Hel lo, I'm actually installing a perl module called HmmCleaner here :
https://metacpan.org/pod/HmmCleaner.pl
for that I use :
/beegfs/data/me/perl-5.30.1/localperl/bin/cpan Bio::MUST::Apps::HmmCleaner
But I'm actually into a shared cluster where we have 2 principal directories :
/beegfs/home/me
And
/beegfs/data/me
and in the home repository I have a threshold of number of chunk files to not
I have a threshold that I cannot exceed of the number of chunk files and when I run the /beegfs/data/me/perl-5.30.1/localperl/bin/cpan Bio::MUST::Apps::HmmCleaner command, for some reason some files are created into the home directory and when I look into the log file I see that something is wrong at this moment :
! Installing Bio::MUST::Core::Utils failed. See /beegfs/home/me/.cpanm/work/1580931498.36405/build.log for details. Retry with --force to force install it.
Warning: unable to close filehandle $out properly: Disk quota exceeded at /beegfs/data/me/perl-5.30.1/localperl/bin/cpanm line 49.
Warning: unable to close filehandle $out properly: Disk quota exceeded at /beegfs/data/me/perl-5.30.1/localperl/bin/cpanm line 49.
Warning: unable to close filehandle $out properly: Disk quota exceeded at /beegfs/data/me/perl-5.30.1/localperl/bin/cpanm line 49.
But when I look into the disk quota in data, both memory and chuck file limit is not reached, but for the home the number of chunk files is exceeded!
Does someone know how can I force to run all the files created in the installation into the data repository instead of home?
Thank you for your help.
for polarbear :
When I do :
/beegfs/data/me/perl-5.30.1/localperl/bin/cpan -D local::lib
I get :
Loading internal logger. Log::Log4perl recommended for better logging
CPAN.pm requires configuration, but most of it can be done automatically.
If you answer 'no' below, you will enter an interactive dialog for each
configuration option instead.
Would you like to configure as much as possible automatically? [yes] yes
Fetching with LWP:
http://www.cpan.org/authors/01mailrc.txt.gz
Reading '/beegfs/home/me/.cpan/sources/authors/01mailrc.txt.gz'
............................................................................DONE
Fetching with LWP:
http://www.cpan.org/modules/02packages.details.txt.gz
Reading '/beegfs/home/me/.cpan/sources/modules/02packages.details.txt.gz'
Database was generated on Thu, 06 Feb 2020 08:41:03 GMT
.............
New CPAN.pm version (v2.27) available.
[Currently running version is v2.22]
You might want to try
install CPAN
reload cpan
to both upgrade CPAN.pm and run the new version without leaving
the current session.
...............................................................DONE
Fetching with LWP:
http://www.cpan.org/modules/03modlist.data.gz
Reading '/beegfs/home/me/.cpan/sources/modules/03modlist.data.gz'
DONE
Writing /beegfs/home/me/.cpan/Metadata
local::lib
-------------------------------------------------------------------------
(no description)
H/HA/HAARG/local-lib-2.000024.tar.gz
(no installation file)
Installed: not installed
CPAN: 2.000024 Not up to date
Graham Knop (HAARG)
haarg#haarg.org
Lets follow next scenario
mv ~/.cpam /beegfs/data/me
ln -s /beegfs/data/me/.cpan ~/.cpan
HOME=/beegfs/data/me perl -Mlocal::lib > ~/.lib_perl
these commands will
move $HOME/.cpan directory from $HOME to /beegfs/data/me
symlink it in $HOME directory
run perl with local::lib module
it will check for $SHELL
output configuration variables to $HOME/.lib_perl file
Now source $HOME/.lib_perl in your shell environment according your $SHELL (bash - .bashrc, csh - .cshrc, ...) on login into system.
As you work remotely you have to logout and login to pickup changes (do it in separate terminal just in case if you do something wrong and you need back door to revert your changes).
At this point you should be able to use cpan to install modules into /beegfs/data/me/perl5 directory.
Check if local::lib is installed with following command
cpan -D local::lib
If it is installed then head to following webpage local::lib and do some reading - pay attention to point #4.
Otherwise check if cpanm is available in your system.
As an option you can set variables manually
PERL_MB_OPT
PERL_MM_OPT
PERL5LIB
PATH
PERL_LOCAL_LIB_ROOT
Before setting private library check that you have write permission on storage directory.
Related
Normally in linux Debian we do sth like this to install a package non-interactively e.g
sudo apt-get install -y Package_x_z
#[-y --assume-yes]
How we can do the same while installing a perl module e.g
sudo perl -MCPAN -e 'install DBI'
That prompt is (typically) coming from ExtUtils::MakeMaker's prompt() function. Stick export PERL_MM_USE_DEFAULT=1 in your .bashrc (or equivalent for your preferred shell) to stop the prompts. The ExUtils::MakeMaker man page documents it thus:
PERL_MM_USE_DEFAULT
If set to a true value then MakeMaker's prompt function will always return the default
without waiting for user input.
