Re: [Bioc-devel] mzR build failure on Windows: missing HDF5 libraries

[Rainer Johannes]

I'll test on mac and windows

cheers, jo

> On 7 Jan 2018, at 22:57, Neumann, Steffen  wrote:
> 
> Hi,
> 
> Following the bug report in 
> https://github.com/sneumann/mzR/issues/143
> 
> there is a branch with a fix in 
> https://github.com/sneumann/mzR/pull/144
> 
> that passes Travis in 
> https://travis-ci.org/sneumann/mzR/builds/324960762
> 
> which we can merge once there is a bit more testing
> on other platforms. Any takers ?
> 
> Yours,
> Steffen
> 
> 
> 
> On Fri, 2018-01-05 at 10:55 -0500, Martin Morgan wrote:
>> Would be great, Steffen, to update mzR to use Rhdf5lib. I believe
>> CRAN 
>> packages with mzR dependencies are also failing to build under devel,
>> as 
>> well as xcms and other mzR dependencies in Bioc.
>> 
>> Martin
>> 
>> On 01/03/2018 04:18 AM, Mike Smith wrote:
>>> Rhdf5lib is in the release branch too.  I'm happy to help try and
>>> get mzR
>>> working with it.
>>> 
>>> On 2 January 2018 at 21:31, Martin Morgan >> k.org>
>>> wrote:
>>> 
 On 01/02/2018 03:16 PM, Neumann, Steffen wrote:
 
> Dear BioC team,
> 
> a happy new year to you as well ;-)
> 
> for a while we have a build error for mzR on windows
> due to missing HDF5 libs:
> https://github.com/sneumann/mzR/issues/143
> 
> I am looking for some hints how to fix this.
> The https://bioconductor.org/packages/release/bioc/html/rhdf5.h
> tml
> package has embedded rhdf5/src/libwin/x64/libhdf5ForBioC-7.dll
> which we could try to use (It does not yet contain H5Cpp.h,
> and we'd have to ask Bernd Fischer et al to include it.
> 
 
 Not a comprehensive answer or solution to release, but in devel
 there is
 Rhdf5lib which contains both the C and C++ headers. (I believe
 that rhdf5
 will move to using this library in the near future) Martin
 
 
> ALternatively, it might already be present on the build
> machines,
> but we didn't have the include path set up:
> https://github.com/r-hub/rhub/issues/91
> "... the location of the hdf5 libraries is defined as
> ${LIB_HDF5}/lib${R_ARCH}. "
> 
> So, any hints which way to go for a fix ?
> 
> Yours,
> Steffen
> 
> 
 
 This email message may contain legally privileged
 and/or...{{dropped:2}}
 
 
 ___
 Bioc-devel@r-project.org mailing list
 https://stat.ethz.ch/mailman/listinfo/bioc-devel
 
>>> 
>>> [[alternative HTML version deleted]]
>>> 
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> 
>> 
>> 
>> This email message may contain legally privileged
>> and/or...{{dropped:2}}
>> 
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> -- 
> 
> IPB HalleAG Massenspektrometrie & Bioinformatik
> Dr. Steffen Neumann  http://www.IPB-Halle.DE
> Weinberg 3   http://msbi.bic-gh.de
> 06120 Halle  Tel. +49 (0) 345 5582 - 1470
>  +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] mzR build failure on Windows: missing HDF5 libraries

[Neumann, Steffen]

Hi,

Following the bug report in 
https://github.com/sneumann/mzR/issues/143

there is a branch with a fix in 
https://github.com/sneumann/mzR/pull/144

that passes Travis in 
https://travis-ci.org/sneumann/mzR/builds/324960762

which we can merge once there is a bit more testing
on other platforms. Any takers ?

