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Bio::SCF installation error !

by jnarayan81 (Sexton)
on Mar 16, 2020 at 10:10 UTC ( #11114335=perlquestion: print w/replies, xml ) Need Help??

jnarayan81 has asked for the wisdom of the Perl Monks concerning the following question:

Hi Monks, I am having difficulties installing Bio::SCF ( https://metacpan.org/release/LDS/Bio-SCF-1.01 ) packages. My earlier attempts were successful (https://bioinformaticsonline.com/pages/view/36185/installing-bioscf-perl-module), but this time it got little messy. It return following errors, can you please enlightens me with your experience.

$/Bio-SCF-1.03$ make cp SCF/Arrays.pm blib/lib/Bio/SCF/Arrays.pm cp SCF.pm blib/lib/Bio/SCF.pm Running Mkbootstrap for SCF () chmod 644 "SCF.bs" "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SCF.bs bli +b/arch/auto/Bio/SCF/SCF.bs 644 "/usr/bin/perl" "/usr/local/share/perl/5.26.1/ExtUtils/xsubpp" -typem +ap '/usr/share/perl/5.26/ExtUtils/typemap' SCF.xs > SCF.xsc Please specify prototyping behavior for SCF.xs (see perlxs manual) mv SCF.xsc SCF.c x86_64-linux-gnu-gcc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv +-fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE - +D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.03\" -DXS_VERSION=\"1.03 +\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.26/CORE" -DLITTLE_ENDIA +N SCF.c In file included from /usr/lib/x86_64-linux-gnu/perl/5.26/CORE/perl.h: +5644:0, from SCF.xs:5: SCF.xs: In function ‘XS_Bio__SCF_get_scf_pointer’: SCF.xs:57:20: warning: cast from pointer to integer of different size +[-Wpointer-to-int-cast] ret_val = newSViv((int)scf_data); ^ /usr/lib/x86_64-linux-gnu/perl/5.26/CORE/embed.h:413:40: note: in defi +nition of macro ‘newSViv’ #define newSViv(a) Perl_newSViv(aTHX_ a) ^ SCF.xs: In function ‘XS_Bio__SCF_get_scf_fpointer’: SCF.xs:80:20: warning: cast from pointer to integer of different size +[-Wpointer-to-int-cast] ret_val = newSViv((int)scf_data); ^ /usr/lib/x86_64-linux-gnu/perl/5.26/CORE/embed.h:413:40: note: in defi +nition of macro ‘newSViv’ #define newSViv(a) Perl_newSViv(aTHX_ a) ^ SCF.xs: In function ‘XS_Bio__SCF_scf_free’: SCF.xs:89:17: warning: cast to pointer from integer of different size +[-Wint-to-pointer-cast] scf_deallocate((Scf *)scf_pointer); ^ SCF.xs: In function ‘XS_Bio__SCF_get_comments’: SCF.xs:95:18: warning: cast to pointer from integer of different size +[-Wint-to-pointer-cast] Scf *scf_data = (Scf *)scf_pointer; ^ SCF.xs: In function ‘XS_Bio__SCF_set_comments’: SCF.xs:108:18: warning: cast to pointer from integer of different size + [-Wint-to-pointer-cast] Scf *scf_data = (Scf *)scf_pointer; ^ SCF.xs: In function ‘XS_Bio__SCF_scf_write’: SCF.xs:121:18: warning: cast to pointer from integer of different size + [-Wint-to-pointer-cast] Scf *scf_data = (Scf *)scf_pointer; ^ SCF.xs: In function ‘XS_Bio__SCF_scf_fwrite’: SCF.xs:137:18: warning: cast to pointer from integer of different size + [-Wint-to-pointer-cast] Scf *scf_data = (Scf *)scf_pointer; ^ SCF.xs: In function ‘XS_Bio__SCF_get_from_header’: SCF.xs:159:18: warning: cast to pointer from integer of different size + [-Wint-to-pointer-cast] Scf *scf_data = (Scf *)scf_pointer; ^ SCF.xs: In function ‘XS_Bio__SCF_get_at’: SCF.xs:186:18: warning: cast to pointer from integer of different size + [-Wint-to-pointer-cast] Scf *scf_data = (Scf *)scf_pointer; ^ SCF.xs: In function ‘XS_Bio__SCF_set_base_at’: SCF.xs:242:18: warning: cast to pointer from integer of different size + [-Wint-to-pointer-cast] Scf *scf_data = (Scf *)scf_pointer; ^ SCF.xs: In function ‘XS_Bio__SCF_set_at’: SCF.xs:255:18: warning: cast to pointer from integer of different size + [-Wint-to-pointer-cast] Scf *scf_data = (Scf *)scf_pointer; ^ rm -f blib/arch/auto/Bio/SCF/SCF.so LD_RUN_PATH="/usr/local/lib" x86_64-linux-gnu-gcc -shared -L/usr/loca +l/lib -fstack-protector-strong SCF.o -o blib/arch/auto/Bio/SCF/SCF. +so \ -lstaden-read -lz \ chmod 755 blib/arch/auto/Bio/SCF/SCF.so Manifying 1 pod document $/Bio-SCF-1.03$ make test "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SCF.bs bli +b/arch/auto/Bio/SCF/SCF.bs 644 PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::H +arness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/l +ib', 'blib/arch')" t/*.t t/scf.t .. Failed 17/18 subtests Test Summary Report ------------------- t/scf.t (Wstat: 139 Tests: 1 Failed: 0) Non-zero wait status: 139 Parse errors: Bad plan. You planned 18 tests but ran 1. Files=1, Tests=1, 1 wallclock secs ( 0.02 usr 0.01 sys + 0.12 cusr + 0.02 csys = 0.17 CPU) Result: FAIL Failed 1/1 test programs. 0/1 subtests failed.

Replies are listed 'Best First'.
Re: Bio::SCF installation error !
by hippo (Bishop) on Mar 16, 2020 at 10:19 UTC

    There are a significant number of test failures, particularly on Linux. You might benefit from reading and following the remedy in this issue as you appear to be on a 64-bit platform. HTH.

Re: Bio::SCF installation error !
by marto (Cardinal) on Mar 16, 2020 at 10:25 UTC
Re: Bio::SCF installation error !
by jnarayan81 (Sexton) on Mar 16, 2020 at 12:17 UTC

    Hi, After exhaustive search, I found updated package at https://launchpad.net/ubuntu/+source/libbio-scf-perl

    Following command works for me on Ubuntu

    sudo apt-get install libbio-scf-perl

      If you are using the system perl you should use your systems package manager to install modules if at all possible. This package includes the patch referenced earlier.

        Corollary: be wary using the OS' perl because that then puts your application (whatever your particular value of "application" might be) at the mercy of the OS' upgrade schedule. If you're doing anything significant use perlbrew or the like to build your own, separate perl; then use that install to install CPAN modules and run your code. You'll be glad for the decoupling when the system upgrade pulls in something that would break your application code.

        The cake is a lie.
        The cake is a lie.
        The cake is a lie.

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