Re: [Bioc-devel] package download stats seem unavailable

2019-11-11 Thread Pages, Herve 
Hi Leonardo,

The download stats are temporarily unavailable and should be back 
tomorrow (as discussed last week on the community-bioc Slack, #general 
channel).

Thanks for your patience,

H.

On 11/11/19 10:23, Leonardo Collado Torres wrote:
> Hi,
> 
> The tabular files with the Bioconductor package statistics seem broken
> right now. For example,
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_packages_stats_bioc_recount_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=upAr-KEcnpFYUqm1Zf56rGah86iEEUKm3UOL6qHiNw0=-BdPEdtYLADOzfp_U4VQlSYBQSa2s6RI-bovMie-tqQ=
>   links
> to 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_packages_stats_bioc_recount_recount-5Fstats.tab=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=upAr-KEcnpFYUqm1Zf56rGah86iEEUKm3UOL6qHiNw0=vmqUUMoSwSUY-T6XNDObItzsiwQF5ypZiPDUHZJFdoA=
> which right now redirects to a "page not found" message at
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_packages_stats_bioc_recount_recount-5Fstats.tab_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=upAr-KEcnpFYUqm1Zf56rGah86iEEUKm3UOL6qHiNw0=emHwGn6PRbXt8ooFXtmph_Qo6Q_yiZtns8S76AdTegk=
> (trailing
> slash).
> 
> I noticed this when I wanted to add the new GenomicState pkg to my CV using
> this R code
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_lcolladotor_cv_blob_gh-2Dpages_en-5FCV-5Flcollado.Rnw-23L87-2DL96=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=upAr-KEcnpFYUqm1Zf56rGah86iEEUKm3UOL6qHiNw0=2et8LWo_FJxTaoaapOWldNpzTq7VqFgUu5vSjH7rOzo=
>  .
> At
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_packages_release_data_annotation_html_GenomicState.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=upAr-KEcnpFYUqm1Zf56rGah86iEEUKm3UOL6qHiNw0=z_7YilykLuxnL4uVyhKd6r1IorqRusOv4al7hZK1cWM=
> the
> link to 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_packages_stats_data-2Dannotation_GenomicState_=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=upAr-KEcnpFYUqm1Zf56rGah86iEEUKm3UOL6qHiNw0=sF1DuzbvLkqkyzWFL1VhKDEKN7-fX7JJ91t9dbU4qM4=
> (from the rank badge) returns an "Access Forbidden" result.
> 
> Best,
> Leo
> 
>   [[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=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=upAr-KEcnpFYUqm1Zf56rGah86iEEUKm3UOL6qHiNw0=imTISDYJBYS5wbRH9D8EUoa812Py7ILj1-5L6oZiJEs=
> 

-- 
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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[Bioc-devel] package download stats seem unavailable

2019-11-11 Thread Leonardo Collado Torres 
Hi,

The tabular files with the Bioconductor package statistics seem broken
right now. For example,
http://bioconductor.org/packages/stats/bioc/recount/ links
to http://bioconductor.org/packages/stats/bioc/recount/recount_stats.tab
which right now redirects to a "page not found" message at
http://bioconductor.org/packages/stats/bioc/recount/recount_stats.tab/
(trailing
slash).

I noticed this when I wanted to add the new GenomicState pkg to my CV using
this R code
https://github.com/lcolladotor/cv/blob/gh-pages/en_CV_lcollado.Rnw#L87-L96.
At
http://bioconductor.org/packages/release/data/annotation/html/GenomicState.html
the
link to http://bioconductor.org/packages/stats/data-annotation/GenomicState/
(from the rank badge) returns an "Access Forbidden" result.

Best,
Leo

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[Bioc-devel] New error appeared on dev without updating the development version

2019-11-11 Thread Christopher John 
Hi

I haven't done an update in a while, but got the following error message
like yesterday just on windows, any ideas? Seems vignette related. Thanks.

