Re: [Bioc-devel] Is there a way to change the name of R package that is already published on bioconductor?

[Marcin Kosiński]

Thanks,

I've changed it to
biocViews: Software, DataImport, DataRepresentation, Preprocessing

Cheers,

Marcin

2015-12-02 22:52 GMT+01:00 Hervé Pagès :

> Hi Marcin,
>
> BTW I noticed that RTCGA has no biocViews (only Software). Populating
> the biocViews field with appropriate and specific terms will make
> your packages show up in the corresponding views here
>
>   http://bioconductor.org/packages/release/BiocViews.html#___Software
>
> and thus will greatly improve the chances that the user in the need
> of functionalities like the ones you provide will discover your package.
>
> Cheers,
> H.
>
>
> On 11/22/2015 10:39 AM, Morgan, Martin wrote:
>
>> Marcin -- I join with Herve in strongly discouraging you from this
>> approach. Because you wish only to change upper versus lower case of your
>> package name, and because some operating systems ignore case, your package
>> will go through a release where it is not available under either upper- or
>> lower-case variant. This will confuse and alienate your users, even more
>> than changing the package name to something completely different. There are
>> a number of packages, including some of our own, where the name could have
>> been chosen more carefully, but we have learned to live with our changes of
>> mind. After all, you can still claim to be consistent with the naming
>> convention of the RTCGA.clinical and RTCGA.mutations package ;)
>>
>> I guess Dario was referring to
>>
>>library(AnnotationHub)
>>hub = AnnotationHub()
>>eset = query(hub, "GSE62944")[[1]]
>>
>> with
>>
>> eset
>>>
>> ExpressionSet (storageMode: lockedEnvironment)
>> assayData: 23368 features, 7706 samples
>>element names: exprs
>> protocolData: none
>> phenoData
>>sampleNames: TCGA-02-0047-01A-01R-1849-01
>>  TCGA-02-0055-01A-01R-1849-01 ... TCGA-ZG-A8QZ-01A-11R-A37L-07 (7706
>>  total)
>>varLabels: bcr_patient_barcode bcr_patient_uuid ... CancerType (421
>>  total)
>>varMetadata: labelDescription
>> featureData: none
>> experimentData: use 'experimentData(object)'
>> Annotation:
>>
>>> table(eset$CancerType)
>>>
>>
>> BLCA BRCA COAD  GBM HNSC KICH KIRC KIRP LAML  LGG LIHC LUAD LUSC   OV
>> PRAD READ
>>   273 1082  468  170  481   66  540  226  164  528  212  514  490  344
>> 423  164
>> SKCM STAD THCA UCEC
>>   373  146  506  536
>>
>>> print(object.size(eset), units="auto")
>>>
>> 264.5 Mb
>>
>>> ov = eset[, eset$CancerType == "OV"]   ## ovarian samples
>>>
>>
>> The data are Rsubread summarized counts from before the May update. In
>> the near term, we are actively expanding offerings derived from that GSE to
>> include the May update; this is in conjunction with efforts to develop an
>> 'ExperimentHub' analog of AnnotationHub, for more experiment-centric,
>> heavily curated resources.
>>
>> It is a little unclear whether the AnnotationHub and your data are
>> redundant or complementary, and whether they can be combined into a single
>> offering. One philosophical difference is the use of semantically rich and
>> integrated ExpressionSet versus basic data structures (data.frame, in your
>> case). We also differ in when we separate data into cancer types; we opted
>> for the entire data set because it is not impossibly large. And our data
>> are AnnotationHub-based rather than package-based. Obviously, avoiding
>> redundant access to the same data is beneficial. One possibility is to
>> collaboratively curate the data into AnnotationHub / ExperimentHub
>> resources, and to tailor access via packages that reference the resource
>> (e.g., one can retrieve the GRASP2 data base through AnnotationHub as
>> resource AH21414, or via grasp2db::GRASP2(); the latter comes with
>> documentation for manipulating the resource).
>>
>> It seems like there are similar opportunities for collaboration and
>> reduced redundancy between the RTCGA, RTCGAToolbox, and TCGAbiolinks
>> packages.
>>
>> Martin Morgan
>> Bioconductor
>>
>> 
>> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Marcin
>> Kosiński [m.p.kosin...@gmail.com]
>> Sent: Sunday, November 22, 2015 11:37 AM
>> To: Dario Strbenac
>> Cc: bioc-devel@r-project.org
>> Subject: Re: [Bioc-devel] Is there a way to change the name of R package
>> that is already published on bioconductor?
>>
>> Hi Herve,
>>
>> I think I would like to proceed with such technical possibility.
>> I'd like to keep consistency with the RTCGA.miRNASeq package that I am
>> uploading to bioconductor with issue 1335.
>> Can we schedule such operation?
>>
>> Best,
>> Marcin
>>
>>
>>
>> Hi Dario,
>>
>> Do you want to tell me that there is a possibility to load RNASeq datasets
>> for all available 38 cancer types/cohorts from the last release date
>> (21-08-2015) of datasets from The Cancer Genome Atlas with the use of
>> AnnotationHub?
>>
>> Is it as simple as:
>>
>> library(AnnotationHub)
>> BRCA.RNASeq -> x
>>
>> ?
>>
>> Best,
>> Marcin
>>
>> 2015-11-17 

Re: [Bioc-devel] Is there a way to change the name of R package that is already published on bioconductor?

