut aussi le compiler et l'installer mais une fois installé, le "--with-build-path" devrait être inutile. Par ailleurs, le premier lien a l'air de donner un fichier corrompu, utilise plutôt le second (http://dev.wormbase.org/cisortho/download/unix/opt-3.19.tar.gz)

MMuy_Bien · 10 juil. 2009

Salut !!

alors j'ai lançé l'installation de gcc (apparement ok)

[root@localhost ~]# yum install gcc-c++ gcc
Loaded plugins: refresh-packagekit
fedora                                                                                                                                 | 2.8 kB     00:00     
updates                                                                                                                                | 3.4 kB     00:00     
Setting up Install Process
Package gcc-4.3.2-7.i386 already installed and latest version
Resolving Dependencies
--> Running transaction check
---> Package gcc-c++.i386 0:4.3.2-7 set to be updated
--> Processing Dependency: libstdc++-devel = 4.3.2-7 for package: gcc-c++-4.3.2-7.i386
--> Running transaction check
---> Package libstdc++-devel.i386 0:4.3.2-7 set to be updated
--> Finished Dependency Resolution

Dependencies Resolved

==============================================================================================================================================================
 Package                                     Arch                             Version                                Repository                          Size
==============================================================================================================================================================
Installing:
 gcc-c++                                     i386                             4.3.2-7                                fedora                             3.9 M
Installing for dependencies:
 libstdc++-devel                             i386                             4.3.2-7                                fedora                             3.8 M

Transaction Summary
==============================================================================================================================================================
Install      2 Package(s)         
Update       0 Package(s)         
Remove       0 Package(s)         

Total download size: 7.7 M
Is this ok [y/N]: y
Downloading Packages:
(1/2): gcc-c++-4.3.2-7.i386.rpm                                                                                                        | 3.9 MB     00:10     
(2/2): libstdc++-devel-4.3.2-7.i386.rpm                                                                                                | 3.8 MB     00:09     
--------------------------------------------------------------------------------------------------------------------------------------------------------------
Total                                                                                                                         369 kB/s | 7.7 MB     00:21     
Running rpm_check_debug
Running Transaction Test
Finished Transaction Test
Transaction Test Succeeded
Running Transaction
  Installing     : libstdc++-devel-4.3.2-7.i386                                                                                                           1/2 
  Installing     : gcc-c++-4.3.2-7.i386                                                                                                                   2/2 

Installed:
  gcc-c++.i386 0:4.3.2-7                                                                                                                                      

Dependency Installed:
  libstdc++-devel.i386 0:4.3.2-7                                                                                                                              

Complete!

Puis j'ai telechargé le fameux opt et fais ceci (untar, configure ..)

