Can't locate DBI.pm - perl

I'm trying to launch this script:
#!/usr/bin/perl
use DBI;
my $dbh = DBI->connect( 'dbi:Oracle:host=lonlin2;sid=TIMFX1AD;port=1524','xbsesdbo','xbsesdbo123' ) || die ( $DBI::errstr . "\n" );
my $query= "SELECT * FROM product_elements WHERE element_id = 1001";
my $queryHandler= $dbh->prepare($query);
my $result= $queryHandler->execute();
open(fileHandler,"> note.txt");
print fileHandler "Risultato query: $result\n";
my $e= $dbh->disconnect();
close(fileHandler);
When I launch this script I receive this error:
Can't locate DBI.pm in #INC (#INC contains: /opt/perl_32/lib/5.8.3/IA64.ARCHREV_0-thread-multi /opt/perl_32/lib/5.8.3 /opt/perl_32/lib/site_perl/5.8.3/IA64.ARCHREV_0-thread-multi /opt/perl_32/lib/site_perl/5.8.3 /opt/perl_32/lib/site_perl /opt/perl_32/lib/vendor_perl/5.8.3/IA64.ARCHREV_0-thread-multi /opt/perl_32/lib/vendor_perl/5.8.3 /opt/perl_32/lib/vendor_perl .) at ./prova.pl line 3.
I've got all installed! DBI.pm is installed!

If you have root, type in console (Debian/Ubuntu):
sudo apt-get install libdbi-perl

If you don't have active perl (and hence don't have ppm), you can also get DBI like this:
perl -MCPAN -e 'install DBI'
You may need to install drivers for Postgres like this:
perl -MCPAN -e 'install DBD::Pg'

For redhat/centos users:
sudo yum -y install perl-DBI

DBI isn't in your #INC path, which tells perl where to look for custom modules. This is probably because you've installed them using the cpan tool as a non-root user, which won't have write access to the default include paths.
You will need to locate DBI.pm and other packages, and move them into your #INC path.
Alternatively, find the packages you've installed and add the install path into your library path, for one time use:
PERL5LIB=/path/to/modules perl yourscript.pl
And for a more permanent solution, add this to ~/.bashrc:
export PERL5LIB=/path/to/modules

For alpine users use perl-dbi: apk add perl-dbi

For arch linux users:
sudo pacman -S perl-dbi

Related

Perl not recognizing module / module path for root user

I am new to Perl so please bear with me. Thank you for your assistance.
I have an Ubuntu machine with Perl on it. I followed the local::lib bootstrapping guide
I used cpanm to install DBI and other modules to my system. I am concerned there may be other DBI modules available on my system which could be part of the problem. This is the result of find / -name 'DBI.pm' 2>/dev/null:
/home/ubuntu/.cpanm/work/16125643.6178/DBI-1.643/blib/lib/DBI.pm
/home/ubuntu/.cpanm/work/16125643.6178/DBI-1.643/blib/lib/Bundle/DBI.pm
/home/ubuntu/.cpanm/work/16125643.6178/DBI-1.643/DBI.pm
/home/ubuntu/.cpanm/work/16125643.6178/DBI-1.643/lib/Bundle/DBI.pm
/home/ubuntu/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/DBI.pm
/home/ubuntu/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Bundle/DBI.pm
I added 2 lines to my .bashrc file. (I added the second line because I broke things for the non-root user and this fixed it; maybe I broke something with local::lib?)
eval "$(perl -I$HOME/perl5/lib/perl5 -Mlocal::lib)"
PERL5LIB="/home/ubuntu/perl5/lib/perl5"
I can run my perl script as a non-root user.
If I run with sudo perlScript.pl I get this error: Can't locate DBI.pm in #INC (you may need to install the DBI module)
I have been troubleshooting #INC for a while now and cannot figure out how to adjust it for the root user. I have tried various things including adding PERL5LIB to .profile and calling my script like so: sudo sh -c '. ~/.profile; perl ~/perlScripts/perlScript.pl "argForScript"' (I verified that PERL5LIB is being set with sudo sh -c '. ~/.profile; echo $PERL5LIB')
However I always get the #INC error. The most obvious thing I have noticed is comparing sudo perl -V and perl -V. The sudo call does not show any ENV vars and the #INC does not include the desired PERL5LIB location. The non-sudo call does show the desired ENV and #INC vars.
I am considering wiping things and doing a fresh install with root privileges for local::lib and cpan. Not really sure what else to try at this point.
These are the commands that ended up working for me. I corrupted my first environment with local::lib / non-sudo cpan install, so I setup a fresh VM.
sudo apt install make
sudo apt install build-essential
sudo apt install libmysqlclient-dev
sudo cpan App::cpanminus
cpanm --sudo DBI
cpanm --sudo Array::Utils
cpanm --sudo DBD::mysql

