Skip Menu |
Report information
Id: 133545
Status: open
Priority: 0/
Queue: perl5

Owner: Nobody
Requestors: patricia.brito [at] nms.unl.pt
Cc:
AdminCc:

Operating System: (no value)
PatchStatus: (no value)
Severity: low
Type: unknown
Perl Version: (no value)
Fixed In: (no value)



Date: Thu, 27 Sep 2018 10:20:44 +0000
Subject: Dumper.c: loadable library and perl binaries are mismatched (got handshake key 0xdb00080, needed 0xde00080)
To: "perlbug [...] perl.org" <perlbug [...] perl.org>
From: Patricia Brito <patricia.brito [...] nms.unl.pt>

Hi,

I  need some help regarding the way to fix some incompatibility issues between loadable library and perl binaries.


End goal is to be able to run the following application:

https://github.com/tseemann/mlst


I am working on a Ubuntu machine and using conda to install the packages that I need. Recently I need to install this mlst software and to avoid incompatibilities between perl versions (!!) decided to do that inside a new virtual environment. I am wondering if perl still reads files outside the virtual environment and if that is the reason for the error message.

Any help is deeply appreciated as I do not know how to fix this.


I pasted below the info from perl -V

Thanks!

Patrícia


Summary of my perl5 (revision 5 version 26 subversion 2) configuration:
   
  Platform:
    osname=linux
    osvers=4.4.0-96-generic
    archname=x86_64-linux-thread-multi
    uname='linux 1d1a811e559a 4.4.0-96-generic #119~14.04.1-ubuntu smp wed sep 13 08:40:48 utc 2017 x86_64 x86_64 x86_64 gnulinux '
    config_args='-de -Dprefix=/home/ubuntu/miniconda3/envs/mlst -Dusethreads -Duserelocatableinc -Dcccdlflags=-fPIC -Dldflags= -Wl,-rpath,/home/ubuntu/miniconda3/envs/mlst/lib -L/home/ubuntu/miniconda3/envs/mlst/lib -Ddefault_inc_excludes_dot=n -Dcc=gcc'
    hint=recommended
    useposix=true
    d_sigaction=define
    useithreads=define
    usemultiplicity=define
    use64bitint=define
    use64bitall=define
    uselongdouble=undef
    usemymalloc=n
    default_inc_excludes_dot=undef
    bincompat5005=undef
  Compiler:
    cc='gcc'
    ccflags ='-D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2'
    optimize='-O2'
    cppflags='-D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include'
    ccversion=''
    gccversion='4.8.2 20140120 (Red Hat 4.8.2-15)'
    gccosandvers=''
    intsize=4
    longsize=8
    ptrsize=8
    doublesize=8
    byteorder=12345678
    doublekind=3
    d_longlong=define
    longlongsize=8
    d_longdbl=define
    longdblsize=16
    longdblkind=3
    ivtype='long'
    ivsize=8
    nvtype='double'
    nvsize=8
    Off_t='off_t'
    lseeksize=8
    alignbytes=8
    prototype=define
  Linker and Libraries:
    ld='gcc'
    ldflags =' -Wl,-rpath,/home/ubuntu/miniconda3/envs/mlst/lib -L/home/ubuntu/miniconda3/envs/mlst/lib -fstack-protector-strong -L/usr/local/lib'
    libpth=/usr/local/lib /opt/rh/devtoolset-2/root/usr/lib /usr/lib /lib/../lib64 /usr/lib/../lib64 /lib /lib64 /usr/lib64 /usr/local/lib64
    libs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
    perllibs=-lpthread -lnsl -ldl -lm -lcrypt -lutil -lc
    libc=libc-2.12.so
    so=so
    useshrplib=false
    libperl=libperl.a
    gnulibc_version='2.12'
  Dynamic Linking:
    dlsrc=dl_dlopen.xs
    dlext=so
    d_dlsymun=undef
    ccdlflags='-Wl,-E'
    cccdlflags='-fPIC'
    lddlflags='-shared -O2 -L/home/ubuntu/miniconda3/envs/mlst/lib -L/usr/local/lib -fstack-protector-strong'


