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,
Related
I'm trying to run unitas_1.7.8.pl, a bioinformatic software available here. Importantly, I've used this software many times in the past successfully on this ubuntu machine. Now when I run the command
perl ~/scripts/unitas_1.7.0.pl -threads 24 -s homo_sapiens -i PCR_Primer_11_S11_L001_R1_001.trim.lng ...
I get the error
Perl module LWP::Simple is not installed on this machine!
Perl module Archive::Extract (in core since 2007-07-07) is not installed on this machine!
Perl modules are available for download at http://www.cpan.org/
If you have CPAN installed try the following:
cpan
install Archive::Extract
exit
If you are on MAC or UNIX you should run cpan with sudo:
sudo cpan
install Archive::Extract
exit
I've followed those instructions and updated AND reinstalled cpan (even though I know it should be fine) without apparent issues. The only thing I can think of that has changed since the last time I successfully used unitas is that the server was hard-rebooted a month ago.
Details:
Distributor ID: Ubuntu
Description: Ubuntu 20.04.2 LTS
Release: 20.04
Codename: focal
$ cpan --version
Loading internal logger. Log::Log4perl recommended for better logging
/home/user/miniconda3/bin/cpan version 1.64 calling Getopt::Std::getopts (version 1.12 [paranoid]),
running under Perl version 5.30.3.
[Now continuing due to backward compatibility and excessive paranoia.
See 'perldoc Getopt::Std' about $Getopt::Std::STANDARD_HELP_VERSION.]
Nothing to install!
$ type -p perl; perl -M5.010 -e'say "$_: $ENV{$_}" for sort grep /^PERL/, keys(%ENV)'; echo 'o conf' | cpan
/home/stewart/miniconda3/bin/perl
[...]
make [/usr/bin/make]
make_arg []
make_install_arg []
make_install_make_command [/usr/bin/make]
makepl_arg [INSTALLDIRS=site]
mbuild_arg []
mbuild_install_arg []
mbuild_install_build_command [./Build]
mbuildpl_arg [--installdirs site]
[...]
$ perl -MLWP::Simple -E 'say $INC{"LWP/Simple.pm"}'
Can't locate LWP/Simple.pm in #INC (you may need to install the LWP::Simple module) (#INC contains: /home/stewart/miniconda3/lib/site_perl/5.30.3/x86_64-linux-thread-multi /home/stewart/miniconda3/lib/site_perl/5.30.3 /home/stewart/miniconda3/lib/5.30.3/x86_64-linux-thread-multi /home/stewart/miniconda3/lib/5.30.3 .).
BEGIN failed--compilation aborted.
$ head -n 1 "$( type -p cpan )"
#!/home/stewart/miniconda3/bin/perl
$ perl -MLWP::Simple -e'print "ok\n"'
Can't locate LWP/Simple.pm in #INC (you may need to install the LWP::Simple module) (#INC contains: /home/stewart/miniconda3/lib/site_perl/5.30.3/x86_64-linux-thread-multi /home/stewart/miniconda3/lib/site_perl/5.30.3 /home/stewart/miniconda3/lib/5.30.3/x86_64-linux-thread-multi /home/stewart/miniconda3/lib/5.30.3 .).
BEGIN failed--compilation aborted.
current state of LWP::Simple and Archive::Extract
$ sudo cpan install LWP::Simple
Loading internal logger. Log::Log4perl recommended for better logging
Reading '/root/.cpan/Metadata'
Database was generated on Tue, 07 Sep 2021 08:55:47 GMT
LWP::Simple is up to date (6.56).
$ sudo cpan install Archive::Extract
Loading internal logger. Log::Log4perl recommended for better logging
Reading '/root/.cpan/Metadata'
Database was generated on Tue, 07 Sep 2021 08:55:47 GMT
Archive::Extract is up to date (0.88).
$ sudo cpan LWP::Simple
Loading internal logger. Log::Log4perl recommended for better logging
Reading '/root/.cpan/Metadata'
Database was generated on Tue, 07 Sep 2021 08:55:47 GMT
LWP::Simple is up to date (6.56).
If you already have Miniconda, then you should install using the Bioconda channel in an isolated environment. Your Perl installation, from conda, is interfering with your system CPAN modules:
conda create -n unitas -c bioconda unitas
conda activate unitas
unitas.pl -threads 24 -s homo_sapiens -i PCR_Primer_11_S11_L001_R1_001.trim.lng ...
conda deactivate
None of the solutions suggested worked for me except calling perl directly from another directory (which already had it installed).
/usr/bin/perl5.30.0 ~/scripts/unitas_1.7.0.pl ...
There may be a way to switch the default perl used when called to this directory with $PATH, but I found this workaround for now. Thanks all for your help.
I am new to Perl so please bear with me. Thank you for your assistance.
I have an Ubuntu machine with Perl on it. I followed the local::lib bootstrapping guide
I used cpanm to install DBI and other modules to my system. I am concerned there may be other DBI modules available on my system which could be part of the problem. This is the result of find / -name 'DBI.pm' 2>/dev/null:
/home/ubuntu/.cpanm/work/16125643.6178/DBI-1.643/blib/lib/DBI.pm
/home/ubuntu/.cpanm/work/16125643.6178/DBI-1.643/blib/lib/Bundle/DBI.pm
/home/ubuntu/.cpanm/work/16125643.6178/DBI-1.643/DBI.pm
/home/ubuntu/.cpanm/work/16125643.6178/DBI-1.643/lib/Bundle/DBI.pm
/home/ubuntu/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/DBI.pm
/home/ubuntu/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Bundle/DBI.pm
I added 2 lines to my .bashrc file. (I added the second line because I broke things for the non-root user and this fixed it; maybe I broke something with local::lib?)
eval "$(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 $PERL5LIB')
However I always get the #INC error. The most obvious thing I have noticed is comparing sudo perl -V and perl -V. The sudo call does not show any ENV vars and the #INC does not include the desired PERL5LIB location. The non-sudo call does show the desired ENV and #INC vars.
I am considering wiping things and doing a fresh install with root privileges for local::lib and cpan. Not really sure what else to try at this point.
These are the commands that ended up working for me. I corrupted my first environment with local::lib / non-sudo cpan install, so I setup a fresh VM.
sudo apt install make
sudo apt install build-essential
sudo apt install libmysqlclient-dev
sudo cpan App::cpanminus
cpanm --sudo DBI
cpanm --sudo Array::Utils
cpanm --sudo DBD::mysql
I'm trying to install Perl modules Geo::ShapeFile and Math::Round but I keep coming across the same error and I can't find a solution that works. I've local::lib installed fine but its not being found or something? Am I doing it in the wrong place?
cian#cian-Aspire-5750:~/Documents/Math-Round-0.07$ 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
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.
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