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The Basics
Id: 30092
Status: resolved
Worked: 5 min
Priority: 0/
Queue: Bio-SCF
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Owner: LDS [...] cpan.org
Requestors: meyniel [...] cervi-lyon.inserm.fr
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Severity: (no value)
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Fixed in: (no value)

History Show all quoted text
  Thu Oct 18 11:09:45 2007 meyniel [...] cervi-lyon.inserm.fr - Ticket created
Subject: Problem with Bio::SCF install
Date: Thu, 18 Oct 2007 17:07:30 -0200 (CEST)
To: bug-Bio-SCF [...] rt.cpan.org
From: meyniel [...] cervi-lyon.inserm.fr
Hello, I'm experiencing problems with the installation of Bio::SCF, can you help me? I downloaded it from http://rt.cpan.org/, then I uncompressed it and tried to install it according to the INSTALL file : $ perl Makefile.PL ------------------ Checking if your kit is complete... Looks good Writing Makefile for Bio::SCF $ make ------ cp SCF.pm blib/lib/Bio/SCF.pm cp SCF/Arrays.pm blib/lib/Bio/SCF/Arrays.pm /usr/bin/perl /usr/lib/perl5/5.8.8/ExtUtils/xsubpp -typemap /usr/lib/perl5/5.8.8/ExtUtils/typemap SCF.xs > SCF.xsc && mv SCF.xsc SCF.c Please specify prototyping behavior for SCF.xs (see perlxs manual) gcc -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -DVERSION=\"1.01\" -DXS_VERSION=\"1.01\" -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE" -DLITTLE_ENDIAN SCF.c Running Mkbootstrap for Bio::SCF () chmod 644 SCF.bs rm -f blib/arch/auto/Bio/SCF/SCF.so gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib SCF.o -o blib/arch/auto/Bio/SCF/SCF.so \ -lread -lz \ chmod 755 blib/arch/auto/Bio/SCF/SCF.so cp SCF.bs blib/arch/auto/Bio/SCF/SCF.bs chmod 644 blib/arch/auto/Bio/SCF/SCF.bs Manifying blib/man3/Bio::SCF.3pm $ make test ----------- PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/scf....Can't load '/home/meyniel/Desktop/Bio-SCF-1.01/blib/arch/auto/Bio/SCF/SCF.so' for module Bio::SCF: /home/meyniel/Desktop/Bio-SCF-1.01/blib/arch/auto/Bio/SCF/SCF.so: undefined symbol: curl_easy_setopt at /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230. at t/scf.t line 23 Compilation failed in require at t/scf.t line 23. BEGIN failed--compilation aborted at t/scf.t line 23. t/scf....dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-18 Failed 18/18 tests, 0.00% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/scf.t 2 512 18 36 200.00% 1-18 Failed 1/1 test scripts, 0.00% okay. 18/18 subtests failed, 0.00% okay. make: *** [test_dynamic] Erreur 2 The informations about my computer are : Fedora core $ uname -a : Linux simap 2.6.18-1.2798.fc6 #1 SMP Mon Oct 16 14:37:32 EDT 2006 i686 i686 i386 GNU/Linux $perl -v : perl, v5.8.8 built for i386-linux-thread-multi If you require any further information, feel free to contact me. Thank you very much, Yours faithfully LM
  Thu Oct 18 11:47:08 2007 LDS [...] cpan.org - Correspondence added 5 min
One of your auxiliary libraries, either libz or libread, seems to have been compiled for libcurl, a library for manipulating URLs. Neither the vanilla libz or libread (Staden) libraries do this, and so I guess that you are using some patched version that is specific to your linux vendor. You can probably fix this by modifying the 'LIBS' option in Makefile.PL to read: 'LIBS' => ['-lcurl -lread -lz'] However, I would be interested in knowing who the culprit is. Could you run the following commands to search for the curl symbols? % strings /usr/lib/libz.a | grep -i curl % strings /usr/local/lib/libread.a | grep -i curl % strings `which perl` | grep -i curl You may need to modify the paths to find the correct libraries and executables on your system. Lincoln On Thu Oct 18 11:09:45 2007, meyniel@cervi-lyon.inserm.fr wrote: Show quoted text
> Hello, > > I'm experiencing problems with the installation of Bio::SCF, can you > help me? > > I downloaded it from http://rt.cpan.org/, then I uncompressed it and > tried > to install it according to the INSTALL file : > > $ perl Makefile.PL > ------------------ > Checking if your kit is complete... > Looks good > Writing Makefile for Bio::SCF > > $ make > ------ > cp SCF.pm blib/lib/Bio/SCF.pm > cp SCF/Arrays.pm blib/lib/Bio/SCF/Arrays.pm > /usr/bin/perl /usr/lib/perl5/5.8.8/ExtUtils/xsubpp -typemap > /usr/lib/perl5/5.8.8/ExtUtils/typemap SCF.xs > SCF.xsc && mv SCF.xsc > SCF.c > Please specify prototyping behavior for SCF.xs (see perlxs manual) > gcc -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe > -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE > -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall > -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic > -fasynchronous-unwind-tables -DVERSION=\"1.01\" > -DXS_VERSION=\"1.01\" > -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE" > -DLITTLE_ENDIAN SCF.c > Running Mkbootstrap for Bio::SCF () > chmod 644 SCF.bs > rm -f blib/arch/auto/Bio/SCF/SCF.so > gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 > -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib SCF.o -o > blib/arch/auto/Bio/SCF/SCF.so \ > -lread -lz \ > > chmod 755 blib/arch/auto/Bio/SCF/SCF.so > cp SCF.bs blib/arch/auto/Bio/SCF/SCF.bs > chmod 644 blib/arch/auto/Bio/SCF/SCF.bs > Manifying blib/man3/Bio::SCF.3pm > > $ make test > ----------- > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/scf....Can't load > '/home/meyniel/Desktop/Bio-SCF-1.01/blib/arch/auto/Bio/SCF/SCF.so' for > module Bio::SCF: > /home/meyniel/Desktop/Bio-SCF-1.01/blib/arch/auto/Bio/SCF/SCF.so: > undefined symbol: curl_easy_setopt at > /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230. > at t/scf.t line 23 > Compilation failed in require at t/scf.t line 23. > BEGIN failed--compilation aborted at t/scf.t line 23. > t/scf....dubious > Test returned status 2 (wstat 512, 0x200) > DIED. FAILED tests 1-18 > Failed 18/18 tests, 0.00% okay > Failed Test Stat Wstat Total Fail Failed List of Failed >
------------------------------------------------------------------------------- Show quoted text
> t/scf.t 2 512 18 36 200.00% 1-18 > Failed 1/1 test scripts, 0.00% okay. 18/18 subtests failed, 0.00% > okay. > make: *** [test_dynamic] Erreur 2 > > The informations about my computer are : > Fedora core > $ uname -a : Linux simap 2.6.18-1.2798.fc6 #1 SMP Mon Oct 16 14:37:32 > EDT > 2006 i686 i686 i386 GNU/Linux > $perl -v : perl, v5.8.8 built for i386-linux-thread-multi > > If you require any further information, feel free to contact me. > > Thank you very much, > > Yours faithfully > > LM > > > > > >
  Thu Oct 18 11:47:10 2007 The RT System itself - Status changed from 'new' to 'open'
  Thu Oct 18 11:47:12 2007 LDS [...] cpan.org - Given to LDS
  Fri Oct 19 04:07:54 2007 meyniel [...] cervi-lyon.inserm.fr - Correspondence added
Subject: Re: [rt.cpan.org #30092] Problem with Bio::SCF install
Date: Fri, 19 Oct 2007 10:05:27 +0200
To: bug-Bio-SCF [...] rt.cpan.org
From: meyniel laurene <meyniel [...] cervi-lyon.inserm.fr>
