proteowizard-developer — Developer discussion

[proteowizard-developer] Maintenance Notice - teamcity.labkey.org - 3/24/26

[Trey C. <tc...@la...>]

On March 24th, we will be performing maintenance on LabKey's TeamCity
servers to improve performance and reliability.

Beginning at 3pm Pacific, the overall outage should last about 1 hour. The
site will still be reachable but at reduced functionality for about 30
minutes. It will then be unreachable for about 15 minutes, while jobs are
able to continue in the background.

Some downloads from https://proteowizard.sourceforge.io/ will also be
unavailable during this window.

We apologize for any inconvenience this may cause.


Thank you,

Trey

-- 

Trey Chadick
Software Test Architect, LabKey
*Pronouns: he/him*

Email: tc...@la...

www.LabKey.com <http://www.labkey.com/>

[proteowizard-developer] Maintenance Notice - teamcity.labkey.org - 2/22/24

[Trey C. <tc...@la...>]

On February 22nd, we will be performing maintenance on our TeamCity server
to improve performance and reliability.
We will pause the queue at 9AM to prepare for the maintenance.
Once the queue has cleared, as early as 11AM, we will take the server
offline and it will be unavailable for a few hours. Downloads from
https://proteowizard.sourceforge.io/ will also be unavailable during this
window.

We apologize for any inconvenience this may cause.

Thank you,
Trey

-- 

Trey Chadick
Test Lead, LabKey
*Pronouns: he/him*

Email: tc...@la...

www.LabKey.com <http://www.labkey.com/>

[proteowizard-developer] TeamCity Maintenance Friday

[Trey C. <tc...@la...>]

We will be performing maintenance on the LabKey TeamCity server on *Friday
2/3/2023 starting at 8 AM PST*. During this maintenance the TeamCity Build
Queue will be paused and no new builds will be started until the
maintenance is completed. We are migrating to a multi-node, high
availability configuration to improve performance and reliability.

The server will be offline periodically throughout the migration. We hope
to have the maintenance complete and validated by 3PM.

Downloads from https://proteowizard.sourceforge.io/ will not be available
during the maintenance.

We apologize for any inconvenience this may cause.

Thank you,
Trey

-- 

Trey Chadick
Test Lead, LabKey
*Pronouns: he/him*

Email: tc...@la...

www.LabKey.com <http://www.labkey.com/>

[proteowizard-developer] Fwd: Teamcity Maintenance - Sunday 12/12/2021

[Trey C. <tc...@la...>]

FYI

---------- Forwarded message ---------
From: Stuart MacDonald <st...@la...>
Date: Fri, Dec 10, 2021 at 9:15 AM
Subject: Teamcity Maintenance - Sunday 12/12/2021
To: LabKey Engineering <eng...@la...>


We will be performing maintenance on TeamCity Sunday 12/122021 between 5 PM
- 8 PM PDT.  During this maintenance window the TeamCity Build Queue will
be paused and no new builds will be started until the maintenance is
completed. Any existing builds running on TeamCity agents will continue and
not be interrupted.

We will be upgrading Postgres and Java.

If you have questions or concerns, please reply to this email or contact me
directly.

Thanks


-- 

Trey Chadick
Test Lead, LabKey
*Pronouns: he/him*

Email: tc...@la...

www.LabKey.com <http://www.labkey.com/>

[proteowizard-developer] Fwd: Teamcity Maintenance Thursday 10/28 5-6PM

[Trey C. <tc...@la...>]

Upcoming TeamCity maintenance.

---------- Forwarded message ---------
From: Stuart MacDonald <st...@la...>
Date: Wed, Oct 27, 2021 at 10:15 AM
Subject: Teamcity Maintenance Thursday 10/28 5-6PM
To: LabKey Engineering <eng...@la...>


We will be performing maintenance on TeamCity Thursday 10/28/2021 between 5
PM - 6 PM PDT.  During this maintenance window the TeamCity Build Queue
will be paused and no new builds will be started until the maintenance is
completed. Any existing builds running on TeamCity agents will continue and
not be interrupted.

We will be updating to TeamCity Release 2021.2, applying Linux Patches and
updating the TLS Certificate.

If you have questions or concerns, please reply to this email or contact me
directly.

Thanks
Stuart



-- 

Trey Chadick
Test Lead, LabKey
*Pronouns: he/him*

Email: tc...@la...

www.LabKey.com <http://www.labkey.com/>

[proteowizard-developer] Fwd: Maintenance Notice - TeamCity Upgrade Monday, June 21st @ 8pm PST

[Trey C. <tc...@la...>]

---------- Forwarded message ---------
From: Isa Farnik <is...@la...>
Date: Mon, Jun 14, 2021 at 12:36 PM
Subject: Maintenance Notice - TeamCity Upgrade Monday, June 21st @ 8pm PST
To: core <co...@la...>


Hey folks,

This is a notice that I'll be performing some routine maintenance on
TeamCity Monday, Jun. 21st at 20:00 PST.