[Hervé Pagès]

Hi Marcin,

BTW I noticed that RTCGA has no biocViews (only Software). Populating
the biocViews field with appropriate and specific terms will make
your packages show up in the corresponding views here

  http://bioconductor.org/packages/release/BiocViews.html#___Software

and thus will greatly improve the chances that the user in the need
of functionalities like the ones you provide will discover your package.

Cheers,
H.

On 11/22/2015 10:39 AM, Morgan, Martin wrote:

Marcin -- I join with Herve in strongly discouraging you from this approach. 
Because you wish only to change upper versus lower case of your package name, 
and because some operating systems ignore case, your package will go through a 
release where it is not available under either upper- or lower-case variant. 
This will confuse and alienate your users, even more than changing the package 
name to something completely different. There are a number of packages, 
including some of our own, where the name could have been chosen more 
carefully, but we have learned to live with our changes of mind. After all, you 
can still claim to be consistent with the naming convention of the 
RTCGA.clinical and RTCGA.mutations package ;)

I guess Dario was referring to

   library(AnnotationHub)
   hub = AnnotationHub()
   eset = query(hub, "GSE62944")[[1]]

with


eset

ExpressionSet (storageMode: lockedEnvironment)
assayData: 23368 features, 7706 samples
   element names: exprs
protocolData: none
phenoData
   sampleNames: TCGA-02-0047-01A-01R-1849-01
 TCGA-02-0055-01A-01R-1849-01 ... TCGA-ZG-A8QZ-01A-11R-A37L-07 (7706
 total)
   varLabels: bcr_patient_barcode bcr_patient_uuid ... CancerType (421
 total)
   varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation:

table(eset$CancerType)


BLCA BRCA COAD  GBM HNSC KICH KIRC KIRP LAML  LGG LIHC LUAD LUSC   OV PRAD READ
  273 1082  468  170  481   66  540  226  164  528  212  514  490  344  423  164
SKCM STAD THCA UCEC
  373  146  506  536

print(object.size(eset), units="auto")

264.5 Mb

ov = eset[, eset$CancerType == "OV"]   ## ovarian samples


The data are Rsubread summarized counts from before the May update. In the near 
term, we are actively expanding offerings derived from that GSE to include the 
May update; this is in conjunction with efforts to develop an 'ExperimentHub' 
analog of AnnotationHub, for more experiment-centric, heavily curated resources.

It is a little unclear whether the AnnotationHub and your data are redundant or 
complementary, and whether they can be combined into a single offering. One 
philosophical difference is the use of semantically rich and integrated 
ExpressionSet versus basic data structures (data.frame, in your case). We also 
differ in when we separate data into cancer types; we opted for the entire data 
set because it is not impossibly large. And our data are AnnotationHub-based 
rather than package-based. Obviously, avoiding redundant access to the same 
data is beneficial. One possibility is to collaboratively curate the data into 
AnnotationHub / ExperimentHub resources, and to tailor access via packages that 
reference the resource (e.g., one can retrieve the GRASP2 data base through 
AnnotationHub as resource AH21414, or via grasp2db::GRASP2(); the latter comes 
with documentation for manipulating the resource).

It seems like there are similar opportunities for collaboration and reduced 
redundancy between the RTCGA, RTCGAToolbox, and TCGAbiolinks packages.

Martin Morgan
Bioconductor


From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Marcin 
Kosiński [m.p.kosin...@gmail.com]
Sent: Sunday, November 22, 2015 11:37 AM
To: Dario Strbenac
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Is there a way to change the name of R package that 
is already published on bioconductor?

Hi Herve,

I think I would like to proceed with such technical possibility.
I'd like to keep consistency with the RTCGA.miRNASeq package that I am
uploading to bioconductor with issue 1335.
Can we schedule such operation?

Best,
Marcin



Hi Dario,

Do you want to tell me that there is a possibility to load RNASeq datasets
for all available 38 cancer types/cohorts from the last release date
(21-08-2015) of datasets from The Cancer Genome Atlas with the use of
AnnotationHub?

Is it as simple as:

library(AnnotationHub)
BRCA.RNASeq -> x

?

Best,
Marcin

2015-11-17 0:00 GMT+01:00 Dario Strbenac :


Hello,

How does your package differ to importing GSE62944 into R with
AnnotationHub
http://bioinformatics.oxfordjournals.org/content/31/22/3666.long ? It
seems like unnecessary duplication.

--
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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Re: [Bioc-devel] Is there a way to change the name of R package that is already published on bioconductor?

