Re: [Bioc-devel] there is no package called 'zlibbioc' on WINDOWS

2016-09-21 Thread Moritz Gerstung 
Hi Dan

Has this problem problem resurrected?

I see many packages depending on zlibbioc fail, including gage, Rhtslib and 
deepSNV.

http://bioconductor.org/checkResults/devel/bioc-LATEST/gage/moscato1-install.html

Cheers

Moritz


> On 1 Jun 2016, at 20:40, Dan Tenenbaum  wrote:
> 
> It's a problem on the server itself. It will not be present in today's build 
> report which should be up in half an hour or so.
> 
> This is an intermittent problem, not a continuous one.
> 
> Dan
> 
> 
> - Original Message -
>> From: "Hartley, Stephen (NIH/NHGRI) [F]" 
>> To: "Dan Tenenbaum" , "Monther Alhamdoosh" 
>> , "bioc-devel"
>> 
>> Sent: Wednesday, June 1, 2016 12:11:27 PM
>> Subject: RE: [Bioc-devel] there is no package called 'zlibbioc' on WINDOWS
> 
>> It looks like the zlibbioc package still won't load on moscato2. This is 
>> causing
>> something a ton of packages to fail at build (almost half?).
>> 
>> Does anyone have any idea what the issue is? Is it a problem with a patch to 
>> the
>> zlibbioc package, or a problem on the server itself?
>> 
>> -Steve
>> 
>> -Original Message-
>> From: Dan Tenenbaum [mailto:dtene...@fredhutch.org]
>> Sent: Thursday, May 26, 2016 9:03 PM
>> To: Monther Alhamdoosh; bioc-devel@r-project.org
>> Subject: Re: [Bioc-devel] there is no package called 'zlibbioc' on WINDOWS
>> 
>> It's an as yet unknown problem with the build system. It's very likely that 
>> it
>> will resolve itself in tonight's builds.
>> 
>> Dan
>> 
>> 
>> On May 26, 2016 5:04:43 PM PDT, Monther Alhamdoosh  
>> wrote:
>>> Hi developers,
>>> 
>>> Our package named EGSEA seems to fail to be built on Windows as it
>>> depends on "gage" which depends on zlibbioc. The problem appears in the
>>> release branch and not in the devel branch.
>>> 
>>> Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck =
>>> vI[[i]])
>>> :
>>> 
>>> there is no package called 'zlibbioc'
>>> 
>>> ERROR: lazy loading failed for package 'gage'
>>> 
>>> Cheers,
>>> Monther
>>> 
>>> [[alternative HTML version deleted]]
>>> 
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>> 
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[Bioc-devel] Job opportunities in translational cancer genomics

2015-08-19 Thread Moritz Gerstung 
DeaR Bioconductor developers

There are currently multiple vacancies for postdoctoral researchers in my new 
research group at the European Bioinformatics Institute close to Cambridge, UK 
(http://www.ebi.ac.uk/research/gerstung). I'm looking for statistically 
inclined researchers to work on methods for translational applications of 
cancer genomics.

This could be part of either the prestigious EBPOD postdoctoral programme, in 
collaboration with the Biomedical Research Campus at the University of 
Cambridge (http://www.ebi.ac.uk/research/postdocs/ebpods, closing on 3 
September), or on a post from my core funding. Funding is based on tax exempt 
EMBL stipend rates.

Interested applicants should send me their short CV including publication list. 
Please forward this to other potential candidates and apologise the spam if 
this is of no interest for you.

Many thanks,

Moritz

--
Moritz Gerstung
Research Group Leader

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton, Cambridgeshire
CB10 1SD 
UK

tel:  +44 (0)1223 49 4636
mail  moritz.gerst...@ebi.ac.uk
web   www.ebi.ac.uk/research/gerstung 
blog  mg14.github.io
c0de  github.com/mg14


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.

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Re: [Bioc-devel] Bioconductor git-svn bridge is available

2014-05-12 Thread Moritz Gerstung 
Hi all

Following Kasper's idea from a couple of months ago: Would it be possible to 
have the git-svn bridge synchronise a branch other than master? 

