in reply to Re^3: How to add path to @INC
in thread How to add path to @INC

Thank you Rob

I had a earlier version of Perl however I needed update it due to a software (CLUMPAK) that asks for modules that only work in Perl 5.24! Really everything worked fine in earlier version but in this one I have problems like that! Even more others modules have problems too: 

cpan[7]> install GraphViz
Running install for module 'GraphViz'
Checksum for /home/uce/.cpan/sources/authors/id/R/RS/RSAVAGE/GraphViz-
+2.20.tgz ok
Configuring R/RS/RSAVAGE/GraphViz-2.20.tgz with Build.PL
Can't exec "dot": Ficheiro ou directoria inexistente at Build.PL line 
+14.
Please install Graphviz from http://www.graphviz.org/.
No 'Build' created  RSAVAGE/GraphViz-2.20.tgz
  /usr/local/bin/perl Build.PL --installdirs site -- NOT OK
Failed during this command:
 RSAVAGE/GraphViz-2.20.tgz                    : writemakefile NO -- No
+ 'Build' created

[download]

or 

cpan[6]> install DB_File
Running install for module 'DB_File'
Checksum for /home/uce/.cpan/sources/authors/id/P/PM/PMQS/DB_File-1.83
+8.tar.gz ok
Configuring P/PM/PMQS/DB_File-1.838.tar.gz with Makefile.PL
Parsing config.in...
Looks Good.
Checking if your kit is complete...
Looks good
'EXPATINCPATH' is not a known MakeMaker parameter name.
'EXPATLIBPATH' is not a known MakeMaker parameter name.
Warning (mostly harmless): No library found for -ldb
Generating a Unix-style Makefile
Writing Makefile for DB_File
Writing MYMETA.yml and MYMETA.json
  PMQS/DB_File-1.838.tar.gz
  /usr/local/bin/perl Makefile.PL EXPATLIBPATH=/non-standard/lib EXPAT
+INCPATH=/non-standard/include -- OK
Running make for P/PM/PMQS/DB_File-1.838.tar.gz
cp DB_File.pm blib/lib/DB_File.pm
Running Mkbootstrap for DB_File ()
chmod 644 "DB_File.bs"
"/usr/local/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- DB_F
+ile.bs blib/arch/auto/DB_File/DB_File.bs 644
cc -c  -I/usr/local/BerkeleyDB/include -fwrapv -fno-strict-aliasing -p
+ipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FIL
+E_OFFSET_BITS=64 -O2   -DVERSION=\"1.838\" -DXS_VERSION=\"1.838\" -fP
+IC "-I/usr/local/lib/perl5/5.24.0/x86_64-linux/CORE"  -D_NOT_CORE  -D
+mDB_Prefix_t=size_t -DmDB_Hash_t=u_int32_t   version.c 
version.c:30:16: fatal error: db.h: Ficheiro ou directoria inexistente
 #include <db.h>
                ^
compilation terminated.
make: ** [version.o] Erro 1
  PMQS/DB_File-1.838.tar.gz
  /usr/bin/make -- NOT OK
Failed during this command:
 PMQS/DB_File-1.838.tar.gz                    : make NO

[download]

summing up, all these modules required for Bio:SeIO fail 

cpan[5]> install Bio::SeqIO
Running install for module 'Bio::SeqIO'
Checksum for /home/uce/.cpan/sources/authors/id/C/CJ/CJFIELDS/BioPerl-
+1.6.924.tar.gz ok
Scanning cache /home/uce/.cpan/build for sizes
......................................................................
+......DONE
Configuring C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz with Build.PL
Checking prerequisites...
  recommends:
    *  DB_File is not installed
    *  GraphViz is not installed
    *  SOAP::Lite is not installed

Checking optional features...
Bio::DB::GFF Tests....disabled
  requires:
    ! DBI is not installed
DB_File Tests.........disabled
  requires:
    ! DB_File is not installed
EntrezGene............disabled
  requires:
    ! Bio::ASN1::EntrezGene is not installed
MySQL Tests...........disabled
  requires:
    ! DBD::mysql is not installed
    ! DBI is not installed
Pg Tests..............disabled
  requires:
    ! DBD::Pg is not installed
    ! DBI is not installed
SQLite Tests..........disabled
  requires:
    ! DBD::SQLite is not installed
    ! DBI is not installed

ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the v
+ersions
of the modules indicated above before proceeding with this installatio
+n

Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractivel
+y? [a] ^CWarning: No success on command[/usr/local/bin/perl Build.PL 
+--installdirs site]
  CJFIELDS/BioPerl-1.6.924.tar.gz
  /usr/local/bin/perl Build.PL --installdirs site -- NOT OK
Failed during this command:
 CJFIELDS/BioPerl-1.6.924.tar.gz              : writemakefile NO '/usr
+/local/bin/perl Build.PL --installdirs site' returned status 2

[download]

However I installed BioPerl-1.6.924 (Bio::SeqIO) from "outside" (without cpan), after to adding the path at PERL5LIB, and it works just fine! When I run all tests everything sounds good! 

