Re: [Bioc-devel] Opinions on a meta-annotation package

[Kasper Daniel Hansen]

>From your description it very much sounds like creating a new package is
the way to go.

On Thu, Oct 24, 2019 at 3:03 PM Pages, Herve  wrote:

> Hi Panagiotis,
>
> Avoiding code repetition is always a good idea. An alternative to the
> creation of a 3rd package would be to have one of the 2 packages depend
> on the other. If that is not a good option (and there might be some
> valid reasons for that) then yes, factorizing out the repeated stuff and
> putting it in a 3rd package is a good option.
>
> Note that your subject line is confusing: You're asking opinions on a
> meta-annotation package but IIUC this is about the creation of a
> **software** package that would provide tools for building and/or
> querying a certain type of annotations right? I think of a
> meta-annotation package as a data package that would contain searchable
> meta data about existing biological annotations but that is not what we
> are talking about here is it?
>
> Also I wonder how much overlap there would be between this new package
> and packages like AnnotationDbi, AnnotationForge, GenomicFeatures,
> ensembldb which also provide functionalities for creating and querying
> annotations. For example AnnotationForge and AnnotationDbi are used to
> create and query the hundreds of "classic" *db packages.
>
> Best,
> H.
>
> On 10/20/19 19:56, Panagiotis Moulos wrote:
> > Dear developers,
> >
> > I maintain two packages (metaseqR, recoup) and about to submit an
> enhanced
> > (but different in many points, thus a new package) version of the 1st
> > (metaseqR2). During their course of development, maintenance and usage,
> > these packages have somehow come to use a common underlying annotation
> > system for the genomic regions they operate on, which of course makes use
> > of Bioconductor facilities and of course structures (GenomicRanges,
> > GenomicAlignments, BSgenome, GenomicFeatures etc.)
> >
> > This annotation system:
> > - Builds a local SQLite database
> > - Supports certain "custom" genomic features which are required for the
> > modeling made by these packages
> > - Is currently embedded to each package
> > - Has almost evolved to a package of its own with respect to independent
> > functionalities
> >
> > The reason for this mail/question is that I would like to ask your
> opinion
> > whether it is worthy to create a new package to host  the annotation
> > functions and detach from the other two. Some points to support this
> idea:
> >
> > 1. It's used in the same manner by two other packages, thus there is a
> lot
> > of code  repetition
> > 2. Users (including myself) often load one of these packages just to use
> it
> > to fetch genomic region annotations for other purposes outside the scope
> of
> > each package (metaseqR - RNA-Seq data analysis, recoup - NGS signal
> > visualization).
> > 3. It automatically constructs the required annotation regions to analyze
> > Lexogen Quant-Seq data (a protocol we are using a lot), a function which
> > may be useful to many others
> > 4. The database created can be expanded with custom user annotations
> using
> > a GTF file to create it (making use of makeTxDbFromGFF)
> > 5. Supports various annotation sources (Ensembl, UCSC, RefSeq, custom) in
> > one place
> > 6. Has a versioning system, allowing transparency and reproducibility
> when
> > required
> >
> > Some (maybe obvious) points against this idea:
> >
> > 1. Bioconductor has already a robust and rich genomic annotation system
> > which can be used and re-used as necessary
> > 2. Maybe there is no need for yet another annotation-related package
> > 3. There is possibly no wide acceptance for such a package, other than my
> > usage in the other two, and maybe a few more users that make use of the
> > annotation functionalities
> > 4. Does not follow standard Bioconductor guidelines for creating
> annotation
> > packages (on the other hand it's not an annotation package in the strict
> > sense, but more a meta-annotation package).
> >
> > Do you have any thoughts or opinions on the best way of action?
> >
> > Best regards,
> >
> > Panagiotis
> >
>
> --
> 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
>


-- 
Best,
Kasper

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Re: [Bioc-devel] Opinions on a meta-annotation package

[Pages, Herve]

Hi Panagiotis,

Avoiding code repetition is always a good idea. An alternative to the 
creation of a 3rd package would be to have one of the 2 packages depend 
on the other. If that is not a good option (and there might be some 
valid reasons for that) then yes, factorizing out the repeated stuff and 
putting it in a 3rd package is a good option.

