error with installing TPP4.5.2

[fangq...@gmail.com]

Hi,

I am installing TPP4.5.2 on my CentOS.  I got the following message when compiling:

mkdir -p /software/TPP-4.5.2/src/../build/CentOS-x86_64
make -C ../extern/xtandem/src TANDEM_PARAMETERS_INSTALL_DIR="/usr/local/tpp/bin/" SRC_ROOT="/software/TPP-4.5.2/src/" ARCH=CentOS-x86_64 BUILD_DIR=/software/TPP-4.5.2/src/../build/CentOS-x86_64 EXPAT_LIB=/software/TPP-4.5.2/src/../build/CentOS-x86_64/libexpat.a ZLIB_INCL="" ZLIB_LIB="-lz " USER_OBJS="/software/TPP-4.5.2/src/../build/CentOS-x86_64/TPPVersionInfo.o"
make[1]: Entering directory `/software/TPP-4.5.2/extern/xtandem/src'
make[1]: Leaving directory `/software/TPP-4.5.2/extern/xtandem/src'
mkdir -p /software/TPP-4.5.2/src/../build/CentOS-x86_64/help
mkdir -p /software/TPP-4.5.2/src/../build/CentOS-x86_64/schema
mkdir -p /software/TPP-4.5.2/src/../build/CentOS-x86_64/images
cd perl_paths; export PERL=perl; make -f perl_paths.makefile all
make[1]: Entering directory `/software/TPP-4.5.2/src/perl_paths'
perl -pe "s/\/cygdrive\/c\/Inetpub\/tpp-bin\//\/usr\/local\/tpp\/cgi\-bin\//g;s/\x24\{base_dir\}users\//\/usr\/local\/tpp\/cgi-bin\/users\//g;s/\/tools\/bin\/TPP\/tpp\//\/usr\/local\/tpp\//g;s/cygpath \-wp //g;s/\"\/cygdrive\/c\/Inetpub\/wwwroot\/\"/\\x24ENV\{\'WEBSERVER_ROOT\'\}\.'\/'/g;s/\/tpp\-bin/\/tpp\/cgi\-bin/g;s/'\/usr\/bin\//'/g;s/'\/bin\//'/g " < ../../CGI/show_nspbin.pl > ../../build/CentOS-x86_64/show_nspbin.pl
perl -c  -I  ../../build/CentOS-x86_64 ../../build/CentOS-x86_64/show_nspbin.pl
Use of ?PATTERN? without explicit operator is deprecated at ../../build/CentOS-x86_64/show_nspbin.pl line 123.
syntax error at ../../build/CentOS-x86_64/show_nspbin.pl line 115, near "$head qw(bin_number nsp_range positive_freq negative_freq positive/negative_ratio)"
syntax error at ../../build/CentOS-x86_64/show_nspbin.pl line 122, near "elsif"
Global symbol "$element" requires explicit package name at ../../build/CentOS-x86_64/show_nspbin.pl line 122.
syntax error at ../../build/CentOS-x86_64/show_nspbin.pl line 146, near "}"
Global symbol "$element" requires explicit package name at ../../build/CentOS-x86_64/show_nspbin.pl line 148.
syntax error at ../../build/CentOS-x86_64/show_nspbin.pl line 152, near "$head qw(bin_number ni_range positive_freq negative_freq positive/negative_ratio)"
syntax error at ../../build/CentOS-x86_64/show_nspbin.pl line 157, near "}"
syntax error at ../../build/CentOS-x86_64/show_nspbin.pl line 179, near "}"
Can't use global @_ in "my" at ../../build/CentOS-x86_64/show_nspbin.pl line 184, near "= @_"
Global symbol "$element" requires explicit package name at ../../build/CentOS-x86_64/show_nspbin.pl line 186.
Global symbol "$element" requires explicit package name at ../../build/CentOS-x86_64/show_nspbin.pl line 190.
Global symbol "$element" requires explicit package name at ../../build/CentOS-x86_64/show_nspbin.pl line 194.
syntax error at ../../build/CentOS-x86_64/show_nspbin.pl line 199, near "}"
../../build/CentOS-x86_64/show_nspbin.pl has too many errors.
make[1]: *** [../../build/CentOS-x86_64/show_nspbin.pl] Error 255
make[1]: *** Deleting file `../../build/CentOS-x86_64/show_nspbin.pl'
make[1]: Leaving directory `/software/TPP-4.5.2/src/perl_paths'
make: *** [perl_paths] Error 2

Can someone have an idea of what to do with this?  I am installing on CentOS6.2.
Thanks a lot,
Qiaojun

[chr12is]

Hi Qiaojun,

I had the same errors when installing the latest version of the TPP on my CentOS cluster. For some reason it throws an error with the qw syntax in the perl files. If you go in those files where it is giving an error, e.g. show_nspbin.pl, and edit the the lines containing qw(variableX variableY) for example, to use the conventional syntax of ('variableX' , 'variableY') removing the qw and using quotes and commas instead it should work...at least it did for me. 

You will have to edit this in a a few different files, like tpp_models.pl...and a couple others I can't remember off the top of my head. But just keep doing 'make' after you fix one, and the next one it has a problem with will appear. 

If any one has a nicer fix for this I would be happy to hear it as it would save me some time!

FYI, this is only a problem, at least for me, in the latest version of the TPP (4.6.3). I was able to compile previous versions without issue. 

Chris

[Joseph Slagel]

Hi Qiaojun,

What version of perl are you using (perl -V)?

-Joe

--
You received this message because you are subscribed to the Google Groups "spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discu...@googlegroups.com.
To post to this group, send email to spctools...@googlegroups.com.
Visit this group at http://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/groups/opt_out.

--

Joe Slagel
Institute for Systems Biology
jsl...@systemsbiology.org
(206) 732-1362

[fangq...@gmail.com]

Hi, Josh,

Thanks for the reply, I am using v5.18.1.  However, I found the PERL_LIB_CORE=/usr/lib64/perl5/5.10.0/x86_64-linux-thread-multi/CORE/

I don't quite understand why it is under 5.10.0 folder, could this be the problem?  How shall I correct this?

Qiaojun

[fangq...@gmail.com]

Hi, Joe,

I am using perl v.15.8. 

$ which perl
/usr/bin/perl

however, the PERL_LIB_CORE=/usr/lib64/perl5/5.10.0/x86_64-linux-thread-multi/CORE/

Not sure why it is installed under 5.10.0, which is the only folder in perl5.  Could this affect the compilation?  How shall I correct it?

Thanks a lot!

Qiaojun


On Monday, November 11, 2013 11:44:35 AM UTC+8, fangq...@gmail.com wrote:

[fangq...@gmail.com]

Hi, Chris,

Thanks for your reply.  Sorry it took a while to reply since connect to this group is slow and often fails from our country.

The version of show_npsbin.pl is different in TPP4.4 or earlier, so I simply replace it with and older version and make it compiled.

However, if you run xinteract, did you get the syntax errors in the tpp_model.pl?  So I think something in my system is configured differently for TPP.

Qiaojun

On Monday, November 11, 2013 11:44:35 AM UTC+8, fangq...@gmail.com wrote: