Re: [Bioc-devel] mzR: pwiz is now the default backend

[Rainer Johannes]

actually, I got quite some segfaults lately with the Ramp backend (was default 
up to now). With the pwiz backend I don't get them anymore.
Also, in xcms we were manually setting the backend to pwiz and did not 
experience any problems.

cheers, jo

On 23 May 2017, at 18:35, Laurent Gatto 
> wrote:


On 23 May 2017 16:26, Vladislav Petyuk wrote:

Are there going to be any noticeable changes for the package users?  Does
it break compatibility?  Do I need to install something extra (like
ProteoWizard)?

In theory, we don't expect any downstream effects: no breaks, no extra
dependencies, ... developers and users shouldn't notice the change at
all. The pwiz backend has been available for many years, but was just
not the default.

Let's see what the practice says...

Laurent

On Tue, May 23, 2017 at 9:10 AM Laurent Gatto 
> wrote:


Dear developer,

For those who use mzR to access raw mass spectrometry data, please note
that we have change the default backend from Ramp to pwiz.

The old backend is still available using

 openMSfile(filename, backend = "Ramp")

See https://github.com/sneumann/mzR/issues/84 for details. Please do
raise any concerns or problems in that issue.

Best wishes,

Laurent

--
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/

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http://lgatto.github.io/

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Re: [Bioc-devel] mzR: pwiz is now the default backend

[Laurent Gatto]

On 23 May 2017 16:26, Vladislav Petyuk wrote:

> Are there going to be any noticeable changes for the package users?  Does
> it break compatibility?  Do I need to install something extra (like
> ProteoWizard)?

In theory, we don't expect any downstream effects: no breaks, no extra
dependencies, ... developers and users shouldn't notice the change at
all. The pwiz backend has been available for many years, but was just
not the default.

Let's see what the practice says...

Laurent

> On Tue, May 23, 2017 at 9:10 AM Laurent Gatto  wrote:
>
>>
>> Dear developer,
>>
>> For those who use mzR to access raw mass spectrometry data, please note
>> that we have change the default backend from Ramp to pwiz.
>>
>> The old backend is still available using
>>
>>   openMSfile(filename, backend = "Ramp")
>>
>> See https://github.com/sneumann/mzR/issues/84 for details. Please do
>> raise any concerns or problems in that issue.
>>
>> Best wishes,
>>
>> Laurent
>>
>> --
>> Laurent Gatto | @lgatt0
>> http://cpu.sysbiol.cam.ac.uk/
>> http://lgatto.github.io/
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>


-- 
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/

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Re: [Bioc-devel] mzR: pwiz is now the default backend

[Vladislav Petyuk]

Are there going to be any noticeable changes for the package users?  Does
it break compatibility?  Do I need to install something extra (like
ProteoWizard)?

On Tue, May 23, 2017 at 9:10 AM Laurent Gatto  wrote:

>
> Dear developer,
>
> For those who use mzR to access raw mass spectrometry data, please note
> that we have change the default backend from Ramp to pwiz.
>
> The old backend is still available using
>
>   openMSfile(filename, backend = "Ramp")
>
> See https://github.com/sneumann/mzR/issues/84 for details. Please do
> raise any concerns or problems in that issue.
>
> Best wishes,
>
> Laurent
>
> --
> Laurent Gatto | @lgatt0
> http://cpu.sysbiol.cam.ac.uk/
> http://lgatto.github.io/
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] mzR: pwiz is now the default backend

[Laurent Gatto]

Dear developer,

For those who use mzR to access raw mass spectrometry data, please note
that we have change the default backend from Ramp to pwiz.

The old backend is still available using

  openMSfile(filename, backend = "Ramp")

See https://github.com/sneumann/mzR/issues/84 for details. Please do
raise any concerns or problems in that issue.

Best wishes,

Laurent

-- 
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/

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