subject:"Re\: \[Bioc\-devel\] Filter classes moved from ensembldb to AnnotationFilter"

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

2017-04-07 Thread Rainer Johannes

Hi Herve

> On 7 Apr 2017, at 07:42, Hervé Pagès  wrote:
> 
> Hi Johannes,
> 
> Thanks for contacting the developers of the packages affected by this
> change. FWIW Pbase is also affected (didn't see it in your list):
> 

I fixed Pbase - changes have not been committed to Bioc yet (asked Laurent for 
that).
I did also fix wiggleplotr and made a pull request, but the developer did not 
yet react to that.

cheers, jo

> https://bioconductor.org/checkResults/3.5/bioc-LATEST/Pbase/malbec2-buildsrc.html
> 
> H.
> 
> 
> On 04/06/2017 01:07 PM, Rainer Johannes wrote:
>> @Florian: nothing you have to change. I checked all packages and 70 of them 
>> have problems related to the relocation of the filters. For 63 of them 
>> everything should be fine once the updated versions of biovizBase and ggbio 
>> are built. This fixes also Gviz and most of the packages with them.
>> 
>> For the remaining packages I either provided patches, pull requests or am in 
>> contact with the developers. I checked these packages and there is not very 
>> much more to do than importing filters from AnnotationFilter instead of 
>> ensembldb.
>> 
>> Fingers crossed - tomorrow everything could be OK again - and sorry again 
>> for all the havoc
>> 
>> cheers, jo
>> 
>> On 6 Apr 2017, at 21:27, Obenchain, Valerie 
>> >
>>  wrote:
>> 
>> We've updated the release schedule and moved the deadline for errors to
>> next Friday, April 14.
>> 
>> Valerie
>> 
>> 
>> On 04/06/2017 10:29 AM, Stian Lågstad wrote:
>> How does the error deadline tomorrow 
>> (https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bioconductor.org_=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=jLQ9KUUm3u9dA66MERqNGNYccQtXR7ieDcLKZZMrSII=mdDgNHoW4wRbQFZFJ4a7r2gUE_n6XQspfZvlgjQ94c8=
>> developers/release-schedule/) affect packages that are still red because of
>> this change? I don't know what else to do other than to wait for changes in
>> Gviz (which my package is dependent on).
>> 
>> Thanks.
>> 
>> On Tue, Apr 4, 2017 at 10:05 PM, Michael Lawrence 
>> 
>> wrote:
>> Sorry I have been traveling. Will get to it soon.
>> 
>> On Apr 4, 2017 12:58 PM, "Rainer Johannes" 
>> >
>> wrote:
>> 
>> Hi Herve,
>> 
>> sorry for all the reds - actually I provided the patches to biovizBase
>> and
>> ggbio, but it did not work out that smoothly that I hoped. For the other
>> packages that depend on ensembldb there's no problem or only small
>> changes
>> required (did contact the developers).
>> Fingers crossed that Michael can patch biovizBase and ggbio soon.
>> 
>> cheers, jo
>> 
>> On 4 Apr 2017, at 21:34, Hervé Pagès 
>> > wrote:
>> 
>> Hi Johannes,
>> 
>> This move is generating a lot of red today on the build report.
>> Hopefully biovizBase and ggbio can be fixed quickly. Note that
>> maybe a smoother path would have been to notify the maintainers
>> of these packages first and wait that they make the required
>> changes (i.e. to import the filters from AnnotationFilter)
>> before modifying ensembldb. Maybe for next time ;-)
>> 
>> Cheers,
>> H.
>> 
>> On 04/04/2017 04:02 AM, Rainer Johannes wrote:
>> 
>> On 4 Apr 2017, at 10:59, Stian Lågstad 
>> > :
>> stianlags...@gmail.com>> wrote:
>> Hi,
>> 
>> Thanks again for notifying me about the changes needed in chimeraviz.
>> Right now I'm having problems installing Gviz - I get these errors:
>> """
>> No methods found in "GenomicAlignments" for requests:
>> pmapFromTranscripts
>> Error : object 'GRangesFilter' is not exported by
>> 'namespace:ensembldb'
>> ERROR: lazy loading failed for package 'Gviz'
>> """
>> 
>> Are these errors caused by the change in ensembldb? If so: Do you know
>> how I can keep developing without having to wait for Gviz?
>> 
>> These come from biovizBase which Gviz imports. I've sent Micheal the
>> fixes for biovizBase and ggbio that should fix this.
>> We need to wait for the changes to be propagated, since also for
>> ensembldb I get today still version 1.99.12 but not the new 1.99.13.
>> On Mon, Apr 3, 2017 at 8:59 AM, Rainer Johannes <
>> johannes.rai...@eurac.edu>
>>  wrote:
>> Dear all,
>> 
>> I've just committed a change in ensembldb (version 1.99.13) that
>> removes all filter classes from it and imports them from the
>> AnnotationFilter package. This change will break biovizBase and ggbio
>> (and
>> all packages downstream of them, e.g. Gviz). I've already sent Michael
>> Lawrence patches to fix both packages, but  there might still be some
>> problems in the upcoming build reports I guess.
>> I've also contacted the developers of the TVTB and chimeraviz

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

2017-04-06 Thread Hervé Pagès

Hi Johannes,

Thanks for contacting the developers of the packages affected by this
change. FWIW Pbase is also affected (didn't see it in your list):

https://bioconductor.org/checkResults/3.5/bioc-LATEST/Pbase/malbec2-buildsrc.html

On 04/06/2017 01:07 PM, Rainer Johannes wrote:

@Florian: nothing you have to change. I checked all packages and 70 of them
have problems related to the relocation of the filters. For 63 of them
everything should be fine once the updated versions of biovizBase and ggbio are
built. This fixes also Gviz and most of the packages with them.