[root@localhost html]# tar xvf opt-3.19.tar.gz 
opt-3.19/
opt-3.19/Makefile.in
opt-3.19/README
opt-3.19/AUTHORS
opt-3.19/COPYING
opt-3.19/ChangeLog
opt-3.19/INSTALL
opt-3.19/Makefile.am
opt-3.19/NEWS
opt-3.19/aclocal.m4
opt-3.19/configure
opt-3.19/configure.in
opt-3.19/install-sh
opt-3.19/mdate-sh
opt-3.19/missing
opt-3.19/mkinstalldirs
opt-3.19/opt.spec.in
opt-3.19/stamp-vti
opt-3.19/texinfo.tex
opt-3.19/version.texi
opt-3.19/opt.texi
opt-3.19/opt.spec
opt-3.19/COPYING.gpl
opt-3.19/src/
opt-3.19/src/Makefile.in
opt-3.19/src/Makefile.am
opt-3.19/src/opt_util.c
opt-3.19/src/opt_reg.c
opt-3.19/src/opt_regt.c
opt-3.19/src/opt_menu.c
opt-3.19/src/opt_proc.c
opt-3.19/src/ag.c
opt-3.19/src/opt_regcc.cc
opt-3.19/src/opt_num.c
opt-3.19/src/opt.h
opt-3.19/src/opt_sf.h
opt-3.19/src/ag.h
opt-3.19/src/opt_p.h
opt-3.19/src/makeopth.pl
opt-3.19/test/
opt-3.19/test/Makefile.am
opt-3.19/test/Makefile.in
opt-3.19/test/t_num.c
opt-3.19/test/testopt.c
opt-3.19/test/birthday.c
opt-3.19/test/hooktest.c
opt-3.19/test/iloop.c
opt-3.19/test/testmain.c
opt-3.19/test/testtypes.c
opt-3.19/test/tstring.c
opt-3.19/test/tnull.c
opt-3.19/test/manyopts.c
opt-3.19/test/tarray.c
opt-3.19/test/testcc.cc
opt-3.19/test/testlong.c
opt-3.19/test/checkopt
opt-3.19/test/checkoptcc
opt-3.19/ext/
opt-3.19/ext/Makefile.in
opt-3.19/ext/Makefile.am
opt-3.19/ext/Opt.pm
opt-3.19/ext/tkopt
opt-3.19/opt.info
opt-3.19/opt.info-1
opt-3.19/opt.info-2
[root@localhost html]# ls
cisortho-0.9.0  ICeE  ICeE_save  ICeE.tar  ICeE_version_1.5  maqgene  opt-3.19  opt-3.19.tar.gz
[root@localhost html]# cd opt-3.19
[root@localhost opt-3.19]# ls
aclocal.m4  configure     COPYING.gpl  install-sh   mdate-sh       NEWS        opt.info-2   opt.texi  stamp-vti    version.texi
AUTHORS     configure.in  ext          Makefile.am  missing        opt.info    opt.spec     README    test
ChangeLog   COPYING       INSTALL      Makefile.in  mkinstalldirs  opt.info-1  opt.spec.in  src       texinfo.tex
[root@localhost opt-3.19]# ./configure 
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

Jusque là ... ça a l'air ok !
Puis j'ai voulu faire le make ... et là ...

[root@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:3:22: error: iostream.h: No such file or directory
testcc.cc: In function 'int go(int, char**)':
testcc.cc:17: error: 'cout' was not declared in this scope
testcc.cc:19: error: 'endl' was not declared in this scope
testcc.cc:23: error: 'cout' was not declared in this scope
testcc.cc:23: error: 'endl' was not declared in this scope
testcc.cc: In function 'int main(int, char**)':
testcc.cc:70: warning: deprecated conversion from string constant to 'char*'
testcc.cc:73: warning: deprecated conversion from string constant to 'char*'
testcc.cc:73: warning: deprecated conversion from string constant to 'char*'
testcc.cc:74: warning: deprecated conversion from string constant to 'char*'
testcc.cc:76: warning: deprecated conversion from string constant to 'char*'
testcc.cc:77: warning: deprecated conversion from string constant to 'char*'
testcc.cc:80: warning: deprecated conversion from string constant to 'char*'
testcc.cc:82: warning: deprecated conversion from string constant to 'char*'
testcc.cc:82: warning: deprecated conversion from string constant to 'char*'
testcc.cc:84: warning: deprecated conversion from string constant to 'char*'
testcc.cc:84: warning: deprecated conversion from string constant to 'char*'
testcc.cc:86: warning: deprecated conversion from string constant to 'char*'
testcc.cc:87: warning: deprecated conversion from string constant to 'char*'
make[1]: *** [testcc.o] Error 1
make[1]: Leaving directory `/var/www/html/opt-3.19/test'
make: *** [all-recursive] Error 1

:-?
Qu'est ce c'est ces tests qui sont deprecated ???
Je vais pas m'en sortir 🙁

Pikachu_2014 · 10 juil. 2009

1) Ne compile pas en root. Jamais.
2) Peux-tu poster le contenu du fichier test/testcc.cc ?

MMuy_Bien · 10 juil. 2009

Pikachu_2014 wrote:1) Ne compile pas en root. Jamais.

Oups ! Pourquoi ?

Pikachu_2014 wrote:2) Peux-tu poster le contenu du fichier test/testcc.cc ?

/* testcc.cc */

#include <iostream.h>
#include <stdio.h>
#include <opt.h>

int month=4;
int day=24;
int year=1993;
int julian=0;
char *who=NULL;
int version=99;

int go(int argc, char **argv)
{
    if (argc>1) {
    cout << 
    "In program: " << argv[0] <<
    "Extra option: " << argv[1] << endl;
    }

    if (optinvoked(&month)) {
    cout << "User set month..." << endl;
    }

    if (month == 9 && day == 11 && year == 1989) {
        printf("Happy birthday, Max\n");
    } else {
        printf("Hello, %s: %4d/%02d/%02d %s\n",(who==NULL ? "world" : who),
               year,month,day,(julian ? "(Julian)" : ""));
    }
    return OPT_OK;
}

int checkyear(void *v)
{
    if (year == 2000) {
        printf("Watch out for that year=2000 bug!\n");
        return OPT_ERROR;
    }
    return OPT_OK;
}
int quit()
{
    printf("Bye...\n");
    return OPT_OK;
}
int write_version(void *v)
{
    /* it's a little hokey that this requires an argument... */
    v = &version; 
    printf("Version %d\n",version);
    optExitNumber(12);
    return OPT_EXIT;
}
int fix_mon(void *v)
{
    int m;
    /* fix whatever int variable v is pointing to */
    m = *((int *)v);
    if (m < 1 || m > 12) 
        m=1;
    *((int *)v) = m;
    return OPT_OK;
} 

int
main(int argc, char **argv)
{
    OptRegister(&month,'m',"month");
    opthook(&month,fix_mon);

    OptRegister(&day,'d',"day","Day");
    opthelp(&day,"Use day of month, should be less than 32");
    
    OptRegister(&year,"year");
    optdescript(&year,"What Year");
    opthook(&year,checkyear);

    OptRegister(&julian,OPT_BOOL,"julian");

    optregp(&who,OPT_STRING,"who","Who to say hello to");

    optexec("version",write_version,"Write version number and exit");

    optEnvVarName( "OPT" );
    optDefaultFile( "testoptrc" ); /* in practice, you do ~/.testoptrc */
    
    optMain(go);
    optQuit(quit);

    opt(&argc,&argv);
    return go(argc,argv);
}

??? Qu'est ce c'est ??

Pikachu_2014 · 10 juil. 2009

J'applique juste le vieil adage qui dit qu'on évite d'être root le plus possible. Et la compilation ne nécessite pas d'être root. C'est plus sûr ainsi, on est à l'abri de mauvaises manipulations.

Dans le fichier que tu as posté, tu vas éditer la ligne 3 :

#include <iostream.h>

et la remplacer par :

#include <iostream>

Relance alors make.

MMuy_Bien · 10 juil. 2009

ok alors make en pas root :-D aprés la modif

[Elegans@localhost opt-3.19]$ make
Making all in src
make[1]: Entering directory `/var/www/html/opt-3.19/src'
make[1]: Nothing to be done for `all'.
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'
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 go(int, char**)':
testcc.cc:17: error: 'cout' was not declared in this scope
testcc.cc:19: error: 'endl' was not declared in this scope
testcc.cc:23: error: 'cout' was not declared in this scope
testcc.cc:23: error: 'endl' was not declared in this scope
testcc.cc: In function 'int main(int, char**)':
testcc.cc:70: warning: deprecated conversion from string constant to 'char*'
testcc.cc:73: warning: deprecated conversion from string constant to 'char*'
testcc.cc:73: warning: deprecated conversion from string constant to 'char*'
testcc.cc:74: warning: deprecated conversion from string constant to 'char*'
testcc.cc:76: warning: deprecated conversion from string constant to 'char*'
testcc.cc:77: warning: deprecated conversion from string constant to 'char*'
testcc.cc:80: warning: deprecated conversion from string constant to 'char*'
testcc.cc:82: warning: deprecated conversion from string constant to 'char*'
testcc.cc:82: warning: deprecated conversion from string constant to 'char*'
testcc.cc:84: warning: deprecated conversion from string constant to 'char*'
testcc.cc:84: warning: deprecated conversion from string constant to 'char*'
testcc.cc:86: warning: deprecated conversion from string constant to 'char*'
testcc.cc:87: warning: deprecated conversion from string constant to 'char*'
make[1]: *** [testcc.o] Error 1
make[1]: Leaving directory `/var/www/html/opt-3.19/test'
make: *** [all-recursive] Error 1

il y a moins d'erreur !!! On (tu) progresse !!!

Pikachu_2014 · 10 juil. 2009

Rajoute cette fois juste après le "#include <iostream>" la ligne "using namespace std;" (désolé pour l'oubli ^^).
Ca devrait passer cette fois. Les messages de warning ne sont pas rédhibitoires, on peut les ignorer, ils n'empêcheront pas a priori la compilation de se poursuivre.

MMuy_Bien · 10 juil. 2009

hey !!!

j'ai fait ce que tu m'as dit... mais il est pas trés bavard enfin il est bavard mais pas dans le meme langue que la mienne pas de ok ou c'est bon !:-D

[root@localhost opt-3.19]# make
Making all in src
make[1]: Entering directory `/var/www/html/opt-3.19/src'
make[1]: Nothing to be done for `all'.
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'
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'
[root@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 /usr/local/lib
 /usr/bin/install -c -m 644 libopt.a /usr/local/lib/libopt.a
 ranlib /usr/local/lib/libopt.a
/bin/sh ../mkinstalldirs /usr/local/include
 /usr/bin/install -c -m 644 opt.h /usr/local/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 /usr/local/info
mkdir /usr/local/info
 /usr/bin/install -c -m 644 ./opt.info /usr/local/info/opt.info
 /usr/bin/install -c -m 644 ./opt.info-1 /usr/local/info/opt.info-1
 /usr/bin/install -c -m 644 ./opt.info-2 /usr/local/info/opt.info-2
 install-info --info-dir=/usr/local/info /usr/local/info/opt.info
install-info: warning: no info dir entry in `/usr/local/info/opt.info'
make[2]: Leaving directory `/var/www/html/opt-3.19'
make[1]: Leaving directory `/var/www/html/opt-3.19'

je lance configure pour cisortho ...

EDIT :
Au fait je viens de réaliser que j'ai encore compiler en root 😐 desolé pas encore le reflex ... j'etais root pour editer le fichier et pis voila ...
pour cisortho ... pas plus bavard ...

[root@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 $(MAKE)... (cached) yes
Using CPPFLAGS = 
checking for --enable-debug... no
checking for --enable-profile... no
checking for --enable-stldebug... no
checking for optMain in -lopt... yes
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking opt.h usability... yes
checking opt.h presence... yes
checking for opt.h... yes
checking for an ANSI C-conforming const... yes
configure: creating ./config.status
config.status: creating src/Makefile
config.status: creating Makefile
config.status: executing depfiles commands
[root@localhost cisortho-0.9.0]# su Elegans
[Elegans@localhost cisortho-0.9.0]$ 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***)'
genome_index.cpp: At global scope:
genome_index.cpp:308: fatal error: opening dependency file .deps/genome_index.Tpo: Permission denied
compilation terminated.
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]$ make install
Making install 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***)'
genome_index.cpp: At global scope:
genome_index.cpp:308: fatal error: opening dependency file .deps/genome_index.Tpo: Permission denied
compilation terminated.
make[1]: *** [genome_index.o] Error 1
make[1]: Leaving directory `/var/www/html/cisortho-0.9.0/src'
make: *** [install-recursive] Error 1

Pikachu_2014 · 10 juil. 2009

Tu as lancé le ./configure en tant que root... Du coup les makefile et autres fichiers de dépendances générés appartiennent à root. Il eut mieux valu continuer en root...

Supprime les sources décompressées en root. Et recommence : décompresse l'archive de sources de cisortho dans ton répertoire personnel. Recommence la compilation, cette fois en tant que simple utilisateur.
De cette façon on aura des logs de compilation plus claires, et plus de parasites à propos de droits ^^.

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 ?