Note that your subject line is confusing: You're asking opinions on a 
meta-annotation package but IIUC this is about the creation of a 
**software** package that would provide tools for building and/or 
querying a certain type of annotations right? I think of a 
meta-annotation package as a data package that would contain searchable 
meta data about existing biological annotations but that is not what we 
are talking about here is it?

Also I wonder how much overlap there would be between this new package 
and packages like AnnotationDbi, AnnotationForge, GenomicFeatures, 
ensembldb which also provide functionalities for creating and querying 
annotations. For example AnnotationForge and AnnotationDbi are used to 
create and query the hundreds of "classic" *db packages.

Best,
H.

On 10/20/19 19:56, Panagiotis Moulos wrote:
> Dear developers,
> 
> I maintain two packages (metaseqR, recoup) and about to submit an enhanced
> (but different in many points, thus a new package) version of the 1st
> (metaseqR2). During their course of development, maintenance and usage,
> these packages have somehow come to use a common underlying annotation
> system for the genomic regions they operate on, which of course makes use
> of Bioconductor facilities and of course structures (GenomicRanges,
> GenomicAlignments, BSgenome, GenomicFeatures etc.)
> 
> This annotation system:
> - Builds a local SQLite database
> - Supports certain "custom" genomic features which are required for the
> modeling made by these packages
> - Is currently embedded to each package
> - Has almost evolved to a package of its own with respect to independent
> functionalities
> 
> The reason for this mail/question is that I would like to ask your opinion
> whether it is worthy to create a new package to host  the annotation
> functions and detach from the other two. Some points to support this idea:
> 
> 1. It's used in the same manner by two other packages, thus there is a lot
> of code  repetition
> 2. Users (including myself) often load one of these packages just to use it
> to fetch genomic region annotations for other purposes outside the scope of
> each package (metaseqR - RNA-Seq data analysis, recoup - NGS signal
> visualization).
> 3. It automatically constructs the required annotation regions to analyze
> Lexogen Quant-Seq data (a protocol we are using a lot), a function which
> may be useful to many others
> 4. The database created can be expanded with custom user annotations using
> a GTF file to create it (making use of makeTxDbFromGFF)
> 5. Supports various annotation sources (Ensembl, UCSC, RefSeq, custom) in
> one place
> 6. Has a versioning system, allowing transparency and reproducibility when
> required
> 
> Some (maybe obvious) points against this idea:
> 
> 1. Bioconductor has already a robust and rich genomic annotation system
> which can be used and re-used as necessary
> 2. Maybe there is no need for yet another annotation-related package
> 3. There is possibly no wide acceptance for such a package, other than my
> usage in the other two, and maybe a few more users that make use of the
> annotation functionalities
> 4. Does not follow standard Bioconductor guidelines for creating annotation
> packages (on the other hand it's not an annotation package in the strict
> sense, but more a meta-annotation package).
> 
> Do you have any thoughts or opinions on the best way of action?
> 
> Best regards,
> 
> Panagiotis
> 

-- 
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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[Bioc-devel] Bioconductor 3.10 OrgDb and TxDb packages now available

[Interdonato, Kayla]

The new OrgDbs and TxDbs for the Bioconductor 3.10 release are now available.

The new OrgDbs are:

GO.db_3.10.0.tar.gz
org.Ag.eg.db_3.10.0.tar.gz
org.At.tair.db_3.10.0.tar.gz
org.Bt.eg.db_3.10.0.tar.gz
org.Ce.eg.db_3.10.0.tar.gz
org.Cf.eg.db_3.10.0.tar.gz
org.Dm.eg.db_3.10.0.tar.gz
org.Dr.eg.db_3.10.0.tar.gz
org.EcK12.eg.db_3.10.0.tar.gz
org.EcSakai.eg.db_3.10.0.tar.gz
org.Gg.eg.db_3.10.0.tar.gz
org.Hs.eg.db_3.10.0.tar.gz
org.Mm.eg.db_3.10.0.tar.gz
org.Mmu.eg.db_3.10.0.tar.gz
org.Pf.plasmo.db_3.10.0.tar.gz
org.Pt.eg.db_3.10.0.tar.gz
org.Rn.eg.db_3.10.0.tar.gz
org.Sc.sgd.db_3.10.0.tar.gz
org.Ss.eg.db_3.10.0.tar.gz
org.Xl.eg.db_3.10.0.tar.gz
PFAM.db_3.10.0.tar.gz