For the remaining packages I either provided patches, pull requests or am in
contact with the developers. I checked these packages and there is not very
much more to do than importing filters from AnnotationFilter instead of
ensembldb.

Fingers crossed - tomorrow everything could be OK again - and sorry again for
all the havoc

cheers, jo

On 6 Apr 2017, at 21:27, Obenchain, Valerie
>
wrote:

We've updated the release schedule and moved the deadline for errors to
next Friday, April 14.

Valerie

On 04/06/2017 10:29 AM, Stian Lågstad wrote:
How does the error deadline tomorrow
(https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bioconductor.org_=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=jLQ9KUUm3u9dA66MERqNGNYccQtXR7ieDcLKZZMrSII=mdDgNHoW4wRbQFZFJ4a7r2gUE_n6XQspfZvlgjQ94c8=
developers/release-schedule/) affect packages that are still red because of
this change? I don't know what else to do other than to wait for changes in
Gviz (which my package is dependent on).

Thanks.

On Tue, Apr 4, 2017 at 10:05 PM, Michael Lawrence

wrote:
Sorry I have been traveling. Will get to it soon.

On Apr 4, 2017 12:58 PM, "Rainer Johannes"
>
wrote:

Hi Herve,

sorry for all the reds - actually I provided the patches to biovizBase
and
ggbio, but it did not work out that smoothly that I hoped. For the other
packages that depend on ensembldb there's no problem or only small
changes
required (did contact the developers).
Fingers crossed that Michael can patch biovizBase and ggbio soon.

cheers, jo

On 4 Apr 2017, at 21:34, Hervé Pagès
> wrote:

Hi Johannes,

This move is generating a lot of red today on the build report.
Hopefully biovizBase and ggbio can be fixed quickly. Note that
maybe a smoother path would have been to notify the maintainers
of these packages first and wait that they make the required
changes (i.e. to import the filters from AnnotationFilter)
before modifying ensembldb. Maybe for next time ;-)

Cheers,
H.

On 04/04/2017 04:02 AM, Rainer Johannes wrote:

On 4 Apr 2017, at 10:59, Stian Lågstad
mailto:stianlags...@gmail.com>>> wrote:
Hi,

Thanks again for notifying me about the changes needed in chimeraviz.
Right now I'm having problems installing Gviz - I get these errors:
"""
No methods found in "GenomicAlignments" for requests:
pmapFromTranscripts
Error : object 'GRangesFilter' is not exported by
'namespace:ensembldb'
ERROR: lazy loading failed for package 'Gviz'
"""

Are these errors caused by the change in ensembldb? If so: Do you know
how I can keep developing without having to wait for Gviz?

These come from biovizBase which Gviz imports. I've sent Micheal the
fixes for biovizBase and ggbio that should fix this.
We need to wait for the changes to be propagated, since also for
ensembldb I get today still version 1.99.12 but not the new 1.99.13.
On Mon, Apr 3, 2017 at 8:59 AM, Rainer Johannes <
johannes.rai...@eurac.edu>
wrote:
Dear all,

I've just committed a change in ensembldb (version 1.99.13) that
removes all filter classes from it and imports them from the
AnnotationFilter package. This change will break biovizBase and ggbio
(and
all packages downstream of them, e.g. Gviz). I've already sent Michael
Lawrence patches to fix both packages, but there might still be some
problems in the upcoming build reports I guess.
I've also contacted the developers of the TVTB and chimeraviz packages
and made them aware of the change. Could be that there are other packages
out there possibly affected by the change. If so, let me know and I'll
assist fixing the problems (if needed).
cheers, jo

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--
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+47 41 80 80

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

2017-04-06 Thread Hahne, Florian

And by Rainer I mean Johannes. It is late…

From: Rainer Johannes <johannes.rai...@eurac.edu>
Date: Thursday, 6 April 2017 at 22:07
To: "Obenchain, Valerie" <valerie.obench...@roswellpark.org>
Cc: Stian Lågstad <stianlags...@gmail.com>, Michael Lawrence 
<lawrence.mich...@gene.com>, "bioc-devel@r-project.org" 
<bioc-devel@r-project.org>, Florian Hahne <florian.ha...@novartis.com>
Subject: Re: [Bioc-devel] Filter classes moved from ensembldb to 
AnnotationFilter

@Florian: nothing you have to change. I checked all packages and 70 of them 
have problems related to the relocation of the filters. For 63 of them 
everything should be fine once the updated versions of biovizBase and ggbio are 
built. This fixes also Gviz and most of the packages with them.

For the remaining packages I either provided patches, pull requests or am in 
contact with the developers. I checked these packages and there is not very 
much more to do than importing filters from AnnotationFilter instead of 
ensembldb.

Fingers crossed - tomorrow everything could be OK again - and sorry again for 
all the havoc

cheers, jo

On 6 Apr 2017, at 21:27, Obenchain, Valerie 
<valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>> 
wrote:

We've updated the release schedule and moved the deadline for errors to
next Friday, April 14.

Valerie

On 04/06/2017 10:29 AM, Stian Lågstad wrote:

How does the error deadline tomorrow (http://www.bioconductor.org/
developers/release-schedule/) affect packages that are still red because of
this change? I don't know what else to do other than to wait for changes in
Gviz (which my package is dependent on).

Thanks.

On Tue, Apr 4, 2017 at 10:05 PM, Michael Lawrence 
<lawrence.mich...@gene.com<mailto:lawrence.mich...@gene.com>

wrote:
Sorry I have been traveling. Will get to it soon.

On Apr 4, 2017 12:58 PM, "Rainer Johannes" 
<johannes.rai...@eurac.edu<mailto:johannes.rai...@eurac.edu>>
wrote:

Hi Herve,

sorry for all the reds - actually I provided the patches to biovizBase
and

ggbio, but it did not work out that smoothly that I hoped. For the other
packages that depend on ensembldb there's no problem or only small
changes

required (did contact the developers).
Fingers crossed that Michael can patch biovizBase and ggbio soon.

cheers, jo

On 4 Apr 2017, at 21:34, Hervé Pagès 
<hpa...@fredhutch.org<mailto:hpa...@fredhutch.org>> wrote:

Hi Johannes,

This move is generating a lot of red today on the build report.
Hopefully biovizBase and ggbio can be fixed quickly. Note that
maybe a smoother path would have been to notify the maintainers
of these packages first and wait that they make the required
changes (i.e. to import the filters from AnnotationFilter)
before modifying ensembldb. Maybe for next time ;-)

Cheers,
H.

On 04/04/2017 04:02 AM, Rainer Johannes wrote:

On 4 Apr 2017, at 10:59, Stian Lågstad 
<stianlags...@gmail.com<mailto:stianlags...@gmail.com>mailto:stianlags...@gmail.com>>> wrote:

Hi,

Thanks again for notifying me about the changes needed in chimeraviz.
Right now I'm having problems installing Gviz - I get these errors:

"""
No methods found in "GenomicAlignments" for requests:
pmapFromTranscripts

Error : object 'GRangesFilter' is not exported by
'namespace:ensembldb'

ERROR: lazy loading failed for package 'Gviz'
"""

Are these errors caused by the change in ensembldb? If so: Do you know
how I can keep developing without having to wait for Gviz?

These come from biovizBase which Gviz imports. I've sent Micheal the
fixes for biovizBase and ggbio that should fix this.

We need to wait for the changes to be propagated, since also for
ensembldb I get today still version 1.99.12 but not the new 1.99.13.

On Mon, Apr 3, 2017 at 8:59 AM, Rainer Johannes <
johannes.rai...@eurac.edu<mailto:johannes.rai...@eurac.edu><mailto:johannes.rai...@eurac.edu>>
 wrote:

Dear all,

I've just committed a change in ensembldb (version 1.99.13) that
removes all filter classes from it and imports them from the
AnnotationFilter package. This change will break biovizBase and ggbio
(and

all packages downstream of them, e.g. Gviz). I've already sent Michael
Lawrence patches to fix both packages, but  there might still be some
problems in the upcoming build reports I guess.

I've also contacted the developers of the TVTB and chimeraviz packages
and made them aware of the change. Could be that there are other packages
out there possibly affected by the change. If so, let me know and I'll
assist fixing the problems (if needed).

cheers, jo

___
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Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

2017-04-06 Thread Rainer Johannes

@Florian: nothing you have to change. I checked all packages and 70 of them 
have problems related to the relocation of the filters. For 63 of them 
everything should be fine once the updated versions of biovizBase and ggbio are 
built. This fixes also Gviz and most of the packages with them.

For the remaining packages I either provided patches, pull requests or am in 
contact with the developers. I checked these packages and there is not very 
much more to do than importing filters from AnnotationFilter instead of 
ensembldb.

Fingers crossed - tomorrow everything could be OK again - and sorry again for 
all the havoc

cheers, jo

On 6 Apr 2017, at 21:27, Obenchain, Valerie 
> 
wrote:

We've updated the release schedule and moved the deadline for errors to
next Friday, April 14.

Valerie

On 04/06/2017 10:29 AM, Stian Lågstad wrote:
How does the error deadline tomorrow (http://www.bioconductor.org/
developers/release-schedule/) affect packages that are still red because of
this change? I don't know what else to do other than to wait for changes in
Gviz (which my package is dependent on).

Thanks.

On Tue, Apr 4, 2017 at 10:05 PM, Michael Lawrence 

wrote:
Sorry I have been traveling. Will get to it soon.

On Apr 4, 2017 12:58 PM, "Rainer Johannes" 
>
wrote:

Hi Herve,

sorry for all the reds - actually I provided the patches to biovizBase
and
ggbio, but it did not work out that smoothly that I hoped. For the other
packages that depend on ensembldb there's no problem or only small
changes
required (did contact the developers).
Fingers crossed that Michael can patch biovizBase and ggbio soon.

cheers, jo

On 4 Apr 2017, at 21:34, Hervé Pagès 
> wrote:

Hi Johannes,

This move is generating a lot of red today on the build report.
Hopefully biovizBase and ggbio can be fixed quickly. Note that
maybe a smoother path would have been to notify the maintainers
of these packages first and wait that they make the required
changes (i.e. to import the filters from AnnotationFilter)
before modifying ensembldb. Maybe for next time ;-)

Cheers,
H.

On 04/04/2017 04:02 AM, Rainer Johannes wrote:

On 4 Apr 2017, at 10:59, Stian Lågstad 
mailto:stianlags...@gmail.com>>> wrote:
Hi,

Thanks again for notifying me about the changes needed in chimeraviz.
Right now I'm having problems installing Gviz - I get these errors:
"""
No methods found in "GenomicAlignments" for requests:
pmapFromTranscripts
Error : object 'GRangesFilter' is not exported by
'namespace:ensembldb'
ERROR: lazy loading failed for package 'Gviz'
"""

Are these errors caused by the change in ensembldb? If so: Do you know
how I can keep developing without having to wait for Gviz?

These come from biovizBase which Gviz imports. I've sent Micheal the
fixes for biovizBase and ggbio that should fix this.
We need to wait for the changes to be propagated, since also for
ensembldb I get today still version 1.99.12 but not the new 1.99.13.
On Mon, Apr 3, 2017 at 8:59 AM, Rainer Johannes <
johannes.rai...@eurac.edu>
 wrote:
Dear all,

I've just committed a change in ensembldb (version 1.99.13) that
removes all filter classes from it and imports them from the
AnnotationFilter package. This change will break biovizBase and ggbio
(and
all packages downstream of them, e.g. Gviz). I've already sent Michael
Lawrence patches to fix both packages, but  there might still be some
problems in the upcoming build reports I guess.
I've also contacted the developers of the TVTB and chimeraviz packages
and made them aware of the change. Could be that there are other packages
out there possibly affected by the change. If so, let me know and I'll
assist fixing the problems (if needed).
cheers, jo

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Program in Computational Biology
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Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

2017-04-06 Thread Obenchain, Valerie

We've updated the release schedule and moved the deadline for errors to
next Friday, April 14.

Valerie


On 04/06/2017 10:29 AM, Stian Lågstad wrote:
> How does the error deadline tomorrow (http://www.bioconductor.org/
> developers/release-schedule/) affect packages that are still red because of
> this change? I don't know what else to do other than to wait for changes in
> Gviz (which my package is dependent on).
>
> Thanks.
>
> On Tue, Apr 4, 2017 at 10:05 PM, Michael Lawrence > wrote:
>> Sorry I have been traveling. Will get to it soon.
>>
>> On Apr 4, 2017 12:58 PM, "Rainer Johannes" 
>> wrote:
>>
>>> Hi Herve,
>>>
>>> sorry for all the reds - actually I provided the patches to biovizBase
>> and
>>> ggbio, but it did not work out that smoothly that I hoped. For the other
>>> packages that depend on ensembldb there's no problem or only small
>> changes
>>> required (did contact the developers).
>>> Fingers crossed that Michael can patch biovizBase and ggbio soon.
>>>
>>> cheers, jo
>>>
 On 4 Apr 2017, at 21:34, Hervé Pagès  wrote:

 Hi Johannes,

 This move is generating a lot of red today on the build report.
 Hopefully biovizBase and ggbio can be fixed quickly. Note that
 maybe a smoother path would have been to notify the maintainers
 of these packages first and wait that they make the required
 changes (i.e. to import the filters from AnnotationFilter)
 before modifying ensembldb. Maybe for next time ;-)

 Cheers,
 H.

 On 04/04/2017 04:02 AM, Rainer Johannes wrote:
>
> On 4 Apr 2017, at 10:59, Stian Lågstad  :
>>> stianlags...@gmail.com>> wrote:
> Hi,
>
> Thanks again for notifying me about the changes needed in chimeraviz.
>>> Right now I'm having problems installing Gviz - I get these errors:
> """
> No methods found in "GenomicAlignments" for requests:
>>> pmapFromTranscripts
> Error : object 'GRangesFilter' is not exported by
>> 'namespace:ensembldb'
> ERROR: lazy loading failed for package 'Gviz'
> """
>
> Are these errors caused by the change in ensembldb? If so: Do you know
>>> how I can keep developing without having to wait for Gviz?
>
> These come from biovizBase which Gviz imports. I've sent Micheal the
>>> fixes for biovizBase and ggbio that should fix this.
> We need to wait for the changes to be propagated, since also for
>>> ensembldb I get today still version 1.99.12 but not the new 1.99.13.
> On Mon, Apr 3, 2017 at 8:59 AM, Rainer Johannes <
>>> johannes.rai...@eurac.edu> wrote:
> Dear all,
>
> I've just committed a change in ensembldb (version 1.99.13) that
>>> removes all filter classes from it and imports them from the
>>> AnnotationFilter package. This change will break biovizBase and ggbio
>> (and
>>> all packages downstream of them, e.g. Gviz). I've already sent Michael
>>> Lawrence patches to fix both packages, but  there might still be some
>>> problems in the upcoming build reports I guess.
> I've also contacted the developers of the TVTB and chimeraviz packages
>>> and made them aware of the change. Could be that there are other packages
>>> out there possibly affected by the change. If so, let me know and I'll
>>> assist fixing the problems (if needed).
> cheers, jo
>
> ___
> Bioc-devel@r-project.org mailing
>> list
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>
>
> --
> Stian Lågstad
> +47 41 80 80 25
>
>
>  [[alternative HTML version deleted]]
>
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 --
 Hervé Pagès

 Program in Computational Biology
 Division of Public Health Sciences
 Fred Hutchinson Cancer Research Center
 1100 Fairview Ave. N, M1-B514
 P.O. Box 19024
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 E-mail: hpa...@fredhutch.org
 Phone:  (206) 667-5791
 Fax:(206) 667-1319
>>> ___
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>>
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>>

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

2017-04-06 Thread Hahne, Florian

I thought that this all originates in biovizBase? So there’s nothing to change 
in Gviz unless I miss a crucial point here.
Florian

On 06.04.17, 19:10, "Bioc-devel on behalf of Stian Lågstad" 
 wrote:

How does the error deadline tomorrow (http://www.bioconductor.org/
developers/release-schedule/) affect packages that are still red because of
this change? I don't know what else to do other than to wait for changes in
Gviz (which my package is dependent on).

Thanks.

On Tue, Apr 4, 2017 at 10:05 PM, Michael Lawrence  wrote:

> Sorry I have been traveling. Will get to it soon.
>
> On Apr 4, 2017 12:58 PM, "Rainer Johannes" 
> wrote:
>
> > Hi Herve,
> >
> > sorry for all the reds - actually I provided the patches to biovizBase
> and
> > ggbio, but it did not work out that smoothly that I hoped. For the other
> > packages that depend on ensembldb there's no problem or only small
> changes
> > required (did contact the developers).
> > Fingers crossed that Michael can patch biovizBase and ggbio soon.
> >
> > cheers, jo
> >
> > > On 4 Apr 2017, at 21:34, Hervé Pagès  wrote:
> > >
> > > Hi Johannes,
> > >
> > > This move is generating a lot of red today on the build report.
> > > Hopefully biovizBase and ggbio can be fixed quickly. Note that
> > > maybe a smoother path would have been to notify the maintainers
> > > of these packages first and wait that they make the required
> > > changes (i.e. to import the filters from AnnotationFilter)
> > > before modifying ensembldb. Maybe for next time ;-)
> > >
> > > Cheers,
> > > H.
> > >
> > > On 04/04/2017 04:02 AM, Rainer Johannes wrote:
> > >>
> > >>
> > >> On 4 Apr 2017, at 10:59, Stian Lågstad  > stianlags...@gmail.com>> wrote:
> > >>
> > >> Hi,
> > >>
> > >> Thanks again for notifying me about the changes needed in chimeraviz.
> > Right now I'm having problems installing Gviz - I get these errors:
> > >>
> > >> """
> > >> No methods found in "GenomicAlignments" for requests:
> > pmapFromTranscripts
> > >> Error : object 'GRangesFilter' is not exported by
> 'namespace:ensembldb'
> > >> ERROR: lazy loading failed for package 'Gviz'
> > >> """
> > >>
> > >> Are these errors caused by the change in ensembldb? If so: Do you 
know
> > how I can keep developing without having to wait for Gviz?
> > >>
> > >>
> > >> These come from biovizBase which Gviz imports. I've sent Micheal the
> > fixes for biovizBase and ggbio that should fix this.
> > >> We need to wait for the changes to be propagated, since also for
> > ensembldb I get today still version 1.99.12 but not the new 1.99.13.
> > >>
> > >> On Mon, Apr 3, 2017 at 8:59 AM, Rainer Johannes <
> > johannes.rai...@eurac.edu> wrote:
> > >> Dear all,
> > >>
> > >> I've just committed a change in ensembldb (version 1.99.13) that
> > removes all filter classes from it and imports them from the
> > AnnotationFilter package. This change will break biovizBase and ggbio
> (and
> > all packages downstream of them, e.g. Gviz). I've already sent Michael
> > Lawrence patches to fix both packages, but  there might still be some
> > problems in the upcoming build reports I guess.
> > >>
> > >> I've also contacted the developers of the TVTB and chimeraviz 
packages
> > and made them aware of the change. Could be that there are other 
packages
> > out there possibly affected by the change. If so, let me know and I'll
> > assist fixing the problems (if needed).
> > >>
> > >> cheers, jo
> > >>
> > >> ___
> > >> Bioc-devel@r-project.org mailing
> list
> > >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.
> > ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAf
> qt84VtBcfhQ=
> > BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=iJ2N4NzAka_Lu8P0_h6XWIy-
> > PpkQJQ6twQd8-on8IrI=TXnXWMXgtHzzTK32JJ1rJ7ayI3US5B9DHGXheFpNXEY=
> > >>
> > >>
> > >>
> > >> --
> > >> Stian Lågstad
> > >> +47 41 80 80 25
> > >>
> > >>
> > >>  [[alternative HTML version deleted]]
> > >>
> > >> ___
> > >> Bioc-devel@r-project.org mailing list
> > >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.
> > ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAf
> qt84VtBcfhQ=
> > BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=iJ2N4NzAka_Lu8P0_h6XWIy-
> >

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

2017-04-06 Thread Stian Lågstad

How does the error deadline tomorrow (http://www.bioconductor.org/
developers/release-schedule/) affect packages that are still red because of
this change? I don't know what else to do other than to wait for changes in
Gviz (which my package is dependent on).