Note that this can come to bite you if you run cpan(1) on a box that's not yet had CPAN repositories configured. It will rattle on and get stuck in a prompt loop at a point where there is no default and you need to make a choice, but have no ability to do so. export PERL_MM_USE_DEFAULT=0 in the shell before running cpan(1) will of course temporarily re-enable input.
To prevent the CPAN client from asking whether to install prerequisites, start it in interactive mode
perl -MCPAN -e shell
and enter the commands:
o conf build_requires_install_policy yes
o conf prerequisites_policy follow
o conf commit
The commit command is optional, but it will update the default configuration, which I suspect is what you want. Without it, you may or may not (depending on whether autocommit is enabled in your CPAN config) need to make this change every time you want to do a prompt-less installation.
These changes will deal with all of the CPAN client's routine questions about whether to install dependencies. For distributions which have questions embedded in their install scripts, you may also want to add
o conf inactivity_timeout 60
to set how long it will wait for a response before automatically going with the default answer to the question. (Set it to 0 to change it back to "wait forever".)
What about just :
$ yes | sudo perl -MCPAN -e 'install DBI'
Ban ! your problem is solved :-)
Appending to an answer here, you can also make these changes in config file located at /usr/share/perl5/CPAN/Config.pm.
'build_requires_install_policy' => q[yes],
'prerequisites_policy' => q[follow],
This helped me to automate installation, since CPAN doesn't have these configuration by default.
I have a problem when i want to install perl module
I make " cpan" to install cpan , but i get this "
Terminal does not support AddHistory.
Your configuration suggests that CPAN.pm should use a working
directory of
/home/cyrine/.cpan
Unfortunately we could not create the lock file
/home/cyrine/.cpan/.lock
due to permission problems.
Please make sure that the configuration variable
$CPAN::Config->{cpan_home}
points to a directory where you can write a .lock file. You can set
this variable in either a CPAN/MyConfig.pm or a CPAN/Config.pm in your
#INC path;
You don't seem to have a user configuration (MyConfig.pm) yet.
i make "y"
then i got this strange message :
mkdir /home/cyrine/.cpan/CPAN: Permission denied at /usr/share/perl/5.10/CPAN/Shell.pm >line 656
Any idea please?
Thank you
The immediate cause of this problem is that you don't have write permissions on /home/cyrine/.cpan. In my experience, this is most often the result of logging in as a normal user, then running cpan for the first time on that account in a su session, causing the CPAN configuration to be created in ~cyrine (because you have cyrine's environment), but owned by root (because su has given you root's permissions). Assuming that is the case, you should be able to resolve this my suing to root, running the command chown -R cyrine.cyrine /home/cyrine/.cpan and then running cpan as user cyrine.
I have installed ActivePerl 5.14.2 on a Windows 32 bit machine running XP. My problem is that I'm trying to install a few modules with PPM and it's not working out.
According to ActiveState's website, all you need to do to install a module from their repository is "ppm install module name" , example: http://code.activestate.com/ppm/Template-Toolkit/
Every time I try this or any other module I get: "No Perl script found in input"
Even when I do just "ppm" I get the same message, even though the GUI should run.
When I run PPM with a GUI from the start menu I get this error: "Failed 500 Can't connect to ppm4.activestate.com:8080 (connect: timeout)”
I though that it might be my connection, so using cmd.exe I used the set HTTP_PROXY command and then tried ppm install, but still no luck. So is there any way I can get these modules installed?
Any advice is appreciated !!
Invoke the cpan prompt from your command prompt. Go to cmd and simply type cpan. If you successfully enter cpan prompt them there is probably no issues with your Perl installation. To install a module from cpan prompt just use
cpan>install Module::Name
Screenshot below shows command to install module Net::Stomp
If the above does not work, check if your FTP data and connection ports needs to be added to the Windows firewall exceptions (Ports 20 (FTP Command port) and 21 (FTP Data port)).
Alternatively (if you don't want to add port 20 21 to exception), you can go to the cpan prompt and use an ftp_proxy by
cpan> o conf ftp_proxy http://your.ftpproxy.com
and then issue install command. Or you can update your ../CPAN/config.pm file to make permanent changes to the ftp_proxy parameter.
The next step would be to try set the FTP_PASSIVE mode to 1. By default the libnetcfg configuration for this is set to 0. To change this find libnetcfg.bat file (should be somewhere C:\Perl\bin), open the file in an editor and replace
ftp_int_passive 0
to
ftp_int_passive 1
Again, looking at you r timeout error it seems that your network is blocking you from accessing the CPAN ftp mirrors, this would happen mostly if you are inside a corporate VPN. The solution to this can only be proxy servers.
Attempting to install the Perl module DBD::mysql on Windows 7
From the Windows command line I executed
perl -MCPAN -e 'install DBD::mysql'
Which downloaded and uncompressed the file -- then gave me this ERROR:
CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.018.tar.gz
Set up gcc environment - 3.4.5 (mingw-vista special r3)
C:\PROGRA~1\MySQL\MYSQLS~1.1\bin\MYSQLA~1.EXE: connect to server at 'localhost'
failed
error: 'Access denied for user 'ODBC'#'localhost' (using password: NO)'
Problem running C:\PROGRA~1\MySQL\MYSQLS~1.1\bin\MYSQLA~1.EXE - aborting ...