Can't locate Bio/SeqIO.pm in #INC

Hi I am trying to install VelvetOptimizer using docker. and it say Can't locate Bio/SeqIO.pm in #INC. It requires the following to be installed:
Velvet >= 0.7.51 ,Perl >= 5.8, BioPerl >= 1.4 and i have installed them
Please find the Dockerfile:
FROM amazonlinux
WORKDIR /shared
RUN yum -y install gcc
ADD http://www.cpan.org/src/5.0/perl-5.16.1.tar.gz /shared
RUN tar -xzf perl-5.16.1.tar.gz
WORKDIR /shared/perl-5.16.1
RUN ./Configure -des -Dprefix=/shared/perl-5.16.1/localperl
RUN make
RUN make test
RUN make install
RUN echo “Perl Installation Complete”
ENV PATH=/shared/perl-5.16.1/localperl/bin/:${PATH}
WORKDIR /shared
ADD http://www.ebi.ac.uk/~zerbino/velvet/velvet_latest.tgz .
RUN tar -xvf /shared/velvet_latest.tgz
WORKDIR /shared/velvet_1.2.10/
RUN make
ENV PATH=${PATH}:/shared/velvet_1.2.10/
WORKDIR /shared
RUN echo "BIO PERL INSTALLATION"
RUN \wget -O - https://install.perlbrew.pl | bash
ENV PATH=${PATH}:/root/perl5/perlbrew/bin/
RUN perlbrew install-cpanm
RUN cpanm Bio::Perl
WORKDIR /shared
ADD http://www.vicbioinformatics.com/VelvetOptimiser-2.2.5.tar.gz .
RUN tar zxvf VelvetOptimiser-2.2.5.tar.gz
ENV PATH=${PATH}:/shared/VelvetOptimiser-2.2.4
When I run the command/shared/VelvetOptimiser-2.2.5/VelvetOptimiser.pl
I get the below error:
Error:
Can't locate Bio/SeqIO.pm in #INC (#INC contains: /shared/VelvetOptimiser-2.2.5 /shared/vcftools/src/perl /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /shared/VelvetOptimiser-2.2.5/VelvetOpt/Assembly.pm line 238.
BEGIN failed--compilation aborted at /shared/VelvetOptimiser-2.2.5/VelvetOpt/Assembly.pm line 238.
Compilation failed in require at /shared/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 37.
BEGIN failed--compilation aborted at /shared/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 37.
But when I use "find" command: I am able to find the files.
./root/.cpanm/work/1501770319.1/BioPerl-1.007001/blib/lib/Bio/SeqIO.pm
./root/.cpanm/work/1501770319.1/BioPerl-1.007001/Bio/SeqIO.pm
./shared/perl-5.16.1/localperl/lib/site_perl/5.16.1/Bio/SeqIO.pm
I think its not be found in Perl's include path, which is represented by the variable named #INC.
Can anyone please let me know how to fix this issue. how to add it in perls include path.
Clearly, /shared/VelvetOptimiser-2.2.5/VelvetOptimiser.pl has
#!/usr/bin/env perl
as its shebang line. So, it will use the first perl it finds in the $PATH.
You likely have a perl in /usr/bin. In your Docker file, you have:
ENV PATH=${PATH}:/root/perl5/perlbrew/bin/
That is, you likely put /usr/bin ahead of the perlbrew directory. So, /usr/bin/env perl is picking up /usr/bin/perl and not the perl you installed via perlbrew (which is also where you installed your new perl).
So, try
ENV PATH=/root/perl5/perlbrew/bin/:${PATH}
In addition, I do not see you actually install a perl via perlbrew:
You need
perlbrew install 5.xx.x
perlbrew switch 5.xx.x
before installing cpanm and installing Bio::Perl.

Installing Perl modules on Ubuntu 16.04

I'm trying to install Perl modules Geo::ShapeFile and Math::Round but I keep coming across the same error and I can't find a solution that works. I've local::lib installed fine but its not being found or something? Am I doing it in the wrong place?
cian#cian-Aspire-5750:~/Documents/Math-Round-0.07$ make install
Manifying 1 pod document
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
ERROR: Can't create '/usr/local/man/man3'
mkdir /usr/local/man/man3: Permission denied at /usr/share/perl/5.22/ExtUtils/Install.pm line 477.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
at -e line 1.
Makefile:697: recipe for target 'pure_site_install' failed
make: *** [pure_site_install] Error 13
I notice in my directory '/usr/local/man' points to 'usr/share/man'. I dunno if this was an issue how to solve it. Thanks.
I've local::lib installed fine
No, you don't. The environment has clearly not by set by local::lib. Make sure the following in your login script:
eval "$(perl -I$HOME/perl5/lib/perl5 -Mlocal::lib)"
(Adjust the path to local::lib if needed.)
Log out and log back in or use the following to pick up the changes:
exec bash -l
If you want to install module systemwide (it's what you do), you should have root privileges. Try sudo make install or install modules locally.
Alternatively you may try a cpanm client, which handles local::lib installs either:
$ cpanm -l ~/ Geo::ShapeFile Math::Round
And then don't forget to adjust perl5lib var to see installed modules:
$ PERL5LIB=~/lib/perl5