[Morgan, Martin]

Marcin -- I join with Herve in strongly discouraging you from this approach. 
Because you wish only to change upper versus lower case of your package name, 
and because some operating systems ignore case, your package will go through a 
release where it is not available under either upper- or lower-case variant. 
This will confuse and alienate your users, even more than changing the package 
name to something completely different. There are a number of packages, 
including some of our own, where the name could have been chosen more 
carefully, but we have learned to live with our changes of mind. After all, you 
can still claim to be consistent with the naming convention of the 
RTCGA.clinical and RTCGA.mutations package ;)

I guess Dario was referring to

  library(AnnotationHub)
  hub = AnnotationHub()
  eset = query(hub, "GSE62944")[[1]]

with

> eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 23368 features, 7706 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: TCGA-02-0047-01A-01R-1849-01
TCGA-02-0055-01A-01R-1849-01 ... TCGA-ZG-A8QZ-01A-11R-A37L-07 (7706
total)
  varLabels: bcr_patient_barcode bcr_patient_uuid ... CancerType (421
total)
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation:  
> table(eset$CancerType)

BLCA BRCA COAD  GBM HNSC KICH KIRC KIRP LAML  LGG LIHC LUAD LUSC   OV PRAD READ 
 273 1082  468  170  481   66  540  226  164  528  212  514  490  344  423  164 
SKCM STAD THCA UCEC 
 373  146  506  536 
> print(object.size(eset), units="auto")
264.5 Mb
> ov = eset[, eset$CancerType == "OV"]   ## ovarian samples

The data are Rsubread summarized counts from before the May update. In the near 
term, we are actively expanding offerings derived from that GSE to include the 
May update; this is in conjunction with efforts to develop an 'ExperimentHub' 
analog of AnnotationHub, for more experiment-centric, heavily curated resources.

It is a little unclear whether the AnnotationHub and your data are redundant or 
complementary, and whether they can be combined into a single offering. One 
philosophical difference is the use of semantically rich and integrated 
ExpressionSet versus basic data structures (data.frame, in your case). We also 
differ in when we separate data into cancer types; we opted for the entire data 
set because it is not impossibly large. And our data are AnnotationHub-based 
rather than package-based. Obviously, avoiding redundant access to the same 
data is beneficial. One possibility is to collaboratively curate the data into 
AnnotationHub / ExperimentHub resources, and to tailor access via packages that 
reference the resource (e.g., one can retrieve the GRASP2 data base through 
AnnotationHub as resource AH21414, or via grasp2db::GRASP2(); the latter comes 
with documentation for manipulating the resource).

It seems like there are similar opportunities for collaboration and reduced 
redundancy between the RTCGA, RTCGAToolbox, and TCGAbiolinks packages.

Martin Morgan
Bioconductor


From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Marcin 
Kosiński [m.p.kosin...@gmail.com]
Sent: Sunday, November 22, 2015 11:37 AM
To: Dario Strbenac
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Is there a way to change the name of R package that 
is already published on bioconductor?

Hi Herve,

I think I would like to proceed with such technical possibility.
I'd like to keep consistency with the RTCGA.miRNASeq package that I am
uploading to bioconductor with issue 1335.
Can we schedule such operation?

Best,
Marcin



Hi Dario,

Do you want to tell me that there is a possibility to load RNASeq datasets
for all available 38 cancer types/cohorts from the last release date
(21-08-2015) of datasets from The Cancer Genome Atlas with the use of
AnnotationHub?

Is it as simple as:

library(AnnotationHub)
BRCA.RNASeq -> x

?

Best,
Marcin

2015-11-17 0:00 GMT+01:00 Dario Strbenac :

> Hello,
>
> How does your package differ to importing GSE62944 into R with
> AnnotationHub
> http://bioinformatics.oxfordjournals.org/content/31/22/3666.long ? It
> seems like unnecessary duplication.
>
> --
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Is there a way to change the name of R package that is already published on bioconductor?

[Hervé Pagès]

Hi Marcin,

It's technically possible to change the name. In order to try to keep
this the less disruptive, we would only do this in devel and we would
need to create a new package there by cloning the current package and
changing its name. Then we would add a deprecation/redirection message
in the old package. If the renaming only involves changing case, it
might cause problems on Windows.

As you can see it's a quite bumpy road. Is it really worth all the
trouble?

Cheers,
H.

On 11/16/2015 08:47 AM, Marcin Kosiński wrote:

I have published `RTCGA.rnaseq` R package that provides datasets from TCGA
project containig RNA sequencing (gene's expressions). I am wondering if
there is a way to change this package name to be more proper like
`RTCGA.RNAseq` and if that's possible, how should I do that and to whom
should I write?

Cheers,

Marcin

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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] Is there a way to change the name of R package that is already published on bioconductor?

[Dario Strbenac]

Hello,

How does your package differ to importing GSE62944 into R with AnnotationHub 
http://bioinformatics.oxfordjournals.org/content/31/22/3666.long ? It seems 
like unnecessary duplication.

--
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel