date:20191015

Re: [Bioc-devel] hook declined

2019-10-15 Thread Cuklina Jelena

Sorry, indeed you have most of the information that I found through 
trial-error-stackoverflow already. Some of these lines when missed cause a lot 
of headache. Thanks for pointing again!

Best regards,
Jelena Čuklina.
On 15 Oct 2019, 15:46 +0200, Shepherd, Lori , 
wrote:
Have you looked at the extensive git documentation and the FAQ we already have 
for reference:
http://bioconductor.org/developers/how-to/git/


There is a page dedicated to BFG:
http://bioconductor.org/developers/how-to/git/remove-large-data/


Nitesh and Herve also commented relating to this back in Sept?
https://stat.ethz.ch/pipermail/bioc-devel/2019-September/015609.html




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Cuklina Jelena 
Sent: Tuesday, October 15, 2019 9:35 AM
To: Michael Lawrence via Bioc-devel ; Shepherd, Lori 

Subject: Re: hook declined

Thanks Lori,

may I ask to add more clarifications to git-related issues on bioconductor 
submission pages? E.g. once explaining what can and cannot be done with 
bioconductor branch (many git commands cannot be executed).

I also believe it would be good to have more advice how to handle bfg 
“correctly”, e.g. what it does exactly and how to keep the remotes in sync if 
bfg is applied locally. History re-writing is not a good practice, so it would 
be good to understand Bioconductors reasons to recommend it, in addition to 
practical implications.

Git versioning with remotes is not straightforward, especially for git-newbies, 
which many biopackage developers are.

Best regards,
Jelena Čuklina.
On 15 Oct 2019, 13:53 +0200, Shepherd, Lori , 
wrote:
There is no RELEASE_3_10 branch yet.   The master branch is the devel 3.10 
branch.  Once we make that branch we will announce it.



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 Cuklina Jelena 

Sent: Tuesday, October 15, 2019 3:33 AM
To: Michael Lawrence via Bioc-devel 
Subject: [Bioc-devel] hook declined

Dear Bioconductor team,

my submission to Release_3_10 branch is declined. Could you please tell why is 
that? I can’t submit to master as I need repo reset due to large file cleaning 
and history re-writing, is this issue related? Or is it the deadline missed?

Error message:
 ! [remote rejected] RELEASE_3_10 -> RELEASE_3_10 (hook declined)
error: failed to push some refs to 
'g...@git.bioconductor.org:packages/proBatch.git'

Best regards,
Jelena Čuklina.

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Re: [Bioc-devel] hook declined

2019-10-15 Thread Shepherd, Lori

Have you looked at the extensive git documentation and the FAQ we already have 
for reference:
http://bioconductor.org/developers/how-to/git/


There is a page dedicated to BFG:
http://bioconductor.org/developers/how-to/git/remove-large-data/


Nitesh and Herve also commented relating to this back in Sept?
https://stat.ethz.ch/pipermail/bioc-devel/2019-September/015609.html




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Cuklina Jelena 
Sent: Tuesday, October 15, 2019 9:35 AM
To: Michael Lawrence via Bioc-devel ; Shepherd, Lori 

Subject: Re: hook declined

Thanks Lori,

may I ask to add more clarifications to git-related issues on bioconductor 
submission pages? E.g. once explaining what can and cannot be done with 
bioconductor branch (many git commands cannot be executed).

I also believe it would be good to have more advice how to handle bfg 
�correctly�, e.g. what it does exactly and how to keep the remotes in sync if 
bfg is applied locally. History re-writing is not a good practice, so it would 
be good to understand Bioconductors reasons to recommend it, in addition to 
practical implications.

Git versioning with remotes is not straightforward, especially for git-newbies, 
which many biopackage developers are.

Best regards,
Jelena �uklina.
On 15 Oct 2019, 13:53 +0200, Shepherd, Lori , 
wrote:
There is no RELEASE_3_10 branch yet.   The master branch is the devel 3.10 
branch.  Once we make that branch we will announce it.



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 Cuklina Jelena 

Sent: Tuesday, October 15, 2019 3:33 AM
To: Michael Lawrence via Bioc-devel 
Subject: [Bioc-devel] hook declined

Dear Bioconductor team,

my submission to Release_3_10 branch is declined. Could you please tell why is 
that? I can�t submit to master as I need repo reset due to large file cleaning 
and history re-writing, is this issue related? Or is it the deadline missed?

Error message:
 ! [remote rejected] RELEASE_3_10 -> RELEASE_3_10 (hook declined)
error: failed to push some refs to 
'g...@git.bioconductor.org:packages/proBatch.git'

Best regards,
Jelena �uklina.

[[alternative HTML version deleted]]

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notify the sender immediately by e-mail and delete this email message from your 
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Re: [Bioc-devel] check fails on arch 'i386'

2019-10-15 Thread Toth, Reka

Thank you Herve, 

I finally was able to reproduce the error and solve it. You are right, it was 
most probably due to the data.table package.
Interestingly, the problem occurs randomly, with different error messages 
(sometimes it is complaining about negative vector size...). I will open an 
issue for data.table, because on these small datasets it shouldn't happen that 
it needs those big vector sizes. 

Thanks again. 

Best, 
Reka 




-Original Message-
From: Pages, Herve [mailto:hpa...@fredhutch.org] 
Sent: Monday, October 14, 2019 7:34 PM
To: Toth, Reka; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] check fails on arch 'i386'

Hi Toth,

Not clear to me what's going on but I kind of suspect this might have 
something to do with the use of data.table.

A few things to keep in mind:

- 'R CMD check' runs all the example in the same R session. This means 
that the outcome of the examples of a given man page can be affected by 
the examples from other man pages.

- A process cannot allocate more than 3 Gb of memory on 32-bit Windows. 
There is no such limit on 64-bit Windows or on the other platforms we 
support (Linux and Mac). On these platforms the maximum amount of memory 
a process can allocate only depends on what's available on the system.

- Generally speaking, sticking to the Bioconductor way of doing things 
(e.g use of GRanges objects instead of data.table objects, use of 
findOverlaps() instead of data.table::foverlaps()) will lead to faster 
code and reduced memory usage. Therefore I would strongly encourage you 
to consider switching to GRanges/findOverlaps() and to avoid the use of 
data.table in methrix.

Best,
H.


On 10/11/19 09:36, Toth, Reka wrote:
> 
> Dear BioC developers,
> 
> The most recent build of methrix fails on Tokay1 server:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_spb-5Freports_methrix-5Fbuildreport-5F20191009174210.html=DwIF-g=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=doO3ej8vD58ZBQWVxkHTaCLk-xipbskav8uofJL2syI=zs3uDnFqyAl-hr_7StB3Yr-tGZW8VPfclbPY_JKtSt8=
> The error message is the following:
> 
> ** running examples for arch 'i386' ... ERROR
> Running examples in 'methrix-Ex.R' failed
> The error most likely occurred in:
> 
>> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
>> ### Name: get_region_summary
>> ### Title: Extract and summarize methylation or coverage info by regions of
>> ###   interest
>> ### Aliases: get_region_summary
>>
>> ### ** Examples
>>
>> data("methrix_data")
>> get_region_summary(m = methrix_data, regions = data.table(chr = "chr21", 
>> start = 27867971, end =  27868103), type = "M", how = "mean")
> -Checking for overlaps..
> Error: cannot allocate vector of size 1.4 Gb
> Execution halted
> 
> I am a bit puzzled what the reasons could be, since it passed this step 
> during the previous builds and I didn't change any of the functions in my 
> last commit.
> When I run the check on our local Windows, I don't get any error. We use a 
> very small dataset as example, it definitely should not use a vector of size 
> 1.4 Gb.
> 
> I would appreciate every input or idea on how to tackle this error.
> Thanks a lot!
> 
> Best,
> Reka
> 
> Dr. Reka Toth
> Computational Epigenomics Group
> Division of Epigenomics and Cancer Risk Factors /C010
> Postdoctoral Fellow
> 
> German Cancer Research Center (DKFZ)
> Foundation under Public Law
> Im Neuenheimer Feld 280
> 69120 Heidelberg
> Germany
> 
> r.t...@dkfz-heidelberg.de
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dkfz.de=DwIF-g=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=doO3ej8vD58ZBQWVxkHTaCLk-xipbskav8uofJL2syI=U7YGBonX7WmBqfyEneCtEsuRUKl1fbTS6Esi3e9XGAI=
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIF-g=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=doO3ej8vD58ZBQWVxkHTaCLk-xipbskav8uofJL2syI=2BO1kFpXuH1gpxwLxHae_ELnR7g_k9JV-qtslgowQMQ=
> 

-- 
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] Converting gene ids to GRanges - ensembl centric TxDb missing for human

2019-10-15 Thread Bhagwat, Aditya via Bioc-devel

Thankyou Lori,

Cheers,

Aditya



From: Shepherd, Lori [lori.sheph...@roswellpark.org]
Sent: Tuesday, October 15, 2019 2:22 PM
To: Bhagwat, Aditya; bioc-devel@r-project.org
Subject: Re: Converting gene ids to GRanges - ensembl centric TxDb missing for 
human

Again we would not recommend posting these types of questions to both the 
mailing list and the support site.
Since this is not a developer question -  the support site was the appropriate 
place -
https://support.bioconductor.org/p/125609/

We have members of the team working on developing the new TxDbs for the release 
and will look into the reasoning and post on the support site thread.



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 Bhagwat, 
Aditya 
Sent: Tuesday, October 15, 2019 8:15 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Converting gene ids to GRanges - ensembl centric TxDb 
missing for human

Dear BioC devel,

I want to convert geneids to GRanges by doing:
GenomicFeatures::genes(txdb)[geneids]

Works wonderfully for mouse, with entrezgene as well ensemblgene-centric TxDbs:
txdb <- 
TxDb.Mmusculus.UCSC.mm10.knownGene::TxDb.Mmusculus.UCSC.mm10.knownGene
GenomicFeatures::genes(txdb)[c('19600', '99889', '99982')]

txdb <- 
TxDb.Mmusculus.UCSC.mm10.ensGene::TxDb.Mmusculus.UCSC.mm10.ensGene
GenomicFeatures::genes(txdb)[c('ENSMUSG001', 
'ENSMUSG003')]

For human, hower, ensembl-centric TxDbs seem to be missing:
txdb <- 
TxDb.Hsapiens.UCSC.hg38.knownGene::TxDb.Hsapiens.UCSC.hg38.knownGene
GenomicFeatures::genes(txdb)[c('1', '10', '100')]

   # No TxDb.Hsapiens.UCSC.hg38.ensGene::TxDb.Hsapiens.UCSC.hg38.ensGene

Has this been a (perhaps recent) design choice to no longer offer the 
ensemble-centric TxDbs?

(The larger context of this question is the development of multicrispr 
(https://gitlab.gwdg.de/loosolab/software/multicrispr))

Thankyou for feedback!

Aditya

[[alternative HTML version deleted]]

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[Bioc-devel] Last build of RELEASE_3_9

2019-10-15 Thread Shepherd, Lori

Tonight is expected to be the last build of the RELEASE_3_9  release branch.   
We will be freezing commits to this branch at 3 PM EST today.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
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recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
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Re: [Bioc-devel] Converting gene ids to GRanges - ensembl centric TxDb missing for human

2019-10-15 Thread Shepherd, Lori

Again we would not recommend posting these types of questions to both the 
mailing list and the support site.
Since this is not a developer question -  the support site was the appropriate 
place -
https://support.bioconductor.org/p/125609/

We have members of the team working on developing the new TxDbs for the release 
and will look into the reasoning and post on the support site thread.



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 Bhagwat, 
Aditya 
Sent: Tuesday, October 15, 2019 8:15 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Converting gene ids to GRanges - ensembl centric TxDb 
missing for human

Dear BioC devel,

I want to convert geneids to GRanges by doing:
GenomicFeatures::genes(txdb)[geneids]

Works wonderfully for mouse, with entrezgene as well ensemblgene-centric TxDbs:
txdb <- 
TxDb.Mmusculus.UCSC.mm10.knownGene::TxDb.Mmusculus.UCSC.mm10.knownGene
GenomicFeatures::genes(txdb)[c('19600', '99889', '99982')]

txdb <- 
TxDb.Mmusculus.UCSC.mm10.ensGene::TxDb.Mmusculus.UCSC.mm10.ensGene
GenomicFeatures::genes(txdb)[c('ENSMUSG001', 
'ENSMUSG003')]

For human, hower, ensembl-centric TxDbs seem to be missing:
txdb <- 
TxDb.Hsapiens.UCSC.hg38.knownGene::TxDb.Hsapiens.UCSC.hg38.knownGene
GenomicFeatures::genes(txdb)[c('1', '10', '100')]

   # No TxDb.Hsapiens.UCSC.hg38.ensGene::TxDb.Hsapiens.UCSC.hg38.ensGene

Has this been a (perhaps recent) design choice to no longer offer the 
ensemble-centric TxDbs?

(The larger context of this question is the development of multicrispr 
(https://gitlab.gwdg.de/loosolab/software/multicrispr))

Thankyou for feedback!

Aditya

[[alternative HTML version deleted]]

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recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
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[Bioc-devel] Converting gene ids to GRanges - ensembl centric TxDb missing for human

2019-10-15 Thread Bhagwat, Aditya

Dear BioC devel,

I want to convert geneids to GRanges by doing:
GenomicFeatures::genes(txdb)[geneids]

Works wonderfully for mouse, with entrezgene as well ensemblgene-centric TxDbs:
txdb <- 
TxDb.Mmusculus.UCSC.mm10.knownGene::TxDb.Mmusculus.UCSC.mm10.knownGene
GenomicFeatures::genes(txdb)[c('19600', '99889', '99982')]

txdb <- 
TxDb.Mmusculus.UCSC.mm10.ensGene::TxDb.Mmusculus.UCSC.mm10.ensGene
GenomicFeatures::genes(txdb)[c('ENSMUSG001', 
'ENSMUSG003')]

For human, hower, ensembl-centric TxDbs seem to be missing:
txdb <- 
TxDb.Hsapiens.UCSC.hg38.knownGene::TxDb.Hsapiens.UCSC.hg38.knownGene
GenomicFeatures::genes(txdb)[c('1', '10', '100')]

   # No TxDb.Hsapiens.UCSC.hg38.ensGene::TxDb.Hsapiens.UCSC.hg38.ensGene

Has this been a (perhaps recent) design choice to no longer offer the 
ensemble-centric TxDbs?

(The larger context of this question is the development of multicrispr 
(https://gitlab.gwdg.de/loosolab/software/multicrispr))

Thankyou for feedback!

Aditya

[[alternative HTML version deleted]]

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Re: [Bioc-devel] hook declined

2019-10-15 Thread Shepherd, Lori

There is no RELEASE_3_10 branch yet.   The master branch is the devel 3.10 
branch.  Once we make that branch we will announce it.



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 Cuklina Jelena 

Sent: Tuesday, October 15, 2019 3:33 AM
To: Michael Lawrence via Bioc-devel 
Subject: [Bioc-devel] hook declined

Dear Bioconductor team,

my submission to Release_3_10 branch is declined. Could you please tell why is 
that? I can�t submit to master as I need repo reset due to large file cleaning 
and history re-writing, is this issue related? Or is it the deadline missed?

Error message:
 ! [remote rejected] RELEASE_3_10 -> RELEASE_3_10 (hook declined)
error: failed to push some refs to 
'g...@git.bioconductor.org:packages/proBatch.git'

Best regards,
Jelena �uklina.

[[alternative HTML version deleted]]

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recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
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[Bioc-devel] hook declined

2019-10-15 Thread Cuklina Jelena

Dear Bioconductor team,

my submission to Release_3_10 branch is declined. Could you please tell why is 
that? I can’t submit to master as I need repo reset due to large file cleaning 
and history re-writing, is this issue related? Or is it the deadline missed?

Error message:
 ! [remote rejected] RELEASE_3_10 -> RELEASE_3_10 (hook declined)
error: failed to push some refs to 
'g...@git.bioconductor.org:packages/proBatch.git'

Best regards,
Jelena Čuklina.

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Re: [Bioc-devel] hook declined

Re: [Bioc-devel] hook declined

Re: [Bioc-devel] check fails on arch 'i386'

Re: [Bioc-devel] Converting gene ids to GRanges - ensembl centric TxDb missing for human

[Bioc-devel] Last build of RELEASE_3_9

Re: [Bioc-devel] Converting gene ids to GRanges - ensembl centric TxDb missing for human

[Bioc-devel] Converting gene ids to GRanges - ensembl centric TxDb missing for human

Re: [Bioc-devel] hook declined

[Bioc-devel] hook declined

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