Yours,
Steffen



On Fri, 2018-01-05 at 10:55 -0500, Martin Morgan wrote:
> Would be great, Steffen, to update mzR to use Rhdf5lib. I believe
> CRAN 
> packages with mzR dependencies are also failing to build under devel,
> as 
> well as xcms and other mzR dependencies in Bioc.
> 
> Martin
> 
> On 01/03/2018 04:18 AM, Mike Smith wrote:
> > Rhdf5lib is in the release branch too.  I'm happy to help try and
> > get mzR
> > working with it.
> > 
> > On 2 January 2018 at 21:31, Martin Morgan  > k.org>
> > wrote:
> > 
> > > On 01/02/2018 03:16 PM, Neumann, Steffen wrote:
> > > 
> > > > Dear BioC team,
> > > > 
> > > > a happy new year to you as well ;-)
> > > > 
> > > > for a while we have a build error for mzR on windows
> > > > due to missing HDF5 libs:
> > > > https://github.com/sneumann/mzR/issues/143
> > > > 
> > > > I am looking for some hints how to fix this.
> > > > The https://bioconductor.org/packages/release/bioc/html/rhdf5.h
> > > > tml
> > > > package has embedded rhdf5/src/libwin/x64/libhdf5ForBioC-7.dll
> > > > which we could try to use (It does not yet contain H5Cpp.h,
> > > > and we'd have to ask Bernd Fischer et al to include it.
> > > > 
> > > 
> > > Not a comprehensive answer or solution to release, but in devel
> > > there is
> > > Rhdf5lib which contains both the C and C++ headers. (I believe
> > > that rhdf5
> > > will move to using this library in the near future) Martin
> > > 
> > > 
> > > > ALternatively, it might already be present on the build
> > > > machines,
> > > > but we didn't have the include path set up:
> > > > https://github.com/r-hub/rhub/issues/91
> > > > "... the location of the hdf5 libraries is defined as
> > > > ${LIB_HDF5}/lib${R_ARCH}. "
> > > > 
> > > > So, any hints which way to go for a fix ?
> > > > 
> > > > Yours,
> > > > Steffen
> > > > 
> > > > 
> > > 
> > > This email message may contain legally privileged
> > > and/or...{{dropped:2}}
> > > 
> > > 
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > 
> > 
> > [[alternative HTML version deleted]]
> > 
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
> 
> 
> This email message may contain legally privileged
> and/or...{{dropped:2}}
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- 

IPB HalleAG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3   http://msbi.bic-gh.de
06120 Halle  Tel. +49 (0) 345 5582 - 1470
  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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Re: [Bioc-devel] git help

[Turaga, Nitesh]

Hi Kevin,

One last message, give me a green light to fix your repository once you have 
had a chance to see my emails.