The new TxDbs are:

TxDb.Btaurus.UCSC.bosTau8.refGene_3.10.0.tar.gz
TxDb.Btaurus.UCSC.bosTau9.refGene_3.10.0.tar.gz
TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.10.0.tar.gz
TxDb.Ggallus.UCSC.galGal4.refGene_3.10.0.tar.gz
TxDb.Ggallus.UCSC.galGal5.refGene_3.10.0.tar.gz
TxDb.Ggallus.UCSC.galGal6.refGene_3.10.0.tar.gz
TxDb.Hsapiens.UCSC.hg38.knownGene_3.10.0.tar.gz
TxDb.Mmulatta.UCSC.rheMac3.refGene_3.10.0.tar.gz
TxDb.Mmulatta.UCSC.rheMac8.refGene_3.10.0.tar.gz
TxDb.Mmulatta.UCSC.rheMac10.refGene_3.10.0.tar.gz
TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0.tar.gz
TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.10.0.tar.gz
TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.10.0.tar.gz
TxDb.Ptroglodytes.UCSC.panTro6.refGene_3.10.0.tar.gz
TxDb.Rnorvegicus.UCSC.rn5.refGene_3.10.0.tar.gz
TxDb.Sscrofa.UCSC.susScr11.refGene_3.10.0.tar.gz
TxDb.Sscrofa.UCSC.susScr3.refGene_3.10.0.tar.gz


Kayla E. Interdonato, MS
Programmer/Analyst
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
(716)845-1300 x4621


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Re: [Bioc-devel] Updating package via git fails

[Spivakov, Mikhail]

Sorry have realised I cloned with https!

Many apologies.

Mikhail

From: "Spivakov, Mikhail" 
Date: Thursday, 24 October 2019 at 17:01
To: "bioc-devel@r-project.org" 
Subject: Updating package via git fails

Hello!

I’ve just made some changes to our Chicago package that help avoid some common 
errors our users have encountered due to mis-specified parameters.

I tried pushing the update to github (push origin master), but it fails with 
“fatal: remote error: FATAL: W any packages/Chicago nobody DENIED by fallthru”.

I have got the username set and the public key uploaded. Could you please 
advise if there is any other obvious reason why this could fail?

Thanks so much,
Mikhail


--
Mikhail Spivakov, PhD
Group Leader and Senior Lecturer (Assoc. Professor)
MRC London Institute of Medical Sciences
Imperial College Faculty of Medicine
Hammersmith Hospital Campus
London W12 0NN


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[Bioc-devel] Updating package via git fails

[Spivakov, Mikhail]

Hello!

I’ve just made some changes to our Chicago package that help avoid some common 
errors our users have encountered due to mis-specified parameters.

I tried pushing the update to github (push origin master), but it fails with 
“fatal: remote error: FATAL: W any packages/Chicago nobody DENIED by fallthru”.

I have got the username set and the public key uploaded. Could you please 
advise if there is any other obvious reason why this could fail?

Thanks so much,
Mikhail


--
Mikhail Spivakov, PhD
Group Leader and Senior Lecturer (Assoc. Professor)
MRC London Institute of Medical Sciences
Imperial College Faculty of Medicine
Hammersmith Hospital Campus
London W12 0NN


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Re: [Bioc-devel] ndexr fails on vignette build on windows

[Vincent Carey]

Thanks for this.  I will try with the upcoming curl from github

On Thu, Oct 24, 2019 at 7:21 AM Florian J. Auer <
florian.a...@informatik.uni-augsburg.de> wrote:

> Hi Vincent,
>
> For me the sollution was quite simple: I just put the protocol to the url,
> i.e. replaced www.ndexbio.org with http://www.ndexbio.org.
>
> I guess providing the protocol would be good practice anyways.
>
> In general, the issue was in curl, which should be fixed in the current
> devel release. For more information see also the curl issue:
>
> https://github.com/jeroen/curl/issues/209#issuecomment-542127937
>
> and the discussion in the httr issue:
>
> https://github.com/r-lib/httr/issues/619
>
> It seems, that this issue still exists in windows:
> *jeroen  *commented 8 days ago
>  •
> edited
>
> On Windows you have to wait for the next release of the r package
>
> https://github.com/jeroen/curl/issues/209#issuecomment-542758288
>
> Greetings
>
> Florian
> Am 23.10.19 um 21:23 schrieb Vincent Carey:
>
> May I ask what is the resolution here?  I have updated curl and httr on my
> windows box and continue
> to see errors unique to windows when requests lack the protocol in the URL.
>
> On Wed, Oct 23, 2019 at 7:28 AM Shepherd, Lori <
> lori.sheph...@roswellpark.org> wrote:
>
>> Thank you for the update.
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Comprehensive Cancer Center
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>>
>> 
>> From: Florian J. Auer 
>> Sent: Wednesday, October 23, 2019 7:25 AM
>> To: Shepherd, Lori 
>> ; bioc-devel@r-project.org <
>> bioc-devel@r-project.org>
>> Subject: Re: [Bioc-devel] ndexr fails on vignette build on windows
>>
>>
>> Hi Lori,
>>
>> Thanks a lot, that really helped!
>>
>> It seems, that the error is caused by httr, and curl in the end.
>>
>>
>> https://github.com/r-lib/httr/issues/619
>>
>>
>> Greetings
>>
>> Florian
>>
>>
>>
>> Am 09.10.19 um 17:37 schrieb Shepherd, Lori:
>> I did a little digging and here is what I've found...
>>
>>
>> I R CMD Stangle the vignette and then sourced the code:
>>
>>
>> > source("ndexr-vignette.R", echo=TRUE)
>>
>> > ## 
>> eval=FALSE-
>> > ## if (!requireNamespace("BiocManager", quietly=TRUE))
>> > ## instal  [TRUNCATED]
>>
>> > ## 
>> eval=FALSE-
>> > ## ## login to the NDEx server
>> > ## ndexcon = ndex_connect("username",  [TRUNCATED]
>> Error in if (is_http) { : argument is of length zero
>> > traceback()
>> 8: request_perform(req, hu$handle$handle)
>> 7: httr::GET(url = url, config = auth_param) at ndex_helper.r#149
>> 6: ndex_helper_httpResponseHandler(httr::GET(url = url, config =
>> auth_param),
>>log_txt, verbose) at ndex_connect.r#84
>> 5: ndex_connect() at ndexr-vignette.R#24
>> 4: eval(ei, envir)
>> 3: eval(ei, envir)
>> 2: withVisible(eval(ei, envir))
>> 1: source("ndexr-vignette.R", echo = TRUE)
>>
>>
>> If I then did a
>> debug(httr:::request_perform)
>>
>> httr:::request_fetch results in different output on windows than on
>> mac/linux
>>
>>
>>
>> #
>> # on linux and mac
>> #
>>
>> Browse[2]> resp
>> $url
>> [1] "HTTP://www.ndexbio.org/v2/admin/status"<
>> HTTP://www.ndexbio.org/v2/admin/status>
>>
>>
>> #
>> # on windows
>> #
>>
>> Browse[2]> resp
>> $url
>> [1] "www.ndexbio.org/v2/admin/status<
>> http://www.ndexbio.org/v2/admin/status>"
>>
>> This causes the eventual error.
>>
>>
>> You might try to come up with a small reproducible example and report as
>> a bug to httr.
>>
>>
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Comprehensive Cancer Center
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>>
>> 
>> From: Bioc-devel > bioc-devel-boun...@r-project.org> on behalf of Florian J. Auer <
>> florian.a...@informatik.uni-augsburg.de>> florian.a...@informatik.uni-augsburg.de>
>> Sent: Thursday, September 26, 2019 7:52 AM
>> To: bioc-devel@r-project.org <
>> bioc-devel@r-project.org>
>> Subject: [Bioc-devel] ndexr fails on vignette build on windows
>>
>> Hi everyone,
>>
>> my package ndexr produces some errors while building the vignette, but
>> only in the Windows build.
>>
>> In particular, the error message shows:
>>
>> Quitting from lines 76-78 (ndexr-vignette.Rmd)
>> Error: processing vignette 'ndexr-vignette.Rmd' failed with diagnostics:
>> argument is of length zero
>> --- failed re-building 'ndexr-vignette.Rmd'
>>
>> Seems like it's occurring in the following lines:
>>
>> ```{r, echo=FALSE, results='hide', message=FALSE}
>> ## login to the NDEx server
>> ndexcon = ndex_connect()
>> ```
>>
>> Is there 

Re: [Bioc-devel] ndexr fails on vignette build on windows

[Florian J. Auer]

Hi Vincent,

For me the sollution was quite simple: I just put the protocol to the
url, i.e. replaced www.ndexbio.org with http://www.ndexbio.org.

