Dumper.c: loadable library and perl binaries are mismatched (got handshake key 0xdb00080, needed 0xde00080)

[p5pRT]

Migrated from rt.perl.org#133545 (status was 'open')

Searchable as RT133545$

[p5pRT]

From [email protected]

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

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
  .

[p5pRT]

From @jkeenan

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.

--
James E Keenan (jkeenan@​cpan.org)

[p5pRT]

The RT System itself - Status changed from 'new' to 'open'

[p5pRT]

From @Leont

On Sun, Sep 30, 2018 at 12​:47 AM James E Keenan via RT
<perlbug-followup@​perl.org> wrote​:

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

[jkeenan]

From @jkeenan

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?

Since we have not heard back from the original poster in more than 2 years, I propose we close this ticket in 14 days. Self-assigning for that purpose.

Thank you very much.
Jim Keenan

[phbrito]

I do not recall to have seen your reply at the time, apologies for that.
You can close this ticket. I am not working with this machine anymore.