Best,

Nitesh 

> On Jan 7, 2018, at 2:17 PM, Turaga, Nitesh  
> wrote:
> 
> Now your version numbers don’t match. You skip versions without those commits
> 
> Your history is supposed to look like this,
> 
> commit 5a1ad6ff08747d1380875840fe96d3633c210ee2 (HEAD -> master)
> Author: khoran 
> Date:   Sun Jan 7 09:44:16 2018 -0800
> 
>History was rolled back 6 months to remove dup commits.
>All changes since then are being re-applied in this one commit.
> 
> commit fb7c8ed13eb09527038e1959737d556a15667771
> Author: Hervé Pagès 
> Date:   Mon Oct 30 12:52:08 2017 -0400
> 
>bump x.y.z versions to odd y after creation of RELEASE_3_6 branch
> 
> commit 73c4cb1d48d9f14598e63a28a9b9184e096f254e
> Author: Hervé Pagès 
> Date:   Mon Oct 30 12:39:24 2017 -0400
> 
>bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch
> 
> commit e3a8d2122a65305c478276e538faace277ea9ed6
> Author: Kevin Horan 
> Date:   Fri Jun 30 20:12:52 2017 +
> 
>Merge branch 'master' into devel
> 
>git-svn-id: 
> file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR@130816
>  bc3139a8-67e5-0310-9ffc-ced21a209358
> 
> ##
> Same for the RELEASE branch. 
> ##
> 
> commit 7111f07cc9c32977f1eca63a0f2a25cb1092f7be (HEAD -> RELEASE_3_6)
> Author: khoran 
> Date:   Sun Jan 7 10:14:49 2018 -0800
> 
>set version for release branch
> 
> commit a2615e98aff83130f6129abc02132a65d99689b9
> Author: Hervé Pagès 
> Date:   Mon Oct 30 12:39:24 2017 -0400
> 
>bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch
> 
> commit e3a8d2122a65305c478276e538faace277ea9ed6
> Author: Kevin Horan 
> Date:   Fri Jun 30 20:12:52 2017 +
> 
>Merge branch 'master' into devel
> 
>git-svn-id: 
> file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR@130816
>  bc3139a8-67e5-0310-9ffc-ced21a209358
> 
> 
> I can make your commit history look like this, but I’m not sure if all the 
> changes in your code are reflected accurately. You might have to make sure 
> manually, and see if your code and package work like you expect.
> 
> Once they work as expected, please don’t do anything with the commit history. 
> Just add the new changes on top of what exists. It becomes extremely 
> complicated and time taking to fix the commit history manually.
> 
> Best,
> 
> Nitesh 
> 
>> On Jan 7, 2018, at 1:32 PM, Turaga, Nitesh  
>> wrote:
>> 
>> Hi Kevin,
>> 
>> It seems you have lost a few commits which are important in tracking 
>> RELEASE’s in Bioconductor.
>> 
>> 
>> commit fb5868c2fdfa607b52e467881212b3619a8b0ae9 (HEAD -> master)
>> Author: Hervé Pagès 
>> Date:   Mon Oct 30 12:52:08 2017 -0400
>> 
>>   bump x.y.z versions to odd y after creation of RELEASE_3_6 branch
>> 
>> commit 46e0a56d1117cca6274fea3b8430eb8d6c7a9976 (RELEASE_3_6)
>> Author: Hervé Pagès 
>> Date:   Mon Oct 30 12:39:24 2017 -0400
>> 
>>   bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch
>> 
>> These commits are important. 
>> 
>> Please wait for further instructions while we figure out how to resolve this 
>> issue. 
>> 
>> Best,
>> 
>> Nitesh 
>> 
>>> On Jan 7, 2018, at 1:20 PM, Kevin Horan  wrote:
>>> 
>>> Nitesh,
>>> 
>>>  I have pushed changes to both the master and RELEASE_3_6 branches now.
>>> 
>>> Kevin
>>> 
>>> 
>>> On 01/05/2018 11:14 AM, Turaga, Nitesh wrote:
 Hi Kevin,
 
 Please overlay the commits so that we can get your package building on our 
 build machines.
 
 Please do this soon. You also have to make RELEASE_3_6 branch now.
 
 We have skipped your package for now, and it won’t show up in the release 
 report.
 Thanks
 
 Nitesh
 
> On Jan 4, 2018, at 10:07 AM, Turaga, Nitesh 
>  wrote:
> 
> Hi Kevin,
> 
> I have your package reset to this commit 
> e3a8d2122a65305c478276e538faace277ea9ed6.
> 
> Please check. You will need to overlay all the commits including the new 
> release on top of this (RELEASE_3_6).
> 
> If you have any questions further on this, please ask before pushing to 
> Bioconductor.
> 
> Best,
> 
> Nitesh
> 
>> On Jan 3, 2018, at 7:10 PM, Kevin Horan  wrote:
>> 
>> Nitesh,
>> 
>> That sounds great, thanks.
>> 
>> Kevin
>> 
>> 
>> On 01/03/2018 01:53 PM, Turaga, Nitesh wrote:
>>> Hi Kevin,
>>> 
>>> I can help you with this. I can take you back to a state before August 
>>> 18th and put that 

Re: [Bioc-devel] git help

[Turaga, Nitesh]