Chris

##
##
###
### Running command:
###
###   chmod a+r M3C -R && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe
CMD build --keep-empty-dirs --no-resave-data M3C
###
##
##


* checking for file 'M3C/DESCRIPTION' ... OK
* preparing 'M3C':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'M3Cvignette.Rmd' using rmarkdown
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:base':

isFALSE

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO:
windows] | Cores 39/40

Attaching package: 'gplots'

The following object is masked from 'package:stats':

lowess

***PCA wrapper function***
running...
done.
***M3C***
method: Monte Carlo simulation
clustering algorithm: pam
annotation: yes
running simulations...
done.
running consensus cluster algorithm for real data...
done.
running clinical analysis type: chi
optimal K: 4
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-7-1.pdf'.
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-8-1.pdf'.
***PCA wrapper function***
running...
done.
***t-SNE wrapper function***
running...
done.
***M3C***
method: penalised stability
clustering algorithm: pam
annotation: none
running consensus cluster algorithm for real data...
done.
optimal K: 5
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-10-1.pdf'.
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-10-2.pdf'.
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-10-3.pdf'.
***clustersim***
computing simulated data using linear combination...
calculating PCs of data and performing kmeans...
computing centroids of clusters and pulling apart...
transforming pulled apart PC co ordinates back to dataset...
finished.
PDFCROP 1.38, 2012/11/02 - Copyright (c) 2002-2012 by Heiko Oberdiek.
==> 1 page written on `M3Cvignette_files/figure-latex/unnamed-chunk-11-1.pdf'.
! Package ifvtex Error: Name clash, \ifvtex is already defined.

Error: processing vignette 'M3Cvignette.Rmd' failed with diagnostics:
Failed to compile M3Cvignette.tex. See
https://yihui.name/tinytex/r/#debugging for debugging tips. See
M3Cvignette.log for more info.
--- failed re-building 'M3Cvignette.Rmd'

SUMMARY: processing the following file failed:
  'M3Cvignette.Rmd'

Error: Vignette re-building failed.
Execution halted

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Re: [Bioc-devel] From Biostring matching to short read mapping

2019-11-11 Thread Bhagwat, Aditya 
True :-)

From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Éric Fournier 
[fournier.eri...@crchudequebec.ulaval.ca]
Sent: Saturday, November 09, 2019 5:12 PM
To: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] From Biostring matching to short read mapping

Hi,

it might be worthwhile to note that the concern about different chromosome 
sizes only applies if you have more workers than chromosomes. If you're running 
on 2-8 threads, the longer chromosome might hold up a thread while another 
processes two short ones.

Cheers,
-Eric




Date: Fri, 8 Nov 2019 18:19:27 +
From: "Pages, Herve" 
To: "Bhagwat, Aditya" ,
"bioc-devel@r-project.org" 
Subject: Re: [Bioc-devel] From Biostring matching to short read
mapping
Message-ID: <84550bd2-9ded-04a3-6ef6-52746c66f...@fredhutch.org>
Content-Type: text/plain; charset="windows-1252"

Hi Aditya,

Should not be too hard to parallelize. With some gotchas: using one
worker per chromosome (which is the easy way to go) wouldn't be optimal
because of the size differences between the chromosomes. So a better
approach is to try to give each worker the same amount of work by
splitting the set of chromosomes in groups of more or less equal sizes.
The split can either preserve full chromosomes or break them in smaller
pieces. The later will allow using a lot more workers than the former.
I'll try to come up with some code that I'll share here.

BTW the *PDict() family in Biostrings is for finding the matches of a
collection of patterns. You say you want to find "all genomic
(mis)matches of a 23-bp candidate Cas9 sequence". Any reason you're not
using vmatchPattern() (or vcountPattern()) for that?

Cheers,
H.


On 11/7/19 02:11, Bhagwat, Aditya wrote:
> Dear bioc-devel,
>
> multicrispr
> 
>  provides
> functions for Crispr/Cas9 gRNA design (and is being prepared for BioC).
> One task involves finding all genomic (mis)matches of a 23-bp candidate
> Cas9 sequence. Currently this is done with `Biostrings::vcountPDict`, an
> approach that is successful, though not fast. An alternative would be to
> switch to short read mapping rather than (Bio)string matching, which
> involves a one-time indexing effort, but subsequent fast alignment.
>
> `Rsubread::align` seems to be limited to max. 16 `nBestLocations`,
> whereas I know from vcountPDict that some Cas9 candidates have hundreds
> of genomic matches.
>
> `QuasR::qAlign` (connecting to Bowtie) does not mention an upper limit
> on `maxHits`.
>
> Feedback request�
>
> Michael, would QuasR/(R)bowtie be a good approach to do this?
>
> Wei, did I overlook a way to do this with Rsubread?
>
> Herve, is there an elegant way to speed up vcountPDict (parallelize?)
>
> Thankyou J
>
> Aditya
>

--
Herv� Pag�s

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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