date:20191211

Re: [Bioc-devel] Making changes to the current release branch

2019-12-11 Thread 유도영



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[Bioc-devel] Making changes to the current release branch

2019-12-11 Thread 유도영



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Re: [Bioc-devel] proposal for additional seqlevelsStyle

2019-12-11 Thread Pages, Herve

Hi Vince, Robert,

Looks like Vince wants the RefSeq accession e.g. NC_17.11 for chrom 
17 in the GRCh38.

@Robert: Is this what you're also interested in?

The problem is that the RefSeq accessions are specific to a particular 
assembly (e.g. NC_17.11 for chrom 17 in GRCh38 but NC_17.10 for 
the same chrom in GRCh37).

Currently seqlevelsStyle() doesn't know how to distinguish between 
different assemblies of the same organism. Not saying it couldn't but it 
would require some thinking and some significant refactoring. It 
wouldn't be just a matter of adding a column to 
genomeStyles()$Homo_sapiens.

H.


On 12/10/19 14:19, Robert Castelo wrote:
> I second this, and would suggest to name the style as 'GRC' for "Genome 
> Reference Consortium".
> 
> thanks Vince for bringing this up, being able to easily switch between 
> genome styles is great.
> 
> if 'paste0()' in R is one of the most influential contributions to 
> statistical computing
> 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__simplystatistics.org_2013_01_31_paste0-2Dis-2Dstatistical-2Dcomputings-2Dmost-2Dinfluential-2Dcontribution-2Dof-2Dthe-2D21st-2Dcentury=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=LCcYSINIz3XXhf8i-26IegXRLkTO1NgVbvzgvnPA3dc=b0_SIu8orJ7ZcCS3TIodFvGTPibt9R8vFL5Y40YSx3Q=
>  
> 
> i think that 'seqlevelsStyle()' from the GenomeInfoDb package is one of 
> the most influential contributions to human genetics, if you think about 
> the time invested by researchers in parsing and changing between 
> different styles of chromosome names :)
> 
> robert.
> 
> On 06/12/2019 15:03, Vincent Carey wrote:
>> I raised this issue previously with little response.
>>
>> I'd propose that we add a column or two to genomeStyles()$Homo_sapiens
>>
>>> head(genomeStyles()$Homo_sapiens, 2)
>>    circular auto   sex NCBI UCSC dbSNP Ensembl
>>
>> 1    FALSE TRUE FALSE    1 chr1   ch1   1
>>
>> 2    FALSE TRUE FALSE    2 chr2   ch2   2
>>
>>
>> that includes the values for "NCBI reference sequence names"
>>
>> See 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_nuccore_568815581=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=LCcYSINIz3XXhf8i-26IegXRLkTO1NgVbvzgvnPA3dc=3Jy-MH7heIcrc_A4qm_izduLvBoPWHSeq4gdxf5nv24=
>>   
>> for one report on chr17,
>> and
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_assembly_GCF-5F01405.39=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=LCcYSINIz3XXhf8i-26IegXRLkTO1NgVbvzgvnPA3dc=y6ut_Xcc4rSbXanckiJhiwLsL0W8neJfKWQa6wnG3aM=
>>  
>>
>> for a table that includes the Genbank labels.
>>
>> Should I just file a PR at 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_GenomeInfoDb_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=LCcYSINIz3XXhf8i-26IegXRLkTO1NgVbvzgvnPA3dc=KMzfo3_8kkJ-wdvRCNP5rUjTVMW87brj07yHaKL5Qb0=
>>   
>> after
>> testing?
>>
> 
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>  
> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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Re: [Bioc-devel] Error in Vignette of package

2019-12-11 Thread Benjamin Jean-Marie Tremblay

Thank you for the fixes, I'm having no issues in the release version. However I
am still getting a vignette error in tokay2 (from Tuesdays build) which is a bit
different from the previous zero-length error:

! Package ifvtex Error: Name clash, \ifvtex is already defined.

