[Bioc-devel] Issue with syncing Github to Bioconductor /devel landing page

[Bohdan Khomtchouk]

I'm following the steps recommended at
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
but getting an unexpected error:

bohdankhomtchouk$ git merge upstream/master

merge: upstream/master - not something we can merge

I just updated https://git.bioconductor.org/packages/geneXtendeR less than
an hour ago so perhaps it takes a bit of time to appear on the Bioconductor
/devel landing page?

In other words, now that git clone
https://git.bioconductor.org/packages/geneXtendeR is giving me what I want
(the most updated version), is there anything else I need to do in order
for the /devel landing page to update itself?

Note: the /devel landing page says v.1.7.2 and I pushed v.1.7.2.  Perhaps
this is a mistake and I should have pushed v.1.7.3 in order for the changes
to be reflected?

-- 
Bohdan Khomtchouk, Ph.D.
AHA Postdoctoral Fellow, Gozani & Assimes Labs
Department of Biology & Department of Medicine
Division of Cardiovascular Medicine
Stanford University
Stanford, CA 94305
https://profiles.stanford.edu/bohdan-khomtchouk


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Re: [Bioc-devel] Error: file larger than 5 Mb.

[Bohdan Khomtchouk]

Looks like that was the issue, thanks Vincent & Martin!

> hub = AnnotationHub()
snapshotDate(): 2018-08-20
> isDevel()
[1] TRUE

> query(hub, "Mus_musculus.GRCm38.93.chr.gtf")
AnnotationHub with 1 record
# snapshotDate(): 2018-08-20
# names(): AH63797
# $dataprovider: Ensembl
# $species: Mus musculus
# $rdataclass: GRanges
# $rdatadateadded: 2018-07-31
# $title: Mus_musculus.GRCm38.93.chr.gtf
# $description: Gene Annotation for Mus musculus
# $taxonomyid: 10090
# $genome: GRCm38
# $sourcetype: GTF
# $sourceurl: ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus...
# $sourcesize: 29183870
# $tags: c("GTF", "ensembl", "Gene", "Transcript", "Annotation")
# retrieve record with 'object[["AH63797"]]'


On Wed, Sep 26, 2018 at 2:01 PM Martin Morgan 
wrote:

> maybe you are not using the 'devel' version of Bioconductor?
>
> On 09/26/2018 03:48 PM, Bohdan Khomtchouk wrote:
> > Martin, I don't see it unfortunately:
> >
> >  > query(hub, "Mus_musculus.GRCm38.93.chr.gtf")
> > AnnotationHub with 0 records
> > # snapshotDate(): 2018-04-30
> >
> > But perhaps it needs to be added to AnnotationHub, because I see other
> > .chr.gtf files that go up to 86 (while I'm using 93 in this original
> post):
> >
> >  > query(hub, c("GTF", "Mus musculus", ".chr.gtf"))
> > AnnotationHub with 112 records
> > # snapshotDate(): 2018-04-30
> > # $dataprovider: Ensembl
> > # $species: Mus musculus
> > # $rdataclass: GRanges
> > # additional mcols(): taxonomyid, genome, description,
> > #   coordinate_1_based, maintainer, rdatadateadded, preparerclass,
> > #   tags, rdatapath, sourceurl, sourcetype
> > # retrieve records with, e.g., 'object[["AH50868"]]'
> >
> >  title
> >AH50868 | Mus_musculus.GRCm38.84.chr.gtf
> >AH51038 | Mus_musculus.GRCm38.85.chr.gtf
> >AH51979 | Mus_musculus.GRCm38.86.chr.gtf
> >AH51983 | Mus_musculus_129s1svimj.129S1_SvImJ_v1.86.chr.gtf
> >AH51986 | Mus_musculus_aj.A_J_v1.86.chr.gtf
> >...   ...
> >AH61202 | Mus_musculus_lpj.LP_J_v1.92.chr.gtf
> >AH61205 | Mus_musculus_nodshiltj.NOD_ShiLtJ_v1.92.chr.gtf
> >AH61208 | Mus_musculus_nzohlltj.NZO_HlLtJ_v1.92.chr.gtf
> >AH61211 | Mus_musculus_pwkphj.PWK_PhJ_v1.92.chr.gtf
> >AH61214 | Mus_musculus_wsbeij.WSB_EiJ_v1.92.chr.gtf
> >
> > So it looks like "AH51979 | Mus_musculus.GRCm38.86.chr.gtf" is the
> > latest one available in AnnotationHub right now.
> >
> >
> > On Tue, Sep 25, 2018 at 10:35 PM Martin Morgan  > > wrote:
> >
> > Good news, the file is in AnnotationHub and can be used from there.
> > There is a download cost the first time but not subsequently.
> >
> > library(AnnotationHub)
> > hub = AnnotationHub()
> > query(hub, "Mus_musculus.GRCm38.93.chr.gtf.gz")
> >
> > ## note 'AH' number, then...
> > gtf = hub[["AH63797"]]
> >
> > Need the path rather than the imported path? use
> cache(hub["AH63797"])
> > instead.
> >
> > Martin
> >
> > On 09/25/2018 09:59 PM, Bohdan Khomtchouk wrote:
> >  > To generate mouse.rda, I used:
> >  >
> >  > library(rtracklayer)
> >  > mouse <- readGFF("
> >  >
> >
> ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.chr.gtf.gz
> >  > ")
> >  >
> >  > And then I saved the object as mouse.rda
> >  >
> >  >
> >  > On Tue, Sep 25, 2018 at 6:33 PM Bohdan Khomtchouk
> > mailto:khomtchouk...@gmail.com>>
> >  > wrote:
> >  >
> >  >> Here it is:
> >  >>
> >
> https://github.com/Bohdan-Khomtchouk/geneXtendeR/blob/master/data/mouse.rda
> >  >>
> >  >>
> >  >> On Tue, Sep 25, 2018 at 6:23 PM Vincent Carey
> > mailto:st...@channing.harvard.edu>>
> >  >> wrote:
> >  >>
> >  >>> (resending with reply all -- please reply to this one)
> >  >>>
> >  >>> Can you say some more about the content of the file?  Perhaps
> > it can be
> >  >>> placed in ExperimentHub.  "mouse.rda" is not very descriptive.
> > is it
> >  >>> in your github repo?
> >  >>>
> >  >>>
> >  >>> On Tue, Sep 25, 2018 at 6:25 PM, Bohdan Khomtchouk <
> >  >>> khomtchouk...@gmail.com >
> wrote:
> >  >>>
> >   I need to include an important .rda file in the /data folder
> of my
> >   Bioconductor package.  However, this .rda file exceeds 5 Mb in
> > size.  Do
> >   I
> >   have any other options besides for deleting it?
> >  
> >   bohdankhomtchouk$ git push origin master
> >  
> >   Counting objects: 65, done.
> >  
> >   Delta compression using up to 8 threads.
> >  
> >   Compressing objects: 100% (65/65), done.
> >  
> >   Writing objects: 100% (65/65), 13.79 MiB | 7.62 MiB/s, done.
> >  
> >   Total 65 (delta 30), reused 0 (delta 0)
> >  
> >   remote: Error: file larger than 5 Mb.
> >  
> >  

Re: [Bioc-devel] Error: file larger than 5 Mb.

[Martin Morgan]

maybe you are not using the 'devel' version of Bioconductor?

On 09/26/2018 03:48 PM, Bohdan Khomtchouk wrote:

Martin, I don't see it unfortunately:

 > query(hub, "Mus_musculus.GRCm38.93.chr.gtf")
AnnotationHub with 0 records
# snapshotDate(): 2018-04-30

But perhaps it needs to be added to AnnotationHub, because I see other 
.chr.gtf files that go up to 86 (while I'm using 93 in this original post):


 > query(hub, c("GTF", "Mus musculus", ".chr.gtf"))
AnnotationHub with 112 records
# snapshotDate(): 2018-04-30
# $dataprovider: Ensembl
# $species: Mus musculus
# $rdataclass: GRanges
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass,
#   tags, rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH50868"]]'

             title
   AH50868 | Mus_musculus.GRCm38.84.chr.gtf
   AH51038 | Mus_musculus.GRCm38.85.chr.gtf
   AH51979 | Mus_musculus.GRCm38.86.chr.gtf
   AH51983 | Mus_musculus_129s1svimj.129S1_SvImJ_v1.86.chr.gtf
   AH51986 | Mus_musculus_aj.A_J_v1.86.chr.gtf
   ...       ...
   AH61202 | Mus_musculus_lpj.LP_J_v1.92.chr.gtf
   AH61205 | Mus_musculus_nodshiltj.NOD_ShiLtJ_v1.92.chr.gtf
   AH61208 | Mus_musculus_nzohlltj.NZO_HlLtJ_v1.92.chr.gtf
   AH61211 | Mus_musculus_pwkphj.PWK_PhJ_v1.92.chr.gtf
   AH61214 | Mus_musculus_wsbeij.WSB_EiJ_v1.92.chr.gtf

So it looks like "AH51979 | Mus_musculus.GRCm38.86.chr.gtf" is the 
latest one available in AnnotationHub right now.



On Tue, Sep 25, 2018 at 10:35 PM Martin Morgan > wrote:


Good news, the file is in AnnotationHub and can be used from there.
There is a download cost the first time but not subsequently.

library(AnnotationHub)
hub = AnnotationHub()
query(hub, "Mus_musculus.GRCm38.93.chr.gtf.gz")

## note 'AH' number, then...
gtf = hub[["AH63797"]]

Need the path rather than the imported path? use cache(hub["AH63797"])
instead.

Martin

On 09/25/2018 09:59 PM, Bohdan Khomtchouk wrote:
 > To generate mouse.rda, I used:
 >
 > library(rtracklayer)
 > mouse <- readGFF("
 >

ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.chr.gtf.gz
 > ")
 >
 > And then I saved the object as mouse.rda
 >
 >
 > On Tue, Sep 25, 2018 at 6:33 PM Bohdan Khomtchouk
mailto:khomtchouk...@gmail.com>>
 > wrote:
 >
 >> Here it is:
 >>
https://github.com/Bohdan-Khomtchouk/geneXtendeR/blob/master/data/mouse.rda
 >>
 >>
 >> On Tue, Sep 25, 2018 at 6:23 PM Vincent Carey
mailto:st...@channing.harvard.edu>>
 >> wrote:
 >>
 >>> (resending with reply all -- please reply to this one)
 >>>
 >>> Can you say some more about the content of the file?  Perhaps
it can be
 >>> placed in ExperimentHub.  "mouse.rda" is not very descriptive. 
is it

 >>> in your github repo?
 >>>
 >>>
 >>> On Tue, Sep 25, 2018 at 6:25 PM, Bohdan Khomtchouk <
 >>> khomtchouk...@gmail.com > wrote:
 >>>
  I need to include an important .rda file in the /data folder of my
  Bioconductor package.  However, this .rda file exceeds 5 Mb in
size.  Do
  I
  have any other options besides for deleting it?
 
  bohdankhomtchouk$ git push origin master
 
  Counting objects: 65, done.
 
  Delta compression using up to 8 threads.
 
  Compressing objects: 100% (65/65), done.
 
  Writing objects: 100% (65/65), 13.79 MiB | 7.62 MiB/s, done.
 
  Total 65 (delta 30), reused 0 (delta 0)
 
  remote: Error: file larger than 5 Mb.
 
  remote:
 
  remote:     File name: 'data/mouse.rda'
 
  remote:     File size: 12.9 Mb
 
  remote:
 
  remote: Please see Biocondcutor guidelines
 
  remote: https://bioconductor.org/developers/package-guidelines/
 
  remote:
 
  To git.bioconductor.org:packages/geneXtendeR
 
    ! [remote rejected] master -> master (pre-receive hook declined)
 
  error: failed to push some refs to 'g...@git.bioconductor.org
:
  packages/geneXtendeR'
 
  --
  Bohdan Khomtchouk, Ph.D.
  AHA Postdoctoral Fellow, Gozani & Assimes Labs
  Department of Biology & Department of Medicine
  Division of Cardiovascular Medicine
  Stanford University
  Stanford, CA 94305
  https://profiles.stanford.edu/bohdan-khomtchouk
 
 
  CONFIDENTIALITY NOTICE: Information contained in this
me...{{dropped:9}}
 
  ___
  Bioc-devel@r-project.org 

Re: [Bioc-devel] Error: file larger than 5 Mb.

[Bohdan Khomtchouk]

Just did, same result:

> hub = AnnotationHub()
snapshotDate(): 2018-04-30

I re-installed AnnotationHub package as well.


