Re: [Bioc-devel] R CMD check error on shinytest package

[Obenchain, Valerie]

Hi Sam,

Yes, this is a problem. Packages you depend on must be in a CRAN or
Bioconductor repository.

Valerie


On 04/12/2017 10:33 PM, Samuel Wieczorek wrote:
> Hi
>
> For the Prostar package, I began to use the funtionnalities of shinytest 
> wich is a package that provides utilities to automatically test shiny apps.
>
> Unfortunately, this package is not available neither on CRAN or 
> Bioconductor (it is available on github 
> https://github.com/rstudio/shinytest).
>
> Thus, I had a an error on all platforms at the CHECK step.Will it be a 
> problem to pass the tests and be in the next release ?
>
>
> Thanks
>
>
> Sam
>
>
>



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Re: [Bioc-devel] Commiting from git to svn

[Lluís Revilla]

Dear Stephanie,

Maybe I didn't pick the right commit but it didn't solve my error, and
the same message appeared.
Thanks for the suggestion.

Lluís

On 6 April 2017 at 18:34, Stephanie M. Gogarten
 wrote:
> Try following the steps under "Dealing with prior history / merge conflicts"
> on the git mirror page:
> http://www.bioconductor.org/developers/how-to/git-mirrors/
>
> Using "git cherry-pick" instead of rebase seems to avoid a lot of errors.
>
> Stephanie
>
>
> On 4/5/17 8:18 AM, Lluís Revilla wrote:
>>
>> Dear all,
>>
>> Short problem: I am a trying to sync my new package BioCor git repository
>> with the Bioconductor svn repository. But I am failing when I do git svn
>> dcommit.
>>
>> Long history of the problem
>> I did some changes on my master branch (where I developed until now) then
>> I
>> used the update_remotes.sh which created a new branch.
>> I changed to that branch (git checkout devel), changed its name (git
>> branch
>> -m devel bioc/devel) and used (git svn rebase) following the instructions.
>> I brought the changes by merging the branches (git merge master)and wanted
>> to push it to the svn server with (git svn dcommit --add-author-from) .
>> As expected I had some merge conflicts (apparently originated because the
>> initial commit to that repository wasn't with the code I submitted)
>> I skipped them (git rebase --skip) until it ended the rebase at the moment
>> I am only with the changes I performed after submitting the package, as
>> compared with the Bioconductor-mirror (previously the branch was ahead of
>> 'bioc/master' by 173 commits):
>> git status
>> Your branch is ahead of 'bioc/master' by 11 commits.
>>
>> However when I try to sync and commit with svn I can't (BTW it wasn't
>> clear
>> to me how to add my username for git svn repository otherwise I am
>> prompted
>> with tue username of my machine, so maybe it is still wrong):
>>
>> git svn dcommit --add-author-from --username l.revilla
>>
>> Authentication realm:  The bioconductor
>> Subversion Repository
>> Password for 'l.revilla':
>>
>> ERROR from SVN:
>> URL access forbidden for unknown reason: POST of '/bioconductor/!svn/me':
>> 403 Forbidden (https://hedgehog.fhcrc.org)
>> W: 3d12099bda0c61d0a63a787ebb9cbe3b2e06770d and refs/remotes/svn differ,
>> using rebase:
>> :04 04 985b6b2986a31a3eff4161563a5585ea10467787
>> c8d818d0ed3196d391f914996dd26354004df665 MR
>> :100644 00 8e2bef6bf185b9bbc9da7e500bdb394396ccad99
>>  Dbio_cor.R
>> :04 04 ed161436ea9089f70f74f2e1ea79e53a796eed5b
>> 378a5b97d68ecfa7430bebdaba2c5b6540e6051e Mman
>> :04 04 65b109ed754cd8aa35a2fcaceea8c05fdbe91899
>> 594d15d7838d2096afda7b5697242e48bb7fce42 Mtests
>> :04 04 474a6a48c23f1bce377071b58e0b87f161b2a5cf
>> 6be3cd535391595a962f610dad103e88b2fc32bd Mvignettes
>> Current branch bioc/devel is up to date.
>> ERROR: Not all changes have been committed into SVN, however the committed
>> ones (if any) seem to be successfully integrated into the working tree.
>> Please see the above messages for details.
>>
>>
>> How can I push the new commits to the svn repository?
>>
>> Many thanks!
>>
>> Lluís
>>
>> [[alternative HTML version deleted]]
>>
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Re: [Bioc-devel] Iterating over BSgenomeViews returns DNAString instead of BSgenomeViews

[Michael Lawrence]

You could eventually point your student to MaskedXString and
oligonucleotideFrequency(). You can mask the repeats and then just run
the latter to count the N-mers. Comparing their original code to the
code based on existing high-level utilities might be a useful
exercise.

Michael


On Wed, Apr 12, 2017 at 8:24 PM, Pariksheet Nanda
 wrote:
> On Fri, Apr 7, 2017 at 1:13 AM, Hervé Pagès  wrote:
>>
>> This is the expected behavior.
>>
>> Some background: BSgenomeViews are list-like objects where the *list
>> elements* (i.e. the elements one extracts with [[) are the DNA
>> sequences from the views
> --snip--
>> The important difference is that with [[ I get a DNAString object
>> (the content of the view) and with [ I get a BSgenomeViews object
>> of length 1.
>
> Thank you, Hervé!
>
> I was failing to make the connection with the `[[` accessor.
>
>
> On Fri, Apr 7, 2017 at 1:16 AM, Michael Lawrence 
> wrote:
>>
>> I'm curious as to why you are looping over the views in the first
>> place. Maybe we could arrive at a vectorized solution, which is often
>> but not always simpler and faster.
>
> Hi Michael!
>
> Broad background is I'm acculturating an undergraduate student to writing a
> bioconductor package and applying software engineering practices of version
> control, unit testing, documenting, dependency setup and validation in a
> different environment on our university HPC cluster, etc.  The student also
> came along to LibrePlanet to better understand the culture of software
> freedom :o)  The package goal is to use Biostrings to look for repeating
> DNA sequences of a fixed kmer size and subset to portions of the genome
> without repeats (an aligner can do this ofc, but the goal is to teach R and
> engineering practices).
>
> I appreciate your thoughtfulness for vectorizing the code to best use
> BSgenomeViews, but please don't spend more than 10 minutes as I have to
> balance changes to the code with the student's learning and coding "voice"
> and may not do proper justice for more of your effort.  My slowness to
> reply was getting the project further along to be more understandable.
> Here was the line which I've updating as Hervé suggested to use seq_along():
> https://github.com/coregenomics/kmap/blob/4adaed6b8007e8ea39f39ff57a42a821445d3d46/R/BiostringsProjectNEW.R#L185
> (I'm having a hard time thinking of how to summarizing a small example out
> of context).
> Although in that line ranges_hits() is only operating on single indices,
> ranges_hits() was written to process groups of indices to reduce
> multi-processor communication.  Generating such sets of indices would
> involve applying width() to the views inside mappable() to break in into
> chunks of, say, a million bases for matchPDict().  Again, I'm linking to
> the code for anything that stands out at you, but I will feel bad if you
> spend a lot of time on it.
>
>
>> H.
>
>> Michael
>
> Pariksheet
>
> [[alternative HTML version deleted]]
>
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