If so, one could use the git subtree command,

git subtree split -P minfi -b biocsvn

to create a branch 'biocsvn' only containing minfi directory [package]. This 
branch would then be synchronised over the git-svn bridge. Changes in the 
biocsvn branch can be merged back into the master branch and the correct 
directory with 

git subtree merge -P minfi biocsvn

I would also fancy a directory structure as Kasper suggested, where the actual 
R package is a subdirectory. This would allow for placing extra files such as 
README.md or Makefile into the root directory and other project related data 
which shouldn't go into the package, but may be useful, in other directories. 
As a side effect one can also screw up the git master branch without breaking 
the devel repository.

I'm not a git guru, so maybe I'm missing something here, but it seems feasible.

Cheers,

Moritz

PS. Resent as it bounced from list before.


On 21 Feb 2014, at 17:00, Kasper Daniel Hansen kasperdanielhan...@gmail.com 
wrote:

 Thanks everyone, it was worth a question.
 
 Perhaps I will figure out how to use submodules.
 
 Kasper
 
 
 On Fri, Feb 21, 2014 at 11:45 AM, Dan Tenenbaum dtene...@fhcrc.org wrote:
 
 
 
 - Original Message -
 From: Sean Davis sdav...@mail.nih.gov
 To: Kasper Daniel Hansen kasperdanielhan...@gmail.com
 Cc: bioc-devel@r-project.org, Dan Tenenbaum dtene...@fhcrc.org
 Sent: Friday, February 21, 2014 7:08:21 AM
 Subject: Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge is available
 
 
 
 I doubt this is possible given the atomic nature of a git repository.
 You might look at using a second git repository and including the
 minfi package as a git submodule of that second repository. Then,
 you can keep things in sync, but the minfi repository remains
 atomic.
 
 
 I think Sean is correct.
 Dan
 
 
 Sean
 On Feb 21, 2014 9:44 AM, Kasper Daniel Hansen 
 kasperdanielhan...@gmail.com  wrote:
 
 
 Question: is it possible to synchronize a subset of a github repos?
 For
 minfi, I would like my github to be
 
 minfi-devel
 /minfi
 OTHER SCRIPTS
 
 where OTHER SCRIPTS could be notes or test scripts I use for internal
 development. I then only want to synchronize the
 minfi-devel/minfi
 directory with Bioc.
 
 Kasper
 
 
 On Sun, Feb 9, 2014 at 9:55 AM, Kasper Daniel Hansen 
 kasperdanielhan...@gmail.com  wrote:
 
 Seems to work for me; I have now populated my github repo.
 
 Thanks for the help,
 Kasper
 
 
 On Sun, Feb 9, 2014 at 2:35 AM, Dan Tenenbaum  dtene...@fhcrc.org
 wrote:
 
 This should be fixed now.
 Thanks.
 Dan
 
 
 - Original Message -
 From: Kasper Daniel Hansen  kasperdanielhan...@gmail.com 
 To: Dan Tenenbaum  dtene...@fhcrc.org 
 Cc: bioc-devel@r-project.org
 Sent: Saturday, February 8, 2014 7:07:44 PM
 Subject: Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge is
 available
 
 
 
 Yes, see screenshot
 
 
 (I do know I have a whitespace in front of the github url and I
 get a
 note and I fixed it.
 
 
 Kasper
 
 
 On Sat, Feb 8, 2014 at 9:56 PM, Dan Tenenbaum 
 dtene...@fhcrc.org 
 wrote:
 
 
 
 https://github.com/kasperdanielhansen/minfi
 
 
 
 
 
 
 [[alternative HTML version deleted]]
 
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 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.

