[Bioc-devel] Error when index duplicate rows in SummarizedExperiment -- is this a bug?

[Elizabeth Purdom]

Hello,

I want to be able to index duplicate rows of an assay of a Summarized 
Experiment (think bootstrapping), something like this:

assay(se[c(1,1,2,2),])

However this gives me an error when the assay contains a data.frame, rather 
than a DataFrame

# > assay(se[c(1,1,2,2),]) #throws error
# Error in `.rowNamesDF<-`(x, value = value) :
#   duplicate 'row.names' are not allowed
# In addition: Warning message:
# non-unique values when setting 'row.names': ‘A1’, ‘A2’

Here’s a simple example:

test <- data.frame(matrix(rnorm(100),ncol=5))
row.names(test) <- paste0("A",1:nrow(test))
se<-SummarizedExperiment(test)

I can pull duplicate rows of the original data.frame:

test[c(1,1,2,2),] # works

I can also index duplicate rows of the SummarizedExperiment

se[c(1,1,2,2),] #works

But I can’t then call `assay` on that object with the duplicated rows:

assay(se[c(1,1,2,2),]) #throws error

# > assay(se[c(1,1,2,2),]) 
# Error in `.rowNamesDF<-`(x, value = value) :
#   duplicate 'row.names' are not allowed
# In addition: Warning message:
# non-unique values when setting 'row.names': ‘A1’, ‘A2’

Of course, I can do

assay(se)[c(1,1,2,2),]

because the underlying data.frame can be indexed that way, but then I am not 
indexing the corresponding `rowData`, which is my goal in indexing `se` 
directly, rather than the `assay`.

On the other hand, I don’t get this problem if the input object is a DataFrame 
or matrix:

se<-SummarizedExperiment(DataFrame(test))
assay(se[c(1,1,2,2),]) #now it works

se<-SummarizedExperiment(data.matrix(test))
assay(se[c(1,1,2,2),]) #now it works

This seems like a bug, but I thought I’d check here. It seems, at a minimum, 
unfortunate that you can call `se[c(1,1,2,2),]` but not 
`assay(se[c(1,1,2,2),])`, especially given that the underlying `data.frame` 
allows this call.

Thanks,
Elizabeth Purdom

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Re: [Bioc-devel] providerVersion error with BSgenome genomes

[Diego Diez]

I found that the providerVersion method has been deprecated (see
commit log below). Is there an official way to obtain that information
now? I could do unique(genome(dm3)) but not sure if this is the best
approach.

Diego

commit f99ceb5d17ca6dcf886600bf1fbf5d7c398de75c
Author: Hervé Pagès 
Date:   Fri Jun 26 18:49:17 2020 -0700

A couple of changes to GenomeDescription objects

- The GenomeDescription() constructor looses its 'provider_version'
  argument.
- The providerVersion() accessor is now deprecated.

On Sat, Jul 18, 2020 at 12:46 AM Diego Diez  wrote:
>
> To add more information, this is what I get for
> showMethods("providerVersion") using Bioc 3.11:
>
> >showMethods("providerVersion")
> Function: providerVersion (package GenomeInfoDb)
> x="BSgenome"
> (inherited from: x="GenomeDescription")
> x="GenomeDescription"
> x="GFFFile"
> x="SNPlocs"
> x="XtraSNPlocs"
>
> But with Bioc devel I get:
>
> showMethods("providerVersion")
> Function: providerVersion (package GenomeInfoDb)
> x="GenomeDescription"
> x="GFFFile"
> x="SNPlocs"
> x="XtraSNPlocs"
>
> So it seems providerVersion has lost the BSgenome method. Is this an
> intentional change or something that needs to be fixed?
>
> Thank you.
> Diego
>
> On Thu, Jul 16, 2020 at 2:38 PM Diego Diez  wrote:
> >
> > Dear all,
> >
> > I am finding an error when running the following code:
> >
> > > library(BSgenome.Dmelanogaster.UCSC.dm3)
> > Loading required package: BSgenome
> > Loading required package: GenomeInfoDb
> > Loading required package: GenomicRanges
> > Loading required package: rtracklayer
> >
> > > dm3 <- BSgenome.Dmelanogaster.UCSC.dm3
> > > providerVersion(dm3)
> > Error in (function (classes, fdef, mtable)  :
> >   unable to find an inherited method for function ‘providerVersion’
> > for signature ‘"BSgenome"’
> >
> > > BiocManager::version()
> > [1] ‘3.12’
> >
> >
> > I am expecting to get "dm3" with this genome. What would be the proper
> > way to do this?
> >
> > Thank you.
> >
> > Best,
> >
> > Diego

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Re: [Bioc-devel] providerVersion error with BSgenome genomes

[Diego Diez]

To add more information, this is what I get for
showMethods("providerVersion") using Bioc 3.11:

>showMethods("providerVersion")
Function: providerVersion (package GenomeInfoDb)
x="BSgenome"
(inherited from: x="GenomeDescription")
x="GenomeDescription"
x="GFFFile"
x="SNPlocs"
x="XtraSNPlocs"

But with Bioc devel I get:

showMethods("providerVersion")
Function: providerVersion (package GenomeInfoDb)
x="GenomeDescription"
x="GFFFile"
x="SNPlocs"
x="XtraSNPlocs"

So it seems providerVersion has lost the BSgenome method. Is this an
intentional change or something that needs to be fixed?

Thank you.
Diego

On Thu, Jul 16, 2020 at 2:38 PM Diego Diez  wrote:
>
> Dear all,
>
> I am finding an error when running the following code:
>
> > library(BSgenome.Dmelanogaster.UCSC.dm3)
> Loading required package: BSgenome
> Loading required package: GenomeInfoDb
> Loading required package: GenomicRanges
> Loading required package: rtracklayer
>
> > dm3 <- BSgenome.Dmelanogaster.UCSC.dm3
> > providerVersion(dm3)
> Error in (function (classes, fdef, mtable)  :
>   unable to find an inherited method for function ‘providerVersion’
> for signature ‘"BSgenome"’
>
> > BiocManager::version()
> [1] ‘3.12’
>
>
> I am expecting to get "dm3" with this genome. What would be the proper
> way to do this?
>
> Thank you.
>
> Best,
>
> Diego

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Re: [Bioc-devel] No access to dorothea package

[Nitesh Turaga]

Hi Christian 

Can you try to upload a new SSH key to your BiocCredentials account? 

It is likely that the SSH private key you are using doesn’t “match” the public 
key we have on record for your account. The easiest way to solve this, you 
upload a new key to BiocCredentials and try again.

Also, when you are sending an email like this, we encourage 
http://bioconductor.org/developers/how-to/git/faq/ 
 #14. It’ll be useful for 
us to help you better if you copy those commands and their results in the email.

If you still have an issue please let me know. 


Nitesh

> On Jul 17, 2020, at 5:05 AM, Christian Holland  wrote:
> 
> Dear Bioc Team,
> 
> I am the maintainer of the dorothea package. 
> 
> This package has been release with 3.11 and now its the first time that I 
> have to update the package. For some reasons I don’t have access anymore. 
> 
> Executing "ssh -T g...@git.bioconductor.org 
> " yields in "g...@git.bioconductor.org: 
> Permission denied (publickey).”. However, the BiocCredentials app states that 
> I am supposed to have access to the dorothea package.
> 
> The ssh key deposit in the app is identical to the key of my GitHub profile.
> 
> I would be grateful for any advice how to get access back.
> 
> Thanks,
> Christian
> 
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] New version in tscR doesn't trigger new build

[Shepherd, Lori]

Please read the top of this page for timing.  It can take up to 36-48 hours to 
appear on the build report depending on when you pushed your changes
http://bioconductor.org/developers/how-to/troubleshoot-build-report/

Based on the information you provided I would expect to see the changes on 
today's report that post approximately 1300 EST

Cheers


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 Fernando P�rez 
Sanz 
Sent: Friday, July 17, 2020 2:09 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] New version in tscR doesn't trigger new build

Hello, bioconductor,

Yesterday around 9.00 am,  I made changes in tscR package to fix a
dependency bug  with another package.

I made :

 >git push upstream RELEASE_3_11
 >git push origin RELEASE_3_11

having changed the version in DESCRIPTION from 1.0.0 to 1.0.1, but it
doesn't seem to have triggered the new build check,
because last build report show check version 1.0.0.

If you clone repository

 >git clone g...@git.bioconductor.org:packages/tscR

the version in master branch is 1.1.1 and in RELEASE_3_11 branch, is 1.0.1.

Can someone help me, please?

Regards

Fenando

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[Bioc-devel] No access to dorothea package

[Christian Holland]

Dear Bioc Team,

I am the maintainer of the dorothea package. 

This package has been release with 3.11 and now its the first time that I have 
to update the package. For some reasons I don’t have access anymore. 

Executing "ssh -T g...@git.bioconductor.org " 
yields in "g...@git.bioconductor.org: Permission denied (publickey).”. However, 
the BiocCredentials app states that I am supposed to have access to the 
dorothea package.

The ssh key deposit in the app is identical to the key of my GitHub profile.

I would be grateful for any advice how to get access back.

Thanks,
Christian


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