On Wed, Sep 26, 2018 at 1:16 PM Vincent Carey 
wrote:

> your annotation hub is out of date.  run hub = AnnotationHub() and try
> again
>
> On Wed, Sep 26, 2018 at 3:48 PM, Bohdan Khomtchouk <
> khomtchouk...@gmail.com> wrote:
>
>> Martin, I don't see it unfortunately:
>>
>> > query(hub, "Mus_musculus.GRCm38.93.chr.gtf")
>> AnnotationHub with 0 records
>> # snapshotDate(): 2018-04-30
>>
>> But perhaps it needs to be added to AnnotationHub, because I see other
>> .chr.gtf files that go up to 86 (while I'm using 93 in this original post):
>>
>> > query(hub, c("GTF", "Mus musculus", ".chr.gtf"))
>> AnnotationHub with 112 records
>> # snapshotDate(): 2018-04-30
>> # $dataprovider: Ensembl
>> # $species: Mus musculus
>> # $rdataclass: GRanges
>> # additional mcols(): taxonomyid, genome, description,
>> #   coordinate_1_based, maintainer, rdatadateadded, preparerclass,
>> #   tags, rdatapath, sourceurl, sourcetype
>> # retrieve records with, e.g., 'object[["AH50868"]]'
>>
>> title
>>   AH50868 | Mus_musculus.GRCm38.84.chr.gtf
>>   AH51038 | Mus_musculus.GRCm38.85.chr.gtf
>>   AH51979 | Mus_musculus.GRCm38.86.chr.gtf
>>   AH51983 | Mus_musculus_129s1svimj.129S1_SvImJ_v1.86.chr.gtf
>>   AH51986 | Mus_musculus_aj.A_J_v1.86.chr.gtf
>>   ...   ...
>>   AH61202 | Mus_musculus_lpj.LP_J_v1.92.chr.gtf
>>   AH61205 | Mus_musculus_nodshiltj.NOD_ShiLtJ_v1.92.chr.gtf
>>   AH61208 | Mus_musculus_nzohlltj.NZO_HlLtJ_v1.92.chr.gtf
>>   AH61211 | Mus_musculus_pwkphj.PWK_PhJ_v1.92.chr.gtf
>>   AH61214 | Mus_musculus_wsbeij.WSB_EiJ_v1.92.chr.gtf
>>
>> So it looks like "AH51979 | Mus_musculus.GRCm38.86.chr.gtf" is the latest
>> one available in AnnotationHub right now.
>>
>>
>> On Tue, Sep 25, 2018 at 10:35 PM Martin Morgan 
>> wrote:
>>
>>> Good news, the file is in AnnotationHub and can be used from there.
>>> There is a download cost the first time but not subsequently.
>>>
>>> library(AnnotationHub)
>>> hub = AnnotationHub()
>>> query(hub, "Mus_musculus.GRCm38.93.chr.gtf.gz")
>>>
>>> ## note 'AH' number, then...
>>> gtf = hub[["AH63797"]]
>>>
>>> Need the path rather than the imported path? use cache(hub["AH63797"])
>>> instead.
>>>
>>> Martin
>>>
>>> On 09/25/2018 09:59 PM, Bohdan Khomtchouk wrote:
>>> > To generate mouse.rda, I used:
>>> >
>>> > library(rtracklayer)
>>> > mouse <- readGFF("
>>> >
>>> ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.chr.gtf.gz
>>> > ")
>>> >
>>> > And then I saved the object as mouse.rda
>>> >
>>> >
>>> > On Tue, Sep 25, 2018 at 6:33 PM Bohdan Khomtchouk <
>>> khomtchouk...@gmail.com>
>>> > wrote:
>>> >
>>> >> Here it is:
>>> >>
>>> https://github.com/Bohdan-Khomtchouk/geneXtendeR/blob/master/data/mouse.rda
>>> >>
>>> >>
>>> >> On Tue, Sep 25, 2018 at 6:23 PM Vincent Carey <
>>> st...@channing.harvard.edu>
>>> >> wrote:
>>> >>
>>> >>> (resending with reply all -- please reply to this one)
>>> >>>
>>> >>> Can you say some more about the content of the file?  Perhaps it can
>>> be
>>> >>> placed in ExperimentHub.  "mouse.rda" is not very descriptive.  is it
>>> >>> in your github repo?
>>> >>>
>>> >>>
>>> >>> On Tue, Sep 25, 2018 at 6:25 PM, Bohdan Khomtchouk <
>>> >>> khomtchouk...@gmail.com> wrote:
>>> >>>
>>>  I need to include an important .rda file in the /data folder of my
>>>  Bioconductor package.  However, this .rda file exceeds 5 Mb in
>>> size.  Do
>>>  I
>>>  have any other options besides for deleting it?
>>> 
>>>  bohdankhomtchouk$ git push origin master
>>> 
>>>  Counting objects: 65, done.
>>> 
>>>  Delta compression using up to 8 threads.
>>> 
>>>  Compressing objects: 100% (65/65), done.
>>> 
>>>  Writing objects: 100% (65/65), 13.79 MiB | 7.62 MiB/s, done.
>>> 
>>>  Total 65 (delta 30), reused 0 (delta 0)
>>> 
>>>  remote: Error: file larger than 5 Mb.
>>> 
>>>  remote:
>>> 
>>>  remote: File name: 'data/mouse.rda'
>>> 
>>>  remote: File size: 12.9 Mb
>>> 
>>>  remote:
>>> 
>>>  remote: Please see Biocondcutor guidelines
>>> 
>>>  remote: https://bioconductor.org/developers/package-guidelines/
>>> 
>>>  remote:
>>> 
>>>  To git.bioconductor.org:packages/geneXtendeR
>>> 
>>>    ! [remote rejected] master -> master (pre-receive hook declined)
>>> 
>>>  error: failed to push some refs to 'g...@git.bioconductor.org:
>>>  packages/geneXtendeR'
>>> 
>>>  --
>>>  Bohdan Khomtchouk, Ph.D.
>>>  AHA Postdoctoral Fellow, Gozani & Assimes Labs
>>>  Department of Biology & Department of Medicine
>>>  Division of Cardiovascular Medicine
>>>  Stanford University
>>>  Stanford, CA 94305
>>>  https://profiles.stanford.edu/bohdan-khomtchouk
>>> 
>>> 
>>>  CONFIDENTIALITY NOTICE: Information contained in this
>>> 

Re: [Bioc-devel] Issue with an illegal version bump message when updating an old experiment data package

[Leonardo Collado Torres]

Hi bioc-devel,

Thanks to Nitesh Turaga we were able to get derfinderData back in
sync. Basically:

* We discarded the previous GitHub repo (deleted forever)
* Re-synced via
http://bioconductor.org/developers/how-to/git/maintain-github-bioc/
* The real issue was a bug in the bump version script back in 2014
that bumped the package from 0.99.3 to 0.101.0 instead of 1.1.0
https://github.com/leekgroup/derfinderData/commit/5ea1d9580a4086ecea44cef696679a7e248ff2ab
* Nitesh fixed this manually:
https://github.com/leekgroup/derfinderData/commit/a9ba347501d92ffb2039d01d53159ebe69924b99
* See all new commits: https://github.com/leekgroup/derfinderData/commits/master

Thanks for the input Marcel!

Best,
Leo

On Tue, Sep 25, 2018 at 10:42 PM Ramos Perez, Marcel
 wrote:
>
>
> Hi Leonardo,
>
> Keep in mind that GitHub and the Bioconductor git server are two
> different animals.
>
> You should be pushing your changes to the git server as you would with
> software
> packages ( `g...@git.bioconductor.org:packages/derfinderData` ).
>
> My guess is that the hook is looking at the version already in the git
> server and
> comparing that to the committed changes (but I could be wrong).
>
> Nitesh can elaborate a bit more on this.
>
> We will look into it on our end.
>
> Regards,
>
> Marcel
>
>
>
>
> On 09/24/2018 10:54 AM, Leonardo Collado Torres wrote:
> > Hi,
> >
> > Marcel Ramos told me a few months ago (July 24, 2018) that experiment
> > data packages are now controlled the same way as software packages via
> > GitHub. Today I finally tried synching the repos following these
> > instructions 
> > http://bioconductor.org/developers/how-to/git/sync-existing-repositories/.
> > I had to use the "git merge --allow-unrelated-histories
> > upstream/master" step and resolve 3 small conflicts. It's almost all
> > working well, the step I'm stuck at is:
> >
> > $ git push upstream master
> > Counting objects: 45, done.
> > Delta compression using up to 4 threads.
> > Compressing objects: 100% (38/38), done.
> > Writing objects: 100% (45/45), 5.98 KiB | 1.50 MiB/s, done.
> > Total 45 (delta 25), reused 5 (delta 4)
> > remote: Error: Illegal version bump from '0.115.0' to '0.115.1'. Check
> > remote: http://bioconductor.org/developers/how-to/version-numbering/
> > remote: for details
> > To git.bioconductor.org:packages/derfinderData.git
> >  ! [remote rejected] master -> master (pre-receive hook declined)
> > error: failed to push some refs to
> > 'g...@git.bioconductor.org:packages/derfinderData.git'
> >
> > My guess is that the hook is looking at
> > https://github.com/leekgroup/derfinderData/commit/90971f8c8f6b4116d939309942a781bc5f55d9d8
> > and thinks that I'm trying to bump from 0.103.1 to 0.115.1 while in
> > reality the version at
> > http://bioconductor.org/packages/devel/data/experiment/html/derfinderData.html
> > is 0.115.0 (updated in
> > https://github.com/leekgroup/derfinderData/commit/dbf71bbd4418be5a80a6060df8f5f16379a01cb3).
> >
> > Is there something I can do to make this work?
> >
> > GitHub: https://github.com/leekgroup/derfinderData
> > Bioc-devel: 
> > http://bioconductor.org/packages/devel/data/experiment/html/derfinderData.html
> >
> > PS I guess that I don't need this file anymore:
> > https://github.com/leekgroup/derfinderData/blob/master/external_data_store.txt
> > nor the currently untracked svn files:
> >
> > $ git status
> > On branch master
> > Your branch is up to date with 'origin/master'.
> >
> > Untracked files:
> >   (use "git add ..." to include in what will be committed)
> >
> > data/.svn/
> > inst/extdata/.svn/
> >
> > Best,
> > Leo
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> This email message may contain legally privileged and/or confidential 
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> agent responsible for the delivery of this message to the intended 
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Re: [Bioc-devel] Error: file larger than 5 Mb.

[Vincent Carey]

your annotation hub is out of date.  run hub = AnnotationHub() and try again

On Wed, Sep 26, 2018 at 3:48 PM, Bohdan Khomtchouk 
wrote:

> Martin, I don't see it unfortunately:
>
> > query(hub, "Mus_musculus.GRCm38.93.chr.gtf")
> AnnotationHub with 0 records
> # snapshotDate(): 2018-04-30
>
> But perhaps it needs to be added to AnnotationHub, because I see other
> .chr.gtf files that go up to 86 (while I'm using 93 in this original post):
>
> > query(hub, c("GTF", "Mus musculus", ".chr.gtf"))
> AnnotationHub with 112 records
> # snapshotDate(): 2018-04-30
> # $dataprovider: Ensembl
> # $species: Mus musculus
> # $rdataclass: GRanges
> # additional mcols(): taxonomyid, genome, description,
> #   coordinate_1_based, maintainer, rdatadateadded, preparerclass,
> #   tags, rdatapath, sourceurl, sourcetype
> # retrieve records with, e.g., 'object[["AH50868"]]'
>
> title
>   AH50868 | Mus_musculus.GRCm38.84.chr.gtf
>   AH51038 | Mus_musculus.GRCm38.85.chr.gtf
>   AH51979 | Mus_musculus.GRCm38.86.chr.gtf
>   AH51983 | Mus_musculus_129s1svimj.129S1_SvImJ_v1.86.chr.gtf
>   AH51986 | Mus_musculus_aj.A_J_v1.86.chr.gtf
>   ...   ...
>   AH61202 | Mus_musculus_lpj.LP_J_v1.92.chr.gtf
>   AH61205 | Mus_musculus_nodshiltj.NOD_ShiLtJ_v1.92.chr.gtf
>   AH61208 | Mus_musculus_nzohlltj.NZO_HlLtJ_v1.92.chr.gtf
>   AH61211 | Mus_musculus_pwkphj.PWK_PhJ_v1.92.chr.gtf
>   AH61214 | Mus_musculus_wsbeij.WSB_EiJ_v1.92.chr.gtf
>
> So it looks like "AH51979 | Mus_musculus.GRCm38.86.chr.gtf" is the latest
> one available in AnnotationHub right now.
>
>
> On Tue, Sep 25, 2018 at 10:35 PM Martin Morgan 
> wrote:
>
>> Good news, the file is in AnnotationHub and can be used from there.
>> There is a download cost the first time but not subsequently.
>>
>> library(AnnotationHub)
>> hub = AnnotationHub()
>> query(hub, "Mus_musculus.GRCm38.93.chr.gtf.gz")
>>
>> ## note 'AH' number, then...
>> gtf = hub[["AH63797"]]
>>
>> Need the path rather than the imported path? use cache(hub["AH63797"])
>> instead.
>>
>> Martin
>>
>> On 09/25/2018 09:59 PM, Bohdan Khomtchouk wrote:
>> > To generate mouse.rda, I used:
>> >
>> > library(rtracklayer)
>> > mouse <- readGFF("
>> > ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/
>> Mus_musculus.GRCm38.93.chr.gtf.gz
>> > ")
>> >
>> > And then I saved the object as mouse.rda
>> >
>> >
>> > On Tue, Sep 25, 2018 at 6:33 PM Bohdan Khomtchouk <
>> khomtchouk...@gmail.com>
>> > wrote:
>> >
>> >> Here it is:
>> >> https://github.com/Bohdan-Khomtchouk/geneXtendeR/blob/
>> master/data/mouse.rda
>> >>
>> >>
>> >> On Tue, Sep 25, 2018 at 6:23 PM Vincent Carey <
>> st...@channing.harvard.edu>
>> >> wrote:
>> >>
>> >>> (resending with reply all -- please reply to this one)
>> >>>
>> >>> Can you say some more about the content of the file?  Perhaps it can
>> be
>> >>> placed in ExperimentHub.  "mouse.rda" is not very descriptive.  is it
>> >>> in your github repo?
>> >>>
>> >>>
>> >>> On Tue, Sep 25, 2018 at 6:25 PM, Bohdan Khomtchouk <
>> >>> khomtchouk...@gmail.com> wrote:
>> >>>
>>  I need to include an important .rda file in the /data folder of my
>>  Bioconductor package.  However, this .rda file exceeds 5 Mb in
>> size.  Do
>>  I
>>  have any other options besides for deleting it?
>> 
>>  bohdankhomtchouk$ git push origin master
>> 
>>  Counting objects: 65, done.
>> 
>>  Delta compression using up to 8 threads.
>> 
>>  Compressing objects: 100% (65/65), done.
>> 
>>  Writing objects: 100% (65/65), 13.79 MiB | 7.62 MiB/s, done.
>> 
>>  Total 65 (delta 30), reused 0 (delta 0)
>> 
>>  remote: Error: file larger than 5 Mb.
>> 
>>  remote:
>> 
>>  remote: File name: 'data/mouse.rda'
>> 
>>  remote: File size: 12.9 Mb
>> 
>>  remote:
>> 
>>  remote: Please see Biocondcutor guidelines
>> 
>>  remote: https://bioconductor.org/developers/package-guidelines/
>> 
>>  remote:
>> 
>>  To git.bioconductor.org:packages/geneXtendeR
>> 
>>    ! [remote rejected] master -> master (pre-receive hook declined)
>> 
>>  error: failed to push some refs to 'g...@git.bioconductor.org:
>>  packages/geneXtendeR'
>> 
>>  --
>>  Bohdan Khomtchouk, Ph.D.
>>  AHA Postdoctoral Fellow, Gozani & Assimes Labs
>>  Department of Biology & Department of Medicine
>>  Division of Cardiovascular Medicine
>>  Stanford University
>>  Stanford, CA 94305
>>  https://profiles.stanford.edu/bohdan-khomtchouk
>> 
>> 
>>  CONFIDENTIALITY NOTICE: Information contained in this
>> me...{{dropped:9}}
>> 
>>  ___
>>  Bioc-devel@r-project.org mailing list
>>  https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
>> >>>
>> >>>
>> >>> The information in this e-mail is intended only for t...{{dropped:17}}
>> >
>> > ___
>> > 

Re: [Bioc-devel] Error: file larger than 5 Mb.

[Bohdan Khomtchouk]

Martin, I don't see it unfortunately:

> query(hub, "Mus_musculus.GRCm38.93.chr.gtf")
AnnotationHub with 0 records
# snapshotDate(): 2018-04-30

But perhaps it needs to be added to AnnotationHub, because I see other
.chr.gtf files that go up to 86 (while I'm using 93 in this original post):

> query(hub, c("GTF", "Mus musculus", ".chr.gtf"))
AnnotationHub with 112 records
# snapshotDate(): 2018-04-30
# $dataprovider: Ensembl
# $species: Mus musculus
# $rdataclass: GRanges
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass,
#   tags, rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH50868"]]'

title
  AH50868 | Mus_musculus.GRCm38.84.chr.gtf
  AH51038 | Mus_musculus.GRCm38.85.chr.gtf
  AH51979 | Mus_musculus.GRCm38.86.chr.gtf
  AH51983 | Mus_musculus_129s1svimj.129S1_SvImJ_v1.86.chr.gtf
  AH51986 | Mus_musculus_aj.A_J_v1.86.chr.gtf
  ...   ...
  AH61202 | Mus_musculus_lpj.LP_J_v1.92.chr.gtf
  AH61205 | Mus_musculus_nodshiltj.NOD_ShiLtJ_v1.92.chr.gtf
  AH61208 | Mus_musculus_nzohlltj.NZO_HlLtJ_v1.92.chr.gtf
  AH61211 | Mus_musculus_pwkphj.PWK_PhJ_v1.92.chr.gtf
  AH61214 | Mus_musculus_wsbeij.WSB_EiJ_v1.92.chr.gtf

So it looks like "AH51979 | Mus_musculus.GRCm38.86.chr.gtf" is the latest
one available in AnnotationHub right now.


On Tue, Sep 25, 2018 at 10:35 PM Martin Morgan 
wrote:

> Good news, the file is in AnnotationHub and can be used from there.
> There is a download cost the first time but not subsequently.
>
> library(AnnotationHub)
> hub = AnnotationHub()
> query(hub, "Mus_musculus.GRCm38.93.chr.gtf.gz")
>
> ## note 'AH' number, then...
> gtf = hub[["AH63797"]]
>
> Need the path rather than the imported path? use cache(hub["AH63797"])
> instead.
>
> Martin
>
> On 09/25/2018 09:59 PM, Bohdan Khomtchouk wrote:
> > To generate mouse.rda, I used:
> >
> > library(rtracklayer)
> > mouse <- readGFF("
> >
> ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.chr.gtf.gz
> > ")
> >
> > And then I saved the object as mouse.rda
> >
> >
> > On Tue, Sep 25, 2018 at 6:33 PM Bohdan Khomtchouk <
> khomtchouk...@gmail.com>
> > wrote:
> >
> >> Here it is:
> >>
> https://github.com/Bohdan-Khomtchouk/geneXtendeR/blob/master/data/mouse.rda
> >>
> >>
> >> On Tue, Sep 25, 2018 at 6:23 PM Vincent Carey <
> st...@channing.harvard.edu>
> >> wrote:
> >>
> >>> (resending with reply all -- please reply to this one)
> >>>
> >>> Can you say some more about the content of the file?  Perhaps it can be
> >>> placed in ExperimentHub.  "mouse.rda" is not very descriptive.  is it
> >>> in your github repo?
> >>>
> >>>
> >>> On Tue, Sep 25, 2018 at 6:25 PM, Bohdan Khomtchouk <
> >>> khomtchouk...@gmail.com> wrote:
> >>>
>  I need to include an important .rda file in the /data folder of my
>  Bioconductor package.  However, this .rda file exceeds 5 Mb in size.
> Do
>  I
>  have any other options besides for deleting it?
> 
>  bohdankhomtchouk$ git push origin master
> 
>  Counting objects: 65, done.
> 
>  Delta compression using up to 8 threads.
> 
>  Compressing objects: 100% (65/65), done.
> 
>  Writing objects: 100% (65/65), 13.79 MiB | 7.62 MiB/s, done.
> 
>  Total 65 (delta 30), reused 0 (delta 0)
> 
>  remote: Error: file larger than 5 Mb.
> 
>  remote:
> 
>  remote: File name: 'data/mouse.rda'
> 
>  remote: File size: 12.9 Mb
> 
>  remote:
> 
>  remote: Please see Biocondcutor guidelines
> 
>  remote: https://bioconductor.org/developers/package-guidelines/
> 
>  remote:
> 
>  To git.bioconductor.org:packages/geneXtendeR
> 
>    ! [remote rejected] master -> master (pre-receive hook declined)
> 
>  error: failed to push some refs to 'g...@git.bioconductor.org:
>  packages/geneXtendeR'
> 
>  --
>  Bohdan Khomtchouk, Ph.D.
>  AHA Postdoctoral Fellow, Gozani & Assimes Labs
>  Department of Biology & Department of Medicine
>  Division of Cardiovascular Medicine
>  Stanford University
>  Stanford, CA 94305
>  https://profiles.stanford.edu/bohdan-khomtchouk
> 
> 
>  CONFIDENTIALITY NOTICE: Information contained in this
> me...{{dropped:9}}
> 
>  ___
>  Bioc-devel@r-project.org mailing list
>  https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> >>>
> >>>
> >>> The information in this e-mail is intended only for t...{{dropped:17}}
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>

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Re: [Bioc-devel] Error: file larger than 5 Mb.

[Tim Triche, Jr.]

hmm, does it make sense to submit the hg19, hg38, and mm10 HMM CpG island
predictions to AnnotationHub?

R> qhs <- query(ah, "island" )
R> qhs
AnnotationHub with 4 records
# snapshotDate(): 2018-08-20
# $dataprovider: UCSC
# $species: Homo sapiens
# $rdataclass: GRanges
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH5086"]]'

   title
  AH5086 | CpG Islands
  AH5204 | CpG Islands
  AH5344 | CpG Islands
  AH5463 | CpG Islands
R> qhs$title
[1] "CpG Islands" "CpG Islands" "CpG Islands" "CpG Islands"
R> qhs$dataprovider
[1] "UCSC" "UCSC" "UCSC" "UCSC"


There's rather a lot of items that might belong in AnnotationHub (and not
any package) now that I think about it.

Does each type of data need to go through
https://www.bioconductor.org/packages/devel/bioc/vignettes/AnnotationHub/inst/doc/CreateAnAnnotationPackage.html
or can items be submitted directly?

Thanks,

--t


On Wed, Sep 26, 2018 at 1:35 AM Martin Morgan 
wrote:

> Good news, the file is in AnnotationHub and can be used from there.
> There is a download cost the first time but not subsequently.
>
> library(AnnotationHub)
> hub = AnnotationHub()
> query(hub, "Mus_musculus.GRCm38.93.chr.gtf.gz")
>
> ## note 'AH' number, then...
> gtf = hub[["AH63797"]]
>
> Need the path rather than the imported path? use cache(hub["AH63797"])
> instead.
>
> Martin
>
> On 09/25/2018 09:59 PM, Bohdan Khomtchouk wrote:
> > To generate mouse.rda, I used:
> >
> > library(rtracklayer)
> > mouse <- readGFF("
> >
> ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus/Mus_musculus.GRCm38.93.chr.gtf.gz
> > ")
> >
> > And then I saved the object as mouse.rda
> >
> >
> > On Tue, Sep 25, 2018 at 6:33 PM Bohdan Khomtchouk <
> khomtchouk...@gmail.com>
> > wrote:
> >
> >> Here it is:
> >>
> https://github.com/Bohdan-Khomtchouk/geneXtendeR/blob/master/data/mouse.rda
> >>
> >>
> >> On Tue, Sep 25, 2018 at 6:23 PM Vincent Carey <
> st...@channing.harvard.edu>
> >> wrote:
> >>
> >>> (resending with reply all -- please reply to this one)
> >>>
> >>> Can you say some more about the content of the file?  Perhaps it can be
> >>> placed in ExperimentHub.  "mouse.rda" is not very descriptive.  is it
> >>> in your github repo?
> >>>
> >>>
> >>> On Tue, Sep 25, 2018 at 6:25 PM, Bohdan Khomtchouk <
> >>> khomtchouk...@gmail.com> wrote:
> >>>
>  I need to include an important .rda file in the /data folder of my
>  Bioconductor package.  However, this .rda file exceeds 5 Mb in size.
> Do
>  I
>  have any other options besides for deleting it?
> 
>  bohdankhomtchouk$ git push origin master
> 
>  Counting objects: 65, done.
> 
>  Delta compression using up to 8 threads.
> 
>  Compressing objects: 100% (65/65), done.
> 
>  Writing objects: 100% (65/65), 13.79 MiB | 7.62 MiB/s, done.
> 
>  Total 65 (delta 30), reused 0 (delta 0)
> 
>  remote: Error: file larger than 5 Mb.
> 
>  remote:
> 
>  remote: File name: 'data/mouse.rda'
> 
>  remote: File size: 12.9 Mb
> 
>  remote:
> 
>  remote: Please see Biocondcutor guidelines
> 
>  remote: https://bioconductor.org/developers/package-guidelines/
> 
>  remote:
> 
>  To git.bioconductor.org:packages/geneXtendeR
> 
>    ! [remote rejected] master -> master (pre-receive hook declined)
> 
>  error: failed to push some refs to 'g...@git.bioconductor.org:
>  packages/geneXtendeR'
> 
>  --
>  Bohdan Khomtchouk, Ph.D.
>  AHA Postdoctoral Fellow, Gozani & Assimes Labs
>  Department of Biology & Department of Medicine
>  Division of Cardiovascular Medicine
>  Stanford University
>  Stanford, CA 94305
>  https://profiles.stanford.edu/bohdan-khomtchouk
> 
> 
>  CONFIDENTIALITY NOTICE: Information contained in this
> me...{{dropped:9}}
> 
>  ___
>  Bioc-devel@r-project.org mailing list
>  https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> >>>
> >>>
> >>> The information in this e-mail is intended only for t...{{dropped:17}}
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] NEWS.md

[Lluís Revilla]

Yes I was arguing if NEWS.md could be used. Only after Lori reply I
realized the changes don't apply for the next release of Bioconductor.
Anyway, thanks Laurent for the command, and the team for considering it in
its due time.

