Hi DAve
Thanks for your mail.
When I look at how InSilicoSpectro is coded, I'm not that proud now....
Anyway, it's working everyday.
It could be a good opportunity to checkout these warnings.
I would happily give you the keys to write on the source code, but
unfortunately, it is hosted on the same cvs server than other code and
my boss would not like that that much...
Anyway, I'll try to find some time to address that quickly.
BTW, we are rewriting some of the InSilicoSpectro spirit: javaprotlib
on sourceforge
cheers
Alex
On Jun 10, 2009, at 2:11 AM, Dave Campbell via RT wrote:
> Tue Jun 09 20:11:04 2009: Request 46816 was acted upon.
> Transaction: Ticket created by dcampbell@systemsbiology.org
> Queue: InSilicoSpectro
> Subject: perl with warnings
> Broken in: (no value)
> Severity: (no value)
> Owner: Nobody
> Requestors: dcampbell@systemsbiology.org
> Status: new
> Ticket <URL:
http://rt.cpan.org/Ticket/Display.html?id=46816 >
>
>
> Hi,
>
> I work on a project called 'PeptideAtlas', perhaps you know Eric
> Deutsch,
> the principal architect. We happily use your InSilicoSpectro
> package, thank
> you for making it.
>
> When we use InSilicoSpecto with warnings on, we get a fair amount of
> output. I wanted to bring this to your attention in case you were
> unaware,
> and if possible ask if you intend to address this issue with the next
> release. If not, do you accept user-contributed fixes?
>
> 1) We think we are using the latest version:
> perl -MInSilicoSpectro -e 'print "$InSilicoSpectro::VERSION\n"'
> 1.3.24
>
> 2) This simple script yeilds the warnings below:
> #!/usr/local/bin/perl -w
> use InSilicoSpectro::InSilico::MassCalculator;
>
> "my" variable $elSite masks earlier declaration in same scope at
> /tools64/lib/perl5/site_perl/5.8.8/InSilicoSpectro/InSilico/
> ModRes.pm line
> 370.
> Subroutine InSilicoSpectro::InSilico::MassCalculator::init redefined
> at
> /tools64/lib/perl5/site_perl/5.8.8/InSilicoSpectro/InSilico/
> ModRes.pm line
> 40
> Subroutine InSilicoSpectro::InSilico::MassCalculator::getFromDico
> redefined
> at /tools64/lib/perl5/site_perl/5.8.8/InSilicoSpectro/InSilico/
> ModRes.pm
> line 40
> Subroutine InSilicoSpectro::InSilico::MassCalculator::getList
> redefined at
> /tools64/lib/perl5/site_perl/5.8.8/InSilicoSpectro/InSilico/
> ModRes.pm line
> 40
> Subroutine init redefined at
> /tools64/lib/perl5/site_perl/5.8.8/InSilicoSpectro/InSilico/
> MassCalculator.pm
> line 134.
> Useless use of private variable in void context at
> /tools64/lib/perl5/site_perl/5.8.8/InSilicoSpectro/InSilico/
> MassCalculator.pm
> line 1144.
>
> Below are the uname and perl -V output. Thanks for your time.
>
> -Dave
>
> Linux dione.systemsbiology.net 2.6.18-128.1.10.el5 #1 SMP Thu May 7
> 10:35:59
> EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
>
> Summary of my perl5 (revision 5 version 8 subversion 8) configuration:
> Platform:
> osname=linux, osvers=2.4.21-47.elsmp, archname=x86_64-linux-ld
> uname='linux odin.systemsbiology.net 2.4.21-47.elsmp #1 smp tue
> aug 1
> 08:12:32 edt 2006 x86_64 x86_64 x86_64 gnulinux '
> config_args=''
> hint=recommended, useposix=true, d_sigaction=define
> usethreads=undef use5005threads=undef useithreads=undef
> usemultiplicity=undef
> useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
> use64bitint=define use64bitall=define uselongdouble=define
> usemymalloc=n, bincompat5005=undef
> Compiler:
> cc='gcc', ccflags ='-fno-strict-aliasing -pipe
> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm',
> optimize='-O2',
> cppflags='-fno-strict-aliasing -pipe -Wdeclaration-after-statement
> -I/usr/local/include -I/usr/include/gdbm'
> ccversion='', gccversion='3.2.3 20030502 (Red Hat Linux 3.2.3-56)',
> gccosandvers=''
> intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678
> d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
> ivtype='long', ivsize=8, nvtype='long double', nvsize=16,
> Off_t='off_t',
> lseeksize=8
> alignbytes=16, prototype=define
> Linker and Libraries:
> ld='gcc', ldflags =''
> libpth=/tools64/lib /usr/local/lib64 /lib64 /usr/lib64
> libs=-lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lc
> perllibs=-lnsl -ldl -lm -lcrypt -lutil -lc
> libc=/lib/libc-2.3.2.so, so=so, useshrplib=false, libperl=libperl.a
> gnulibc_version='2.3.2'
> Dynamic Linking:
> dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
> cccdlflags='-fpic', lddlflags='-shared'
>
>
> Characteristics of this binary (from libperl):
> Compile-time options: PERL_MALLOC_WRAP USE_64_BIT_ALL USE_64_BIT_INT
> USE_LARGE_FILES USE_LONG_DOUBLE USE_PERLIO
> Built under linux
> Compiled at Jan 17 2007 15:21:34
> @INC:
> /tools64/lib/perl5/5.8.8/x86_64-linux-ld
> /tools64/lib/perl5/5.8.8
> /tools64/lib/perl5/site_perl/5.8.8/x86_64-linux-ld
> /tools64/lib/perl5/site_perl/5.8.8
> /tools64/lib/perl5/site_perl
> .
>
> Hi,
>
> I work on a project called 'PeptideAtlas', perhaps you know Eric
> Deutsch, the principal architect. We happily use your
> InSilicoSpectro package, thank you for making it.
>
> When we use InSilicoSpecto with warnings on, we get a fair amount
> of output. I wanted to bring this to your attention in case you
> were unaware, and if possible ask if you intend to address this
> issue with the next release. If not, do you accept user-contributed
> fixes?
>
> 1) We think we are using the latest version:
> perl -MInSilicoSpectro -e 'print "$InSilicoSpectro::VERSION\n"'
> 1.3.24
>
> 2) This simple script yeilds the warnings below:
> #!/usr/local/bin/perl -w
> use InSilicoSpectro::InSilico::MassCalculator;
>
> "my" variable $elSite masks earlier declaration in same scope at /
> tools64/lib/perl5/site_perl/5.8.8/InSilicoSpectro/InSilico/ModRes.pm
> line 370.
> Subroutine InSilicoSpectro::InSilico::MassCalculator::init redefined
> at /tools64/lib/perl5/site_perl/5.8.8/InSilicoSpectro/InSilico/
> ModRes.pm line 40
> Subroutine InSilicoSpectro::InSilico::MassCalculator::getFromDico
> redefined at /tools64/lib/perl5/site_perl/5.8.8/InSilicoSpectro/
> InSilico/ModRes.pm line 40
> Subroutine InSilicoSpectro::InSilico::MassCalculator::getList
> redefined at /tools64/lib/perl5/site_perl/5.8.8/InSilicoSpectro/
> InSilico/ModRes.pm line 40
> Subroutine init redefined at /tools64/lib/perl5/site_perl/5.8.8/
> InSilicoSpectro/InSilico/MassCalculator.pm line 134.
> Useless use of private variable in void context at /tools64/lib/
> perl5/site_perl/5.8.8/InSilicoSpectro/InSilico/MassCalculator.pm
> line 1144.
>
> Below are the uname and perl -V output. Thanks for your time.
>
> -Dave
>
> Linux dione.systemsbiology.net 2.6.18-128.1.10.el5 #1 SMP Thu May 7
> 10:35:59 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
>
> Summary of my perl5 (revision 5 version 8 subversion 8) configuration:
> Platform:
> osname=linux, osvers=2.4.21-47.elsmp, archname=x86_64-linux-ld
> uname='linux odin.systemsbiology.net 2.4.21-47.elsmp #1 smp tue
> aug 1 08:12:32 edt 2006 x86_64 x86_64 x86_64 gnulinux '
> config_args=''
> hint=recommended, useposix=true, d_sigaction=define
> usethreads=undef use5005threads=undef useithreads=undef
> usemultiplicity=undef
> useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
> use64bitint=define use64bitall=define uselongdouble=define
> usemymalloc=n, bincompat5005=undef
> Compiler:
> cc='gcc', ccflags ='-fno-strict-aliasing -pipe -Wdeclaration-
> after-statement -I/usr/local/include -D_LARGEFILE_SOURCE -
> D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm',
> optimize='-O2',
> cppflags='-fno-strict-aliasing -pipe -Wdeclaration-after-
> statement -I/usr/local/include -I/usr/include/gdbm'
> ccversion='', gccversion='3.2.3 20030502 (Red Hat Linux
> 3.2.3-56)', gccosandvers=''
> intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678
> d_longlong=define, longlongsize=8, d_longdbl=define,
> longdblsize=16
> ivtype='long', ivsize=8, nvtype='long double', nvsize=16,
> Off_t='off_t', lseeksize=8
> alignbytes=16, prototype=define
> Linker and Libraries:
> ld='gcc', ldflags =''
> libpth=/tools64/lib /usr/local/lib64 /lib64 /usr/lib64
> libs=-lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lc
> perllibs=-lnsl -ldl -lm -lcrypt -lutil -lc
> libc=/lib/libc-2.3.2.so, so=so, useshrplib=false,
> libperl=libperl.a
> gnulibc_version='2.3.2'
> Dynamic Linking:
> dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
> cccdlflags='-fpic', lddlflags='-shared'
>
>
> Characteristics of this binary (from libperl):
> Compile-time options: PERL_MALLOC_WRAP USE_64_BIT_ALL USE_64_BIT_INT
> USE_LARGE_FILES USE_LONG_DOUBLE USE_PERLIO
> Built under linux
> Compiled at Jan 17 2007 15:21:34
> @INC:
> /tools64/lib/perl5/5.8.8/x86_64-linux-ld
> /tools64/lib/perl5/5.8.8
> /tools64/lib/perl5/site_perl/5.8.8/x86_64-linux-ld
> /tools64/lib/perl5/site_perl/5.8.8
> /tools64/lib/perl5/site_perl
> .
>