This maintenance includes but is not limited to:
  - upgrading to TeamCity 2021.1 (Build: 92597) What's New
<https://www.jetbrains.com/help/teamcity/2021.1/what-s-new-in-teamcity.html>
 | Release Notes
<https://www.jetbrains.com/help/teamcity/2021.1/teamcity-2021-1-release-notes.html>
  - renewal of the SSL certificate

In fair weather conditions, this voyage should only last ~30 minutes. On
rough seas, 2 hours.

As always, I'll message once again when beginning the work and once more
when the work is complete or is continuing unexpectedly.

Cross posting to the announcements forum shortly.

Thanks in advance for your patience,
~Isa

-- 

Isa Farnik
Cloud Infrastructure Engineer, LabKey
*Pronouns: he/him/his*

Email: is...@la...

www.LabKey.com


-- 

Trey Chadick
Test Lead, LabKey
*Pronouns: he/him*

Email: tc...@la...

www.LabKey.com <http://www.labkey.com/>

[proteowizard-developer] Fwd: Maintenance Notice - Upgrade of TeamCity for Monday, Feb 8th @ 20:00 PST

[Trey C. <tc...@la...>]

---------- Forwarded message ---------
From: Isa Farnik <is...@la...>
Date: Mon, Feb 8, 2021 at 10:51 AM
Subject: Maintenance Notice - Upgrade of TeamCity for Monday, Feb 8th @
20:00 PST
To: core <co...@la...>


Hey folks,

Sorry for the late notice on this.

There will be some maintenance done on TeamCity tonight at 8pm PST:
  - Upgrade to 2020.2.2 (build 85899)
  - A refresh of the TeamCity SSL cert

This is mostly routine so it ideally shouldn't take more than 30 minutes
with a maximum of 2 hours if something goes awry and a rollback is required.

As always, I'll message again when the work starts and again when the work
completes.

Thanks for your patience and sorry again for the late notice,
~Isa

-- 

Isa Farnik
Cloud Infrastructure Engineer, LabKey
*Pronouns: he/him/his*

Email: is...@la...

www.LabKey.com


-- 

Trey Chadick
Test Lead, LabKey
*Pronouns: he/him*

Email: tc...@la...
Phone: 206.489.2577

www.LabKey.com <http://www.labkey.com/>

[proteowizard-developer] Fwd: TeamCity Maintenance Sat. 1/10 @ 8pm PST

[Trey C. <tc...@la...>]

---------- Forwarded message ---------
From: Isa Farnik <is...@la...>
Date: Thu, Jan 7, 2021 at 11:13 AM
Subject: TeamCity Maintenance Sat. 1/10 @ 8pm PST
To: core <co...@la...>


Hey folks,

I'll be doing an upgrade of TeamCity to get us onto 2020.2.x this Saturday
Jan. 10th at 20:00 PST.

As always, I'll message again when the work begins and once more after that
to indicate the work has completed. Ideally this is a 30 minute affair but
could take up to 2 hours.

Please forward this message to interested parties who otherwise wouldn't be
notified.

Thanks

-- 

Isa Farnik
Cloud Infrastructure Engineer, LabKey
*Pronouns: he/him/his*

Email: is...@la...

www.LabKey.com


-- 

Trey Chadick
Test Lead, LabKey
*Pronouns: he/him*

Email: tc...@la...
Phone: 206.489.2577

www.LabKey.com <http://www.labkey.com/>

Re: [proteowizard-developer] [proteowizard-support] Exploris data cannot use MSConvert

[Chambers, M. <mat...@gm...>]

Posts like this are why I want to switch to GitHub issues, where we can provide a template to prompt users to provide relevant information, 
like what version they used, what error message they got, at least...

On 12/3/2020 11:16 AM, ZOU Juan wrote:
>
> Hi,
>
> I could not use MSConvert to process Exploris 480 data. Is anything you can do?
>
> Best wishes
>
> Juan
>

Re: [proteowizard-developer] TeamCity Maintenance Mon. 9/14 @ 8pm PDT

[Trey C. <tc...@la...>]

Maintenance was completed successfully.

Thank you,
Trey

On Thu, Sep 10, 2020 at 4:06 PM Trey Chadick <tc...@la...> wrote:

> Hey there folks,
>
> It's time again for some TeamCity maintenance.
>
> This go round, we'll be:
>   - upgrading TeamCity from version 2019.x to 2020.1.4.
>   - refreshing TeamCity's SSL certificate
>
> If all goes well, the work should be complete within 30 minutes, but could
> run as long as 90 minutes.
>
> Thank you,
> Trey
>
> --
>
> Trey Chadick
> Test Lead, LabKey
> *Pronouns: he/him*
>
> Email: tc...@la...
>
> www.LabKey.com <http://www.labkey.com/>
>
>

-- 

Trey Chadick
Test Lead, LabKey
*Pronouns: he/him*

Email: tc...@la...
Phone: 206.489.2577

www.LabKey.com <http://www.labkey.com/>

Re: [proteowizard-developer] TeamCity Maintenance Mon. 9/14 @ 8pm PST

[Isa F. <is...@la...>]

This work is now complete!

"I repeat, we have normality. Anything you still can't cope with is
therefore your own problem."

