Re: [Bioc-devel] Why should Bioconductor developers re-use core classes?

[Dario Strbenac]

Good day,

It might be useful to readers to have a comparison table (ticks and crosses) in 
the MultiAssayExperiment vignette that compares the features available in it to 
those available in SummarizedExperiment, to allow quicker decision making.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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Re: [Bioc-devel] Help with R CMD check NOTEs

[Pariksheet Nanda]

Hi Anusha,

On Wed, Oct 18, 2017 at 2:30 PM, Anusha Nagari <
anusha.nag...@utsouthwestern.edu> wrote:
>
> Can you please let me know how to go about the following NOTE. Or if this
is something that should be really taken care of for a successful package
build and install:
>
> * checking re-building of vignette outputs ... NOTE
> Warnings in re-building vignettes:
>   Warning: file stem ‘/fig2’ is not portable
>   Warning: file stem ‘/fig3’ is not portable
>
> @Pariksheet: I am working on the groHMM package.
https://github.com/Kraus-Lab/groHMM

My best guess is you might want to revise your figure label names without
the number.  LaTeX commands like macro names consider numbers to be an
invalid character class.  So you could try replacing instances of fig2 and
fig3 in the vignette with something like figTwo and figThree.

I couldn't reproduce the build NOTE to confirm the fault / fix.  The
bioconductor.org 1.10.0 tarball doesn't see to produce the error, BiocCheck
fails, and I had trouble building the vignette from the GitHub master
branch.

Hope that helps.


> Anusha

 Pariksheet

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Re: [Bioc-devel] Updating Rsamtools to support BAMs with >65535 CIGAR operators

[Heng Li]

> Sounds great; please make a pull request against
> 
>  https://github.com/Bioconductor/Rsamtools

I will send a pull request tomorrow. I will probably have some technical 
questions on testing and may ask you there on github. Thanks for the quick 
response.

Heng

> On Oct 18, 2017, at 16:40, Martin Morgan  
> wrote:
> 
> On 10/18/2017 04:32 PM, Heng Li wrote:
>> Hi,
>> I am not sure whether I should send the request to this mailing list in this 
>> case, but I am not sure what is the best place to ask.
>> Anyway, an alignment with >65535 operators can't be encoded in the current 
>> BAM format. Unfortunately, a tiny fraction of ultra-long nanopore reads will 
>> be aligned with >65535 ops, which means none of the existing BAM readers 
>> works with ultra-long reads. To address this issue, we can move long CIGAR 
>> to a tag in the file and move it back in memory when the file is read.
>> I can update Rsamtools to support long-cigar BAMs with the approach above. 
>> The update will keep API the same but will slightly alter ABI – struct 
>> bam1_core_t in samtools/bam.c needs to be enlarged. If you think it is ok, I 
>> can generate a patch file against the git.bioconductor.org HEAD.
>> What do you (or the current maintainer) think? What is the best way to send 
>> this patch?
> 
> Sounds great; please make a pull request against
> 
>  https://github.com/Bioconductor/Rsamtools
> 
> or as a simple diff to me (martin.morgan @ roswellpark.org)
> 
> Martin
> 
>> Thanks in advance,
>> Heng
> 
> 
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Re: [Bioc-devel] Updating Rsamtools to support BAMs with >65535 CIGAR operators

[Martin Morgan]

On 10/18/2017 04:32 PM, Heng Li wrote:

Hi,

I am not sure whether I should send the request to this mailing list in this 
case, but I am not sure what is the best place to ask.

Anyway, an alignment with >65535 operators can't be encoded in the current BAM 
format. Unfortunately, a tiny fraction of ultra-long nanopore reads will be aligned 
with >65535 ops, which means none of the existing BAM readers works with 
ultra-long reads. To address this issue, we can move long CIGAR to a tag in the file 
and move it back in memory when the file is read.

I can update Rsamtools to support long-cigar BAMs with the approach above. The 
update will keep API the same but will slightly alter ABI – struct bam1_core_t 
in samtools/bam.c needs to be enlarged. If you think it is ok, I can generate a 
patch file against the git.bioconductor.org HEAD.

What do you (or the current maintainer) think? What is the best way to send 
this patch?


Sounds great; please make a pull request against

  https://github.com/Bioconductor/Rsamtools

or as a simple diff to me (martin.morgan @ roswellpark.org)

Martin



Thanks in advance,

Heng




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[Bioc-devel] Updating Rsamtools to support BAMs with >65535 CIGAR operators

[Heng Li]

Hi,

I am not sure whether I should send the request to this mailing list in this 
case, but I am not sure what is the best place to ask.

Anyway, an alignment with >65535 operators can't be encoded in the current BAM 
format. Unfortunately, a tiny fraction of ultra-long nanopore reads will be 
aligned with >65535 ops, which means none of the existing BAM readers works 
with ultra-long reads. To address this issue, we can move long CIGAR to a tag 
in the file and move it back in memory when the file is read.

I can update Rsamtools to support long-cigar BAMs with the approach above. The 
update will keep API the same but will slightly alter ABI – struct bam1_core_t 
in samtools/bam.c needs to be enlarged. If you think it is ok, I can generate a 
patch file against the git.bioconductor.org HEAD.

What do you (or the current maintainer) think? What is the best way to send 
this patch?

Thanks in advance,

Heng
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Re: [Bioc-devel] Why should Bioconductor developers re-use core classes?

[Levi Waldron]

>
> On Wed, Oct 18, 2017 at 10:26 AM, Ryan Thompson 
> wrote:
>
>> I think the main reason for reusing/subclassing core classes that users
>> can
>> appreciate is that it makes it much easier for users to integrate multiple
>> packages into a single workflow. Only the most basic of pipelines uses
>> just
>> a single Bioconductor package. For instance, an "edgeR" pipeline obviously
>> uses the edgeR package, but it likely also uses several other packages,
>> like sva, RUV, variancePartition, etc. The more these different packages
>> operate on the same core data structures, the less work the user has to do
>> to use them together. And to bring that back around to an incentive for
>> developers, making your package interoperate with other packages more
>> easily means that users will be more likely to use your package.
>>
>
My impression is that the interoperability argument may already be more
widely appreciated, because in the pipeline example you can have several
packages operating on the same data class. It seems less obvious when you
are doing something different that requires defining a new class, why you
should extend an existing class to meet your needs. Although I guess your
point extends to interoperability with other packages providing methods for
the parent class, and the ability to use coercion methods defined for the
parent class, which I didn't mention...

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Re: [Bioc-devel] Help with R CMD check NOTEs

[Anusha Nagari]

Hi Herve,

Thank you for your response.

>In other words putting everything in Imports can hurt
>usability/friendliness. The approach should be more nuanced. It's
>good that the 'R CMD check' NOTE reminds us about the Depends vs
>Imports trade-off but for Bioconductor packages the choices made
>by the developers will not always please 'R CMD check'.

I will leave them as dependencies in the Description file.

Can you please let me know how to go about the following NOTE. Or if this is 
something that should be really taken care of for a successful package build 
and install:
* checking re-building of vignette outputs ... NOTE
Warnings in re-building vignettes:
  Warning: file stem ‘/fig2’ is not portable
  Warning: file stem ‘/fig3’ is not portable

@Pariksheet: I am working on the groHMM package. 
https://github.com/Kraus-Lab/groHMM

Thank you,
Anusha

From: Anusha Nagari 

Hi,

On 10/18/2017 09:19 AM, Pariksheet Nanda wrote:
> Hi Anusha
>
> On Wed, Oct 18, 2017 at 12:04 PM, Anusha Nagari
>  utsouthwestern.edu> wrote:
>>
>> Depends: includes the non-default packages:
>>‘MASS’ ‘parallel’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’
>>‘GenomicRanges’ ‘GenomicAlignments’ ‘rtracklayer’
>> Adding so many packages to the search path is excessive and importing
>> selectively is preferable.
>
> Move those to the "Imports" section in your package DESCRIPTION file.

It's important to realize that this will remove all the functionalities
provided by these packages from the search path e.g. your users will
need to explicitly library(MASS) or library(parallel) etc... before
they can access things defined in these packages. The code in your
examples (man page and vignettes) and possibly in your unit tests will
also need to be modified to reflect this.

In other words putting everything in Imports can hurt
usability/friendliness. The approach should be more nuanced. It's
good that the 'R CMD check' NOTE reminds us about the Depends vs
Imports trade-off but for Bioconductor packages the choices made
by the developers will not always please 'R CMD check'.

Cheers,
H.

>
>
>> * checking re-building of vignette outputs ... NOTE
>> Warnings in re-building vignettes:
>>Warning: file stem ‘/fig2’ is not portable
>>Warning: file stem ‘/fig3’ is not portable
>
> Hmm... I think we'll have to look at the exact vignette to see what's
> going on.  Presumably that's a LaTeX vignette.  Can you advise the
> package name you are working on and/or link to the the source code?
>
>
>> Anusha
>
> Pariksheet
>
> ---
> Pariksheet Nanda
> PhD Candidate in Genetics and Genomics
> System Administrator, Storrs HPC Cluster
> University of Connecticut
>
> ___
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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: hpages at 
fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319


From: Anusha Nagari 
Date: Wednesday, October 18, 2017 at 11:04 AM
To: "bioc-devel@r-project.org" 
Subject: Help with R CMD check NOTEs

Hello,

I am getting the following NOTES at R CMD check step:

NOTE1:
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘MASS’ ‘parallel’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’
  ‘GenomicRanges’ ‘GenomicAlignments’ ‘rtracklayer’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

NOTE2:
* checking re-building of vignette outputs ... NOTE
Warnings in re-building vignettes:
  Warning: file stem ‘/fig2’ is not portable
  Warning: file stem ‘/fig3’ is not portable

Can anyone suggest how I can fix these? Thanks in advance!

Best,
Anusha



UT Southwestern


Medical Center



The future of medicine, today.


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Re: [Bioc-devel] Why should Bioconductor developers re-use core classes?

[Michael Lawrence]

Good points. I think Levi hit on the direct reuse argument (via inheritance
and composition), and, you're right, interoperability is another big one.

On Wed, Oct 18, 2017 at 10:26 AM, Ryan Thompson 
wrote:

> I think the main reason for reusing/subclassing core classes that users can
> appreciate is that it makes it much easier for users to integrate multiple
> packages into a single workflow. Only the most basic of pipelines uses just
> a single Bioconductor package. For instance, an "edgeR" pipeline obviously
> uses the edgeR package, but it likely also uses several other packages,
> like sva, RUV, variancePartition, etc. The more these different packages
> operate on the same core data structures, the less work the user has to do
> to use them together. And to bring that back around to an incentive for
> developers, making your package interoperate with other packages more
> easily means that users will be more likely to use your package.
>
> On Tue, Oct 17, 2017 at 4:55 PM Levi Waldron 
> wrote:
>
> > I'm putting together a presentation with a demo on why Bioconductor
> > developers should re-use and extend core classes whenever possible. It
> > includes a demo of some real-life consequences from two packages I use a
> > lot, metagenomeSeq and phyloseq. These are far from the only examples,
> many
> > Bioconductor packages have created new classes from scratch, and I think
> as
> > a community we should greatly reduce that practice. I would welcome any
> > feedback:
> >
> > https://www.slideshare.net/LeviWaldron/why-reuse-core-classes
> >
> > (sorry the slides are a little Frankenstein - in the interest of speed I
> > made part of it in Powerpoint and part in Beamer, and used pdftk to
> > concatenate these! In practice I would do the Beamer part as a live-demo,
> > and take advantage of some animations in PPT)
> >
> >
> > --
> > Levi Waldron
> > http://www.waldronlab.org
> > Assistant Professor of Biostatistics CUNY School of Public Health
> > US: +1 646-364-9616 <(646)%20364-9616>
> >Skype:
> > levi.waldron
> >
> > [[alternative HTML version deleted]]
> >
> > ___
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] Help with R CMD check NOTEs

[Hervé Pagès]

Hi,

On 10/18/2017 09:19 AM, Pariksheet Nanda wrote:

Hi Anusha

On Wed, Oct 18, 2017 at 12:04 PM, Anusha Nagari
 wrote:


Depends: includes the non-default packages:
   ‘MASS’ ‘parallel’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’
   ‘GenomicRanges’ ‘GenomicAlignments’ ‘rtracklayer’
Adding so many packages to the search path is excessive and importing
selectively is preferable.