Lluís


On Wed, 26 Sep 2018 at 13:22, Shepherd, Lori 
wrote:

> As mentioned by Henrik,  The code referenced seems only implemented in
> R-devel currently.   Bioconductor will look at updating the code we use on
> our systems to match when our Bioconductor version is being built against
> R-devel  (after the October release) .
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Cancer Institute
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> --
> *From:* Henrik Bengtsson 
> *Sent:* Tuesday, September 25, 2018 7:01:36 PM
> *To:* lg...@cam.ac.uk
> *Cc:* Shepherd, Lori; lluis.revi...@gmail.com; bioc-devel@r-project.org
> *Subject:* Re: [Bioc-devel] NEWS.md
>
> Forgot to mention that here's how news() select which file to parse if
> there are several:
>
> ## Look for new-style inst/NEWS.Rd installed as NEWS.Rd
> ## If not found, look for NEWS.md.
> ## If not found, look at old-style
> ## NEWS inst/NEWS
> ## installed as NEWS (and ignore ChangeLog files).
>
> Source:
> https://github.com/wch/r-source/blob/d20943d71407f9209cb6c7581ac0fce3b3517419/src/library/tools/R/news.R#L62-L66
>
> /Henrik
> On Tue, Sep 25, 2018 at 3:58 PM Henrik Bengtsson
>  wrote:
> >
> > Note that in R-devel, we have that
> > (https://cran.r-project.org/doc/manuals/r-devel/NEWS.html):
> >
> > * news() gains support for ‘NEWS.md’ files.
> >
> > That is, news(package = pkg) not only finds NEWS.md (as before) but
> > also parses it (into sections etc.) analogously to how it parses
> > NEWS.Rd and NEWS.
> >
> > Because of this, I'd say a package should use only one of the NEWS,
> > NEWS.Rd, and NEWS.md files.
> >
> > Also, I believe CRAN has parsed NEWS.md files for quite a while now
> > and rendered them as HTML.  I think Bioconductor should do the same
> > thing (sounds like this is what Lluís argued for), especially with the
> > new NEWS.md support by news().
> >
> > /Henrik
> > On Tue, Sep 25, 2018 at 2:08 PM Laurent Gatto  wrote:
> > >
> > >
> > > Dear all,
> > >
> > > My experience (and things may have changed since I set this up) is that
> > > NEWS and NEWS.md serve different purposes despite a very similar
> > > syntax. The former is used by news() and displayed on the Bioconductor
> > > page (would NEWS.md be used if NEWS was absent?), while the one with
> the
> > > md extension displays nicely (including links) on github and in pkgdown
> > > sites.
> > >
> > > My solution is a Makefile recipe [1] (contributed by Sebastian Gibb)
> > > that converts NEWS.md into NEWS while updating the syntax and removing
> > > markdown links (typically to github issues, that are automatically
> > > expanded from #123 to a full URL via a github hook).
> > >
> > > NEWS: #' create plain text NEWS from NEWS.md if available
> > > test -f ${PKGDIR}/NEWS.md && sed '/^# .*$$/d; /^## .*$$/{s/^##
> //g; p; s/./-/g}; /^###\+/{s/./\u&/g}; s/^##\+ //g;
> 1,2{/^[[:space:]]*$$/d}; s/\[\(#[0-9]\+\)\]([^)]\+)/\1/g' ${PKGDIR}/NEWS.md
> > ${PKGDIR}/NEWS
> > >
> > > (where ${PKGDIR} is the package directory)
> > >
> > > Unsure whether this helps or adds further to the confusion.
> > >
> > > Best wishes,
> > >
> > > Laurent
> > >
> > > [1] https://github.com/ComputationalProteomicsUnit/maker
> > >
> > >
> > > On 25 September 2018 13:55, Shepherd, Lori wrote:
> > >
> > > > It can be used currently.  If you remove the .md extension but keep
> the format in should be recognized.  As described in the ?news help page
> > > >
> > > >
> > > >
> > > >  If 'package' is '"R"' (default), a news db is built with the
> news
> > > >  since the 3.0.0 release of R (corresponding to R's top-level
> > > >  'NEWS' file).  Otherwise, if the given add-on package can be
> found
> > > >  in the given libraries, it is attempted to read its news in
> > > >  structured form from files 'inst/NEWS.Rd', 'NEWS' or 'inst/NEWS'
> > > >  (in that order).
> > > >
> > > >
> > > >
> > > > Please also note your news file is formatted incorrectly.  from the
> ?news
> > > >
> > > >
> > > >  The plain text 'NEWS' files in add-on packages use a variety of
> > > >  different formats; the default news reader should be capable to
> > > >  extract individual news entries from a majority of packages from
> > > >  the standard repositories, which use (slight variations of) the
> > > >  following format:
> > > >
> > > > • Entries are grouped according to version, with version
> header
> > > >   "Changes in version" at the beginning of a line, followed
> by
> > > >   a version number, optionally followed by an ISO 8601 format
> > > >   date, possibly parenthesized.
> > > >
> > > > • Entries may be grouped 

Re: [Bioc-devel] Dependency to PEER

[Martin Morgan]

On 09/25/2018 07:07 PM, Christian Mertes wrote:

Hi,

thanks for the answers.

Since we only use 5 functions from the package within one function in our 
package, I hoped to get around it by masking this function in a special way.


not sure what that means; better not to be devious if that is what 
'special' means.


I think an appropriate thing to do would be to illustrate installation / 
evaluation functionality in a non-evaluated code chunk in the vignette. 
Your reviewer will be understanding.


Martin



The package is not dependent on PEER and works without it perfectly. Its just 
to make it easier for the user if he wants to use a different normalisation 
method.