Thanks,

BT

On Wed, 2019-12-11 at 00:37 -0500, Simina Boca wrote:
> The tokay error is fixed now. Thank you all! Sergio, best wishes for
> getting the other error fixed as well!
> 
> Cheers,
> Simina
> 
> On Mon, Dec 9, 2019 at 5:25 PM Sergio Picart Armada <
> sergi.pic...@upc.edu
> >
> wrote:
> 
> > Hi all,
> > 
> > I've also followed this thread as the FELLA package has problems with the
> > vignette as well.
> > I have two issues (link
> > <
> > http://bioconductor.org/checkResults/devel/bioc-LATEST/FELLA/tokay2-buildsrc.html
> > >
> > )
> > First:
> > 
> > Invalid Parameter - /figure-html
> > Warning in shell(paste(c(cmd, args), collapse = " ")) :
> >   'convert "quickstart_files/figure-html/unnamed-chunk-12-1.png" -trim
> > "quickstart_files/figure-html/unnamed-chunk-12-1.png"' execution failed with
> > error code 4
> > Invalid Parameter - /figure-html
> > Warning in shell(paste(c(cmd, args), collapse = " ")) :
> >   'convert "quickstart_files/figure-html/unnamed-chunk-13-1.png" -trim
> > "quickstart_files/figure-html/unnamed-chunk-13-1.png"' execution failed with
> > error code 4
> > Invalid Parameter - /figure-html
> > Warning in shell(paste(c(cmd, args), collapse = " ")) :
> >   'convert "quickstart_files/figure-html/unnamed-chunk-14-1.png" -trim
> > "quickstart_files/figure-html/unnamed-chunk-14-1.png"' execution failed with
> > error code 4
> > --- finished re-building 'quickstart.Rmd'
> > 
> > (but I believe this one does not prevent the vignette from building) And the
> > second:
> > 
> > Error: processing vignette 'zebrafish.Rmd' failed with diagnostics:
> > argument is of length zero
> > 
> > This is the same one reported by Simina, in tokay2 too.
> > 
> > I hope the new adjustement fixes at least the second one.
> > 
> > Thank you Andrzej,
> > Sergi
> > 
> > 
> > On Monday, December 09, 2019 11:37 CET, Andrzej Oleś <
> > andrzej.o...@gmail.com
> > > wrote:
> > 
> > 
> > Hi Simina,
> > 
> > thank you for reporting the remaining problem on Windows builders. I have
> > just made an adjustment to BiocStyle which should resolve the issue.
> > 
> > Cheers,
> > Andrzej
> > 
> > On Sun, Dec 8, 2019 at 4:18 PM Simina Boca <
> > smb...@georgetown.edu
> > > wrote:
> > 
> > > Hi all,
> > > I've been following this conversation as I was having the same issue for
> > > the swfdr package. Happy to see that it's now fixed on malbec and merida,
> > > though I now see a different error on tokay, also referring to the
> > > vignettes. I looked around a bit, and a bunch of other packages now have
> > > the tokay error, which is:
> > > 
> > > * creating vignettes ... ERROR
> > > --- re-building 'swfdrQ.Rmd' using rmarkdown
> > > Error: processing vignette 'swfdrQ.Rmd' failed with diagnostics:
> > > argument is of length zero
> > > --- failed re-building 'swfdrQ.Rmd'
> > > 
> > > 
> > > 
> > 
> > https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/swfdr/tokay1-buildsrc.html
> > 
> > > 
> > > Thanks!
> > > Cheers,
> > > Simina
> > > 
> > > 
> > > 
> > > On Fri, Dec 6, 2019 at 3:18 PM Pages, Herve <
> > > hpa...@fredhutch.org
> > > >
> > 
> > wrote:
> > > > Great news Andrzej! We'll keep a close eye on the build reports in the
> > > > next few days. Fingers crossed. Thanks!
> > > > 
> > > > H.
> > > > 
> > > > 
> > > > On 12/6/19 03:46, Andrzej Oleś wrote:
> > > > > Dear Package Developers,
> > > > > 
> > > > > An updated version of BiocStyle has been deployed to both the
> > > > 
> > > > development
> > > > > and the release branch. The fix addresses vignette build errors
> > > > 
> > > > occurring
> > > > > with rmarkdown v1.18, these should clear up within the next build
> > 
> > cycle.
> > > > > Cheers,
> > > > > Andrzej
> > > > > 
> > > > > On Wed, Dec 4, 2019 at 2:31 PM Andrzej Oleś <
> > > > > andrzej.o...@gmail.com
> > > > > >
> > > > 
> > > > wrote:
> > > > > > Dear Package Developers,
> > > > > > 
> > > > > > BiocStyle will be patched within the next couple of days to address
> > 
> > the
> > > > > > observed errors. Until then please refrain from making any changes
> > > > > > to
> > > > 
> > > > your
> > > > > > package, the issue should resolve itself once BiocStyle is updated.
> > > > > > 
> > > > > > Cheers,
> > > > > > Andrzej
> > > > > > 
> > > > > > On Mon, Dec 2, 2019 at 11:20 AM Andrzej Oleś <
> > > > > > andrzej.o...@gmail.com
> > > > > > 
> > > > > > wrote:
> > > > > > 
> > > > > > > Hi,
> > > > > > > 
> > > > > > > the error seems to be related to some recent changes in the
> > > > > > > upstream
> > > > > > > package rmarkdown v1.18. I will give you an update once I know
> > > > > > > more
> > > > 
> > > > details.
> > > > > > > Cheers,
> > > > > > > Andrzej
> > > > > > > 
> > > > > > > 
> > > > > > > On Sun,

Re: [Bioc-devel] Add collaborator

2019-12-11 Thread Turaga, Nitesh

You have been added and given permissions Pedro.

Please check for a private email with credentials.

--
Nitesh Turaga
Senior Programmer Analyst
Bioconductor core team
Roswell Park


From: Bioc-devel  on behalf of Turaga, Nitesh 

Sent: Wednesday, December 11, 2019 10:56:26 AM
To: Pedro Russo 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] Add collaborator

I'll create one for you Pedro and send you a private email about access.

Nitesh

--
Nitesh Turaga
Senior Programmer Analyst
Bioconductor core team
Roswell Park


From: Pedro Russo 
Sent: Wednesday, December 11, 2019 6:00:48 AM
To: Turaga, Nitesh 
Cc: Helder Nakaya ; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] Add collaborator

Hi Nitesh,

No, I don't believe I do, how can I create one?

Thanks,
Pedro

On Wed, Dec 11, 2019 at 11:47 AM Turaga, Nitesh 
mailto:nitesh.tur...@roswellpark.org>> wrote:
Hi,

I'll help you with this. Does Pedro have a Bioccredentials account already?

Best

Nitesh

--
Nitesh Turaga
Senior Programmer Analyst
Bioconductor core team
Roswell Park


From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Helder Nakaya mailto:hnak...@usp.br>>
Sent: Wednesday, December 11, 2019 6:52:00 AM
To: bioc-devel@r-project.org 
mailto:bioc-devel@r-project.org>>
Cc: Pedro Russo mailto:pedrostru...@gmail.com>>
Subject: [Bioc-devel] Add collaborator

Hi,

I would like to add one collaborator for our CEMiTool package.
https://bioconductor.org/packages/release/bioc/html/CEMiTool.html

Below is the contact information.
Collaborator: Pedro Russo
email: pedrostru...@gmail.com (cc'd in this 
email)

Best,

Helder Nakaya

==
Helder Nakaya, Ph.D.
Associate Professor

School of Pharmaceutical Sciences
University of Sao Paulo, Brazil

Computational Systems Biology Laboratory 

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Re: [Bioc-devel] Error in Vignette of package

2019-12-11 Thread Pages, Herve

All the "VerbBar" LaTeX errors have cleared up in release and devel. 
Thanks again Andrzej!

Cheers,
H.


On 12/6/19 12:17, Hervé Pagès wrote:
> Great news Andrzej! We'll keep a close eye on the build reports in the 
> next few days. Fingers crossed. Thanks!
> 
> H.
> 
> 
> On 12/6/19 03:46, Andrzej Oleś wrote:
>> Dear Package Developers,
>>
>> An updated version of BiocStyle has been deployed to both the development
>> and the release branch. The fix addresses vignette build errors occurring
>> with rmarkdown v1.18, these should clear up within the next build cycle.
>>
>> Cheers,
>> Andrzej
>>
>> On Wed, Dec 4, 2019 at 2:31 PM Andrzej Oleś  
>> wrote:
>>
>>> Dear Package Developers,
>>>
>>> BiocStyle will be patched within the next couple of days to address the
>>> observed errors. Until then please refrain from making any changes to 
>>> your
>>> package, the issue should resolve itself once BiocStyle is updated.
>>>
>>> Cheers,
>>> Andrzej
>>>
>>> On Mon, Dec 2, 2019 at 11:20 AM Andrzej Oleś 
>>> wrote:
>>>
 Hi,

 the error seems to be related to some recent changes in the upstream
 package rmarkdown v1.18. I will give you an update once I know more 
 details.