Characteristics of this binary (from libperl):
  Compile-time options:
    HAS_TIMES
    MULTIPLICITY
    PERLIO_LAYERS
    PERL_COPY_ON_WRITE
    PERL_DONT_CREATE_GVSV
    PERL_IMPLICIT_CONTEXT
    PERL_MALLOC_WRAP
    PERL_OP_PARENT
    PERL_PRESERVE_IVUV
    USE_64_BIT_ALL
    USE_64_BIT_INT
    USE_ITHREADS
    USE_LARGE_FILES
    USE_LOCALE
    USE_LOCALE_COLLATE
    USE_LOCALE_CTYPE
    USE_LOCALE_NUMERIC
    USE_LOCALE_TIME
    USE_PERLIO
    USE_PERL_ATOF
    USE_REENTRANT_API
  Built under linux
  Compiled at Jul  6 2018 15:53:32
  %ENV:
    PERL5LIB="/home/ubuntu/miniconda3/lib/perl5/site_perl/5.22.0"
  @INC:
    /home/ubuntu/miniconda3/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi
    /home/ubuntu/miniconda3/lib/perl5/site_perl/5.22.0
    /home/ubuntu/miniconda3/envs/mlst/lib/site_perl/5.26.2/x86_64-linux-thread-multi
    /home/ubuntu/miniconda3/envs/mlst/lib/site_perl/5.26.2
    /home/ubuntu/miniconda3/envs/mlst/lib/5.26.2/x86_64-linux-thread-multi
    /home/ubuntu/miniconda3/envs/mlst/lib/5.26.2
    .




RT-Send-CC: perl5-porters [...] perl.org
On Thu, 27 Sep 2018 10:21:17 GMT, patricia.brito@nms.unl.pt wrote: Show quoted text
> Hi, > > I need some help regarding the way to fix some incompatibility issues > between loadable library and perl binaries. > > > End goal is to be able to run the following application: > > <https://github.com/tseemann/mlst/blob/master/README.md>https://github.com/tseemann/mlst > > > I am working on a Ubuntu machine and using conda to install the > packages that I need. Recently I need to install this mlst software > and to avoid incompatibilities between perl versions (!!) decided to > do that inside a new virtual environment. I am wondering if perl still > reads files outside the virtual environment and if that is the reason > for the error message. > > Any help is deeply appreciated as I do not know how to fix this. > > > I pasted below the info from perl -V > > Thanks! > > Patrícia >
Can you provide more of the sequence of commands that culminated in the error message? Thank you very much. -- James E Keenan (jkeenan@cpan.org)
To: perlbug <perlbug-followup [...] perl.org>
Subject: Re: [perl #133545] Dumper.c: loadable library and perl binaries are mismatched (got handshake key 0xdb00080, needed 0xde00080)
Date: Sun, 30 Sep 2018 01:32:12 +0200
From: Leon Timmermans <fawaka [...] gmail.com>
CC: Perl5 Porters <perl5-porters [...] perl.org>
Download (untitled) / with headers
text/plain 1.2k
On Sun, Sep 30, 2018 at 12:47 AM James E Keenan via RT <perlbug-followup@perl.org> wrote: Show quoted text
> On Thu, 27 Sep 2018 10:21:17 GMT, patricia.brito@nms.unl.pt wrote:
> > Hi, > > > > I need some help regarding the way to fix some incompatibility issues > > between loadable library and perl binaries. > > > > > > End goal is to be able to run the following application: > > > > <https://github.com/tseemann/mlst/blob/master/README.md>https://github.com/tseemann/mlst > > > > > > I am working on a Ubuntu machine and using conda to install the > > packages that I need. Recently I need to install this mlst software > > and to avoid incompatibilities between perl versions (!!) decided to > > do that inside a new virtual environment. I am wondering if perl still > > reads files outside the virtual environment and if that is the reason > > for the error message. > > > > Any help is deeply appreciated as I do not know how to fix this. > > > > > > I pasted below the info from perl -V > > > > Thanks! > > > > Patrícia > >
> > Can you provide more of the sequence of commands that culminated in the error message? > > Thank you very much.
It's sounds like a cousin of #133440, though indeed we need more information to understand what's going on. Leon


This service is sponsored and maintained by Best Practical Solutions and runs on Perl.org infrastructure.

For issues related to this RT instance (aka "perlbug"), please contact perlbug-admin at perl.org