Best,
Christian


On 25. Sep 2018, at 13:39, Robert Castelo  wrote:

hi,

it seems that the PEER repository hasn't been updated in the last 7 years and that 
the package is distributed under a GPL-2 license. if i'm interpreting this 
correctly, you could copy that code into your package redistributing it 
under the GPL-2 license and asking the users of PEER to cite the PEER paper when 
using it.

cheers,

robert.

On 25/09/2018 18:55, Kasper Daniel Hansen wrote:

It is a major weakness of PEER that it has not been submitted to a standard
repository. Of course, that is up to the PEER developers, but the community
should put pressure on them.

On Tue, Sep 25, 2018 at 12:40 PM Christian Mertes  wrote:


Hi all,

Im the developer of OUTRIDER. Our package normalises RNA-seq count data
and finds expression outliers within the population.
During the development we compared our approach against PCA and PEER. The
later one is a well established method to normalise RNA-seq data.

https://github.com/gagneurlab/OUTRIDER <
https://github.com/gagneurlab/OUTRIDER>
https://github.com/PMBio/peer 

For PEER, an R package exists on GitHub, but it is not in CRAN nor
Bioconductor, even it would fit really well with Bioconductor.

We would like to leave the user the option to switch between the different
normalisation methods within our package (auto encoder, peer, pca, sea, …).
But since the Bioconductor requirements are that all loaded libraries need
to be within CRAN or BioC, my question is how we should implement this.

Is there a best practice for this? Does we have to ask the developer of
PEER to push it on CRAN or do we get around this? Or can we flag one
function to be not checked by Bioconductor for dependencies and use
require(peer) within the function?

Thanks for any advices in advance!

Best,
Christian




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Re: [Bioc-devel] NEWS.md

[Shepherd, Lori]

As mentioned by Henrik,  The code referenced seems only implemented in R-devel 
currently.   Bioconductor will look at updating the code we use on our systems 
to match when our Bioconductor version is being built against R-devel  (after 
the October release) .


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Henrik Bengtsson 
Sent: Tuesday, September 25, 2018 7:01:36 PM
To: lg...@cam.ac.uk
Cc: Shepherd, Lori; lluis.revi...@gmail.com; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] NEWS.md

Forgot to mention that here's how news() select which file to parse if
there are several:

## Look for new-style inst/NEWS.Rd installed as NEWS.Rd
## If not found, look for NEWS.md.
## If not found, look at old-style
## NEWS inst/NEWS
## installed as NEWS (and ignore ChangeLog files).

Source: 
https://github.com/wch/r-source/blob/d20943d71407f9209cb6c7581ac0fce3b3517419/src/library/tools/R/news.R#L62-L66

/Henrik
On Tue, Sep 25, 2018 at 3:58 PM Henrik Bengtsson
 wrote:
>
> Note that in R-devel, we have that
> (https://cran.r-project.org/doc/manuals/r-devel/NEWS.html):
>
> * news() gains support for �NEWS.md� files.
>
> That is, news(package = pkg) not only finds NEWS.md (as before) but
> also parses it (into sections etc.) analogously to how it parses
> NEWS.Rd and NEWS.
>
> Because of this, I'd say a package should use only one of the NEWS,
> NEWS.Rd, and NEWS.md files.
>
> Also, I believe CRAN has parsed NEWS.md files for quite a while now
> and rendered them as HTML.  I think Bioconductor should do the same
> thing (sounds like this is what Llu�s argued for), especially with the
> new NEWS.md support by news().
>
> /Henrik
> On Tue, Sep 25, 2018 at 2:08 PM Laurent Gatto  wrote:
> >
> >
> > Dear all,
> >
> > My experience (and things may have changed since I set this up) is that
> > NEWS and NEWS.md serve different purposes despite a very similar
> > syntax. The former is used by news() and displayed on the Bioconductor
> > page (would NEWS.md be used if NEWS was absent?), while the one with the
> > md extension displays nicely (including links) on github and in pkgdown
> > sites.
> >
> > My solution is a Makefile recipe [1] (contributed by Sebastian Gibb)
> > that converts NEWS.md into NEWS while updating the syntax and removing
> > markdown links (typically to github issues, that are automatically
> > expanded from #123 to a full URL via a github hook).
> >
> > NEWS: #' create plain text NEWS from NEWS.md if available
> > test -f ${PKGDIR}/NEWS.md && sed '/^# .*$$/d; /^## .*$$/{s/^## //g; 
> > p; s/./-/g}; /^###\+/{s/./\u&/g}; s/^##\+ //g; 1,2{/^[[:space:]]*$$/d}; 
> > s/\[\(#[0-9]\+\)\]([^)]\+)/\1/g' ${PKGDIR}/NEWS.md > ${PKGDIR}/NEWS
> >
> > (where ${PKGDIR} is the package directory)
> >
> > Unsure whether this helps or adds further to the confusion.
> >
> > Best wishes,
> >
> > Laurent
> >
> > [1] https://github.com/ComputationalProteomicsUnit/maker
> >
> >
> > On 25 September 2018 13:55, Shepherd, Lori wrote:
> >
> > > It can be used currently.  If you remove the .md extension but keep the 
> > > format in should be recognized.  As described in the ?news help page
> > >
> > >
> > >
> > >  If 'package' is '"R"' (default), a news db is built with the news
> > >  since the 3.0.0 release of R (corresponding to R's top-level
> > >  'NEWS' file).  Otherwise, if the given add-on package can be found
> > >  in the given libraries, it is attempted to read its news in
> > >  structured form from files 'inst/NEWS.Rd', 'NEWS' or 'inst/NEWS'
> > >  (in that order).
> > >
> > >
> > >
> > > Please also note your news file is formatted incorrectly.  from the ?news
> > >
> > >
> > >  The plain text 'NEWS' files in add-on packages use a variety of
> > >  different formats; the default news reader should be capable to
> > >  extract individual news entries from a majority of packages from
> > >  the standard repositories, which use (slight variations of) the
> > >  following format:
> > >
> > > � Entries are grouped according to version, with version header
> > >   "Changes in version" at the beginning of a line, followed by
> > >   a version number, optionally followed by an ISO 8601 format
> > >   date, possibly parenthesized.
> > >
> > > � Entries may be grouped according to category, with a category
> > >   header (different from a version header) starting at the
> > >   beginning of a line.
> > >
> > > � Entries are written as itemize-type lists, using one of 'o',
> > >   '*', '-' or '+' as item tag.  Entries must be indented, and
> > >   ideally use a common indentation for the item texts.
> > >
> > >
> > >
> > >
> > > Please remove the pound sign (# ) from the header entry -  and use 
> > > "Changes in version"  not "BioCor"
> > >
> > >