Enabling PNG support while installing GD.pm in Perl

I have already installed GD.pm. I want to make sure it supports PNG.
So to check that I do this:
$ perl -e 'use GD; $im=GD::Image->new(); print $im->can("png") ? "yes" : "no" , "\n";'
no
As you see. It prints no.
Then I download the latest GD from CPAN with the following process:
> wget http://search.cpan.org/CPAN/authors/id/L/LD/LDS/GD-2.53.tar.gz
> tar xvfz GD-2.53.tar.gz
> cd GD-2.44
> perl Makefile.PL
> make
> make test
> make install
I expect it to contain the line like this which is a hallmark of the installed PNG support:
Included Features: GD_XPM GD_JPEG GD_FONTCONFIG GD_FREETYPE
GD_PNG GD_GIF GD_GIFANIM GD_OPENPOLYGON GD_UNCLOSEDPOLY GD_ANIMGIF
GD_FTCIRCLE VERSION_33
But instead I got this only:
Included Features: GD_GIF GD_GIFANIM GD_OPENPOLYGON
I wasn't successful with this command either sudo perl Makefile.PL -options "JPEG,FT,PNG".
It didn't show GD_PNG.
What's the way to install GD.pm with PNG support?
I need it to run circos.
Update:
After installing libpng and rebuilding GD
$ brew update && brew upgrade
$ brew install gd
$ brew install libpng
$ sudo cpan
cpan > force install GD
as adviced, I got this error:
$ perl -e 'use GD; $im=GD::Image->new(); print $im->can("png") ? "yes" : "no" , "\n";'
Can't load '/Library/Perl/5.16/darwin-thread-multi-2level/auto/GD/GD.bundle' for module GD: dlopen(/Library/Perl/5.16/darwin-thread-multi-2level/auto/GD/GD.bundle, 1): Library not loaded: libpng15.15.dylib
Referenced from: /usr/local/lib/libfreetype.6.dylib
Reason: image not found at /System/Library/Perl/5.16/darwin-thread-multi-2level/DynaLoader.pm line 194.
at -e line 1.
Compilation failed in require at -e line 1.
BEGIN failed--compilation aborted at -e line 1.
Update 2:
Finally I fixed the problem by doing this:
$ locate libpng15.15.dylib
/anaconda/lib/libpng15.15.dylib
/anaconda/pkgs/libpng-1.5.13-1/lib/libpng15.15.dylib
/opt/X11/lib/libpng15.15.dylib
/opt/local/lib/libpng15.15.dylib
$ ln -s /opt/X11/lib/libpng15.15.dylib /usr/local/lib/libpng15.15.dylib
$ perl -e 'use GD; $im=GD::Image->new(); print $im->can("png") ? "yes" : "no" , "\n";'
yes
You need libraries as dependencies before making GD.pm. In this particular case libpng is obviously missing.
Because of that dependency, I recommend that you use package managers, not CPAN, if your perl is the one that comes with your OS:
MacPorts or homebrew for OS X
apt-get for Debian and Ubuntu.
yum for RHEL, Cent-OS.

Need help installing Spreadsheet::ParseExcel

I am trying to install Spreadsheet::ParseExcel to use with ExcelLatex. This is what I did:
Installed Active perl, Then install CPAN.pm by perl -MCPAN -e shell
I was asked for configuration and mirror site and I let perl do the auoconfoguration. At the end I got the following message: Autoconfiguration complete.Then I tried:
perl -MCPAN -e 'install "Spreadsheet::WriteExcel"'
And it tried to install it but at the end I got the following error:
ERROR: Can't create '/Library/Perl/5.12/Spreadsheet'
mkdir /Library/Perl/5.12/Spreadsheet: Permission denied at /System/Library/Perl/5.12/ExtUtils/Install.pm line 494
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
at -e line 1
make: *** [pure_site_install] Error 13
JMCNAMARA/Spreadsheet-WriteExcel-2.37.tar.gz
/usr/bin/make install -- NOT OK
I really appreciate it one please help me how I can solve the problem
It is trying to create a directory in the root (mkdir /Library/Perl/5.12/Spreadsheet)
You have to be root to be able to do that.
You may could use PerlBrew or local::lib to install your perl libs into your home dir.
# Install Spreadsheet::WriteExcel and its missing dependencies to the '~/perl5' directory
perl -MCPAN -Mlocal::lib -e 'CPAN::install(Spreadsheet::WriteExcel)'
# Just print out useful shell commands
$ perl -Mlocal::lib
export PERL_MB_OPT='--install_base /home/username/perl5'
export PERL_MM_OPT='INSTALL_BASE=/home/username/perl5'
export PERL5LIB='/home/username/perl5/lib/perl5/i386-linux:/home/username/perl5/lib/perl5'
export PATH="/home/username/perl5/bin:$PATH"
#create a environment setting script and execute it.
perl -Mlocal::lib > ~/.setenv && . ~/.setenv
Regards,