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[Bioc-devel] VariantAnnotation bug when loading multiple regions from vcf

2013-03-05 Thread Moritz Gerstung 
Hi,

I discovered the following problem in the geno() elements of the VCF object 
when I load multiple regions from a .vcf file:

## Correct
 tmp = readVcf(system.file(extdata, chr22.vcf.gz, 
 package=VariantAnnotation), hg19)[1:10]
 geno(tmp)$GT
   HG00096 HG00097 HG00099 HG00100 HG00101
rs7410291   0|0   0|0   1|0   0|0   0|0  
rs147922003 0|0   0|0   0|0   0|0   0|0  
rs114143073 0|0   0|0   0|0   0|0   0|0  
rs141778433 0|0   0|0   0|0   0|0   0|0  
rs182170314 0|0   0|0   0|0   0|0   0|0  
rs115145310 0|0   0|0   0|0   0|0   0|0  
rs186769856 0|0   0|0   0|0   0|0   0|0  
rs77627744  0|0   0|0   0|0   0|0   0|0  
rs193230365 0|0   0|0   0|0   0|0   0|0  
rs9627788   0|0   0|0   1|0   0|0   0|0  

## Wrong: Load regions separately using ScanVcfParam(which= )
 tmp2 = readVcf(system.file(extdata, chr22.vcf.gz, 
 package=VariantAnnotation), hg19, param=ScanVcfParam(which=rowData(tmp)))
 geno(tmp2)$GT
   HG00096 HG00097 HG00099 HG00100 HG00101
rs7410291   0|0   0|0   0|0   0|0   0|0  
rs147922003 0|0   0|0   0|0   0|0   0|0  
rs114143073 1|0   0|0   0|0   0|0   0|0  
rs141778433 0|0   0|0   0|0   0|0   0|0  
rs182170314 0|0   0|0   0|0   0|0   0|0  
rs115145310 0|0   0|0   0|0   0|0   0|0  
rs186769856 0|0   0|0   0|0   0|0   0|0  
rs77627744  0|0   0|0   0|0   0|0   1|0  
rs193230365 0|0   0|0   0|0   0|0   0|0  
rs9627788   0|0   0|0   0|0   0|0   0|0  

Note how the elements have been added by column instead of by row.

The following solved the issue for me:

$svn diff VariantAnnotation/
Index: VariantAnnotation/R/AllUtilities.R
===
--- VariantAnnotation/R/AllUtilities.R  (revision 73920)
+++ VariantAnnotation/R/AllUtilities.R  (working copy)
@@ -62,8 +62,8 @@
cmb
} else {
trans - lapply(elt, t)
-cmb - matrix(t(do.call(c, trans)), 
-  length(lst[[rowData]]), d[2])
+cmb - matrix(do.call(c, trans), 
+  length(lst[[rowData]]), d[2], byrow=TRUE)
cmb
}
}) 


My suspicion is that the transposition t() on line 65 didn't do the desired 
job, as do.call() returned a vector.. 

I don't fully understand the code, so it may be worth double checking.
For example, I didn't check the case when the individual geno entries contain 
more than a single value for each variant and sample.

The same problem also occurred for VariantAnnotation_1.4.9.

Best wishes,

Moritz



P.S.

 sessionInfo()
R Under development (unstable) (2013-02-05 r61843)
Platform: x86_64-apple-darwin11.4.2 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] parallel  stats graphics  grDevices utils datasets  methods  
[8] base 

other attached packages:
[1] VariantAnnotation_1.5.41 Rsamtools_1.11.20Biostrings_2.27.11  
[4] biomaRt_2.15.0   GenomicRanges_1.11.34IRanges_1.17.35 
[7] BiocGenerics_0.5.6   BiocInstaller_1.9.6  RColorBrewer_1.0-5  

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.21.12   Biobase_2.19.2  bitops_1.0-5   
[4] BSgenome_1.27.1 DBI_0.2-5   GenomicFeatures_1.11.13
[7] RCurl_1.95-3RSQLite_0.11.2  rtracklayer_1.19.9 
[10] stats4_3.0.0tools_3.0.0 XML_3.95-0.1   
[13] zlibbioc_1.5.0 



---
Moritz Gerstung
Postdoctoral Fellow

Cancer Genome Project
Wellcome Trust Sanger Institute
Wellcome Trust Genome Campus
Hinxton, Cambridgeshire
CB10 1SA
UK



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.

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