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This queue is for tickets about the Metabolomics-Fragment-Annotation CPAN distribution.

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The Basics
Id: 131468
Status: resolved
Priority: 0/
Queue: Metabolomics-Fragment-Annotation
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Owner: pfem.bioinfo [...] gmail.com
Requestors: SREZIC [...] cpan.org
Cc:
AdminCc:
Bug Information
Severity: (no value)
Broken in: 0.2
Fixed in: 0.3

History Show all quoted text
  Tue Jan 14 14:46:26 2020 SREZIC [...] cpan.org - Ticket created
Subject: Test failure with -Duselongdouble
If perl is compiled with increased floating point accuracy (using the configuration option -Duselongdouble), then the test suite fails: ... # Failed test 'Method 'compareExpMzToTheoMzList' works with peak list and Ab initio fragments content' # at t/Fragment-Annotation.t line 145. # Structures begin differing at: # $got->{_EXP_PEAK_LIST_}[0]{_PPM_ERROR_} = '111.703012965368715' # $expected->{_EXP_PEAK_LIST_}[0]{_PPM_ERROR_} = '111.703012965369' [WARN] the method _getPeak_ANNOTATION_IN_NEG_MODE can't _getPeak a undef or null string value # Failed test 'Method 'compareExpMzToTheoMzList' works with peak list file and Contaminant content' # at t/Fragment-Annotation.t line 259. # Structures begin differing at: # $got->{_EXP_PEAK_LIST_}[0]{_PPM_ERROR_} = '0.0979864278998715888' # $expected->{_EXP_PEAK_LIST_}[0]{_PPM_ERROR_} = '0.0979864278998716' ...
  Wed Oct 07 08:54:08 2020 pfem.bioinfo [...] gmail.com - Correspondence added
On Tue Jan 14 14:46:26 2020, SREZIC wrote: Show quoted text
> If perl is compiled with increased floating point accuracy (using the > configuration option -Duselongdouble), then the test suite fails: > > ... > # Failed test 'Method 'compareExpMzToTheoMzList' works with peak > list and Ab initio fragments content' > # at t/Fragment-Annotation.t line 145. > # Structures begin differing at: > # $got->{_EXP_PEAK_LIST_}[0]{_PPM_ERROR_} = > '111.703012965368715' > # $expected->{_EXP_PEAK_LIST_}[0]{_PPM_ERROR_} = > '111.703012965369' > [WARN] the method _getPeak_ANNOTATION_IN_NEG_MODE can't _getPeak a > undef or null string value >
This bug was fixed in 0.3 module version. (double are standardized with lower float numbers and in metabolomics float > 7 is a great precision value...) Show quoted text
> # Failed test 'Method 'compareExpMzToTheoMzList' works with peak > list file and Contaminant content' > # at t/Fragment-Annotation.t line 259. > # Structures begin differing at: > # $got->{_EXP_PEAK_LIST_}[0]{_PPM_ERROR_} = > '0.0979864278998715888' > # $expected->{_EXP_PEAK_LIST_}[0]{_PPM_ERROR_} = > '0.0979864278998716' > ...
  Wed Oct 07 08:54:09 2020 The RT System itself - Status changed from 'new' to 'open'
  Wed Oct 07 08:54:09 2020 pfem.bioinfo [...] gmail.com - Fixed in 0.3 added
  Wed Oct 07 09:21:04 2020 pfem.bioinfo [...] gmail.com - Correspondence added
On Wed Oct 07 08:54:08 2020, GIACOMONI wrote: Show quoted text
> On Tue Jan 14 14:46:26 2020, SREZIC wrote:
> > If perl is compiled with increased floating point accuracy (using the > > configuration option -Duselongdouble), then the test suite fails: > > > > ... > > # Failed test 'Method 'compareExpMzToTheoMzList' works with peak > > list and Ab initio fragments content' > > # at t/Fragment-Annotation.t line 145. > > # Structures begin differing at: > > # $got->{_EXP_PEAK_LIST_}[0]{_PPM_ERROR_} = > > '111.703012965368715' > > # $expected->{_EXP_PEAK_LIST_}[0]{_PPM_ERROR_} = > > '111.703012965369' > > [WARN] the method _getPeak_ANNOTATION_IN_NEG_MODE can't _getPeak a > > undef or null string value > >
> > This bug was fixed in 0.3 module version. (double are standardized > with lower float numbers and in metabolomics float > 7 is a great > precision value...) >
> > # Failed test 'Method 'compareExpMzToTheoMzList' works with peak > > list file and Contaminant content' > > # at t/Fragment-Annotation.t line 259. > > # Structures begin differing at: > > # $got->{_EXP_PEAK_LIST_}[0]{_PPM_ERROR_} = > > '0.0979864278998715888' > > # $expected->{_EXP_PEAK_LIST_}[0]{_PPM_ERROR_} = > > '0.0979864278998716' > > ...
Fixed and ticket closed
  Wed Oct 07 09:21:05 2020 pfem.bioinfo [...] gmail.com - Status changed from 'open' to 'resolved'
  Wed Oct 07 09:21:05 2020 pfem.bioinfo [...] gmail.com - Taken