 Cheers,
 Andrzej


 On Sun, Dec 1, 2019 at 5:00 PM Benjamin Jean-Marie Tremblay <
 b2tremb...@uwaterloo.ca> wrote:

> Not using BiocStyle::pdf_document means you can’t use the 
> helpers/macros.
> Try this in a fresh interactive session:
>
>    library(BiocStyle)
>    rmarkdown::render("yourvignette.Rmd")
>
> This should make the helpers/macros available. It won’t fix the issue
> for passing R CMD check, but at least it’ll confirm what the issue 
> is and
> thus you’ll know to wait for BiocStyle to update.
>
> BT
>
>> Le 1 déc. 2019 à 10:47, Ioannis Vardaxis  a écrit
> :
>>
>> Thanks for the answer. However replacing it resulted in another error
> for me:
>>
>> Quitting from lines 2-41 (MACPET.Rmd)
>> Error in doc_date() : could not find function "doc_date"
>> Calls:  ... inline_exec -> hook_eval -> withVisible -> 
>> eval
> -> eval
>> Execution halted
>>
>> Should I wait until BiocStyle is updated?
>>
>> Best,
>> Ioannis
>>
>> Fra: Martin Morgan 
>> Sendt: søndag 1. desember 2019 11:51
>> Til: Benjamin Jean-Marie Tremblay ; Ioannis
> Vardaxis 
>> Kopi: bioc-devel@r-project.org 
>> Emne: Re: [Bioc-devel] Error in Vignette of package
>>
>> Thanks for that insight, we'll try to solve the issue with BiocStyle.
>>
>> Martin
>>
>> On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie
> Tremblay"  b2tremb...@uwaterloo.ca> wrote:
>>
>>  I’ve been getting the exact same error for compiling the 
>> Rmarkdown
>>  vignettes in my own package. Some partial testing before the
> weekend
>>  revealed that in my case the error could be circumvented 
>> simply by
> not
>>  using
>>
>>  output: BiocStyle::pdf_document
>>
>>  but instead
>>
>>  output: pdf_document
>>
>>  in the yaml header. I’m not quite sure why, but when 
>> BiocStyle is
> used
>>  some of the latex code for code highlighting is repeated, 
>> leading
> to the
>>  'already defined' error. I’ve not updated my package since 
>> before
> this
>>  error started.
>>
>>  BT
>>
>>  > Le 30 nov. 2019 à 10:25, Ioannis Vardaxis 
> a écrit :
>>  >
>>  > Hey,
>>  >
>>  > I am trying to build my package Vegnette and I get the 
>> following
> error:
>>  >
>>  > ! LaTeX Error: Command \VerbBar already defined.
>>  >   Or name \end... illegal, see p.192 of the 
>> manual.
>>  >
>>  > I tried to find what this means with no luck.
>>  >
>>  > Best,
>>  > Ioannis
>>  >
>>  >
>>  >    [[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=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=JsBc-iL36QFx_Aqpb62zZVHaZB5IN1kYdWe9Jm_OV6k=v4uVRNgws7ncN1VtLeiBc5vMT9El_E8b4jI-HNncD54=
>>  
>>
>>
>>  ___
>>  Bioc-devel@r-project.org mailing list
>>  
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=JsBc-iL36QFx_Aqpb62zZVHaZB5IN1kYdWe9Jm_OV6k=v4uVRNgws7ncN1VtLeiBc5vMT9El_E8b4jI-HNncD54=
>>  
>>
>

Re: [Bioc-devel] Add collaborator

2019-12-11 Thread Turaga, Nitesh

I'll create one for you Pedro and send you a private email about access.

Nitesh

--
Nitesh Turaga
Senior Programmer Analyst
Bioconductor core team
Roswell Park


From: Pedro Russo 
Sent: Wednesday, December 11, 2019 6:00:48 AM
To: Turaga, Nitesh 
Cc: Helder Nakaya ; bioc-devel@r-project.org 

Subject: Re: [Bioc-devel] Add collaborator

Hi Nitesh,

No, I don't believe I do, how can I create one?

