Re: [Bioc-devel] Don't have access to new package

[Obenchain, Valerie]

Hi John,

The error was on our end. I've cleaned this up and you should now have access 
to multiHiCcompare and HiCcompare.

Valerie


On 08/27/2018 11:13 PM, John Stansfield wrote:

I recently had a new package accepted to Bioconductor, however when I try
to push changes upstream I get the following error:

FATAL: W any packages/multiHiCcompare j.stansfield DENIED by fallthru
(or you mis-spelled the reponame)

I also checked on the bioconductor git credentials and under packages I
have access to, only my first Bioconductor package is listed. My new
package, multiHiCcompare, does not show up and when checking my read write
privileges I only have read access to multiHiCcompare. I added my SSH key
to my github account and I can push to my other package, it is only the new
package that I cannot access.

What do I need to do gain write access to my new package?

Thank you,
John Stansfield

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[Bioc-devel] updating development version package

[zzrickli]

Hi There,

I need to make a few minor change to my INDEED package, which has already
been accepted. I want to know if I need to do anything other than modify
the codes and bump up the version number.

Thanks
ZL

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Re: [Bioc-devel] updating development version package

[Shepherd, Lori]

You need to push any associated changes to the Bioconductor git server.

See the help pages found here:

http://bioconductor.org/developers/how-to/git/



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of 
zzric...@gmail.com 
Sent: Tuesday, August 28, 2018 12:46:03 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] updating development version package

Hi There,

I need to make a few minor change to my INDEED package, which has already
been accepted. I want to know if I need to do anything other than modify
the codes and bump up the version number.

Thanks
ZL

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Re: [Bioc-devel] Logolas package broken for R (3.4) users

[Obenchain, Valerie]

You could use an AMI with R 3.4 installed. See the 'AMI IDs' section:

https://www.bioconductor.org/help/bioconductor-cloud-ami/#ami_ids

Valerie


On 08/27/2018 11:48 AM, kushal kumar dey wrote:

Hi,

I just found based on user reports that the old version of my package
Logolas for R 3.4 and Bioc 3.6 is broken. It does install fine but the main
function does not run. Everything seems to be fine however for R 3.5 and
Bioc 3.7. I would like to produce either an error message if someone < R
3.5 tries to install Logolas, or to mend the old version. Can you please
let me know what is the procedure for either of these cases?

Thanks so much.

Kushal





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Re: [Bioc-devel] Help with class lost after subsetting.

[Hervé Pagès]

On 08/27/2018 11:01 PM, Martin Morgan wrote:



On 08/28/2018 12:19 AM, Charles Plessy wrote:

Dear Bioconductor developers,

In the CAGEr package, I created a "CAGEexp" class that extends
"MultiAssayExperiment" without adding new slots, in order to define 
generic

functions that require CAGEr-specific contents in the colData slot.

Unfortunately, when run in the development branch of Bioconductor,
the CAGEexp objects lose their class when they are subsetted.  Here
is an example:


CAGEr::exampleCAGEexp

A CAGEexp object of 4 listed
(...)


CAGEr::exampleCAGEexp[,1]

A MultiAssayExperiment object of 4 listed
(...)

This breaks examples in the package, as well as existing code.

I am lost on how to troubleshoot this.  May I ask for your help ?


I debugged this using first `selectMethod("[", "MultiAssayExperiment")` 
and then `showMethod()` / `selectMethod()` to arrive at 
`subsetByColData,MultiAssayExperiment,ANY-method`.


The problem is that this line

https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_waldronlab_MultiAssayExperiment_blob_master_R_subsetBy-2Dmethods.R-23L261&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=BFHgkPpGkkRZx_me9V6pN2aTIxXYDgkUBG5jJTKLugc&s=6XrUMqkUrT5cepxjwAwSXVXdjOeyRdWAjdpGaasVqc0&e= 



returns a MultiAssayExperiment; what it should do is probably closer to 
the 'copy constructor' functionality of `initialize()`, along the lines of


   initialize(x, ExperimentList = ..., )

This could be opened as an issue on the MultiAssayExperiment github 
repository; maybe Herve or Michael or others might comment on the best 
implementation.


Yep. Personally I tend to prefer BiocGenerics:::replaceSlots()
over initialize() because the former can be called with check=FALSE
in order to skip a possibly expensive validation. So:

BiocGenerics:::replaceSlots(x
ExperimentList = harmon[["experiments"]],
colData = harmon[["colData"]],
sampleMap = harmon[["sampleMap"]],
metadata = metadata(x),
check = FALSE)

If you know that the replacement values are valid (because of the way
you prepared them), then validation should not be needed.

Also when only **some** of the slots are updated (which is not the
case in the above example where all the slots are being replaced),
I find that the use of initialize() is misleading from a readability
point of view.

See https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011496.html
for a discussion about this about 1 year ago.

H.



Martin



Best regards,



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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] Help with class lost after subsetting.

[Hervé Pagès]

On 08/28/2018 11:46 AM, Hervé Pagès wrote:

On 08/27/2018 11:01 PM, Martin Morgan wrote:



On 08/28/2018 12:19 AM, Charles Plessy wrote:

Dear Bioconductor developers,

In the CAGEr package, I created a "CAGEexp" class that extends
"MultiAssayExperiment" without adding new slots, in order to define 
generic

functions that require CAGEr-specific contents in the colData slot.

Unfortunately, when run in the development branch of Bioconductor,
the CAGEexp objects lose their class when they are subsetted.  Here
is an example:


CAGEr::exampleCAGEexp

A CAGEexp object of 4 listed
(...)


CAGEr::exampleCAGEexp[,1]

A MultiAssayExperiment object of 4 listed
(...)

This breaks examples in the package, as well as existing code.

I am lost on how to troubleshoot this.  May I ask for your help ?


I debugged this using first `selectMethod("[", 
"MultiAssayExperiment")` and then `showMethod()` / `selectMethod()` to 
arrive at `subsetByColData,MultiAssayExperiment,ANY-method`.


The problem is that this line

https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_waldronlab_MultiAssayExperiment_blob_master_R_subsetBy-2Dmethods.R-23L261&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=BFHgkPpGkkRZx_me9V6pN2aTIxXYDgkUBG5jJTKLugc&s=6XrUMqkUrT5cepxjwAwSXVXdjOeyRdWAjdpGaasVqc0&e= 



returns a MultiAssayExperiment; what it should do is probably closer 
to the 'copy constructor' functionality of `initialize()`, along the 
lines of


   initialize(x, ExperimentList = ..., )

This could be opened as an issue on the MultiAssayExperiment github 
repository; maybe Herve or Michael or others might comment on the best 
implementation.


Yep. Personally I tend to prefer BiocGenerics:::replaceSlots()
over initialize() because the former can be called with check=FALSE
in order to skip a possibly expensive validation. So:

     BiocGenerics:::replaceSlots(x
     ExperimentList = harmon[["experiments"]],
     colData = harmon[["colData"]],
     sampleMap = harmon[["sampleMap"]],
     metadata = metadata(x),
     check = FALSE)

If you know that the replacement values are valid (because of the way
you prepared them), then validation should not be needed.

Also when only **some** of the slots are updated (which is not the
case in the above example where all the slots are being replaced),


ERRATA: It seems that MultiAssayExperiment have one more slot,
the "drops" slot, that the code above does not modify so this would
be one more reason IMO to use BiocGenerics:::replaceSlots() instead
of something like initialize(x, ExperimentList = ..., ) or
new(class(x),ExperimentList = ..., ).

H.


I find that the use of initialize() is misleading from a readability
point of view.

See 
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2017-2DSeptember_011496.html&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=OlbCmHfOSsvIe5QU8cUQjnV7NeLHnJ9GndGatxMWmXQ&s=fV9PeZDYz9qEIxeLk00LcjpNNgzQy_kzi6aFEKBvlds&e= 


for a discussion about this about 1 year ago.

H.



Martin



Best regards,



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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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