Can't locate JSON/RPC/Client.pm in @INC

[jpaganini]

I'm having an issue when running the command

echo "kb|g.0" | genomes_to_contigs | contigs_to_sequences > E_coli.contig
the error is

Can't locate JSON/RPC/Client.pm in @inc (you may need to install the JSON::RPC::Client module) (@inc contains: /usr/share/rasttk/deployment/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /usr/share/rasttk/deployment/lib/Bio/KBase/CDMI/Client.pm line 3.
BEGIN failed--compilation aborted at /usr/share/rasttk/deployment/lib/Bio/KBase/CDMI/Client.pm line 3.
Compilation failed in require at /usr/share/rasttk/deployment/lib/Bio/KBase/CDMI/CDMIClient.pm line 4.
BEGIN failed--compilation aborted at /usr/share/rasttk/deployment/lib/Bio/KBase/CDMI/CDMIClient.pm line 4.
Compilation failed in require at /usr/share/rasttk/deployment/plbin/genomes_to_contigs.pl line 58.
BEGIN failed--compilation aborted at /usr/share/rasttk/deployment/plbin/genomes_to_contigs.pl line 58.
Can't locate JSON/RPC/Client.pm in @inc (you may need to install the JSON::RPC::Client module) (@inc contains: /usr/share/rasttk/deployment/lib /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /usr/share/rasttk/deployment/lib/Bio/KBase/CDMI/Client.pm line 3.
BEGIN failed--compilation aborted at /usr/share/rasttk/deployment/lib/Bio/KBase/CDMI/Client.pm line 3.
Compilation failed in require at /usr/share/rasttk/deployment/lib/Bio/KBase/CDMI/CDMIClient.pm line 4.
BEGIN failed--compilation aborted at /usr/share/rasttk/deployment/lib/Bio/KBase/CDMI/CDMIClient.pm line 4.
Compilation failed in require at /usr/share/rasttk/deployment/plbin/contigs_to_sequences.pl line 64.
BEGIN failed--compilation aborted at /usr/share/rasttk/deployment/plbin/contigs_to_sequences.pl line 64.

I have already downloaded the json rpc client v 0.96 and installed it in my home directory. I also defined the enviromental variable PERL5LIB in .bashrc to include the location of the module JSON::RPC::Client, as follows:

export PERL5LIB=/home/location_of_the_file

I'm really lost here guys. Thanks in advance for any help you can provide.

[olsonanl]

Which release did you install, and on which operating system?

[jpaganini]

HI there, I installed the release 1.3.0 on Ubuntu 16.04

[olsonanl]

If you can, please try installing this:

https://github.com/PATRIC3/PATRIC-distribution/releases/tag/1.018

Depending on what you are trying to do, you should see the basic functionality you're looking for in the PATRIC CLI releases.

What is it you are trying to run? Your example was from looking up KBase data from its database; that project is no longer maintaining the genome database in that form.

There is documentation available here:

http://docs.patricbrc.org/cli_tutorial/cli_installation.html

[mjoppich]

One question: did installing PATRIC3 help?

I only solved this issue when installing an old package for libjson-rpc-perl RPM Seek

Apparently newer versions of libjson-rpc have a different API ....

[glucksfall]

I really too late, but...
For the perl missing library, install with sudo cpanm JSON::RPC::Client

[EthanGladius]

I really too late, but... For the perl missing library, install with sudo cpanm JSON::RPC::Client

Hi @glucksfall, seems that cpanm doesn't have the module JSON::RPC::Clientanymore... any alternatives?

[glucksfall]

Hi @EthanGladius,

That's a big problem. If you find a replacement from cpan (can it be this https://metacpan.org/pod/JSON::RPC::Legacy::Client??), you will need to modify manually all the matches to the new dependency:

data/usr/share/rasttk/deployment/lib/IDServerAPIClient.pm:use JSON::RPC::Client;
data/usr/share/rasttk/deployment/lib/IDServerAPIClient.pm:	client => JSON::RPC::Client->new,
data/usr/share/rasttk/deployment/lib/Bio/ModelSEED/MSSeedSupportServer/Client.pm:use JSON::RPC::Client;
data/usr/share/rasttk/deployment/lib/Bio/ModelSEED/MSSeedSupportServer/Client.pm:use base 'JSON::RPC::Client';
data/usr/share/rasttk/deployment/lib/Bio/ModelSEED/MSSeedSupportServer/Client.pm:# Override JSON::RPC::Client::call because it doesn't handle error returns properly.
data/usr/share/rasttk/deployment/lib/Bio/ModelSEED/MSSeedSupportServer/Client.pm:            $obj->{id} = $self->id || ($self->id('JSON::RPC::Client'));
data/usr/share/rasttk/deployment/lib/Bio/KBase/userandjobstate/Client.pm:use JSON::RPC::Client;
data/usr/share/rasttk/deployment/lib/Bio/KBase/userandjobstate/Client.pm:use base 'JSON::RPC::Client';
data/usr/share/rasttk/deployment/lib/Bio/KBase/userandjobstate/Client.pm:# Override JSON::RPC::Client::call because it doesn't handle error returns properly.
data/usr/share/rasttk/deployment/lib/Bio/KBase/userandjobstate/Client.pm:            $obj->{id} = $self->id || ($self->id('JSON::RPC::Client'));
data/usr/share/rasttk/deployment/lib/Bio/KBase/fbaModelServices/Client.pm:use JSON::RPC::Client;
data/usr/share/rasttk/deployment/lib/Bio/KBase/fbaModelServices/Client.pm:use base 'JSON::RPC::Client';
data/usr/share/rasttk/deployment/lib/Bio/KBase/fbaModelServices/Client.pm:# Override JSON::RPC::Client::call because it doesn't handle error returns properly.
data/usr/share/rasttk/deployment/lib/Bio/KBase/fbaModelServices/Client.pm:            $obj->{id} = $self->id || ($self->id('JSON::RPC::Client'));
data/usr/share/rasttk/deployment/lib/Bio/KBase/AbstractHandle/Client.pm:use JSON::RPC::Client;
data/usr/share/rasttk/deployment/lib/Bio/KBase/AbstractHandle/Client.pm:use base 'JSON::RPC::Client';
data/usr/share/rasttk/deployment/lib/Bio/KBase/AbstractHandle/Client.pm:# Override JSON::RPC::Client::call because it doesn't handle error returns properly.
data/usr/share/rasttk/deployment/lib/Bio/KBase/AbstractHandle/Client.pm:            $obj->{id} = $self->id || ($self->id('JSON::RPC::Client'));
data/usr/share/rasttk/deployment/lib/Bio/KBase/CDMI/Client.pm:use JSON::RPC::Client;
data/usr/share/rasttk/deployment/lib/Bio/KBase/CDMI/Client.pm:use base 'JSON::RPC::Client';
data/usr/share/rasttk/deployment/lib/Bio/KBase/CDMI/Client.pm:# Override JSON::RPC::Client::call because it doesn't handle error returns properly.
data/usr/share/rasttk/deployment/lib/Bio/KBase/CDMI/Client.pm:            $obj->{id} = $self->id || ($self->id('JSON::RPC::Client'));
data/usr/share/rasttk/deployment/lib/Bio/KBase/workspace/Client.pm:use JSON::RPC::Client;
data/usr/share/rasttk/deployment/lib/Bio/KBase/workspace/Client.pm:use base 'JSON::RPC::Client';
data/usr/share/rasttk/deployment/lib/Bio/KBase/workspace/Client.pm:# Override JSON::RPC::Client::call because it doesn't handle error returns properly.
data/usr/share/rasttk/deployment/lib/Bio/KBase/workspace/Client.pm:            $obj->{id} = $self->id || ($self->id('JSON::RPC::Client'));
data/usr/share/rasttk/deployment/lib/Bio/KBase/KIDL/client_stub.tt:use JSON::RPC::Client;
data/usr/share/rasttk/deployment/lib/Bio/KBase/KIDL/client_stub.tt:use base 'JSON::RPC::Client';
data/usr/share/rasttk/deployment/lib/Bio/KBase/KIDL/client_stub.tt:# Override JSON::RPC::Client::call because it doesn't handle error returns properly.
data/usr/share/rasttk/deployment/lib/Bio/KBase/KIDL/client_stub.tt:            $obj->{id} = $self->id || ($self->id('JSON::RPC::Client'));
data/usr/share/rasttk/deployment/lib/Bio/KBase/GenomeAnnotation/Client.pm:use JSON::RPC::Client;
data/usr/share/rasttk/deployment/lib/Bio/KBase/GenomeAnnotation/Client.pm:use base 'JSON::RPC::Client';
data/usr/share/rasttk/deployment/lib/Bio/KBase/GenomeAnnotation/Client.pm:# Override JSON::RPC::Client::call because it doesn't handle error returns properly.
data/usr/share/rasttk/deployment/lib/Bio/KBase/GenomeAnnotation/Client.pm:            $obj->{id} = $self->id || ($self->id('JSON::RPC::Client'));
data/usr/share/rasttk/deployment/lib/Bio/KBase/KmerAnnotationByFigfam/Client.pm:use JSON::RPC::Client;
data/usr/share/rasttk/deployment/lib/Bio/KBase/KmerAnnotationByFigfam/Client.pm:use base 'JSON::RPC::Client';
data/usr/share/rasttk/deployment/lib/Bio/KBase/KmerAnnotationByFigfam/Client.pm:# Override JSON::RPC::Client::call because it doesn't handle error returns properly.
data/usr/share/rasttk/deployment/lib/Bio/KBase/KmerAnnotationByFigfam/Client.pm:            $obj->{id} = $self->id || ($self->id('JSON::RPC::Client'));
data/usr/share/rasttk/deployment/lib/Bio/KBase/KmerEval/Client.pm:use JSON::RPC::Client;
data/usr/share/rasttk/deployment/lib/Bio/KBase/KmerEval/Client.pm:use base 'JSON::RPC::Client';
data/usr/share/rasttk/deployment/lib/Bio/KBase/KmerEval/Client.pm:# Override JSON::RPC::Client::call because it doesn't handle error returns properly.
data/usr/share/rasttk/deployment/lib/Bio/KBase/KmerEval/Client.pm:            $obj->{id} = $self->id || ($self->id('JSON::RPC::Client'));
data/usr/share/rasttk/deployment/lib/Bio/KBase/InvocationService/Client.pm:use JSON::RPC::Client;
data/usr/share/rasttk/deployment/lib/Bio/KBase/InvocationService/Client.pm:use base 'JSON::RPC::Client';
data/usr/share/rasttk/deployment/lib/Bio/KBase/InvocationService/Client.pm:# Override JSON::RPC::Client::call because it doesn't handle error returns properly.
data/usr/share/rasttk/deployment/lib/Bio/KBase/InvocationService/Client.pm:            $obj->{id} = $self->id || ($self->id('JSON::RPC::Client'));
data/usr/share/rasttk/deployment/lib/Bio/KBase/InvocationService/.#Client.pm.1.2:use JSON::RPC::Client;
data/usr/share/rasttk/deployment/lib/Bio/KBase/InvocationService/.#Client.pm.1.2:use base 'JSON::RPC::Client';
data/usr/share/rasttk/deployment/lib/Bio/KBase/InvocationService/.#Client.pm.1.2:# Override JSON::RPC::Client::call because it doesn't handle error returns properly.
data/usr/share/rasttk/deployment/lib/Bio/KBase/IDServer/Client.pm:use JSON::RPC::Client;
data/usr/share/rasttk/deployment/lib/Bio/KBase/IDServer/Client.pm:use base 'JSON::RPC::Client';
data/usr/share/rasttk/deployment/lib/Bio/KBase/IDServer/Client.pm:# Override JSON::RPC::Client::call because it doesn't handle error returns properly.
data/usr/share/rasttk/deployment/lib/Bio/KBase/IDServer/Client.pm:            $obj->{id} = $self->id || ($self->id('JSON::RPC::Client'));

Could you try https://github.com/PATRIC3/PATRIC-distribution? I don't think it's a good idea try to repair an old software.

[cpplyqz]

I'm sorry too late to answer you
I agree with you ,but now ,there is a good software which named BV/BRC, it can use rasttk's any command. And you can get it from this web:https://www.bv-brc.org/docs/cli_tutorial/cli_installation.html#cli-installation
also tutotrial for using rasttk:https://www.bv-brc.org/docs/cli_tutorial/rasttk_getting_started.html