Thanks,
Pedro

On Wed, Dec 11, 2019 at 11:47 AM Turaga, Nitesh 
mailto:nitesh.tur...@roswellpark.org>> wrote:
Hi,

I'll help you with this. Does Pedro have a Bioccredentials account already?

Best

Nitesh

--
Nitesh Turaga
Senior Programmer Analyst
Bioconductor core team
Roswell Park


From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>> on 
behalf of Helder Nakaya mailto:hnak...@usp.br>>
Sent: Wednesday, December 11, 2019 6:52:00 AM
To: bioc-devel@r-project.org 
mailto:bioc-devel@r-project.org>>
Cc: Pedro Russo mailto:pedrostru...@gmail.com>>
Subject: [Bioc-devel] Add collaborator

Hi,

I would like to add one collaborator for our CEMiTool package.
https://bioconductor.org/packages/release/bioc/html/CEMiTool.html

Below is the contact information.
Collaborator: Pedro Russo
email: pedrostru...@gmail.com (cc'd in this 
email)

Best,

Helder Nakaya

==
Helder Nakaya, Ph.D.
Associate Professor

School of Pharmaceutical Sciences
University of Sao Paulo, Brazil

Computational Systems Biology Laboratory 

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Re: [Bioc-devel] Add collaborator

2019-12-11 Thread Pedro Russo

Hi Nitesh,

No, I don't believe I do, how can I create one?

Thanks,
Pedro

On Wed, Dec 11, 2019 at 11:47 AM Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:

> Hi,
>
> I'll help you with this. Does Pedro have a Bioccredentials account already?
>
> Best
>
> Nitesh
>
> --
> Nitesh Turaga
> Senior Programmer Analyst
> Bioconductor core team
> Roswell Park
>
> --
> *From:* Bioc-devel  on behalf of Helder
> Nakaya 
> *Sent:* Wednesday, December 11, 2019 6:52:00 AM
> *To:* bioc-devel@r-project.org 
> *Cc:* Pedro Russo 
> *Subject:* [Bioc-devel] Add collaborator
>
> Hi,
>
> I would like to add one collaborator for our CEMiTool package.
> https://bioconductor.org/packages/release/bioc/html/CEMiTool.html
>
> Below is the contact information.
> Collaborator: Pedro Russo
> email: pedrostru...@gmail.com (cc'd in this email)
>
> Best,
>
> Helder Nakaya
>
> ==
> Helder Nakaya, Ph.D.
> Associate Professor
>
> School of Pharmaceutical Sciences
> University of Sao Paulo, Brazil
>
> Computational Systems Biology Laboratory 
>
> [[alternative HTML version deleted]]
>
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> agent responsible for the delivery of this message to the intended
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Re: [Bioc-devel] Add collaborator

2019-12-11 Thread Turaga, Nitesh

Hi,

I'll help you with this. Does Pedro have a Bioccredentials account already?

Best

Nitesh

--
Nitesh Turaga
Senior Programmer Analyst
Bioconductor core team
Roswell Park


From: Bioc-devel  on behalf of Helder Nakaya 

Sent: Wednesday, December 11, 2019 6:52:00 AM
To: bioc-devel@r-project.org 
Cc: Pedro Russo 
Subject: [Bioc-devel] Add collaborator

Hi,

I would like to add one collaborator for our CEMiTool package.
https://bioconductor.org/packages/release/bioc/html/CEMiTool.html

Below is the contact information.
Collaborator: Pedro Russo
email: pedrostru...@gmail.com (cc'd in this email)

Best,

Helder Nakaya

==
Helder Nakaya, Ph.D.
Associate Professor

School of Pharmaceutical Sciences
University of Sao Paulo, Brazil

Computational Systems Biology Laboratory 

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[Bioc-devel] Add collaborator

2019-12-11 Thread Helder Nakaya

Hi,

I would like to add one collaborator for our CEMiTool package.
https://bioconductor.org/packages/release/bioc/html/CEMiTool.html

Below is the contact information.
Collaborator: Pedro Russo
email: pedrostru...@gmail.com (cc'd in this email)

Best,

Helder Nakaya

==
Helder Nakaya, Ph.D.
Associate Professor

School of Pharmaceutical Sciences
University of Sao Paulo, Brazil

Computational Systems Biology Laboratory 

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