Warning: No success on command[C:\Perl\bin\perl.exe Makefile.PL INSTALLDIRS=site
]
Guessing the issue is that MySQL's root user has a password, but what's not clear is how I resolve the issue.
Questions, feedback, requests -- just comment, thanks!!
----------
UPDATE (1): RE: force install DBD::mysql
cpan> force install DBD::mysql
Running install for module 'DBD::mysql'
Running make for C/CA/CAPTTOFU/DBD-mysql-4.018.tar.gz
Has already been unwrapped into directory C:\Perl\cpan\build\DBD-mysql-4.018-A
1T8Uh
'C:\Perl\bin\perl.exe Makefile.PL INSTALLDIRS=site' returned status 256, won't
make
Running make test
Make had some problems, won't test
Running make install
Make had some problems, won't install
On other platforms, the build process runs the mysql_config command to get necessary information about the mysql installation without need of a user and password; on win32, if you have a mysql_config command, you have to explicitly tell Makefile.PL about it with a --mysql_config yourpathname parameter. If you don't, it looks for the mysqladmin program and uses its location to determine as much as it can but runs mysqladmin version to get the mysql version. You can provide a user/password for it to be able to do this using --testuser and --testpassword parameters to Makefile.PL.
Following up on "Robert P" comment, I checked the install guide for installing DBD::MySQL in ActivePerl on Win32; on 64, but doesn't appear to have mattered.
Command that did the job was:
ppm install DBD::mysql
The only way I've got round this in the past is a forced install. It always feels like a bodge but I haven't been able to find a better way.
Open up a CPAN shell:
perl -MCPAN -e 'shell'
Then do a force install
force install DBD::mysql
quit gets you back out of the shell.
as ysth said , maybe try this :
cd C:\Perl\cpan\build\DBD-mysql-4.018-A
and run
perl Makefile.PL --testuser validuser --testpassword validpassword
and then try to make - make test - make install,
or its equivalents on windows
Doesn't work with other modules, but to give an example. I installed Text::CSV_XS with a CPAN setting:
'makepl_arg' => q[PREFIX=~/lib],
When I try running a test.pl script:
$ perl test.pl
#!/usr/bin/perl
use lib "/homes/foobar/lib/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi";
use Text::CSV_XS;
print "test";
I get
Can't load '/homes/foobar/lib/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/Text/CSV_XS/CSV_XS.so' for module Text::CSV_XS: /homes/foobar/lib/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/Text/CSV_XS/CSV_XS.so: cannot open shared object file: No such file or directory at /www/common/perl/lib/5.8.2/i686-linux/DynaLoader.pm line 229.
at test.pl line 6
Compilation failed in require at test.pl line 6.
BEGIN failed--compilation aborted at test.pl line 6.
I traced the error back to DynaLoader.pm it happens at this line:
# Many dynamic extension loading problems will appear to come from
# this section of code: XYZ failed at line 123 of DynaLoader.pm.
# Often these errors are actually occurring in the initialisation
# C code of the extension XS file. Perl reports the error as being
# in this perl code simply because this was the last perl code
# it executed.
my $libref = dl_load_file($file, $module->dl_load_flags) or
croak("Can't load '$file' for module $module: ".dl_error());
CSV_XS.so exists in the above directory
When you installed the module, did you watch the output? Where did it say it installed the module? Look in lib. Do you see the next directory you expect?
Look in ~/lib to see where eveything ended up to verify that you have the right directory name in your use lib statement:
% find ~/lib -name CSV_XS.so
Once you see where it is installed, use that directory name in your use lib (or PERL5LIB or whatever).
I expect you have a lib/lib in there somehow. The PREFIX is just the, well, prefix, and the installer appends other directory portions to that base path. That includes lib, man, bin, etc.
Personally I would suggest to use local::lib. :)
Try this instead:
'makepl_arg' => q[PREFIX=~/]
PREFIX sets the base for all the directories you will be installing into (bin, lib, and so forth.)
You may also be running into shell expansion problems with your '~'. You can try to expand it yourself:
'makepl_arg' => q[PREFIX=/home/users/foobar]
It would also be helpful if you included the commands you used to get the error you are asking about.
It looks from the error message ("at /www/common ...") that your script is a CGI or mod_perl script. The web server is probably not running as the user 'foo', under whose home directory you've installed the module - that could result in the web server being unable to read that directory.
It may also be running in a "chroot jail", which would mean that the directory in which you've installed the module may not be visible to the script.
In other words, just because you can see the module, does not mean that the web server, and therefore your script, can do so. You should check the relevant file permissions, and if the server is chrooted, whether your module directory is mounted within the virtual file system.
Does the file in question (CSV_XS.so) exist?
Does it exist at the listed location?
If you do:
set |grep PERL
What is the output?
Have you successfully installed other local perl modules?
I strongly suggest installing your own perl in your own home directory, if you have space. Then you can keep everything under your control and keep your own module set, as well as escaping if the admins are keeping you on an older version of perl. (Not to mention preserving yourself if they upgrade some day and leave out all the modules you are relying on.)