date:20200707

[Bioc-devel] Bioconductor Developers Forum - Thursday 16th July

2020-07-07 Thread Mike Smith

Dear all,

The next Bioconductor Developers' Forum is scheduled for Thursday 16th July
at 09:00 PDT/ 12:00 EDT / 18:00 CEST
Calendar invite available from https://bit.ly/3gCsFXO

We will be using BlueJeans and the meeting can be joined via:
https://bluejeans.com/114067881 (Meeting ID: 114 067 881)

This month we'll be focusing on continuous integration with Github Actions
and how we can use this relatively new platform for a wide variety of
development tasks, including cross-platform testing of code and website
deployment.

Remember you can join the discussion any time in #developers-forum on
Bioconductor Slack (https://bioc-community.herokuapp.com/).

Best wishes,

Mike

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Re: [Bioc-devel] Unable to replicate Windows build error on new package.

2020-07-07 Thread Shepherd, Lori

Your reviewer should be aware to ignore the error and will review your package 
shortly.

Cheers


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Erik Christensen 
Sent: Tuesday, July 7, 2020 3:10 PM
To: Shepherd, Lori ; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] Unable to replicate Windows build error on new 
package.

Thanks,

Do I need to bump the version or do anything to trigger a rebuild or just wait 
for review now?


--

Erik Christensen mailto:echr...@uwo.ca>>

-Original Message-
From: "Shepherd, Lori" 
mailto:%22Shepherd,%20lori%22%20%3clori.sheph...@roswellpark.org%3e>>
To: Erik Christensen 
mailto:erik%20christensen%20%3cechr...@uwo.ca%3e>>, 
bioc-devel@r-project.org 
mailto:%22bioc-de...@r-project.org%22%20%3cbioc-de...@r-project.org%3e>>
Subject: Re: [Bioc-devel] Unable to replicate Windows build error on new 
package.
Date: Mon, 06 Jul 2020 11:56:49 +

Please ignore the build bin ERROR.  I think this is an issue on the 
Bioconductor build system rather than directly related to your package.


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 Erik 
Christensen 
Sent: Friday, July 3, 2020 4:39 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Unable to replicate Windows build error on new package.

Hi,

I'm working on a new R package 
(https://secure-web.cisco.com/1HFmLtrnT-HzI71X6sTuc9lAzhWM5lqF6PVrvPG22uGJQ6qshZL6PR6Me8GyEEZ2jjOcVzxmleHFajMBY7Bsfbi9WOEra50LcQj-wHINOt3_vsxO5Jak5M-WWZOZPSKD1yLCGYgI8tAUMBUN4gTuhZ2XHAhvzhqMAZ-aLyL_Yktw-mtQPnMhh_P1V2x1vytIErFrJfUhS0pchwLBiWBzXjFSQHsBKtyULnKTpmLadc_-6INJ9cs9f7TCsDGjlEsfxalQxXoMgPVVqe0mcIqP2n3_a12ssip5U57a9QXImssNUY3LUAQb3xMOybkkNQqN_PRtKBu8Kl02VXmYAUucRBA/https%3A%2F%2Fgithub.com%2Fshooshtarilab%2FTMExplorer)
 and don't quite understand the build error I'm getting. I'm able to build the 
binary package without problems on my Windows install (I'm primarily a Linux 
dev) but the Bioconductor build system fails.

Here is a link to the build report: 
http://secure-web.cisco.com/1wu17svsUuFvP8L1S81mY0Gcj-x0keg5i7w30tL03XB1VhAvG334oGtc4DefhDqvqCFxS9MWXaVtJnuGNqYOmqTayhjkWmwH7ZY8rb8Z_rl8n8i9KWL6U2oTMYPjwNKESb-sgZoQ2waoUvFrAIx4zp_3Jqa9Rbrwqg_fzpwTkZSfV2yn9MQThig1wkKXYiAcvlDw34RyYjBDKt8XrIW0CmmpBSxindCwBJIlrD9nbOSciI_Lkb5rIrzU7II4muU1vEY5hGgufnH8euwo9VB0rqsgrXHP2NLbbxoAP5U9AHG-_5PFz7tdqm5kayxJ4nPf6BNm-j8dey4tl2JM4Q8QXYWhMnPZuHRZhaP1Vz8CqbqQ/http%3A%2F%2Fbioconductor.org%2Fspb_reports%2FTMExplorer_buildreport_20200703160041.html%23tokay1_buildbin_anchor

How should I interpret this error so I can fix the package?