Thanks.

On Tue, Apr 4, 2017 at 10:05 PM, Michael Lawrence  wrote:

> Sorry I have been traveling. Will get to it soon.
>
> On Apr 4, 2017 12:58 PM, "Rainer Johannes" 
> wrote:
>
> > Hi Herve,
> >
> > sorry for all the reds - actually I provided the patches to biovizBase
> and
> > ggbio, but it did not work out that smoothly that I hoped. For the other
> > packages that depend on ensembldb there's no problem or only small
> changes
> > required (did contact the developers).
> > Fingers crossed that Michael can patch biovizBase and ggbio soon.
> >
> > cheers, jo
> >
> > > On 4 Apr 2017, at 21:34, Hervé Pagès  wrote:
> > >
> > > Hi Johannes,
> > >
> > > This move is generating a lot of red today on the build report.
> > > Hopefully biovizBase and ggbio can be fixed quickly. Note that
> > > maybe a smoother path would have been to notify the maintainers
> > > of these packages first and wait that they make the required
> > > changes (i.e. to import the filters from AnnotationFilter)
> > > before modifying ensembldb. Maybe for next time ;-)
> > >
> > > Cheers,
> > > H.
> > >
> > > On 04/04/2017 04:02 AM, Rainer Johannes wrote:
> > >>
> > >>
> > >> On 4 Apr 2017, at 10:59, Stian Lågstad  > stianlags...@gmail.com>> wrote:
> > >>
> > >> Hi,
> > >>
> > >> Thanks again for notifying me about the changes needed in chimeraviz.
> > Right now I'm having problems installing Gviz - I get these errors:
> > >>
> > >> """
> > >> No methods found in "GenomicAlignments" for requests:
> > pmapFromTranscripts
> > >> Error : object 'GRangesFilter' is not exported by
> 'namespace:ensembldb'
> > >> ERROR: lazy loading failed for package 'Gviz'
> > >> """
> > >>
> > >> Are these errors caused by the change in ensembldb? If so: Do you know
> > how I can keep developing without having to wait for Gviz?
> > >>
> > >>
> > >> These come from biovizBase which Gviz imports. I've sent Micheal the
> > fixes for biovizBase and ggbio that should fix this.
> > >> We need to wait for the changes to be propagated, since also for
> > ensembldb I get today still version 1.99.12 but not the new 1.99.13.
> > >>
> > >> On Mon, Apr 3, 2017 at 8:59 AM, Rainer Johannes <
> > johannes.rai...@eurac.edu> wrote:
> > >> Dear all,
> > >>
> > >> I've just committed a change in ensembldb (version 1.99.13) that
> > removes all filter classes from it and imports them from the
> > AnnotationFilter package. This change will break biovizBase and ggbio
> (and
> > all packages downstream of them, e.g. Gviz). I've already sent Michael
> > Lawrence patches to fix both packages, but  there might still be some
> > problems in the upcoming build reports I guess.
> > >>
> > >> I've also contacted the developers of the TVTB and chimeraviz packages
> > and made them aware of the change. Could be that there are other packages
> > out there possibly affected by the change. If so, let me know and I'll
> > assist fixing the problems (if needed).
> > >>
> > >> cheers, jo
> > >>
> > >> ___
> > >> Bioc-devel@r-project.org mailing
> list
> > >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.
> > ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAf
> qt84VtBcfhQ=
> > BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=iJ2N4NzAka_Lu8P0_h6XWIy-
> > PpkQJQ6twQd8-on8IrI=TXnXWMXgtHzzTK32JJ1rJ7ayI3US5B9DHGXheFpNXEY=
> > >>
> > >>
> > >>
> > >> --
> > >> Stian Lågstad
> > >> +47 41 80 80 25
> > >>
> > >>
> > >>  [[alternative HTML version deleted]]
> > >>
> > >> ___
> > >> Bioc-devel@r-project.org mailing list
> > >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.
> > ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAf
> qt84VtBcfhQ=
> > BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=iJ2N4NzAka_Lu8P0_h6XWIy-
> > PpkQJQ6twQd8-on8IrI=TXnXWMXgtHzzTK32JJ1rJ7ayI3US5B9DHGXheFpNXEY=
> > >>
> > >
> > > --
> > > Hervé Pagès
> > >
> > > Program in Computational Biology
> > > Division of Public Health Sciences
> > > Fred Hutchinson Cancer Research Center
> > > 1100 Fairview Ave. N, M1-B514
> > > P.O. Box 19024
> > > Seattle, WA 98109-1024
> > >
> > > E-mail: hpa...@fredhutch.org
> > > Phone:  (206) 667-5791
> > > Fax:(206) 667-1319
> >
> > ___
> > 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
>

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

2017-04-04 Thread Michael Lawrence

Sorry I have been traveling. Will get to it soon.

On Apr 4, 2017 12:58 PM, "Rainer Johannes" 
wrote:

> Hi Herve,
>
> sorry for all the reds - actually I provided the patches to biovizBase and
> ggbio, but it did not work out that smoothly that I hoped. For the other
> packages that depend on ensembldb there's no problem or only small changes
> required (did contact the developers).
> Fingers crossed that Michael can patch biovizBase and ggbio soon.
>
> cheers, jo
>
> > On 4 Apr 2017, at 21:34, Hervé Pagès  wrote:
> >
> > Hi Johannes,
> >
> > This move is generating a lot of red today on the build report.
> > Hopefully biovizBase and ggbio can be fixed quickly. Note that
> > maybe a smoother path would have been to notify the maintainers
> > of these packages first and wait that they make the required
> > changes (i.e. to import the filters from AnnotationFilter)
> > before modifying ensembldb. Maybe for next time ;-)
> >
> > Cheers,
> > H.
> >
> > On 04/04/2017 04:02 AM, Rainer Johannes wrote:
> >>
> >>
> >> On 4 Apr 2017, at 10:59, Stian Lågstad > wrote:
> >>
> >> Hi,
> >>
> >> Thanks again for notifying me about the changes needed in chimeraviz.
> Right now I'm having problems installing Gviz - I get these errors:
> >>
> >> """
> >> No methods found in "GenomicAlignments" for requests:
> pmapFromTranscripts
> >> Error : object 'GRangesFilter' is not exported by 'namespace:ensembldb'
> >> ERROR: lazy loading failed for package 'Gviz'
> >> """
> >>
> >> Are these errors caused by the change in ensembldb? If so: Do you know
> how I can keep developing without having to wait for Gviz?
> >>
> >>
> >> These come from biovizBase which Gviz imports. I've sent Micheal the
> fixes for biovizBase and ggbio that should fix this.
> >> We need to wait for the changes to be propagated, since also for
> ensembldb I get today still version 1.99.12 but not the new 1.99.13.
> >>
> >> On Mon, Apr 3, 2017 at 8:59 AM, Rainer Johannes <
> johannes.rai...@eurac.edu> wrote:
> >> Dear all,
> >>
> >> I've just committed a change in ensembldb (version 1.99.13) that
> removes all filter classes from it and imports them from the
> AnnotationFilter package. This change will break biovizBase and ggbio (and
> all packages downstream of them, e.g. Gviz). I've already sent Michael
> Lawrence patches to fix both packages, but  there might still be some
> problems in the upcoming build reports I guess.
> >>
> >> I've also contacted the developers of the TVTB and chimeraviz packages
> and made them aware of the change. Could be that there are other packages
> out there possibly affected by the change. If so, let me know and I'll
> assist fixing the problems (if needed).
> >>
> >> cheers, jo
> >>
> >> ___
> >> Bioc-devel@r-project.org mailing list
> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.
> ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=
> BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=iJ2N4NzAka_Lu8P0_h6XWIy-
> PpkQJQ6twQd8-on8IrI=TXnXWMXgtHzzTK32JJ1rJ7ayI3US5B9DHGXheFpNXEY=
> >>
> >>
> >>
> >> --
> >> Stian Lågstad
> >> +47 41 80 80 25
> >>
> >>
> >>  [[alternative HTML version deleted]]
> >>
> >> ___
> >> Bioc-devel@r-project.org mailing list
> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.
> ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=
> BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=iJ2N4NzAka_Lu8P0_h6XWIy-
> PpkQJQ6twQd8-on8IrI=TXnXWMXgtHzzTK32JJ1rJ7ayI3US5B9DHGXheFpNXEY=
> >>
> >
> > --
> > Hervé Pagès
> >
> > Program in Computational Biology
> > Division of Public Health Sciences
> > Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N, M1-B514
> > P.O. Box 19024
> > Seattle, WA 98109-1024
> >
> > E-mail: hpa...@fredhutch.org
> > Phone:  (206) 667-5791
> > Fax:(206) 667-1319
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

2017-04-04 Thread Rainer Johannes

Hi Herve,

sorry for all the reds - actually I provided the patches to biovizBase and 
ggbio, but it did not work out that smoothly that I hoped. For the other 
packages that depend on ensembldb there's no problem or only small changes 
required (did contact the developers).
Fingers crossed that Michael can patch biovizBase and ggbio soon.