Thank you very much for your quick answer. Before I tried to install Bio::SCF, I had installed the Staden Package, and the Io-lib because I missed the lread library. I modified the line in Makefile.PL, now the command '$ make test' indicates an other problem : $ make test ($ perl Makefile.PL, $ make and $ make test run by root) -------------- PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/scf....Can't load '/home/meyniel/Desktop/Bio-SCF-1.01/blib/arch/auto/Bio/SCF/SCF.so' for module Bio::SCF: /home/meyniel/Desktop/Bio-SCF-1.01/blib/arch/auto/Bio/SCF/SCF.so: ne peut restaurer le segment prot après reloc: Permission non accordée at /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230. at t/scf.t line 23 Compilation failed in require at t/scf.t line 23. BEGIN failed--compilation aborted at t/scf.t line 23. t/scf....dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-18 Failed 18/18 tests, 0.00% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/scf.t 2 512 18 36 200.00% 1-18 Failed 1/1 test scripts, 0.00% okay. 18/18 subtests failed, 0.00% okay. make: *** [test_dynamic] Erreur 2 I have run the commands about the curl symbols (the paths are OK) : $ strings /usr/lib/libz.a | grep -i curl --------------------------------------------- [nothing] $ strings /usr/local/lib/libread.a | grep -i curl -------------------------------------------------------- /usr/include/curl curl.h CURL curl_init curl_init.6081 curl_easy_setopt curl_global_init curl_easy_init curl_easy_perform $ strings `which perl` | grep -i curl -------------------------------------------- [nothing] Can you help me again? Yours faithfully, LM Lincoln_D_Stein via RT a écrit : Show quoted text
> <URL: http://rt.cpan.org/Ticket/Display.html?id=30092 > > > One of your auxiliary libraries, either libz or libread, seems to have > been compiled for libcurl, a library for manipulating URLs. Neither the > vanilla libz or libread (Staden) libraries do this, and so I guess that > you are using some patched version that is specific to your linux vendor. > > You can probably fix this by modifying the 'LIBS' option in Makefile.PL > to read: > > 'LIBS' => ['-lcurl -lread -lz'] > > However, I would be interested in knowing who the culprit is. Could you > run the following commands to search for the curl symbols? > > % strings /usr/lib/libz.a | grep -i curl > % strings /usr/local/lib/libread.a | grep -i curl > % strings `which perl` | grep -i curl > > You may need to modify the paths to find the correct libraries and > executables on your system. > > Lincoln > > On Thu Oct 18 11:09:45 2007, meyniel@cervi-lyon.inserm.fr wrote: >
>> Hello, >> >> I'm experiencing problems with the installation of Bio::SCF, can you >> help me? >> >> I downloaded it from http://rt.cpan.org/, then I uncompressed it and >> tried >> to install it according to the INSTALL file : >> >> $ perl Makefile.PL >> ------------------ >> Checking if your kit is complete... >> Looks good >> Writing Makefile for Bio::SCF >> >> $ make >> ------ >> cp SCF.pm blib/lib/Bio/SCF.pm >> cp SCF/Arrays.pm blib/lib/Bio/SCF/Arrays.pm >> /usr/bin/perl /usr/lib/perl5/5.8.8/ExtUtils/xsubpp -typemap >> /usr/lib/perl5/5.8.8/ExtUtils/typemap SCF.xs > SCF.xsc && mv SCF.xsc >> SCF.c >> Please specify prototyping behavior for SCF.xs (see perlxs manual) >> gcc -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe >> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE >> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector >> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic >> -fasynchronous-unwind-tables -DVERSION=\"1.01\" >> -DXS_VERSION=\"1.01\" >> -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE" >> -DLITTLE_ENDIAN SCF.c >> Running Mkbootstrap for Bio::SCF () >> chmod 644 SCF.bs >> rm -f blib/arch/auto/Bio/SCF/SCF.so >> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions >> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 >> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib SCF.o -o >> blib/arch/auto/Bio/SCF/SCF.so \ >> -lread -lz \ >> >> chmod 755 blib/arch/auto/Bio/SCF/SCF.so >> cp SCF.bs blib/arch/auto/Bio/SCF/SCF.bs >> chmod 644 blib/arch/auto/Bio/SCF/SCF.bs >> Manifying blib/man3/Bio::SCF.3pm >> >> $ make test >> ----------- >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> t/scf....Can't load >> '/home/meyniel/Desktop/Bio-SCF-1.01/blib/arch/auto/Bio/SCF/SCF.so' for >> module Bio::SCF: >> /home/meyniel/Desktop/Bio-SCF-1.01/blib/arch/auto/Bio/SCF/SCF.so: >> undefined symbol: curl_easy_setopt at >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230. >> at t/scf.t line 23 >> Compilation failed in require at t/scf.t line 23. >> BEGIN failed--compilation aborted at t/scf.t line 23. >> t/scf....dubious >> Test returned status 2 (wstat 512, 0x200) >> DIED. FAILED tests 1-18 >> Failed 18/18 tests, 0.00% okay >> Failed Test Stat Wstat Total Fail Failed List of Failed >> >>
> ------------------------------------------------------------------------------- >
>> t/scf.t 2 512 18 36 200.00% 1-18 >> Failed 1/1 test scripts, 0.00% okay. 18/18 subtests failed, 0.00% >> okay. >> make: *** [test_dynamic] Erreur 2 >> >> The informations about my computer are : >> Fedora core >> $ uname -a : Linux simap 2.6.18-1.2798.fc6 #1 SMP Mon Oct 16 14:37:32 >> EDT >> 2006 i686 i686 i386 GNU/Linux >> $perl -v : perl, v5.8.8 built for i386-linux-thread-multi >> >> If you require any further information, feel free to contact me. >> >> Thank you very much, >> >> Yours faithfully >> >> LM >> >> >> >> >> >> >>
> > > > >
  Fri Oct 19 04:30:54 2007 meyniel [...] cervi-lyon.inserm.fr - Correspondence added
Subject: Re: [rt.cpan.org #30092] Problem with Bio::SCF install
Date: Fri, 19 Oct 2007 10:28:25 +0200
To: bug-Bio-SCF [...] rt.cpan.org
From: meyniel laurene <meyniel [...] cervi-lyon.inserm.fr>
I precise (if necessary) that I have already disabled the SELinux protection for httpd daemon. LM Lincoln_D_Stein via RT a écrit : Show quoted text
> <URL: http://rt.cpan.org/Ticket/Display.html?id=30092 > > > One of your auxiliary libraries, either libz or libread, seems to have > been compiled for libcurl, a library for manipulating URLs. Neither the > vanilla libz or libread (Staden) libraries do this, and so I guess that > you are using some patched version that is specific to your linux vendor. > > You can probably fix this by modifying the 'LIBS' option in Makefile.PL > to read: > > 'LIBS' => ['-lcurl -lread -lz'] > > However, I would be interested in knowing who the culprit is. Could you > run the following commands to search for the curl symbols? > > % strings /usr/lib/libz.a | grep -i curl > % strings /usr/local/lib/libread.a | grep -i curl > % strings `which perl` | grep -i curl > > You may need to modify the paths to find the correct libraries and > executables on your system. > > Lincoln > > On Thu Oct 18 11:09:45 2007, meyniel@cervi-lyon.inserm.fr wrote: >
>> Hello, >> >> I'm experiencing problems with the installation of Bio::SCF, can you >> help me? >> >> I downloaded it from http://rt.cpan.org/, then I uncompressed it and >> tried >> to install it according to the INSTALL file : >> >> $ perl Makefile.PL >> ------------------ >> Checking if your kit is complete... >> Looks good >> Writing Makefile for Bio::SCF >> >> $ make >> ------ >> cp SCF.pm blib/lib/Bio/SCF.pm >> cp SCF/Arrays.pm blib/lib/Bio/SCF/Arrays.pm >> /usr/bin/perl /usr/lib/perl5/5.8.8/ExtUtils/xsubpp -typemap >> /usr/lib/perl5/5.8.8/ExtUtils/typemap SCF.xs > SCF.xsc && mv SCF.xsc >> SCF.c >> Please specify prototyping behavior for SCF.xs (see perlxs manual) >> gcc -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe >> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE >> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector >> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic >> -fasynchronous-unwind-tables -DVERSION=\"1.01\" >> -DXS_VERSION=\"1.01\" >> -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE" >> -DLITTLE_ENDIAN SCF.c >> Running Mkbootstrap for Bio::SCF () >> chmod 644 SCF.bs >> rm -f blib/arch/auto/Bio/SCF/SCF.so >> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions >> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 >> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib SCF.o -o >> blib/arch/auto/Bio/SCF/SCF.so \ >> -lread -lz \ >> >> chmod 755 blib/arch/auto/Bio/SCF/SCF.so >> cp SCF.bs blib/arch/auto/Bio/SCF/SCF.bs >> chmod 644 blib/arch/auto/Bio/SCF/SCF.bs >> Manifying blib/man3/Bio::SCF.3pm >> >> $ make test >> ----------- >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> t/scf....Can't load >> '/home/meyniel/Desktop/Bio-SCF-1.01/blib/arch/auto/Bio/SCF/SCF.so' for >> module Bio::SCF: >> /home/meyniel/Desktop/Bio-SCF-1.01/blib/arch/auto/Bio/SCF/SCF.so: >> undefined symbol: curl_easy_setopt at >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230. >> at t/scf.t line 23 >> Compilation failed in require at t/scf.t line 23. >> BEGIN failed--compilation aborted at t/scf.t line 23. >> t/scf....dubious >> Test returned status 2 (wstat 512, 0x200) >> DIED. FAILED tests 1-18 >> Failed 18/18 tests, 0.00% okay >> Failed Test Stat Wstat Total Fail Failed List of Failed >> >>
> ------------------------------------------------------------------------------- >
>> t/scf.t 2 512 18 36 200.00% 1-18 >> Failed 1/1 test scripts, 0.00% okay. 18/18 subtests failed, 0.00% >> okay. >> make: *** [test_dynamic] Erreur 2 >> >> The informations about my computer are : >> Fedora core >> $ uname -a : Linux simap 2.6.18-1.2798.fc6 #1 SMP Mon Oct 16 14:37:32 >> EDT >> 2006 i686 i686 i386 GNU/Linux >> $perl -v : perl, v5.8.8 built for i386-linux-thread-multi >> >> If you require any further information, feel free to contact me. >> >> Thank you very much, >> >> Yours faithfully >> >> LM >> >> >> >> >> >> >>
> > > > >
  Fri Oct 19 09:32:35 2007 meyniel [...] cervi-lyon.inserm.fr - Correspondence added
Subject: Re: [rt.cpan.org #30092] Problem with Bio::SCF install
Date: Fri, 19 Oct 2007 15:29:52 +0200
To: bug-Bio-SCF [...] rt.cpan.org
From: meyniel laurene <meyniel [...] cervi-lyon.inserm.fr>
I have disabled the firewall and the SELinux protection, the tests are successfull and the install too :) Thank you for your help abour lcurl! LM Lincoln_D_Stein via RT a écrit : Show quoted text
> <URL: http://rt.cpan.org/Ticket/Display.html?id=30092 > > > One of your auxiliary libraries, either libz or libread, seems to have > been compiled for libcurl, a library for manipulating URLs. Neither the > vanilla libz or libread (Staden) libraries do this, and so I guess that > you are using some patched version that is specific to your linux vendor. > > You can probably fix this by modifying the 'LIBS' option in Makefile.PL > to read: > > 'LIBS' => ['-lcurl -lread -lz'] > > However, I would be interested in knowing who the culprit is. Could you > run the following commands to search for the curl symbols? > > % strings /usr/lib/libz.a | grep -i curl > % strings /usr/local/lib/libread.a | grep -i curl > % strings `which perl` | grep -i curl > > You may need to modify the paths to find the correct libraries and > executables on your system. > > Lincoln > > On Thu Oct 18 11:09:45 2007, meyniel@cervi-lyon.inserm.fr wrote: >
>> Hello, >> >> I'm experiencing problems with the installation of Bio::SCF, can you >> help me? >> >> I downloaded it from http://rt.cpan.org/, then I uncompressed it and >> tried >> to install it according to the INSTALL file : >> >> $ perl Makefile.PL >> ------------------ >> Checking if your kit is complete... >> Looks good >> Writing Makefile for Bio::SCF >> >> $ make >> ------ >> cp SCF.pm blib/lib/Bio/SCF.pm >> cp SCF/Arrays.pm blib/lib/Bio/SCF/Arrays.pm >> /usr/bin/perl /usr/lib/perl5/5.8.8/ExtUtils/xsubpp -typemap >> /usr/lib/perl5/5.8.8/ExtUtils/typemap SCF.xs > SCF.xsc && mv SCF.xsc >> SCF.c >> Please specify prototyping behavior for SCF.xs (see perlxs manual) >> gcc -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe >> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE >> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall >> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector >> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic >> -fasynchronous-unwind-tables -DVERSION=\"1.01\" >> -DXS_VERSION=\"1.01\" >> -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE" >> -DLITTLE_ENDIAN SCF.c >> Running Mkbootstrap for Bio::SCF () >> chmod 644 SCF.bs >> rm -f blib/arch/auto/Bio/SCF/SCF.so >> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions >> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 >> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib SCF.o -o >> blib/arch/auto/Bio/SCF/SCF.so \ >> -lread -lz \ >> >> chmod 755 blib/arch/auto/Bio/SCF/SCF.so >> cp SCF.bs blib/arch/auto/Bio/SCF/SCF.bs >> chmod 644 blib/arch/auto/Bio/SCF/SCF.bs >> Manifying blib/man3/Bio::SCF.3pm >> >> $ make test >> ----------- >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> t/scf....Can't load >> '/home/meyniel/Desktop/Bio-SCF-1.01/blib/arch/auto/Bio/SCF/SCF.so' for >> module Bio::SCF: >> /home/meyniel/Desktop/Bio-SCF-1.01/blib/arch/auto/Bio/SCF/SCF.so: >> undefined symbol: curl_easy_setopt at >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line 230. >> at t/scf.t line 23 >> Compilation failed in require at t/scf.t line 23. >> BEGIN failed--compilation aborted at t/scf.t line 23. >> t/scf....dubious >> Test returned status 2 (wstat 512, 0x200) >> DIED. FAILED tests 1-18 >> Failed 18/18 tests, 0.00% okay >> Failed Test Stat Wstat Total Fail Failed List of Failed >> >>
> ------------------------------------------------------------------------------- >
>> t/scf.t 2 512 18 36 200.00% 1-18 >> Failed 1/1 test scripts, 0.00% okay. 18/18 subtests failed, 0.00% >> okay. >> make: *** [test_dynamic] Erreur 2 >> >> The informations about my computer are : >> Fedora core >> $ uname -a : Linux simap 2.6.18-1.2798.fc6 #1 SMP Mon Oct 16 14:37:32 >> EDT >> 2006 i686 i686 i386 GNU/Linux >> $perl -v : perl, v5.8.8 built for i386-linux-thread-multi >> >> If you require any further information, feel free to contact me. >> >> Thank you very much, >> >> Yours faithfully >> >> LM >> >> >> >> >> >> >>
> > > > >
  Fri Oct 19 12:19:47 2007 LDS [...] cpan.org - Correspondence added
From: LDS [...] cpan.org
It must be SELinux that was causing the problem. Sorry I didn't think of that! On Fri Oct 19 09:32:35 2007, meyniel@cervi-lyon.inserm.fr wrote: Show quoted text
> I have disabled the firewall and the SELinux protection, the tests are > successfull and the install too :) > > Thank you for your help abour lcurl! > > LM > > Lincoln_D_Stein via RT a écrit :
> > <URL: http://rt.cpan.org/Ticket/Display.html?id=30092 > > > > > One of your auxiliary libraries, either libz or libread, seems to
> have
> > been compiled for libcurl, a library for manipulating URLs. Neither
> the
> > vanilla libz or libread (Staden) libraries do this, and so I guess
> that
> > you are using some patched version that is specific to your linux
> vendor.
> > > > You can probably fix this by modifying the 'LIBS' option in
> Makefile.PL
> > to read: > > > > 'LIBS' => ['-lcurl -lread -lz'] > > > > However, I would be interested in knowing who the culprit is. Could
> you
> > run the following commands to search for the curl symbols? > > > > % strings /usr/lib/libz.a | grep -i curl > > % strings /usr/local/lib/libread.a | grep -i curl > > % strings `which perl` | grep -i curl > > > > You may need to modify the paths to find the correct libraries and > > executables on your system. > > > > Lincoln > > > > On Thu Oct 18 11:09:45 2007, meyniel@cervi-lyon.inserm.fr wrote: > >
> >> Hello, > >> > >> I'm experiencing problems with the installation of Bio::SCF, can
> you
> >> help me? > >> > >> I downloaded it from http://rt.cpan.org/, then I uncompressed it
> and
> >> tried > >> to install it according to the INSTALL file : > >> > >> $ perl Makefile.PL > >> ------------------ > >> Checking if your kit is complete... > >> Looks good > >> Writing Makefile for Bio::SCF > >> > >> $ make > >> ------ > >> cp SCF.pm blib/lib/Bio/SCF.pm > >> cp SCF/Arrays.pm blib/lib/Bio/SCF/Arrays.pm > >> /usr/bin/perl /usr/lib/perl5/5.8.8/ExtUtils/xsubpp -typemap > >> /usr/lib/perl5/5.8.8/ExtUtils/typemap SCF.xs > SCF.xsc && mv
> SCF.xsc
> >> SCF.c > >> Please specify prototyping behavior for SCF.xs (see perlxs manual) > >> gcc -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe > >> -Wdeclaration-after-statement -I/usr/local/include
> -D_LARGEFILE_SOURCE
> >> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall > >> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > >> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic > >> -fasynchronous-unwind-tables -DVERSION=\"1.01\" > >> -DXS_VERSION=\"1.01\" > >> -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE" > >> -DLITTLE_ENDIAN SCF.c > >> Running Mkbootstrap for Bio::SCF () > >> chmod 644 SCF.bs > >> rm -f blib/arch/auto/Bio/SCF/SCF.so > >> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
> -fexceptions
> >> -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 > >> -mtune=generic -fasynchronous-unwind-tables -L/usr/local/lib SCF.o
> -o
> >> blib/arch/auto/Bio/SCF/SCF.so \ > >> -lread -lz \ > >> > >> chmod 755 blib/arch/auto/Bio/SCF/SCF.so > >> cp SCF.bs blib/arch/auto/Bio/SCF/SCF.bs > >> chmod 644 blib/arch/auto/Bio/SCF/SCF.bs > >> Manifying blib/man3/Bio::SCF.3pm > >> > >> $ make test > >> ----------- > >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > >> t/scf....Can't load > >> '/home/meyniel/Desktop/Bio-SCF-1.01/blib/arch/auto/Bio/SCF/SCF.so'
> for
> >> module Bio::SCF: > >> /home/meyniel/Desktop/Bio-SCF-1.01/blib/arch/auto/Bio/SCF/SCF.so: > >> undefined symbol: curl_easy_setopt at > >> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/DynaLoader.pm line
> 230.
> >> at t/scf.t line 23 > >> Compilation failed in require at t/scf.t line 23. > >> BEGIN failed--compilation aborted at t/scf.t line 23. > >> t/scf....dubious > >> Test returned status 2 (wstat 512, 0x200) > >> DIED. FAILED tests 1-18 > >> Failed 18/18 tests, 0.00% okay > >> Failed Test Stat Wstat Total Fail Failed List of Failed > >> > >>
> >
>
------------------------------------------------------------------------------- Show quoted text
> >
> >> t/scf.t 2 512 18 36 200.00% 1-18 > >> Failed 1/1 test scripts, 0.00% okay. 18/18 subtests failed, 0.00% > >> okay. > >> make: *** [test_dynamic] Erreur 2 > >> > >> The informations about my computer are : > >> Fedora core > >> $ uname -a : Linux simap 2.6.18-1.2798.fc6 #1 SMP Mon Oct 16
> 14:37:32
> >> EDT > >> 2006 i686 i686 i386 GNU/Linux > >> $perl -v : perl, v5.8.8 built for i386-linux-thread-multi > >> > >> If you require any further information, feel free to contact me. > >> > >> Thank you very much, > >> > >> Yours faithfully > >> > >> LM > >> > >> > >> > >> > >> > >> > >>
> > > > > > > > > >
>
  Fri Oct 19 12:20:30 2007 LDS [...] cpan.org - Status changed from 'open' to 'resolved'