Move those to the "Imports" section in your package DESCRIPTION file.


It's important to realize that this will remove all the functionalities
provided by these packages from the search path e.g. your users will
need to explicitly library(MASS) or library(parallel) etc... before
they can access things defined in these packages. The code in your
examples (man page and vignettes) and possibly in your unit tests will
also need to be modified to reflect this.

In other words putting everything in Imports can hurt
usability/friendliness. The approach should be more nuanced. It's
good that the 'R CMD check' NOTE reminds us about the Depends vs
Imports trade-off but for Bioconductor packages the choices made
by the developers will not always please 'R CMD check'.

Cheers,
H.





* checking re-building of vignette outputs ... NOTE
Warnings in re-building vignettes:
   Warning: file stem ‘/fig2’ is not portable
   Warning: file stem ‘/fig3’ is not portable


Hmm... I think we'll have to look at the exact vignette to see what's
going on.  Presumably that's a LaTeX vignette.  Can you advise the
package name you are working on and/or link to the the source code?



Anusha


Pariksheet

---
Pariksheet Nanda
PhD Candidate in Genetics and Genomics
System Administrator, Storrs HPC Cluster
University of Connecticut

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Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
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E-mail: hpa...@fredhutch.org
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Re: [Bioc-devel] Why should Bioconductor developers re-use core classes?

[Ryan Thompson]

I think the main reason for reusing/subclassing core classes that users can
appreciate is that it makes it much easier for users to integrate multiple
packages into a single workflow. Only the most basic of pipelines uses just
a single Bioconductor package. For instance, an "edgeR" pipeline obviously
uses the edgeR package, but it likely also uses several other packages,
like sva, RUV, variancePartition, etc. The more these different packages
operate on the same core data structures, the less work the user has to do
to use them together. And to bring that back around to an incentive for
developers, making your package interoperate with other packages more
easily means that users will be more likely to use your package.

On Tue, Oct 17, 2017 at 4:55 PM Levi Waldron 
wrote:

> I'm putting together a presentation with a demo on why Bioconductor
> developers should re-use and extend core classes whenever possible. It
> includes a demo of some real-life consequences from two packages I use a
> lot, metagenomeSeq and phyloseq. These are far from the only examples, many
> Bioconductor packages have created new classes from scratch, and I think as
> a community we should greatly reduce that practice. I would welcome any
> feedback:
>
> https://www.slideshare.net/LeviWaldron/why-reuse-core-classes
>
> (sorry the slides are a little Frankenstein - in the interest of speed I
> made part of it in Powerpoint and part in Beamer, and used pdftk to
> concatenate these! In practice I would do the Beamer part as a live-demo,
> and take advantage of some animations in PPT)
>
>
> --
> Levi Waldron
> http://www.waldronlab.org
> Assistant Professor of Biostatistics CUNY School of Public Health
> US: +1 646-364-9616 <(646)%20364-9616>
>Skype:
> levi.waldron
>
> [[alternative HTML version deleted]]
>
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>

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Re: [Bioc-devel] Help with R CMD check NOTEs

[Pariksheet Nanda]

Hi Anusha

On Wed, Oct 18, 2017 at 12:04 PM, Anusha Nagari
 wrote:
>
> Depends: includes the non-default packages:
>   ‘MASS’ ‘parallel’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’
>   ‘GenomicRanges’ ‘GenomicAlignments’ ‘rtracklayer’
> Adding so many packages to the search path is excessive and importing
> selectively is preferable.

Move those to the "Imports" section in your package DESCRIPTION file.


> * checking re-building of vignette outputs ... NOTE
> Warnings in re-building vignettes:
>   Warning: file stem ‘/fig2’ is not portable
>   Warning: file stem ‘/fig3’ is not portable

Hmm... I think we'll have to look at the exact vignette to see what's
going on.  Presumably that's a LaTeX vignette.  Can you advise the
package name you are working on and/or link to the the source code?