All tests successful.
Files=334, Tests=21522, 120 wallclock secs ( 3.39 usr  0.47 sys + 107.
+39 cusr  4.43 csys = 115.68 CPU)
Result: PASS

[download]

What you think about all this?

Best, TSN

Replies are listed 'Best First'.
Re^5: How to add path to @INC
by syphilis (Archbishop) on May 22, 2016 at 01:52 UTC
    Can't exec "dot": Ficheiro ou directoria inexistente at Build.PL line 14.

    On Ubuntu, I also don't have "dot": 
    $ dot --help
The program 'dot' is currently not installed. You can install it by ty
+ping:
sudo apt-get install graphviz
$

    [download]
    Not sure what the intent of Build.PL is, but if I wanted to install GraphViz then I would first install "dot".
    I think that should enable installation of that module.

    version.c:30:16: fatal error: db.h: Ficheiro ou directoria inexistente #include <db.h>

    db.h is not being found - you can fix this by adding the location of db.h to the CPATH environment variable: 
    export CPATH=/wherever/it/is:$CPATH

    [download]
    I think you'll subsequently find that the DB library is also unlocatable - which will result in unresolved symbols when you try to run the module (eg during 'make test' stage of the build).
    That being so, I would try adding the location of the DB library's .so file to the LD_LIBRARY_PATH environment variable: 
    export LD_LIBRARY_PATH=/wherever/it/is:$LD_LIBRARY_PATH

    [download]
    Or maybe you need to add the location of the static DB library (.a) to the LIBRARY_PATH environment variable.
    I'm a little unsure as I've never managed to properly understand the way linking is effected on Linux - I just usually stuff around with things until I find something that works.
    Maybe someone else can chime in here with some more definitive advice.

    Cheers,
    Rob
[reply]
[d/l]
[select]
      One more question Rob

      Now I have this: 

      cpan[3]> install DB_File
Running install for module 'DB_File'
  PMQS/DB_File-1.838.tar.gz
  Has already been unwrapped into directory /home/uce/.cpan/build/DB_F
+ile-1.838-yBmp3Q
  PMQS/DB_File-1.838.tar.gz
  Has already been prepared
  PMQS/DB_File-1.838.tar.gz
  Could not make: Unknown error

      [download]

      What can I do to fix it?

      Best,

      TSN

[reply]
[d/l]
        Has already been unwrapped into directory /home/uce/.cpan/build/DB_File-1.838-yBmp3Q

        Not sure ... I'm not at all that familiar with these cpan* shells.
        However, I think it means that it wouldn't unpack PMQS/DB_File-1.838.tar.gz into /home/uce/.cpan/build/DB_File-1.838-yBmp3Q because that directory already exists.
        That being so, removing that DB_File-1.838-yBmp3Q directory should work. (Or perhaps opening a new instance of the CPAN shell and re-running the same command will unpack into a different location and therefore succeed.)

        Cheers,
        Rob
[reply]
Re^5: How to add path to @INC
by syphilis (Archbishop) on May 22, 2016 at 04:21 UTC
    CJFIELDS/BioPerl-1.6.924.tar.gz
    : writemakefile NO '/usr/local/bin/perl Build.PL --installdirs site' returned status 2

    This looks like an issue with Module::Build.
    Apparently your version of Module::Build cannot handle the --installdirs site arguments.
    Perhaps your version of Module::Build is too old or too new.

    If you need additional information about that I think you should take it up with the BioPerl folk (or maybe someone else will update this thread with better information).

    Sorry - I can't even look properly at Module::Build issues.
    Such is my loathing of that module that any attempt to diagnose problems with it just leaves me wanting to throw a brick through the console, and I'm not prepared to waste a perfectly good brick over Module::Build.

    If Module::Build gets in the way of allowing a module to install, then I just go without that module.
    Thankully, so far, this policy has not meant that I've had to do without a module that I really want.

    Cheers,
    Rob
[reply]
[d/l]
      Thanks a lot Rob

      you have been a good helper!

      Cheers,

      TSN

[reply]
      Hi Rob!

      Now I have a new problem with the module GD

      When I try install de module GD::Text I have this:

       Can't load '/usr/local/lib/perl5/site_perl/5.24.0/x86_64-linux/auto/GD/GD.so' for module GD: /usr/local/lib/perl5/site_perl/5.24.0/x86_64-linux/auto/GD/GD.so: undefined symbol: PL_thr_key at /usr/local/lib/perl5/5.24.0/x86_64-linux/DynaLoader.pm line 193. When I try  cpan install GD

      GD is up to date (2.56)

      I really need to fix this to run a software!

      Can you help me once more?

      Cheers

      TSN

[reply]
[d/l]
[select]
        you're mixing incompatible perls, a GD compiled against a threaded perl, being run from a non-threaded perl, it won't work, can't mix threaded/non threaded, can't mix versions (ex 5.22 and 5.24.1) you need to recompile/reinstall GD with the version of perl you're trying to run
[reply]

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