--

Erik Christensen 
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Re: [Bioc-devel] Unable to replicate Windows build error on new package.

2020-07-07 Thread Erik Christensen

Thanks, 
Do I need to bump the version or do anything to trigger a rebuild or just wait 
for review now?

-Original Message-From: "Shepherd, Lori" 
To: Erik Christensen , 
bioc-devel@r-project.org Subject: Re: [Bioc-devel] 
Unable to replicate Windows build error on new package.Date: Mon, 06 Jul 2020 
11:56:49 +


 P {margin-top:0;margin-bottom:0;} 



Please ignore the build bin ERROR.  I think this is an issue on the 
Bioconductor build system rather than directly related to your package.  









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 Erik 
Christensen 

Sent: Friday, July 3, 2020 4:39 PM

To: bioc-devel@r-project.org 

Subject: [Bioc-devel] Unable to replicate Windows build error on new package.
 


Hi,



I'm working on a new R package 
(https://secure-web.cisco.com/1HFmLtrnT-HzI71X6sTuc9lAzhWM5lqF6PVrvPG22uGJQ6qshZL6PR6Me8GyEEZ2jjOcVzxmleHFajMBY7Bsfbi9WOEra50LcQj-wHINOt3_vsxO5Jak5M-WWZOZPSKD1yLCGYgI8tAUMBUN4gTuhZ2XHAhvzhqMAZ-aLyL_Yktw-mtQPnMhh_P1V2x1vytIErFrJfUhS0pchwLBiWBzXjFSQHsBKtyULnKTpmLadc_-6INJ9cs9f7TCsDGjlEsfxalQxXoMgPVVqe0mcIqP2n3_a12ssip5U57a9QXImssNUY3LUAQb3xMOybkkNQqN_PRtKBu8Kl02VXmYAUucRBA/https%3A%2F%2Fgithub.com%2Fshooshtarilab%2FTMExplorer)
 and don't quite understand the build error I'm getting. I'm able to build the 
binary package without problems on my Windows install (I'm primarily a Linux 
dev) but the Bioconductor build system fails.



Here is a link to the build report: 
http://secure-web.cisco.com/1wu17svsUuFvP8L1S81mY0Gcj-x0keg5i7w30tL03XB1VhAvG334oGtc4DefhDqvqCFxS9MWXaVtJnuGNqYOmqTayhjkWmwH7ZY8rb8Z_rl8n8i9KWL6U2oTMYPjwNKESb-sgZoQ2waoUvFrAIx4zp_3Jqa9Rbrwqg_fzpwTkZSfV2yn9MQThig1wkKXYiAcvlDw34RyYjBDKt8XrIW0CmmpBSxindCwBJIlrD9nbOSciI_Lkb5rIrzU7II4muU1vEY5hGgufnH8euwo9VB0rqsgrXHP2NLbbxoAP5U9AHG-_5PFz7tdqm5kayxJ4nPf6BNm-j8dey4tl2JM4Q8QXYWhMnPZuHRZhaP1Vz8CqbqQ/http%3A%2F%2Fbioconductor.org%2Fspb_reports%2FTMExplorer_buildreport_20200703160041.html%23tokay1_buildbin_anchor



How should I interpret this error so I can fix the package?



--



Erik Christensen 

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Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

2020-07-07 Thread Bhagwat, Aditya

Fantastic - thankyou Herve!

Aditya

From: Hervé Pagès [hpa...@fredhutch.org]
Sent: Tuesday, July 07, 2020 11:55 AM
To: Bhagwat, Aditya; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in 
bioc-devel?

On 7/7/20 02:50, Hervé Pagès wrote:
>
>
> On 7/7/20 02:46, Bhagwat, Aditya wrote:
>> Thankyou Herve!
>>
>> I guess that means that I can pull the fix in a day or two, is that
>> right?
>
> Yes, as soon as BSgenome 1.57.4 propagates, which should take between
> 24h and 48h.

To be clear: BSgenome 1.57.4 will become available for installation with
BiocManager::install("BSgenome") only in a couple of days but you can
get it now by installing directly from GitHub with
BiocManager::install("Bioconductor/BSgenome").

H.

>
> H.
>
>>
>> Aditya
>> 
>> From: Hervé Pagès [hpa...@fredhutch.org]
>> Sent: Tuesday, July 07, 2020 11:45 AM
>> To: Bhagwat, Aditya; bioc-devel@r-project.org
>> Subject: Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in
>> bioc-devel?
>>
>> Hi Aditya,
>>
>> This change was not intended, sorry. Should be fixed in BSgenome 1.57.4.
>>
>> Cheers,
>> H.
>>
>> On 7/7/20 01:53, Bhagwat, Aditya wrote:
>>> Sorry, my earlier email had a copy/paste error - corrected now
>>> 
>>> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of
>>> Bhagwat, Aditya [aditya.bhag...@mpi-bn.mpg.de]
>>> Sent: Tuesday, July 07, 2020 10:50 AM
>>> To: bioc-devel@r-project.org
>>> Subject: Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in
>>> bioc-devel?
>>>
>>> It's the BSgenome to GenomeDescription coercer that seems to be
>>> missing - is this on purpose?
>>>
>>> # bsgenomeName(BSgenomeObj) FAILS
>>> #---
>>> bsname <- GenomeInfoDb::bsgenomeName(bsgenome)
>>> index_genome(bsgenome, indexedgenomesdir = tempdir())
>>> Error in h(simpleError(msg, call)) :
>>> unable to find an inherited method for function 'bsgenomeName'
>>> for signature '"BSgenome"
>>>
>>> # as(bsgenome, 'GenomeDescription') also FAILS
>>> #
>>> bsname <- GenomeInfoDb::bsgenomeName(as(bsgenome,
>>> 'GenomeDescription')) # ALSO FAILS
>>> index_genome(bsgenome, indexedgenomesdir = tempdir())
>>> Error in h(simpleError(msg, call)) :
>>> error in evaluating the argument 'x' in selecting a method for
>>> function 'bsgenomeName': no method or default for coercing "BSgenome"
>>> to "GenomeDescription"
>>>
>>> Aditya
>>>
>>> 
>>> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of
>>> Bhagwat, Aditya [aditya.bhag...@mpi-bn.mpg.de]
>>> Sent: Tuesday, July 07, 2020 10:22 AM
>>> To: bioc-devel@r-project.org
>>> Subject: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in
>>> bioc-devel?
>>>
>>> Dear bioc-devel,
>>>
>>> multicrispr is having an error on the bioc-devel build
>>> machines>> >, caused by:
>>>
>>> unable to find an inherited method for function 'bsgenomeName' for
>>> signature '"BSgenome"
>>>
>>> This is a bit strange, because normally a BSgenome object gets
>>> automatically converted to a GenomeDescription object before being
>>> sent to the method bsgenomeName. In bioc-devel, for some reason this
>>> mechanism seems to be broken. Is it on purpose? What would be the
>>> best fix/patch?
>>>
>>> Right now, I'm checking whether explicitation fixes things:
>>> bsname <-
>>> GenomeInfoDb::bsgenomeName(bsgenome)
>>> # FAILS
>>> bsname <- GenomeInfoDb::bsgenomeName(as(bsgenome,
>>> 'GenomeDescription')) # WORKS ? (VERIFYING)
>>>
>>> Thank you for feedback :-)
>>>
>>> Aditya
>>>
>>>   [[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=DwIFAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=_1eFc4UGidLaNS3zXQqjaaIUIU5zu68VT0g6PN0b24E=aAOK1NFWIMal4FrsocE13hvo95BTk3RL18eVMCncRzk=
>>>
>>>
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>>>
>>>
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>>> Bioc-devel@r-project.org mailing list
>>>

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

2020-07-07 Thread Hervé Pagès


On 7/7/20 02:50, Hervé Pagès wrote:



On 7/7/20 02:46, Bhagwat, Aditya wrote:

Thankyou Herve!

I guess that means that I can pull the fix in a day or two, is that 
right?


Yes, as soon as BSgenome 1.57.4 propagates, which should take between 
24h and 48h.


To be clear: BSgenome 1.57.4 will become available for installation with 
BiocManager::install("BSgenome") only in a couple of days but you can 
get it now by installing directly from GitHub with 
BiocManager::install("Bioconductor/BSgenome").


H.



H.



Aditya

From: Hervé Pagès [hpa...@fredhutch.org]
Sent: Tuesday, July 07, 2020 11:45 AM
To: Bhagwat, Aditya; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in 
bioc-devel?


Hi Aditya,

This change was not intended, sorry. Should be fixed in BSgenome 1.57.4.

Cheers,
H.

On 7/7/20 01:53, Bhagwat, Aditya wrote:

Sorry, my earlier email had a copy/paste error - corrected now

From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of 
Bhagwat, Aditya [aditya.bhag...@mpi-bn.mpg.de]

Sent: Tuesday, July 07, 2020 10:50 AM
To: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in 
bioc-devel?


It's the BSgenome to GenomeDescription coercer that seems to be 
missing - is this on purpose?


# bsgenomeName(BSgenomeObj) FAILS
#---
bsname <- GenomeInfoDb::bsgenomeName(bsgenome)
index_genome(bsgenome, indexedgenomesdir = tempdir())
Error in h(simpleError(msg, call)) :
    unable to find an inherited method for function 'bsgenomeName' 
for signature '"BSgenome"


# as(bsgenome, 'GenomeDescription') also FAILS
#
bsname <- GenomeInfoDb::bsgenomeName(as(bsgenome, 
'GenomeDescription')) # ALSO FAILS

index_genome(bsgenome, indexedgenomesdir = tempdir())
Error in h(simpleError(msg, call)) :
    error in evaluating the argument 'x' in selecting a method for 
function 'bsgenomeName': no method or default for coercing "BSgenome" 
to "GenomeDescription"


Aditya


From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of 
Bhagwat, Aditya [aditya.bhag...@mpi-bn.mpg.de]

Sent: Tuesday, July 07, 2020 10:22 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in 
bioc-devel?


Dear bioc-devel,

multicrispr is having an error on the bioc-devel build 
machines, caused by:


unable to find an inherited method for function 'bsgenomeName' for 
signature '"BSgenome"


This is a bit strange, because normally a BSgenome object gets 
automatically converted to a GenomeDescription object before being 
sent to the method bsgenomeName. In bioc-devel, for some reason this 
mechanism seems to be broken. Is it on purpose? What would be the 
best fix/patch?


Right now, I'm checking whether explicitation fixes things:
bsname <- 
GenomeInfoDb::bsgenomeName(bsgenome) 
# FAILS
bsname <- GenomeInfoDb::bsgenomeName(as(bsgenome, 
'GenomeDescription')) # WORKS ? (VERIFYING)


Thank you for feedback :-)

Aditya

  [[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
Seattle, WA 98109-1024

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





--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

2020-07-07 Thread Hervé Pagès





On 7/7/20 02:46, Bhagwat, Aditya wrote:

Thankyou Herve!

I guess that means that I can pull the fix in a day or two, is that right?


Yes, as soon as BSgenome 1.57.4 propagates, which should take between 
24h and 48h.


H.



Aditya

From: Hervé Pagès [hpa...@fredhutch.org]
Sent: Tuesday, July 07, 2020 11:45 AM
To: Bhagwat, Aditya; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in 
bioc-devel?

Hi Aditya,

This change was not intended, sorry. Should be fixed in BSgenome 1.57.4.

Cheers,
H.

On 7/7/20 01:53, Bhagwat, Aditya wrote:

Sorry, my earlier email had a copy/paste error - corrected now

From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, 
Aditya [aditya.bhag...@mpi-bn.mpg.de]
Sent: Tuesday, July 07, 2020 10:50 AM
To: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in 
bioc-devel?

It's the BSgenome to GenomeDescription coercer that seems to be missing - is 
this on purpose?

# bsgenomeName(BSgenomeObj) FAILS
#---
bsname <- GenomeInfoDb::bsgenomeName(bsgenome)
index_genome(bsgenome, indexedgenomesdir = tempdir())
Error in h(simpleError(msg, call)) :
unable to find an inherited method for function 'bsgenomeName' for signature 
'"BSgenome"

# as(bsgenome, 'GenomeDescription') also FAILS
#
bsname <- GenomeInfoDb::bsgenomeName(as(bsgenome, 'GenomeDescription')) # ALSO 
FAILS
index_genome(bsgenome, indexedgenomesdir = tempdir())
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'bsgenomeName': no 
method or default for coercing "BSgenome" to "GenomeDescription"

Aditya


From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, 
Aditya [aditya.bhag...@mpi-bn.mpg.de]
Sent: Tuesday, July 07, 2020 10:22 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Dear bioc-devel,

multicrispr is having an error on the bioc-devel build 
machines, caused by:

unable to find an inherited method for function 'bsgenomeName' for signature 
'"BSgenome"

This is a bit strange, because normally a BSgenome object gets automatically 
converted to a GenomeDescription object before being sent to the method 
bsgenomeName. In bioc-devel, for some reason this mechanism seems to be broken. 
Is it on purpose? What would be the best fix/patch?

Right now, I'm checking whether explicitation fixes things:
bsname <- GenomeInfoDb::bsgenomeName(bsgenome)  
   # FAILS
bsname <- GenomeInfoDb::bsgenomeName(as(bsgenome, 'GenomeDescription')) # WORKS 
? (VERIFYING)

Thank you for feedback :-)

Aditya

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



--
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] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

2020-07-07 Thread Bhagwat, Aditya

Thankyou Herve!

I guess that means that I can pull the fix in a day or two, is that right?

Aditya

From: Hervé Pagès [hpa...@fredhutch.org]
Sent: Tuesday, July 07, 2020 11:45 AM
To: Bhagwat, Aditya; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in 
bioc-devel?

Hi Aditya,

This change was not intended, sorry. Should be fixed in BSgenome 1.57.4.

Cheers,
H.

On 7/7/20 01:53, Bhagwat, Aditya wrote:
> Sorry, my earlier email had a copy/paste error - corrected now
> 
> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, 
> Aditya [aditya.bhag...@mpi-bn.mpg.de]
> Sent: Tuesday, July 07, 2020 10:50 AM
> To: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in 
> bioc-devel?
>
> It's the BSgenome to GenomeDescription coercer that seems to be missing - is 
> this on purpose?
>
> # bsgenomeName(BSgenomeObj) FAILS
> #---
> bsname <- GenomeInfoDb::bsgenomeName(bsgenome)
> index_genome(bsgenome, indexedgenomesdir = tempdir())
> Error in h(simpleError(msg, call)) :
>unable to find an inherited method for function 'bsgenomeName' for 
> signature '"BSgenome"
>
> # as(bsgenome, 'GenomeDescription') also FAILS
> #
> bsname <- GenomeInfoDb::bsgenomeName(as(bsgenome, 'GenomeDescription')) # 
> ALSO FAILS
> index_genome(bsgenome, indexedgenomesdir = tempdir())
> Error in h(simpleError(msg, call)) :
>error in evaluating the argument 'x' in selecting a method for function 
> 'bsgenomeName': no method or default for coercing "BSgenome" to 
> "GenomeDescription"
>
> Aditya
>
> 
> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, 
> Aditya [aditya.bhag...@mpi-bn.mpg.de]
> Sent: Tuesday, July 07, 2020 10:22 AM
> To: bioc-devel@r-project.org
> Subject: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?
>
> Dear bioc-devel,
>
> multicrispr is having an error on the bioc-devel build 
> machines  >, caused by:
>
> unable to find an inherited method for function 'bsgenomeName' for signature 
> '"BSgenome"
>
> This is a bit strange, because normally a BSgenome object gets automatically 
> converted to a GenomeDescription object before being sent to the method 
> bsgenomeName. In bioc-devel, for some reason this mechanism seems to be 
> broken. Is it on purpose? What would be the best fix/patch?
>
> Right now, I'm checking whether explicitation fixes things:
> bsname <- GenomeInfoDb::bsgenomeName(bsgenome)
>  # FAILS
> bsname <- GenomeInfoDb::bsgenomeName(as(bsgenome, 'GenomeDescription')) # 
> WORKS ? (VERIFYING)
>
> Thank you for feedback :-)
>
> Aditya
>
>  [[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
Seattle, WA 98109-1024

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

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Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

2020-07-07 Thread Hervé Pagès


Hi Aditya,

This change was not intended, sorry. Should be fixed in BSgenome 1.57.4.

Cheers,
H.

On 7/7/20 01:53, Bhagwat, Aditya wrote:

Sorry, my earlier email had a copy/paste error - corrected now

From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, 
Aditya [aditya.bhag...@mpi-bn.mpg.de]
Sent: Tuesday, July 07, 2020 10:50 AM
To: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in 
bioc-devel?

It's the BSgenome to GenomeDescription coercer that seems to be missing - is 
this on purpose?

# bsgenomeName(BSgenomeObj) FAILS
#---
bsname <- GenomeInfoDb::bsgenomeName(bsgenome)
index_genome(bsgenome, indexedgenomesdir = tempdir())
Error in h(simpleError(msg, call)) :
   unable to find an inherited method for function 'bsgenomeName' for signature 
'"BSgenome"

# as(bsgenome, 'GenomeDescription') also FAILS
#
bsname <- GenomeInfoDb::bsgenomeName(as(bsgenome, 'GenomeDescription')) # ALSO 
FAILS
index_genome(bsgenome, indexedgenomesdir = tempdir())
Error in h(simpleError(msg, call)) :
   error in evaluating the argument 'x' in selecting a method for function 'bsgenomeName': no 
method or default for coercing "BSgenome" to "GenomeDescription"

Aditya


From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, 
Aditya [aditya.bhag...@mpi-bn.mpg.de]
Sent: Tuesday, July 07, 2020 10:22 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Dear bioc-devel,

multicrispr is having an error on the bioc-devel build 
machines, caused by:

unable to find an inherited method for function 'bsgenomeName' for signature 
'"BSgenome"

This is a bit strange, because normally a BSgenome object gets automatically 
converted to a GenomeDescription object before being sent to the method 
bsgenomeName. In bioc-devel, for some reason this mechanism seems to be broken. 
Is it on purpose? What would be the best fix/patch?

Right now, I'm checking whether explicitation fixes things:
bsname <- GenomeInfoDb::bsgenomeName(bsgenome)  
   # FAILS
bsname <- GenomeInfoDb::bsgenomeName(as(bsgenome, 'GenomeDescription')) # WORKS 
? (VERIFYING)

Thank you for feedback :-)

Aditya

 [[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
Seattle, WA 98109-1024

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

___
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Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

2020-07-07 Thread Bhagwat, Aditya

Sorry, my earlier email had a copy/paste error - corrected now

From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, 
Aditya [aditya.bhag...@mpi-bn.mpg.de]
Sent: Tuesday, July 07, 2020 10:50 AM
To: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in 
bioc-devel?

It's the BSgenome to GenomeDescription coercer that seems to be missing - is 
this on purpose?

# bsgenomeName(BSgenomeObj) FAILS
#---
bsname <- GenomeInfoDb::bsgenomeName(bsgenome)
index_genome(bsgenome, indexedgenomesdir = tempdir())
Error in h(simpleError(msg, call)) :
  unable to find an inherited method for function 'bsgenomeName' for signature 
'"BSgenome"

# as(bsgenome, 'GenomeDescription') also FAILS
#
bsname <- GenomeInfoDb::bsgenomeName(as(bsgenome, 'GenomeDescription')) # ALSO 
FAILS
index_genome(bsgenome, indexedgenomesdir = tempdir())
Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'x' in selecting a method for function 
'bsgenomeName': no method or default for coercing "BSgenome" to 
"GenomeDescription"

Aditya

From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, 
Aditya [aditya.bhag...@mpi-bn.mpg.de]
Sent: Tuesday, July 07, 2020 10:22 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Dear bioc-devel,

multicrispr is having an error on the bioc-devel build 
machines,
 caused by:

unable to find an inherited method for function 'bsgenomeName' for signature 
'"BSgenome"

This is a bit strange, because normally a BSgenome object gets automatically 
converted to a GenomeDescription object before being sent to the method 
bsgenomeName. In bioc-devel, for some reason this mechanism seems to be broken. 
Is it on purpose? What would be the best fix/patch?

Right now, I'm checking whether explicitation fixes things:
bsname <- GenomeInfoDb::bsgenomeName(bsgenome)  
   # FAILS
bsname <- GenomeInfoDb::bsgenomeName(as(bsgenome, 'GenomeDescription')) # WORKS 
? (VERIFYING)

Thank you for feedback :-)

Aditya

[[alternative HTML version deleted]]

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Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

2020-07-07 Thread Bhagwat, Aditya

It's the BSgenome to GenomeDescription coercer that seems to be missing - is 
this on purpose?

# bsgenomeName(BSgenomeObj) FAILS
#---
bsname <- GenomeInfoDb::bsgenomeName(bsgenome)
index_genome(bsgenome, indexedgenomesdir = tempdir())
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 
'bsgenomeName': no method or default for coercing "BSgenome" to 
"GenomeDescription"

# as(bsgenome, 'GenomeDescription') also FAILS
#
bsname <- GenomeInfoDb::bsgenomeName(as(bsgenome, 'GenomeDescription')) # ALSO 
FAILS
index_genome(bsgenome, indexedgenomesdir = tempdir())
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 
'bsgenomeName': no method or default for coercing "BSgenome" to 
"GenomeDescription"

Aditya


From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, 
Aditya [aditya.bhag...@mpi-bn.mpg.de]
Sent: Tuesday, July 07, 2020 10:22 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Dear bioc-devel,

multicrispr is having an error on the bioc-devel build 
machines,
 caused by:

unable to find an inherited method for function 'bsgenomeName' for signature 
'"BSgenome"

This is a bit strange, because normally a BSgenome object gets automatically 
converted to a GenomeDescription object before being sent to the method 
bsgenomeName. In bioc-devel, for some reason this mechanism seems to be broken. 
Is it on purpose? What would be the best fix/patch?

Right now, I'm checking whether explicitation fixes things:
bsname <- GenomeInfoDb::bsgenomeName(bsgenome)  
   # FAILS
bsname <- GenomeInfoDb::bsgenomeName(as(bsgenome, 'GenomeDescription')) # WORKS 
? (VERIFYING)

Thank you for feedback :-)

Aditya

[[alternative HTML version deleted]]

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[Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

2020-07-07 Thread Bhagwat, Aditya

Dear bioc-devel,

multicrispr is having an error on the bioc-devel build 
machines,
 caused by:

unable to find an inherited method for function 'bsgenomeName' for signature 
'"BSgenome"

This is a bit strange, because normally a BSgenome object gets automatically 
converted to a GenomeDescription object before being sent to the method 
bsgenomeName. In bioc-devel, for some reason this mechanism seems to be broken. 
Is it on purpose? What would be the best fix/patch?

Right now, I'm checking whether explicitation fixes things:
bsname <- GenomeInfoDb::bsgenomeName(bsgenome)  
   # FAILS
bsname <- GenomeInfoDb::bsgenomeName(as(bsgenome, 'GenomeDescription')) # WORKS 
? (VERIFYING)

Thank you for feedback :-)

Aditya

[[alternative HTML version deleted]]

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[Bioc-devel] Bioconductor Developers Forum - Thursday 16th July

Re: [Bioc-devel] Unable to replicate Windows build error on new package.

Re: [Bioc-devel] Unable to replicate Windows build error on new package.

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

[Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

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