Now your version numbers don’t match. You skip versions without those commits

Your history is supposed to look like this,

commit 5a1ad6ff08747d1380875840fe96d3633c210ee2 (HEAD -> master)
Author: khoran 
Date:   Sun Jan 7 09:44:16 2018 -0800

History was rolled back 6 months to remove dup commits.
All changes since then are being re-applied in this one commit.

commit fb7c8ed13eb09527038e1959737d556a15667771
Author: Hervé Pagès 
Date:   Mon Oct 30 12:52:08 2017 -0400

bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

commit 73c4cb1d48d9f14598e63a28a9b9184e096f254e
Author: Hervé Pagès 
Date:   Mon Oct 30 12:39:24 2017 -0400

bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

commit e3a8d2122a65305c478276e538faace277ea9ed6
Author: Kevin Horan 
Date:   Fri Jun 30 20:12:52 2017 +

Merge branch 'master' into devel

git-svn-id: 
file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR@130816
 bc3139a8-67e5-0310-9ffc-ced21a209358

##
Same for the RELEASE branch. 
##

commit 7111f07cc9c32977f1eca63a0f2a25cb1092f7be (HEAD -> RELEASE_3_6)
Author: khoran 
Date:   Sun Jan 7 10:14:49 2018 -0800

set version for release branch

commit a2615e98aff83130f6129abc02132a65d99689b9
Author: Hervé Pagès 
Date:   Mon Oct 30 12:39:24 2017 -0400

bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

commit e3a8d2122a65305c478276e538faace277ea9ed6
Author: Kevin Horan 
Date:   Fri Jun 30 20:12:52 2017 +

Merge branch 'master' into devel

git-svn-id: 
file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChemmineR@130816
 bc3139a8-67e5-0310-9ffc-ced21a209358


I can make your commit history look like this, but I’m not sure if all the 
changes in your code are reflected accurately. You might have to make sure 
manually, and see if your code and package work like you expect.

Once they work as expected, please don’t do anything with the commit history. 
Just add the new changes on top of what exists. It becomes extremely 
complicated and time taking to fix the commit history manually.

Best,

Nitesh 

> On Jan 7, 2018, at 1:32 PM, Turaga, Nitesh  
> wrote:
> 
> Hi Kevin,
> 
> It seems you have lost a few commits which are important in tracking 
> RELEASE’s in Bioconductor.
> 
> 
> commit fb5868c2fdfa607b52e467881212b3619a8b0ae9 (HEAD -> master)
> Author: Hervé Pagès 
> Date:   Mon Oct 30 12:52:08 2017 -0400
> 
>bump x.y.z versions to odd y after creation of RELEASE_3_6 branch
> 
> commit 46e0a56d1117cca6274fea3b8430eb8d6c7a9976 (RELEASE_3_6)
> Author: Hervé Pagès 
> Date:   Mon Oct 30 12:39:24 2017 -0400
> 
>bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch
> 
> These commits are important. 
> 
> Please wait for further instructions while we figure out how to resolve this 
> issue. 
> 
> Best,
> 
> Nitesh 
> 
>> On Jan 7, 2018, at 1:20 PM, Kevin Horan  wrote:
>> 
>> Nitesh,
>> 
>>   I have pushed changes to both the master and RELEASE_3_6 branches now.
>> 
>> Kevin
>> 
>> 
>> On 01/05/2018 11:14 AM, Turaga, Nitesh wrote:
>>> Hi Kevin,
>>> 
>>> Please overlay the commits so that we can get your package building on our 
>>> build machines.
>>> 
>>> Please do this soon. You also have to make RELEASE_3_6 branch now.
>>> 
>>> We have skipped your package for now, and it won’t show up in the release 
>>> report.
>>> Thanks
>>> 
>>> Nitesh
>>> 
 On Jan 4, 2018, at 10:07 AM, Turaga, Nitesh 
  wrote:
 
 Hi Kevin,
 
 I have your package reset to this commit 
 e3a8d2122a65305c478276e538faace277ea9ed6.
 
 Please check. You will need to overlay all the commits including the new 
 release on top of this (RELEASE_3_6).
 
 If you have any questions further on this, please ask before pushing to 
 Bioconductor.
 
 Best,
 
 Nitesh
 
> On Jan 3, 2018, at 7:10 PM, Kevin Horan  wrote:
> 
> Nitesh,
> 
>  That sounds great, thanks.
> 
> Kevin
> 
> 
> On 01/03/2018 01:53 PM, Turaga, Nitesh wrote:
>> Hi Kevin,
>> 
>> I can help you with this. I can take you back to a state before August 
>> 18th and put that repository up on our Git server.
>> 
>> From that point onwards you’d have to reapply all the changes on that 
>> repository from "commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389" and 
>> onwards.
>> 
>> commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389
>> Merge: 643e470 f1785fb
>> Author: tgirke 
>> Date:   Sat Aug 19 16:32:35 2017 -0700
>> 
>>   resolved conflicts
>> 

Re: [Bioc-devel] git help

[Turaga, Nitesh]

Hi Kevin,

It seems you have lost a few commits which are important in tracking RELEASE’s 
in Bioconductor.


commit fb5868c2fdfa607b52e467881212b3619a8b0ae9 (HEAD -> master)
Author: Hervé Pagès 
Date:   Mon Oct 30 12:52:08 2017 -0400

bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

commit 46e0a56d1117cca6274fea3b8430eb8d6c7a9976 (RELEASE_3_6)
Author: Hervé Pagès 
Date:   Mon Oct 30 12:39:24 2017 -0400

bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

These commits are important. 

Please wait for further instructions while we figure out how to resolve this 
issue. 

Best,

Nitesh 

> On Jan 7, 2018, at 1:20 PM, Kevin Horan  wrote:
> 
> Nitesh,
> 
>I have pushed changes to both the master and RELEASE_3_6 branches now.
> 
> Kevin
> 
> 
> On 01/05/2018 11:14 AM, Turaga, Nitesh wrote:
>> Hi Kevin,
>> 
>> Please overlay the commits so that we can get your package building on our 
>> build machines.
>> 
>> Please do this soon. You also have to make RELEASE_3_6 branch now.
>> 
>> We have skipped your package for now, and it won’t show up in the release 
>> report.
>>  Thanks
>> 
>> Nitesh
>> 
>>> On Jan 4, 2018, at 10:07 AM, Turaga, Nitesh  
>>> wrote:
>>> 
>>> Hi Kevin,
>>> 
>>> I have your package reset to this commit 
>>> e3a8d2122a65305c478276e538faace277ea9ed6.
>>> 
>>> Please check. You will need to overlay all the commits including the new 
>>> release on top of this (RELEASE_3_6).
>>> 
>>> If you have any questions further on this, please ask before pushing to 
>>> Bioconductor.
>>> 
>>> Best,
>>> 
>>> Nitesh
>>> 
 On Jan 3, 2018, at 7:10 PM, Kevin Horan  wrote:
 
 Nitesh,
 
   That sounds great, thanks.
 
 Kevin
 
 
 On 01/03/2018 01:53 PM, Turaga, Nitesh wrote:
> Hi Kevin,
> 
> I can help you with this. I can take you back to a state before August 
> 18th and put that repository up on our Git server.
> 
> From that point onwards you’d have to reapply all the changes on that 
> repository from "commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389" and 
> onwards.
> 
> commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389
> Merge: 643e470 f1785fb
> Author: tgirke 
> Date:   Sat Aug 19 16:32:35 2017 -0700
> 
>resolved conflicts
> 
> I can do this tomorrow and send you an email.
> 
> 
> Best,
> 
> Nitesh
> 
> 
> 
> 
>> On Jan 3, 2018, at 4:28 PM, Kevin Horan  wrote:
>> 
>> Nitesh,
>> 
>>   I tried to re-construct the repo starting from what is left in the SVN 
>> repository, but I couldn't get all the branches to come over and it just 
>> generally looks too different to easily replace the bioc repo.
>> 
>>   I was thinking though, if its easy for you to clobber the current bioc 
>> repo for ChemmineR and re-create it from the old SVN repo (ie, because 
>> you might have scripts from having done it the first time), then that 
>> might be an easier fix. Then I can check it out, apply the recent 
>> changes and push it back.
>> 
>>   But if you don't think that's a good idea, then I'll take your offer 
>> of help and we can try to figure out how to get rid of the duplicate 
>> commits. Thanks.
>> 
>> 
>> Kevin
>> 
>> 
>> On 01/03/2018 11:55 AM, Turaga, Nitesh wrote:
>>> Hi Kevin,
>>> 
>>> I’ll try to help you. I’ll take a look at your package and get back to 
>>> you. Please forward this message to bioc-devel so that it’s public and 
>>> other maintainers/users know that there is an issue with your package.
>>> 
>>> Best,
>>> 
>>> Nitesh
>>> 
 On Jan 3, 2018, at 2:31 PM, Kevin Horan  
 wrote:
 
 Nitesh,
 
   I am one of the maintainers for the ChemmineR package on 
 bioconductor. I have a bad duplicate commit problem I was wondering if 
 you could help me with. Basically, it seems one string of 1000 or so 
 commits has been duplicated twice in the repository, so that there are 
 now 3 copies of each of these commits. This mess is already in the 
 bioconductor repository because in order to allow me to get some last 
 minute changes in for the last release, someone at boic disabled the 
 duplicate commit check for me. That was before I understood the extend 
 of the problem.
 
   I'm not sure if its really your job to help with this sort of thing, 
 as I understand that it's not a bioconductor problem. So if not that 
 is fine. I've spent 6 hours trying to fix it myself ( and I am 
 generally good with  GIT), but I've only succeeded in make more 
 

Re: [Bioc-devel] git help

[Kevin Horan]

Nitesh,

I have pushed changes to both the master and RELEASE_3_6 branches now.

Kevin


On 01/05/2018 11:14 AM, Turaga, Nitesh wrote:

Hi Kevin,

Please overlay the commits so that we can get your package building on our 
build machines.

Please do this soon. You also have to make RELEASE_3_6 branch now.

We have skipped your package for now, and it won’t show up in the release 
report.
  
Thanks


Nitesh


On Jan 4, 2018, at 10:07 AM, Turaga, Nitesh  
wrote:

Hi Kevin,

I have your package reset to this commit 
e3a8d2122a65305c478276e538faace277ea9ed6.

Please check. You will need to overlay all the commits including the new 
release on top of this (RELEASE_3_6).

If you have any questions further on this, please ask before pushing to 
Bioconductor.

Best,

Nitesh


On Jan 3, 2018, at 7:10 PM, Kevin Horan  wrote:

Nitesh,

   That sounds great, thanks.

Kevin


On 01/03/2018 01:53 PM, Turaga, Nitesh wrote:

Hi Kevin,

I can help you with this. I can take you back to a state before August 18th and 
put that repository up on our Git server.

 From that point onwards you’d have to reapply all the changes on that repository from 
"commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389" and onwards.

commit ae93b1e9bcc574b5c8e9fc13b914286464ff4389
Merge: 643e470 f1785fb
Author: tgirke 
Date:   Sat Aug 19 16:32:35 2017 -0700

resolved conflicts

I can do this tomorrow and send you an email.


Best,

Nitesh





On Jan 3, 2018, at 4:28 PM, Kevin Horan  wrote:

Nitesh,

   I tried to re-construct the repo starting from what is left in the SVN 
repository, but I couldn't get all the branches to come over and it just 
generally looks too different to easily replace the bioc repo.

   I was thinking though, if its easy for you to clobber the current bioc repo 
for ChemmineR and re-create it from the old SVN repo (ie, because you might 
have scripts from having done it the first time), then that might be an easier 
fix. Then I can check it out, apply the recent changes and push it back.

   But if you don't think that's a good idea, then I'll take your offer of help 
and we can try to figure out how to get rid of the duplicate commits. Thanks.


Kevin


On 01/03/2018 11:55 AM, Turaga, Nitesh wrote:

Hi Kevin,

I’ll try to help you. I’ll take a look at your package and get back to you. 
Please forward this message to bioc-devel so that it’s public and other 
maintainers/users know that there is an issue with your package.

Best,

Nitesh


On Jan 3, 2018, at 2:31 PM, Kevin Horan  wrote:

Nitesh,

   I am one of the maintainers for the ChemmineR package on bioconductor. I 
have a bad duplicate commit problem I was wondering if you could help me with. 
Basically, it seems one string of 1000 or so commits has been duplicated twice 
in the repository, so that there are now 3 copies of each of these commits. 
This mess is already in the bioconductor repository because in order to allow 
me to get some last minute changes in for the last release, someone at boic 
disabled the duplicate commit check for me. That was before I understood the 
extend of the problem.

   I'm not sure if its really your job to help with this sort of thing, as I 
understand that it's not a bioconductor problem. So if not that is fine. I've 
spent 6 hours trying to fix it myself ( and I am generally good with  GIT), but 
I've only succeeded in make more duplicates. So I think I'd need to toss all 
the history up to the last release, which I image I'd need your help to reset 
the repo on the bioc side as well.

   If you can help, there are more specifics I can give you, just let me know.

Thanks.


Kevin Horan


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Re: [Bioc-devel] Can I push a new branch to Bioconductor git?

[Turaga, Nitesh]

Hi Stian,

You cannot push to any branch other than “master” and RELEASE_3_6. Bioconductor 
regulates the branches that are available on our GIT server. 

You cannot push an additional branch, we recommend you do that on your GitHub, 
and merge with master when you are ready, and then push to Bioconductor.

You also seem to have duplicate commits on your repository. You should probably 
take a look at why that is happening.

Best,

Nitesh 

> On Jan 7, 2018, at 5:43 AM, Stian Lågstad  wrote:
> 
> I'm trying to push a new branch with some changes to origin, but I'm
> getting this error:
> 
> ```
> ➜  chimeraviz-bioconductor git:(starfusionffpm) git push --set-upstream
> origin starfusionffpm
> Counting objects: 7, done.
> Delta compression using up to 8 threads.
> Compressing objects: 100% (7/7), done.
> Writing objects: 100% (7/7), 998 bytes | 0 bytes/s, done.
> 
> Total 7 (delta 5), reused 0 (delta 0)
> remote: Error: duplicate commits.
> remote:
> remote: There are duplicate commits in your commit history, These cannot be
> remote: pushed to the Bioconductor git server. Please make sure that this is
> remote: resolved.
> remote:
> remote: Take a look at the documentation to fix this,
> remote:
> https://bioconductor.org/developers/how-to/git/sync-existing-repositories/,
> remote: particularly, point #8 (force Bioconductor master to Github master).
> remote:
> remote: For more information, or help resolving this issue, contact
> remote: . Provide the error, the package name and
> remote: any other details we might need.
> remote:
> remote: Use
> remote:
> remote: git show 248742bd41a1b1d862d29e612baa067c50c55e5b
> remote: git show 81ee14920be186caf4f2949e7dacfad68db64ed2
> remote:
> remote: to see body of commits.
> remote:
> To g...@git.bioconductor.org:packages/chimeraviz
> 
> ! [remote rejected] starfusionffpm -> starfusionffpm (pre-receive hook
> declined)
> error: failed to push some refs to 'g...@git.bioconductor.org:
> packages/chimeraviz'
> ```
> 
> I'm not syncing anything with an existing Github repository. I just wanted
> to store a couple of changes that I might merge into master later.
> 
> I haven't done anything locally since my last successful push to master, so
> I should be in sync:
> ```
> ➜  chimeraviz-bioconductor git:(starfusionffpm) git checkout master
> Switched to branch 'master'
> Your branch is up-to-date with 'origin/master'.
> ➜  chimeraviz-bioconductor git:(master) git pull
> Already up-to-date.
> ➜  chimeraviz-bioconductor git:(master) git branch -a
>  RELEASE_3_6
> * master
>  starfusionffpm
>  remotes/origin/HEAD -> origin/master
>  remotes/origin/RELEASE_3_5
>  remotes/origin/RELEASE_3_6
>  remotes/origin/master
> ➜  chimeraviz-bioconductor git:(master) git checkout RELEASE_3_6
> Switched to branch 'RELEASE_3_6'
> Your branch is up-to-date with 'origin/RELEASE_3_6'.
> ➜  chimeraviz-bioconductor git:(RELEASE_3_6) git pull
> Already up-to-date.
> ```
> 
> Are we allowed to push new branches to Bioconductor, or should we avoid
> doing that?
> 
> -- 
> Stian Lågstad
> +47 41 80 80 25
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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Re: [Bioc-devel] search - was: differential expression tools for proteins