> Anusha

Pariksheet

---
Pariksheet Nanda
PhD Candidate in Genetics and Genomics
System Administrator, Storrs HPC Cluster
University of Connecticut

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[Bioc-devel] Fail to push changes on RELEASE_3_5

[mohammed Elsiddieg]

Hi every one

I am Mohammed OE the maintainer of cellbaseR package.

I am getting this error while trying to push a bug fix to RELEASE branch


remote: FATAL: W refs/heads/RELEASE_3_5 packages/cellbaseR m.abdallah
DENIED by fallthru
remote: error: hook declined to update refs/heads/RELEASE_3_5
To g...@git.bioconductor.org:packages/cellbaseR.git
 ! [remote rejected] RELEASE_3_5 -> RELEASE_3_5 (hook declined

Best regards

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Re: [Bioc-devel] ShortRead readFasta UniProt Incorrect Import

[Hervé Pagès]

Hi,

I just modified the Sequence Data workflow to suggest the
use of readDNAStringSet() and family to read in a FASTA file.

Cheers,
H.

On 10/18/2017 08:03 AM, Martin Morgan wrote:

On 10/18/2017 01:00 AM, Dario Strbenac wrote:

Good day,

If I have a FASTA file that contains


sp|Q9NYW0|T2R10_HUMAN Taste receptor type 2 member 10 OS=Homo sapiens
GN=TAS2R10 PE=1 SV=3

MLRVVEGIFIFVVVSESVFGVLGNGFIGLVNCIDCAKNKLSTIGFILTGLAISRIFLIWI
IITDGFIQIFSPNIYASGNLIEYISYFWVIGNQSSMWFATSLSIFYFLKIANFSNYIFLW
LKSRTNMVLPFMIVFLLISSLLNFAYIAKILNDYKTKNDTVWDLNMYKSEYFIKQILLNL
GVIFFFTLSLITCIFLIISLWRHNRQMQSNVTGLRDSNTEAHVKAMKVLISFIILFILYF
IGMAIEISCFTVRENKLLLMFGMTTTAIYPWGHSFILILGNSKLKQASLRVLQQLKCCEK
RKNLRVT

readFasta fails to import it with the warning

proteins <- readFasta('.', "test.fasta")

Warning message:
In .Call2("fasta_index", filexp_list, nrec, skip, seek.first.rec,  :
   reading FASTA file test.fasta: ignored 129 invalid one-letter
sequence codes

Also, the amino acid sequence is incomplete. There are 308 amino
acids, but


width(proteins)

[1] 178

It's undesirable for users that some amino acids are discarded.
Hopefully, they notice the warning message before proceeding with the
analysis.

Admittedly, readFasta is in ShortRead, so is designed to work with
high througput sequencing reads. But, perhaps it would be better
suited to a infrastructure package such as Biobase and generalised to
correctly import any FASTA file. There's even a Bioconductor workflow
at
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor.org_help_workflows_sequencing_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=PQf2b4ItE83XXwu2NechRSckpuQ_eISbAf4B017Xrp4=zjUnVdFrQnCYVhojezx1OQ3ulJox_FLqiv8GAl_gzsg=
which has a section titled "DNA/amino acid sequence from FASTA files"
and demonstrates the use of readFasta.


See Biostrings::readAAStringSet (and friends).




I used version 1.34.2 of ShortRead which is the newest one.

