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, [email protected] 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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