[Wolfgang Huber]

7.1.18 12:46, Wolfgang Huber scripsit:
Thank you for your question. It would however be more appropriate for 
the support forum, not for the developer mailing list. Would you mind 
moving it there, perhaps also the responses so far?


I just saw you posted on the forum, after browsing it.
I had searched for your name using the "search" function of the forum 
webpage before sending the previous, but that did not turn up this post.


Wouldn't it be great if our search box worked better? Or would just 
convert the search into an URL like


https://www.google.com/search?q=Cardin+site%3Asupport.bioconductor.org=date

Wolfgang

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Re: [Bioc-devel] differential expression tools for proteins

[Wolfgang Huber]

Dear Julie

Thank you for your question. It would however be more appropriate for 
the support forum, not for the developer mailing list. Would you mind 
moving it there, perhaps also the responses so far?


There is no "in-principle" reason why DESeq2 shouldn't produce useful 
results also for count data from technologies that are not 
DNA-sequencing based. It's error model (Gamma-Poisson, GP) is quite generic.


As always, you should do model fit diagnostics though, to see whether 
the residuals for each protein across replicates and conditions (after 
fitting the GLM) are reasonably consistent with the GP, in particular, 
that they look unimodal.


One issue to check is also whether the normalization (size factors) is 
appropriate.


There is another bit of irony afaIu: If you have enough replicates (or: 
degrees of freedom) that you can actually "see" deviations from the GP 
assumption (i.e. >=dozens), then you probably don't need a parametric 
method, and could switch to something non-parametric.


Kind regards
Wolfgang

6.1.18 18:45, Cardin Julie via Bioc-devel scripsit:

Hi,
I have experienced very good results with DESeq2 for my RNASeq analysis. As 
far as I understand, it is a tool that normalise our data from sequencing to 
make them comparable.

I have a new project implicating proteins counts.
I have  couple of data sets. For each sample we have:
rows with proteins names (instead of genes), with their respective counts.

My goal is again to make a differential expression between treated groups 
versus controls.
I wonder if I can use DESeq2 to do a differential expression for proteins?
Or if the correcting factor that is used by DESeq2 to correct counts for RNASeq 
is specific to DNA sequencing and it is not applicable to proteins?

Is there a tool that do the exact same thing as DESeq2 but for proteins?

Thank you very much for your help and time,
Best regards and happy new year!

Julie Cardin
Bioinforamatician
IRCM



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--
With thanks in advance-
Wolfgang

---
Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany

wolfgang.hu...@embl.de
http://www.huber.embl.de

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