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Camperdown NSW 2050
Australia

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Re: [Bioc-devel] ShortRead readFasta UniProt Incorrect Import

[Martin Morgan]

On 10/18/2017 01:00 AM, Dario Strbenac wrote:

Good day,

If I have a FASTA file that contains


sp|Q9NYW0|T2R10_HUMAN Taste receptor type 2 member 10 OS=Homo sapiens 
GN=TAS2R10 PE=1 SV=3

MLRVVEGIFIFVVVSESVFGVLGNGFIGLVNCIDCAKNKLSTIGFILTGLAISRIFLIWI
IITDGFIQIFSPNIYASGNLIEYISYFWVIGNQSSMWFATSLSIFYFLKIANFSNYIFLW
LKSRTNMVLPFMIVFLLISSLLNFAYIAKILNDYKTKNDTVWDLNMYKSEYFIKQILLNL
GVIFFFTLSLITCIFLIISLWRHNRQMQSNVTGLRDSNTEAHVKAMKVLISFIILFILYF
IGMAIEISCFTVRENKLLLMFGMTTTAIYPWGHSFILILGNSKLKQASLRVLQQLKCCEK
RKNLRVT

readFasta fails to import it with the warning

proteins <- readFasta('.', "test.fasta")

Warning message:
In .Call2("fasta_index", filexp_list, nrec, skip, seek.first.rec,  :
   reading FASTA file test.fasta: ignored 129 invalid one-letter sequence codes

Also, the amino acid sequence is incomplete. There are 308 amino acids, but


width(proteins)

[1] 178

It's undesirable for users that some amino acids are discarded. Hopefully, they 
notice the warning message before proceeding with the analysis.

Admittedly, readFasta is in ShortRead, so is designed to work with high througput 
sequencing reads. But, perhaps it would be better suited to a infrastructure package such 
as Biobase and generalised to correctly import any FASTA file. There's even a 
Bioconductor workflow at https://www.bioconductor.org/help/workflows/sequencing/ which 
has a section titled "DNA/amino acid sequence from FASTA files" and 
demonstrates the use of readFasta.


See Biostrings::readAAStringSet (and friends).




I used version 1.34.2 of ShortRead which is the newest one.

--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia

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Re: [Bioc-devel] EXTERNAL: Cardinal duplicate commits

[Turaga, Nitesh]

Hi Kylie,

I have reset your package to its original state. The best way to proceed is 
with this documentation, 
http://master.bioconductor.org/developers/how-to/git/sync-existing-repositories/

You specifically want to take a look at point#8 
(http://master.bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-).

It is the process of switching your master branch, on your Github. Feel free to 
ask questions on bioc-devel. 

Best,

Nitesh 

> On Oct 17, 2017, at 5:14 PM, Turaga, Nitesh  
> wrote:
> 
> Hi Kylie,
> 
> I will take a look at your package and get back to you. Avoid making any 
> changes till I give you further notice. 
> 
> Best,
> 
> Nitesh 
> 
>> On Oct 17, 2017, at 1:13 PM, Bemis, Kylie  wrote:
>> 
>> Hi all,
>> 
>> I have a problem with duplicate commits in my package “Cardinal”. So far I 
>> have avoided making more commits to my other package “matter” until I am 
>> sure how to avoid this again.
>> 
>> Soon after the git transition, I made a few small commits to the 
>> Bioconductor git repo, which I notice now included duplicate commits in the 
>> history. They were not rejected at the time. New commits now are rejected 
>> for me.
>> 
>> Locally and on my own Github repo (https://github.com/kuwisdelu/Cardinal) I 
>> have reverted to a commit from before I merged the Bioconductor master, to 
>> get a clean history without duplicate commits.
>> 
>> I have been trying to push this with
>> 
>> 
>> git push -f upstream
>> 
>> from the “Abandon changes” help page.
>> 
>> This is being rejected with:
>> 
>> kuwisdelu$ git push --force upstream master
>> Total 0 (delta 0), reused 0 (delta 0)
>> remote: FATAL: + refs/heads/master packages/Cardinal k.bemis DENIED by 
>> fallthru
>> remote: error: hook declined to update refs/heads/master
>> To git.bioconductor.org:packages/Cardinal.git
>> ! [remote rejected] master -> master (hook declined)
>> error: failed to push some refs to 
>> 'g...@git.bioconductor.org:packages/Cardinal.git'
>> 
>> What is the best way to get a clean history and avoid this happening again?
>> 
>> Thank you,
>> Kylie
>> 
>> ~~~
>> Kylie Ariel Bemis
>> Future Faculty Fellow
>> College of Computer and Information Science
>> Northeastern University
>> kuwisdelu.github.io
>> 
>> 
>> 
>> 
>> 
>>  [[alternative HTML version deleted]]
>> 
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Re: [Bioc-devel] EXTERNAL: FW: attract problems reported by the "Build/check report" for BioC 3.5

[Samuel E Zimmerman]

Thank you very much!