Thanks for your patience,
~Isa

On Mon, Sep 14, 2020 at 7:55 PM Isa Farnik <is...@la...> wrote:

> I'll be beginning this work shortly.
>
> On Thu, Sep 10, 2020 at 2:47 PM Isa Farnik <is...@la...> wrote:
>
>> Hey there folks,
>>
>> It's time again for some TeamCity maintenance.
>>
>> This go round, I'll be:
>>   - upgrading TeamCity from version 2019.x to 2020.1.4.
>>   - refreshing TeamCity's SSL certificate
>>
>> As usual, I'll be messaging again when work starts and a third time when
>> the work is complete.
>> If all goes well, the work should be complete within 30 minutes, but
>> could run as long as 90 minutes.
>>
>> Thanks in advance for your patience,
>> ~Isa
>>
>> P.S.:
>> I'll be posting a similar message to the Premium Support forums shortly.
>> But please ensure other vested parties are notified if they aren't on
>> Core or the forum.
>>
>> --
>>
>> Isa Farnik
>> Cloud Infrastructure Engineer, LabKey
>> *Pronouns: he/him/his*
>>
>> Email: is...@la...
>>
>> www.LabKey.com
>>
>
>
> --
>
> Isa Farnik
> Cloud Infrastructure Engineer, LabKey
> *Pronouns: he/him/his*
>
> Email: is...@la...
>
> www.LabKey.com
>


-- 

Isa Farnik
Cloud Infrastructure Engineer, LabKey
*Pronouns: he/him/his*

Email: is...@la...

www.LabKey.com

[proteowizard-developer] TeamCity Maintenance Mon. 9/14 @ 8pm PDT

[Trey C. <tc...@la...>]

Hey there folks,

It's time again for some TeamCity maintenance.

This go round, we'll be:
  - upgrading TeamCity from version 2019.x to 2020.1.4.
  - refreshing TeamCity's SSL certificate

If all goes well, the work should be complete within 30 minutes, but could
run as long as 90 minutes.

Thank you,
Trey

-- 

Trey Chadick
Test Lead, LabKey
*Pronouns: he/him*

Email: tc...@la...

www.LabKey.com <http://www.labkey.com/>

[proteowizard-developer] C++17 removes bind2nd (follow-up)

[Filippo R. <lis...@la...>]

Greetings,

as a follow-up to my previous mail, I would like to get a confirmation that the
following replacements are ok (they seem to compile fine, but that certainly is
not enough :-)


pwiz/utility/findmf/base/filter/utilities/gauss.hpp
===================================================

         template<typename TReal>
         TReal getGaussWorker( TReal sigma,
                               std::vector<TReal> &gauss,
                               std::vector<TReal> &x )
         {
           //generate response
           Gauss<TReal> g(0.,sigma);
           gauss.resize(x.size());
           std::transform(x.begin(),x.end(),gauss.begin(),g);

           //ensure that are of gaussian is one...
           TReal sum = std::accumulate(gauss.begin() , gauss.end() , 0.);
old->          //std::transform(gauss.begin(),gauss.end(),gauss.begin(),std::bind2nd(std::divides<TReal>(),sum )) ;
new->          std::transform(gauss.begin(),gauss.end(),gauss.begin(), [sum] (const TReal &real){ return (real / sum);});
           TReal sumfilter = std::accumulate(gauss.begin(),gauss.end(),0.);
           return sumfilter;
         }


         template<typename TReal>
         void scaleDerivative(
             std::vector<TReal> &mh //the wavelet to scale
             )
         {
           //do this so that the sum of wavelet equals zero
           TReal sum = std::accumulate(mh.begin() , mh.end() , 0.);
           sum /= mh.size();
old->          //std::transform(mh.begin(),mh.end(),mh.begin(),std::bind2nd(std::minus<TReal>(), sum )) ;
new->          std::transform(mh.begin(),mh.end(),mh.begin(), [sum] (const TReal &real) { return (real / sum) ; });
           //compute sum of square...
           TReal sumAbs = 0;
           for(typename std::vector<TReal>::iterator it = mh.begin() ;it != mh.end(); ++it)
             {
               sumAbs += fabs(*it);
             }
old->          //std::transform(mh.begin(),mh.end(),mh.begin(),std::bind2nd(std::divides<TReal>(), sumAbs )) ;
new->          std::transform(mh.begin(),mh.end(),mh.begin(), [sumAbs] (const TReal &real){ return (real / sumAbs);});
         }



pwiz/utility/findmf/base/base/scale.hpp
=======================================
       /**
         scale centers and/or scales all values from begin in to end.
       */
       template<typename InputIterator>
       void scale(
           InputIterator begin,
           InputIterator end,
           std::pair<typename std::iterator_traits<InputIterator>::value_type,typename std::iterator_traits<InputIterator>::value_type> & scaled, //!<[out] scaled.first = center, scaled.second = scale
           bool center = true,//!<[in] either a logical value or a numeric vector of length equal to the number of columns of x.
           bool scale = true //!<[in] 	either a logical value or a numeric vector of length equal to the number of columns of x.
           )
       {
         typedef typename std::iterator_traits<InputIterator>::value_type TReal;
         std::vector<TReal> tmp;

         if(center)
           {
             scaled.first = ralab::base::base::mean( begin , end);
old->            //std::transform(begin, end, begin, std::bind2nd( std::minus<TReal>(), scaled.first));
new->            std::transform(begin, end, begin, [scaled] (const TReal &real) {return (real - scaled.first);});
           }
         else
           {
             scaled.first = std::numeric_limits<TReal>::quiet_NaN();
           }
         if(scale)
           {
             scaled.second = rootMeanSquare( begin , end );
old->            //std::transform(begin, end, begin , std::bind2nd(std::divides<TReal>(), scaled.second) );
new->            std::transform(begin, end, begin , [scaled] (const TReal &real) { return (real / scaled.second);});
           }
         else
           {
             scaled.second = std::numeric_limits<TReal>::quiet_NaN();
           }
       }


Thank you for your patience,

Sincerely,
Filippo

-- 

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Research scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄⠀⠀⠀⠀  http://msxpertsuite.org
           http://www.debian.org

[proteowizard-developer] C++17 removes bind2nd

[Filippo R. <lis...@la...>]

Greetings Fellow Developers,

I am trying to build pwiz on MacOSX and I would like to compile the code using
the C++17 standard. That standard has removed the std::bind2nd function.

In file 

pwiz/utility/findmf/base/filter/utilities/gauss.hpp

lines 103--107:

           //ensure that are of gaussian is one...
           TReal sum = std::accumulate(gauss.begin() , gauss.end() , 0.);
           std::transform(gauss.begin(),gauss.end(),gauss.begin(),std::bind2nd(std::divides<TReal>(),sum )) ;
           TReal sumfilter = std::accumulate(gauss.begin(),gauss.end(),0.);
           return sumfilter;

I would like to replace the std::transform call using a lambda, something like
this:

std::transform(gauss.begin(),gauss.end(),gauss.begin(), [ ] () { ;});

Unfortunately, my acquaintance with the code does not allow me to write that
call correctly.

Is there any good soul who would help me with this ?

Thanks for reading up to here,

Sincerely,
Filippo

-- 

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Research scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄⠀⠀⠀⠀  http://msxpertsuite.org
           http://www.debian.org

[proteowizard-developer] License (actually no license) for file in libpwiz source

[Filippo R. <fil...@un...>]

Greetings, Fellow Develoopers,

In Debian, each file that goes in a package is checked for its Copyright notice
and License.

Some files do not have that information or have only remarks that are legally
invalid.

This mail is to inform you that the file below is in the Public Domain, as
stated by the author of the code whom I requested to clarify the copyright
status of the contents of the 

http://erdani.org/publications/adapting_automation_arrays.html

page from which the code was drawn.

You may update the copyright notice in that specific file by reproducing the
text below.

Regards,

Filippo 

Files:  src/pwiz/utility/misc/automation_vector.h
Copyright: Andrei Alexandrescu
License: Public-domain-email
  http://erdani.org/publications/adapting_automation_arrays.html
  Sent an email to ask for a copyright notice.
  .
  Date: Wed, 3 Jun 2020 16:45:19 -0400
  From: Andrei Alexandrescu <an...@er...>
  To: Filippo Rusconi <fil...@un...>
  Cc: Andrei Alexandrescu <an...@me...>
  Subject: Re: Copyright notice for your work ?
  . 
  Public domain. You can use this email as confirmation. Have fun!
  . 
  On Wed, Jun 3, 2020 at 1:32 PM Filippo Rusconi <
  fil...@un...> wrote:
  . 
  > Greetings, Mr Alexandrescu,
  >
  > I am currently packaging a software for Debian GNU/Linux and am seeing
  > that some
  > code from http://erdani.org/publications/adapting_automation_arrays.html
  > is
  > included in that software.
  >
  > Could you please tell me what is the license of that page ? Is the code
  > freely
  > redistributable with a Free Software license or is it in the public domain
  > ?
  >
  > Looking forward to your answer, and with my best regards,
  >
  > Filippo Rusconi
  >
  > --
  >
  > ⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
  > ⣾⠁⢠⠒⠀⣿⡁   Research scientist at CNRS
  > ⢿⡄⠘⠷⠚⠋⠀   Debian Developer
  > ⠈⠳⣄⠀⠀⠀⠀  http://msxpertsuite.org
  >            http://www.debian.org

-- 

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Research scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄⠀⠀⠀⠀  http://msxpertsuite.org
           http://www.debian.org

~~~~
book: http://www.lavoisier.fr/livre/notice.asp?id=3LKW2OAR2KROWZ
http://books.google.fr/books?id=2NmguxmEI1sC&printsec=frontcover&dq=rusconi+f+lavoisier&hl=fr&sa=X&ei=nGGOUt2SH_Ly0gX0uIHoBQ&ved=0CDUQ6AEwAA#v=onepage&q&f=false
~~~~
Génétique Quantitative et Évolution & Plateforme PAPPSO
UMR CNRS 8120 – INRA – Université Paris-Sud – AgroParisTech - Université Paris-Saclay
http://moulon.inra.fr/ & http://pappso.inra.fr/
Ferme du Moulon
91190 Gif-sur-Yvette
France
Tel : +33 (0)1 69 33 23 54
Fax : +33 (0)1 69 33 23 40

Re: [proteowizard-developer] Msconvert

[Neumann, S. <sne...@ip...>]

Hi,

I looked at the mzML and gave some interpretation at 
https://github.com/mzmine/mzmine2/issues/788#issuecomment-579954787

While the <chromatogram> representation of the MRMs looks fine, 
the <spectrum> encoding as MS1 looks like not covered by the
specification. Not sure whether that is in the WIFF or in the msconvert
conversion. 

Thoughts ?

Yours,
Steffen


On Wed, 2020-01-29 at 08:48 +0000, Neumann, Steffen wrote:
> Hi,
> 
> The file you sent to me was mzXML. Please test mzML,
> I would expect the support on both msconvert and mzmine 
> to be much better for mzML.
> 
> Yours, 
> Steffen
> 
> On Tue, 2020-01-28 at 08:31 +0000, Omar AHMED wrote:
> > Dear
> > 
> > I have an issue concerning the use of MSconvert to convert Wiff
> > files
> > to MzmL to upload them to Mzmine. The problem is when I use MZmine,
> > the peaks appear with the transition number instead of showing the
> > mass. I already contacted Mzmine developer and they said to me that
> > the problem came from MS convert.
> > 
> > Any ideas?
> > 
> > 
> > Regards
> > Omar S.AHMED
> > _______________________________________________
> > proteowizard-developer mailing list
> > pro...@li...
> > https://lists.sourceforge.net/lists/listinfo/proteowizard-developer
-- 

Current bits of interest:

* Computational Metabolomics PhD Position
  
* Leibniz Plant Biochemistry Symposium, 14./15.05.2020, Halle
  https://events.ipb-halle.de/event/60/

* HUPO PSI spring meeting, 23.-25.03.2020, San Diego, CA
  http://www.psidev.info/hupo-psi-meeting-2020

* International Metabolomics Society conferemce, 06.-07.07.2020,
Shanghai, China
  http://metabolomics2020.org/

---
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
06120 Halle                       +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

Re: [proteowizard-developer] Msconvert

[Neumann, S. <sne...@ip...>]

Hi,

The file you sent to me was mzXML. Please test mzML,
I would expect the support on both msconvert and mzmine 
to be much better for mzML.

Yours, 
Steffen

On Tue, 2020-01-28 at 08:31 +0000, Omar AHMED wrote:
> Dear
> 
> I have an issue concerning the use of MSconvert to convert Wiff files
> to MzmL to upload them to Mzmine. The problem is when I use MZmine,
> the peaks appear with the transition number instead of showing the
> mass. I already contacted Mzmine developer and they said to me that
> the problem came from MS convert.
> 
> Any ideas?
> 
> 
> Regards
> Omar S.AHMED
> _______________________________________________
> proteowizard-developer mailing list
> pro...@li...
> https://lists.sourceforge.net/lists/listinfo/proteowizard-developer
-- 

Current bits of interest:

* Computational Metabolomics PhD Position
  
* Leibniz Plant Biochemistry Symposium, 14./15.05.2020, Halle
  https://events.ipb-halle.de/event/60/

* HUPO PSI spring meeting, 23.-25.03.2020, San Diego, CA
  http://www.psidev.info/hupo-psi-meeting-2020

* International Metabolomics Society conferemce, 06.-07.07.2020,
Shanghai, China
  http://metabolomics2020.org/

---
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
06120 Halle                       +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

Re: [proteowizard-developer] Msconvert

[Neumann, S. <sne...@ip...>]

Hi,
can you provide an example mzML file ?
Yours,
Steffen

On Tue, 2020-01-28 at 08:31 +0000, Omar AHMED wrote:
> Dear
> 
> I have an issue concerning the use of MSconvert to convert Wiff files
> to MzmL to upload them to Mzmine. The problem is when I use MZmine,
> the peaks appear with the transition number instead of showing the
> mass. I already contacted Mzmine developer and they said to me that
> the problem came from MS convert.
> 
> Any ideas?
> 
> 
> Regards
> Omar S.AHMED
> _______________________________________________
> proteowizard-developer mailing list
> pro...@li...
> https://lists.sourceforge.net/lists/listinfo/proteowizard-developer
-- 

Current bits of interest:

* Computational Metabolomics PhD Position
  
* Leibniz Plant Biochemistry Symposium, 14./15.05.2020, Halle
  https://events.ipb-halle.de/event/60/

* HUPO PSI spring meeting, 23.-25.03.2020, San Diego, CA
  http://www.psidev.info/hupo-psi-meeting-2020

* International Metabolomics Society conferemce, 06.-07.07.2020,
Shanghai, China
  http://metabolomics2020.org/

---
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
06120 Halle                       +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

[proteowizard-developer] Msconvert

[Omar A. <oma...@ho...>]

Dear

I have an issue concerning the use of MSconvert to convert Wiff files to MzmL to upload them to Mzmine. The problem is when I use MZmine, the peaks appear with the transition number instead of showing the mass. I already contacted Mzmine developer and they said to me that the problem came from MS convert.

Any ideas?


Regards
Omar S.AHMED

[proteowizard-developer] Fwd: TeamCity Maintenance 9/4 15:00 PST

[Trey C. <tc...@la...>]

---------- Forwarded message ---------
From: Isa Farnik <is...@la...>
Date: Tue, Sep 3, 2019 at 1:13 PM
Subject: TeamCity Maintenance 9/4 15:00 PST
To: core <co...@la...>


Hey All,

This is just a heads up that I'll be doing some maintenance on TeamCity
starting tomorrow at 3pm (PST). This should be a relatively painless
upgrade to "2019.1.3." But I'd rather have the time blocked off than not.
If all goes well, there shouldn't be more than ~10 minutes of "downtime"
(wherein running builds won't be disrupted but the TeamCity webui will be
inaccessible).

Please forward notification to effected parties.
~Isa

-- 

Isa Farnik
Cloud Infrastructure Engineer, LabKey
*Pronouns: he/him/his*

Email: is...@la...

www.LabKey.com


-- 

Trey Chadick
Test Lead, LabKey
*Pronouns: he/him*

Email: tc...@la...
Phone: 206.489.2577

www.LabKey.com <http://www.labkey.com/>

[proteowizard-developer] TeamCity Maintenance

[Trey C. <tc...@la...>]

We will be doing some maintenance on TeamCity
<https://teamcity.labkey.org/project.html?projectId=ProteoWizard> this
*Saturday,
April 14th, starting at 11am*. During this maintenance builds will not be
running and TeamCity itself may be inaccessible. Downloads from
http://proteowizard.sourceforge.net/download.html will also be unavailable
during this period

The maintenance is to bring us up to the latest major release: "2018.2.4
(build 61678)"

Thank you,
Trey

-- 

Trey Chadick
Test Lead, LabKey
*Pronouns: he/him*

Email: tc...@la...
Phone: 206.489.2577

www.LabKey.com <http://www.labkey.com/>

[proteowizard-developer] TeamCity Maintenance (1/20/2019)

[Trey C. <tc...@la...>]

teamcity.labkey.org will be down for maintenance starting at 13:00 PST on
Sunday, January 20th. The maintenance is expected to take a few hours.

Thank you,
Trey

-- 

Trey Chadick
Test Lead, LabKey
*Pronouns: he/him*

Email: tc...@la...
Phone: 206.489.2577

www.LabKey.com <http://www.labkey.com/>

[proteowizard-developer] svm.h not found during autotools build

[Filippo R. <fil...@u-...>]

Greetings, Fellow Developers,

this mail is to report on the (finally successful) build of libpwiz on a Debian
box starting from the bjam build.

I followed the instructions and started running make_nonbjam_build.sh, which
succeeded to the autotools-based source tarball creation.

Then, the configure step suceeded also.

Then I got this compilation error:

libtool: compile:  g++ -DPACKAGE_NAME=\"libpwiz\" -DPACKAGE_TARNAME=\"libpwiz\" -DPACKAGE_VERSION=\"3.0.18341\" "-DPACKAGE_STRING=\"libpwiz 3.0.18341\"" -DPACKAGE_BUGREPORT=\"pro...@li...\" -DPACKAGE_URL=\"\" -DPACKAGE=\"libpwiz\" -DVERSION=\"3.0.18341\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_FCNTL_H=1 -DHAVE_FLOAT_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_LIMITS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_NETINET_IN_H=1 -DHAVE_STDINT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_IOCTL_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -Drestrict=__restrict -DHAVE_PTRDIFF_T=1 -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_SYS_TIME_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ALARM=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DHAVE_ATEXIT=1 -DHAVE_MEMMOVE=1 -DHAVE_MEMSET=1 -DHAVE_MKDIR=1 -DHAVE_MODF=1 -DHAVE_STRCASECMP=1 -DHAVE_STRCHR=1 -DHAVE_STRDUP=1 -DHAVE_STRERROR=1 -DHAVE_STRPBRK=1 -DHAVE_STRRCHR=1 -DHAVE_STRSTR=1 -DHAVE_STRTOL=1 -DHAVE_STRTOUL=1 -DHAVE_STRTOULL=1 -DHAVE_BOOST=1 -DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1 -DHAVE_BOOST_THREAD_HPP=1 -DHAVE_BOOST_THREAD=1 -DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1 -DHAVE_BOOST_FILESYSTEM_PATH_HPP=1 -DHAVE_BOOST_FILESYSTEM=1 -DHAVE_BOOST_REGEX_HPP=1 -DHAVE_BOOST_REGEX=1 -DHAVE_BOOST_ARCHIVE_TEXT_OARCHIVE_HPP=1 -DHAVE_BOOST_SERIALIZATION=1 -DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1 -DHAVE_BOOST_IOSTREAMS_DEVICE_FILE_DESCRIPTOR_HPP=1 -DHAVE_BOOST_IOSTREAMS=1 -DHAVE_BOOST_DATE_TIME_POSIX_TIME_POSIX_TIME_HPP=1 -DHAVE_BOOST_DATE_TIME=1 -DHAVE_BOOST_PROGRAM_OPTIONS_HPP=1 -DHAVE_BOOST_PROGRAM_OPTIONS=1 -DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1 -DHAVE_BOOST_CHRONO_HPP=1 -DHAVE_BOOST_CHRONO=1 -I. -Iautotools -pthread -Ilibraries/boost_aux -Ipwiz/data/msdata/ramp -Ilibraries/Eigen -Ilibraries/CSpline -DWITHOUT_MZ5 -DBOOST_DISABLE_ASSERTS -DBOOST_NOWIDE_NO_LIB=1 -DNO_MASCOT_READER -g -O2 -MT pwiz/analysis/spectrum_processing/SpectrumList_ChargeStateCalculator.lo -MD -MP -MF pwiz/analysis/spectrum_processing/.deps/SpectrumList_ChargeStateCalculator.Tpo -c pwiz/analysis/spectrum_processing/SpectrumList_ChargeStateCalculator.cpp  -fPIC -DPIC -o pwiz/analysis/spectrum_processing/.libs/SpectrumList_ChargeStateCalculator.o
pwiz/analysis/spectrum_processing/SpectrumList_ChargeStateCalculator.cpp:40:10: fatal error: svm.h: No such file or directory
 #include "svm.h"

Looking at the include directories, I can see -Ilibraries/Eigen
-Ilibraries/CSpline, but no -Ilibraries/libsvm-3.0.

By adding that include directory to the AM_CPPFLAGS line in the Makefile, I
could go on.

Then the link step failed because the path to libboost was not found:

libtool:   error: require no space between '-L' and '-version-info'

So I edited the Makefile in order to change

BOOST_LDPATH = 

into

BOOST_LDPATH = /usr/lib/x86_64-linux-gnu

At that point the build went fine up to the .la and .so libs.

I recall that I always had that BOOST_LDPATH problem. How could we make sure
that it is detected and set properly ? The following command gives that
directory: 

gcc -dumpmachine

Maybe that could be integrated in the bjam->autotools script ?

Anyways, as usual thanks for your hard work and for that libpwiz library that it
is a pleasure to work with.

Cheers,
Filippo

-- 

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄⠀⠀⠀⠀  http://msxpertsuite.org
          http://www.debian.org

~~~~
book: http://www.lavoisier.fr/livre/notice.asp?id=3LKW2OAR2KROWZ
http://books.google.fr/books?id=2NmguxmEI1sC&printsec=frontcover&dq=rusconi+f+lavoisier&hl=fr&sa=X&ei=nGGOUt2SH_Ly0gX0uIHoBQ&ved=0CDUQ6AEwAA#v=onepage&q&f=false
~~~~
Génétique Quantitative et Évolution & Plateforme PAPPSO
UMR CNRS 8120 – INRA – Université Paris-Sud – AgroParisTech - Université Paris-Saclay
http://moulon.inra.fr/ & http://pappso.inra.fr/
Ferme du Moulon
91190 Gif-sur-Yvette
France
Tel : +33 (0)1 69 33 23 54
Fax : +33 (0)1 69 33 23 40

Re: [proteowizard-developer] TeamCity Maintenance

[Juan F. A. <arg...@gm...>]

Hello,
Could someone please help me to get removed from the mailing list. I have
tried unsuccessfully. Thanks so much.
Juan

On Mon, Jul 23, 2018 at 9:02 AM Trey Chadick <tc...@la...> wrote:

> TeamCity is back up and all of the build agents have been updated.
> We had several successful builds over the weekend, so I think everything's
> good to go on that end.
>
> It looks like there is a configuration issue with download redirects from
> sourceforge. I'm working with Matt Chambers to resolve that problem.
>
> I will let you all know when I have more information.
>
> Thank you,
> Trey
>
>
> On Fri, Jul 20, 2018 at 5:12 PM, Trey Chadick <tc...@la...> wrote:
>
>> Ran into some snags. I have the server back up but the build agents need
>> to be updated.
>> I'm going to make the server available but will leave the queue paused
>> until I can update the agents later this evening.
>>
>> Thank you for your continued patience,
>> Trey
>>
>> On Wed, Jul 18, 2018 at 4:09 PM, Trey Chadick <tc...@la...> wrote:
>>
>>> *IMPORTANT!*
>>>
>>> We will take TeamCity <http://teamcity.labkey.org> down tomorrow; *5PM Thursday,
>>> July 19th*. We will begin disabling agents at 3PM to make sure no
>>> builds are running when we take TeamCity down.
>>> We will take a backup overnight and upgrade the server on Friday.
>>> TeamCity should be back online before *EOD Friday*.
>>>
>>> Thank you,
>>> Trey
>>>
>>> On Mon, Jul 16, 2018 at 2:21 PM, Trey Chadick <tc...@la...> wrote:
>>>
>>>> We plan on upgrading TeamCity later this week.
>>>> In preparation, I may need to take it offline briefly over the next day
>>>> or two. I will send out a warning an hour before any such outage. They
>>>> should last no more than 15 minutes; in-progress builds will be unaffected
>>>> and the server should pick up right where it left off once it comes back up.
>>>>
>>>> The upgrade itself may take the better part of a day (sorry, we don't
>>>> do this level of maintenance on TeamCity very often so don't have a
>>>> well-known, reliable redeployment process in place at the moment).
>>>> I will send a notice at least *24 hours before* we start the upgrade
>>>> process.
>>>>
>>>> Thank you,
>>>> Trey
>>>>
>>>> PS If you know of anybody who should be aware of this but isn't CC'd,
>>>> please point them to the developer forum post
>>>> <https://www.labkey.org/home/Support/Developer%20Forum/announcements-thread.view?rowId=18010>
>>>> on labkey.org
>>>>
>>>> --
>>>> Trey Chadick
>>>> Test Manager, LabKey
>>>> tc...@la...
>>>> 206.489.2577
>>>>
>>>
>>>
>>>
>>> --
>>> Trey Chadick
>>> Test Manager, LabKey
>>> tc...@la...
>>> 206.489.2577
>>>
>>
>>
>>
>> --
>> Trey Chadick
>> Test Manager, LabKey
>> tc...@la...
>> 206.489.2577
>>
>
>
>
> --
> Trey Chadick
> Test Manager, LabKey
> tc...@la...
> 206.489.2577
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> proteowizard-developer mailing list
> pro...@li...
> https://lists.sourceforge.net/lists/listinfo/proteowizard-developer
>

Re: [proteowizard-developer] TeamCity Maintenance

[Trey C. <tc...@la...>]

Update: the download links are good to go.

Please let me know if you have any problems with the new version of
TeamCity or if something is broken that was working last week.

Thank you,
Trey

On Mon, Jul 23, 2018 at 9:01 AM, Trey Chadick <tc...@la...> wrote:

> TeamCity is back up and all of the build agents have been updated.
> We had several successful builds over the weekend, so I think everything's
> good to go on that end.
>
> It looks like there is a configuration issue with download redirects from
> sourceforge. I'm working with Matt Chambers to resolve that problem.
>
> I will let you all know when I have more information.
>
> Thank you,
> Trey
>
>
> On Fri, Jul 20, 2018 at 5:12 PM, Trey Chadick <tc...@la...> wrote:
>
>> Ran into some snags. I have the server back up but the build agents need
>> to be updated.
>> I'm going to make the server available but will leave the queue paused
>> until I can update the agents later this evening.
>>
>> Thank you for your continued patience,
>> Trey
>>
>> On Wed, Jul 18, 2018 at 4:09 PM, Trey Chadick <tc...@la...> wrote:
>>
>>> *IMPORTANT!*
>>>
>>> We will take TeamCity <http://teamcity.labkey.org> down tomorrow; *5PM Thursday,
>>> July 19th*. We will begin disabling agents at 3PM to make sure no
>>> builds are running when we take TeamCity down.
>>> We will take a backup overnight and upgrade the server on Friday.
>>> TeamCity should be back online before *EOD Friday*.
>>>
>>> Thank you,
>>> Trey
>>>
>>> On Mon, Jul 16, 2018 at 2:21 PM, Trey Chadick <tc...@la...> wrote:
>>>
>>>> We plan on upgrading TeamCity later this week.
>>>> In preparation, I may need to take it offline briefly over the next day
>>>> or two. I will send out a warning an hour before any such outage. They
>>>> should last no more than 15 minutes; in-progress builds will be unaffected
>>>> and the server should pick up right where it left off once it comes back up.
>>>>
>>>> The upgrade itself may take the better part of a day (sorry, we don't
>>>> do this level of maintenance on TeamCity very often so don't have a
>>>> well-known, reliable redeployment process in place at the moment).
>>>> I will send a notice at least *24 hours before* we start the upgrade
>>>> process.
>>>>
>>>> Thank you,
>>>> Trey
>>>>
>>>> PS If you know of anybody who should be aware of this but isn't CC'd,
>>>> please point them to the developer forum post
>>>> <https://www.labkey.org/home/Support/Developer%20Forum/announcements-thread.view?rowId=18010>
>>>> on labkey.org
>>>>
>>>> --
>>>> Trey Chadick
>>>> Test Manager, LabKey
>>>> tc...@la...
>>>> 206.489.2577
>>>>
>>>
>>>
>>>
>>> --
>>> Trey Chadick
>>> Test Manager, LabKey
>>> tc...@la...
>>> 206.489.2577
>>>
>>
>>
>>
>> --
>> Trey Chadick
>> Test Manager, LabKey
>> tc...@la...
>> 206.489.2577
>>
>
>
>
> --
> Trey Chadick
> Test Manager, LabKey
> tc...@la...
> 206.489.2577
>



-- 
Trey Chadick
Test Manager, LabKey
tc...@la...
206.489.2577