I guess providing the protocol would be good practice anyways.

In general, the issue was in curl, which should be fixed in the current
devel release. For more information see also the curl issue:

https://github.com/jeroen/curl/issues/209#issuecomment-542127937

and the discussion in the httr issue:

https://github.com/r-lib/httr/issues/619

It seems, that this issue still exists in windows:


  *jeroen  *commented 8 days ago
   • 
  edited 

On Windows you have to wait for the next release of the r package

https://github.com/jeroen/curl/issues/209#issuecomment-542758288

Greetings

Florian

Am 23.10.19 um 21:23 schrieb Vincent Carey:
> May I ask what is the resolution here?  I have updated curl and httr
> on my windows box and continue
> to see errors unique to windows when requests lack the protocol in the
> URL.
>
> On Wed, Oct 23, 2019 at 7:28 AM Shepherd, Lori
> mailto:lori.sheph...@roswellpark.org>>
> wrote:
>
> Thank you for the update.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Florian J. Auer  >
> Sent: Wednesday, October 23, 2019 7:25 AM
> To: Shepherd, Lori ;
> bioc-devel@r-project.org 
> mailto:bioc-devel@r-project.org>>
> Subject: Re: [Bioc-devel] ndexr fails on vignette build on windows
>
>
> Hi Lori,
>
> Thanks a lot, that really helped!
>
> It seems, that the error is caused by httr, and curl in the end.
>
>
> https://github.com/r-lib/httr/issues/619
>
>
> Greetings
>
> Florian
>
>
>
> Am 09.10.19 um 17:37 schrieb Shepherd, Lori:
> I did a little digging and here is what I've found...
>
>
> I R CMD Stangle the vignette and then sourced the code:
>
>
> > source("ndexr-vignette.R", echo=TRUE)
>
> > ## 
> eval=FALSE-
> > ## if (!requireNamespace("BiocManager", quietly=TRUE))
> > ##     instal  [TRUNCATED]
>
> > ## 
> eval=FALSE-
> > ## ## login to the NDEx server
> > ## ndexcon = ndex_connect("username",  [TRUNCATED]
> Error in if (is_http) { : argument is of length zero
> > traceback()
> 8: request_perform(req, hu$handle$handle)
> 7: httr::GET(url = url, config = auth_param) at ndex_helper.r#149
> 6: ndex_helper_httpResponseHandler(httr::GET(url = url, config =
> auth_param),
>        log_txt, verbose) at ndex_connect.r#84
> 5: ndex_connect() at ndexr-vignette.R#24
> 4: eval(ei, envir)
> 3: eval(ei, envir)
> 2: withVisible(eval(ei, envir))
> 1: source("ndexr-vignette.R", echo = TRUE)
>
>
> If I then did a
> debug(httr:::request_perform)
>
> httr:::request_fetch results in different output on windows than
> on mac/linux
>
>
>
> #
> # on linux and mac
> #
>
> Browse[2]> resp
> $url
> [1]
> 
> "HTTP://www.ndexbio.org/v2/admin/status"
>
>
> #
> # on windows
> #
>
> Browse[2]> resp
> $url
> [1] "www.ndexbio.org/v2/admin/status
> 
> "
>
> This causes the eventual error.
>
>
> You might try to come up with a small reproducible example and
> report as a bug to httr.
>
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Bioc-devel  
> > > on behalf of Florian J.
> Auer  
> > >
> Sent: Thursday, September 26, 2019 7:52 AM
> To: bioc-devel@r-project.org
>  >  > >
> Subject: [Bioc-devel] ndexr fails on vignette build on windows
>
> Hi everyone,
>
> my package ndexr produces some errors while building the vignette, but
> only in the Windows build.
>
> In particular, the error