Best,
Sam

On Oct 17, 2017, at 9:58 PM, Obenchain, Valerie 
> 
wrote:

Yes, if all is green on the build report you can ignore it.
Thanks.
Valerie

On 10/17/2017 11:46 AM, Samuel E Zimmerman wrote:

Hi all,

The below email was sent to me regarding an error in my package attract. I 
haven't updated the package in several months but this is the first time I am 
seeing an error reported. I also went to the link below to check the build 
report and everything returns OK. Should I ignore this error message?

Thank you.

Best,
Sam

From: bbs-nore...@bioconductor.org 
[bbs-nore...@bioconductor.org]
Sent: Tuesday, October 17, 2017 2:35 PM
To: Samuel E Zimmerman
Subject: attract problems reported by the "Build/check report" for BioC 3.5

[This is an automatically generated email. Please don't reply.]

Hi attract maintainer,

According to the "Build/check report" for BioC 3.5,
the attract package has the following problem(s):

  o ERROR for 'R CMD check' on malbec2. See the details here:
  
http://master.bioconductor.org/checkResults/3.5/bioc-LATEST/attract/malbec2-checksrc.html

Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org

Notes:

  * This was the status of your package at the time this email was sent to you.
Given that the online report is updated daily (in normal conditions) you
could see something different when you visit the URL(s) above, especially if
you do so several days after you received this email.

  * It is possible that the problems reported in this report are false 
positives,
either because another package (from CRAN or Bioconductor) breaks your
package (if yours depends on it) or because of a Build System problem.
If this is the case, then you can ignore this email.

  * Please check the report again 24h after you've committed your changes to the
package and make sure that all the problems have gone.

  * If you have questions about this report or need help with the
maintenance of your package, please use the Bioc-devel mailing list:

  https://bioconductor.org/help/mailing-list/

(all package maintainers are requested to subscribe to this list)

For immediate notification of package build status, please
subscribe to your package's RSS feed. Information is at:

https://bioconductor.org/developers/rss-feeds/

Thanks for contributing to the Bioconductor project!


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Re: [Bioc-devel] EXTERNAL: Git push error and duplicate commits

[Turaga, Nitesh]

Hi Matthew,

I’ve reset your package to the original clean state. Same place we were last 
time when this happened. 

I encourage you to ask questions on bioc-devel if you are not sure about a 
certain command, or are facing problems.

Best,

Nitesh 

> On Oct 13, 2017, at 3:31 PM, Turaga, Nitesh  
> wrote:
> 
> Yes. That is correct. 
> 
> 
>> On Oct 13, 2017, at 2:59 PM, Matthew Myint  
>> wrote:
>> 
>> Hi,
>> 
>> Thanks for the explanation! To clarify, the proper step after the
>> first time you helped restore my repository was to change the Github
>> branch (with duplicates) to master_deprecated, and switch in the
>> restored one as master?> id="DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2">
>> 
>>  
>>   > href="https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail;
>> target="_blank">> src="https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif;
>> alt="" width="46" height="29" style="width: 46px; height: 29px;"
>> />
>>  Virus-free. > href="https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail;
>> target="_blank" style="color: #4453ea;">www.avast.com
>>  
>>  
>> > height="1">
>> Regards
>> Matthew Myint
>> Life Science Undergraduate, Year 4
>> NUS
>> 
>> 
>> On Sat, Oct 14, 2017 at 2:49 AM, Turaga, Nitesh
>>  wrote:
>>> Hi Matthew,
>>> 
>>> After closer inspection of “cytofkit”, it was this commit which caused the 
>>> duplicates.
>>> 
>>> commit 4050c245d04af30705245f48931e677a6b4ae159
>>> Merge: 467f659 e6cef6c
>>> Author: Hervé Pagès 
>>> Date:   Wed Sep 20 13:19:45 2017 -0700
>>> 
>>>   Merge branch 'master' of git.bioconductor.org:packages/cytofkit
>>> 
>>> 
>>> It was a fetch and merge. So, it means that the GitHub repository hosted 
>>> (https://github.com/JinmiaoChenLab/cytofkit) did not deprecate the “master” 
>>> with duplicate commits by Sept 20th. This was not done till Sept 27th, 
>>> based on your GitHub 
>>> logs(https://github.com/JinmiaoChenLab/cytofkit/commits/master_deprecated).
>>> 
>>> 
>>> Best,
>>> 
>>> Nitesh
>>> 
>>> 
 On Oct 13, 2017, at 2:18 PM, Turaga, Nitesh 
  wrote:
 
 Hi Matthew,
 
 I’ll have to fix your branch again, for this I need some time. Do not push 
 any more changes.
 
 *When you pull from the upstream (g...@git.bioconductor.org), you are not 
 supposed to get any duplicate commits.*
 
 If a merge is giving you duplicate commits, it means that you didn’t 
 switch your master branch out. Or forgot to checkout the non-duplicate 
 master.
 
 Best,
 
 Nitesh
 
 
 
> On Oct 13, 2017, at 2:13 PM, Matthew Myint  
> wrote:
> 
> Hi,
> 
> After you helped me fix my repository, whenever I had updates I would use 
> the steps from 
> https://master.bioconductor.org/developers/how-to/git/push-to-github-bioc/
> 
> 1) note down what files needed to be updated in the repository
> 
> 2) pull from upstream and merge to local branch 
> https://master.bioconductor.org/developers/how-to/git/pull-upstream-changes/
> 
> 3) update the needed files in the repository and commit
> 
> 4) push to both origin and upstream
> 
> Also, just to clarify, the branch pushing I was referring to was the 
> “switcheroo” in the link 
> https://github.com/Bioconductor/bioc_git_transition/blob/master/doc/scenario-6-abandon-changes.md
> 
> Thanks and regards
> Matthew
> Sent from my iPhone
> 
> On 13 Oct 2017, at 22:35, Turaga, Nitesh  
> wrote:
> 
>> Hi Matthew,
>> 
>> I remember fixing this repository for you a few weeks ago.
>> 
>> You cannot push branches to the Bioconductor repository, that is in the 
>> FAQ, and documentation.
>> 
>> Can you tell me what exactly are the steps you are trying that, you are 
>> getting duplicate commits again?
>> 
>> Best,
>> 
>> Nitesh
>> 
>>> On Oct 13, 2017, at 3:39 AM, Matthew Myint  
>>> wrote:
>>> 
>>> Hi,
>>> 
>>> Recently I noticed in hindsight that my repository had duplicate
>>> commits, but I missed this during my normal package updating
>>> procedures.
>>> 
>>> It was odd that the hook didn't reject these, so I made a clean branch
>>> from a commit before the problem occurred and cherry-picking commits
>>> to the present state. However, trying to push this to bioconductor git
>>> returned an error
>>> 
 remote: FATAL: + refs/heads/master packages/cytofkit c.hao DENIED by 
 fallthru
 remote: error: hook declined to update refs/heads/master
 

Re: [Bioc-devel] EXTERNAL: Needs access to devel Git Repository

[Turaga, Nitesh]

We process the keys manually at noon EST every business day.

You submitted at 17/10/2017 21:54:46 . Please wait.

Best,

Nitesh 

> On Oct 17, 2017, at 11:33 PM, Yang Liao  wrote:
> 
> Dear Bioconductor maintainers,
> 
> 
> I'm the co-maintainer of the Rsubread package. When we're preparing Rsubread 
> for the new release, I found that I don't have the access to the "devel" Git 
> Repository (g...@git.bioconductor.org:packages/Rsubread).
> 
> 
> My SVN account is "y.liao", and my GitHub account is "dbpz". The SSH keys 
> have been set up on GitHub. Can anyone please change my settings so I can 
> clone and submit the changes to our Rsubread package?
> 
> 
> Cheers,
> 
> 
> Yang
> 
>   [[alternative HTML version deleted]]
> 
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