cheers, jo

> On 4 Apr 2017, at 21:34, Hervé Pagès  wrote:
> 
> Hi Johannes,
> 
> This move is generating a lot of red today on the build report.
> Hopefully biovizBase and ggbio can be fixed quickly. Note that
> maybe a smoother path would have been to notify the maintainers
> of these packages first and wait that they make the required
> changes (i.e. to import the filters from AnnotationFilter)
> before modifying ensembldb. Maybe for next time ;-)
> 
> Cheers,
> H.
> 
> On 04/04/2017 04:02 AM, Rainer Johannes wrote:
>> 
>> 
>> On 4 Apr 2017, at 10:59, Stian Lågstad 
>> > wrote:
>> 
>> Hi,
>> 
>> Thanks again for notifying me about the changes needed in chimeraviz. Right 
>> now I'm having problems installing Gviz - I get these errors:
>> 
>> """
>> No methods found in "GenomicAlignments" for requests: pmapFromTranscripts
>> Error : object 'GRangesFilter' is not exported by 'namespace:ensembldb'
>> ERROR: lazy loading failed for package 'Gviz'
>> """
>> 
>> Are these errors caused by the change in ensembldb? If so: Do you know how I 
>> can keep developing without having to wait for Gviz?
>> 
>> 
>> These come from biovizBase which Gviz imports. I've sent Micheal the fixes 
>> for biovizBase and ggbio that should fix this.
>> We need to wait for the changes to be propagated, since also for ensembldb I 
>> get today still version 1.99.12 but not the new 1.99.13.
>> 
>> On Mon, Apr 3, 2017 at 8:59 AM, Rainer Johannes 
>> > wrote:
>> Dear all,
>> 
>> I've just committed a change in ensembldb (version 1.99.13) that removes all 
>> filter classes from it and imports them from the AnnotationFilter package. 
>> This change will break biovizBase and ggbio (and all packages downstream of 
>> them, e.g. Gviz). I've already sent Michael Lawrence patches to fix both 
>> packages, but  there might still be some problems in the upcoming build 
>> reports I guess.
>> 
>> I've also contacted the developers of the TVTB and chimeraviz packages and 
>> made them aware of the change. Could be that there are other packages out 
>> there possibly affected by the change. If so, let me know and I'll assist 
>> fixing the problems (if needed).
>> 
>> cheers, jo
>> 
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=iJ2N4NzAka_Lu8P0_h6XWIy-PpkQJQ6twQd8-on8IrI=TXnXWMXgtHzzTK32JJ1rJ7ayI3US5B9DHGXheFpNXEY=
>> 
>> 
>> 
>> --
>> Stian Lågstad
>> +47 41 80 80 25
>> 
>> 
>>  [[alternative HTML version deleted]]
>> 
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=iJ2N4NzAka_Lu8P0_h6XWIy-PpkQJQ6twQd8-on8IrI=TXnXWMXgtHzzTK32JJ1rJ7ayI3US5B9DHGXheFpNXEY=
>> 
> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319

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Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

2017-04-04 Thread Hervé Pagès

Hi Johannes,

Cheers,
H.

On 04/04/2017 04:02 AM, Rainer Johannes wrote:

On 4 Apr 2017, at 10:59, Stian Lågstad
> wrote:

Hi,

Thanks again for notifying me about the changes needed in chimeraviz. Right now
I'm having problems installing Gviz - I get these errors:

"""
No methods found in "GenomicAlignments" for requests: pmapFromTranscripts
Error : object 'GRangesFilter' is not exported by 'namespace:ensembldb'
ERROR: lazy loading failed for package 'Gviz'
"""

Are these errors caused by the change in ensembldb? If so: Do you know how I
can keep developing without having to wait for Gviz?

These come from biovizBase which Gviz imports. I've sent Micheal the fixes for
biovizBase and ggbio that should fix this.
We need to wait for the changes to be propagated, since also for ensembldb I
get today still version 1.99.12 but not the new 1.99.13.

On Mon, Apr 3, 2017 at 8:59 AM, Rainer Johannes
> wrote:
Dear all,

I've also contacted the developers of the TVTB and chimeraviz packages and made
them aware of the change. Could be that there are other packages out there
possibly affected by the change. If so, let me know and I'll assist fixing the
problems (if needed).

cheers, jo

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--
Stian Lågstad
+47 41 80 80 25

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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319

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Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

2017-04-04 Thread Rainer Johannes

On 4 Apr 2017, at 10:59, Stian Lågstad 
> wrote:

Hi,

Thanks again for notifying me about the changes needed in chimeraviz. Right now 
I'm having problems installing Gviz - I get these errors:

"""
No methods found in "GenomicAlignments" for requests: pmapFromTranscripts
Error : object 'GRangesFilter' is not exported by 'namespace:ensembldb'
ERROR: lazy loading failed for package 'Gviz'
"""

Are these errors caused by the change in ensembldb? If so: Do you know how I 
can keep developing without having to wait for Gviz?

These come from biovizBase which Gviz imports. I've sent Micheal the fixes for 
biovizBase and ggbio that should fix this.
We need to wait for the changes to be propagated, since also for ensembldb I 
get today still version 1.99.12 but not the new 1.99.13.

On Mon, Apr 3, 2017 at 8:59 AM, Rainer Johannes 
> wrote:
Dear all,

I've just committed a change in ensembldb (version 1.99.13) that removes all 
filter classes from it and imports them from the AnnotationFilter package. This 
change will break biovizBase and ggbio (and all packages downstream of them, 
e.g. Gviz). I've already sent Michael Lawrence patches to fix both packages, 
but  there might still be some problems in the upcoming build reports I guess.

I've also contacted the developers of the TVTB and chimeraviz packages and made 
them aware of the change. Could be that there are other packages out there 
possibly affected by the change. If so, let me know and I'll assist fixing the 
problems (if needed).

cheers, jo

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--
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+47 41 80 80 25

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

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