Hi Qiaojun,
What version of perl are you using (perl -V)?
-Joe
On Mon, Nov 11, 2013 at 3:11 AM, chr12is <chrishu...@gmail.com> wrote:
> 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
>
>
>
> On Monday, November 11, 2013 4:44:35 AM UTC+1, fangq...@gmail.com wrote:
>>
>> 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.plline
>> 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
>>
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--
Joe Slagel
Institute for Systems Biology
jsla...@systemsbiology.org
(206) 732-1362
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