Re: [Bioc-devel] as.list of a GRanges

2018-02-15 Thread Bernat Gel 

Hi Hervé and others,

Thanks for the responses.

I woudn't call as.list() of a GRanges an "obscure behaviour" but more a 
"works as expected, even if not clearly documented" behaviour.


In any case I can change the code to as(gr, "GRangesList") as suggested.

Thanks again for the responses and discussion :)

Bernat


*Bernat Gel Moreno*
Bioinformatician

Hereditary Cancer Program
Program of Predictive and Personalized Medicine of Cancer (PMPPC)
Germans Trias i Pujol Research Institute (IGTP)

Campus Can Ruti
Carretera de Can Ruti, Camí de les Escoles s/n
08916 Badalona, Barcelona, Spain

Tel: (+34) 93 554 3068
Fax: (+34) 93 497 8654
08916 Badalona, Barcelona, Spain
b...@igtp.cat 
www.germanstrias.org 









El 02/15/2018 a las 11:19 PM, Hervé Pagès escribió:

On 02/15/2018 01:57 PM, Michael Lawrence wrote:



On Thu, Feb 15, 2018 at 1:45 PM, Hervé Pagès > wrote:


    On 02/15/2018 11:53 AM, Cook, Malcolm wrote:

    Hi,

    Can I ask, is this change under discussion in current release or
    so far in Bioconductor devel only (my assumption)?


    Bioconductor devel only.


   > On 02/15/2018 08:37 AM, Michael Lawrence wrote:
   > > So is as.list() no longer supported for GRanges objects?
    I have found it
   > > useful in places.
   >
   > Very few places. I found a dozen of them in the entire
    software repo.

    However there are probably more in the wild...


    What as.list() was doing on a GRanges object was not documented. 
Relying

    on some kind of obscure undocumented feature is never a good idea.


There's just too much that is documented implicitly through inherited 
behaviors, or where we say things like "this data structure behaves 
as one would expect given base R". It's not fair to claim that those 
features are undocumented. Our documentation is not complete enough 
to use it as an excuse.


It's not fair to suggest that this is a widely used feature either.

I've identified all the places in the 1500 software packages where
this was used, and, as I said, there were very few places. BTW I
fixed most of them but my plan is to fix all of them. Some of the
code that is outside the Bioc package corpus might be affected but
it's fair to assume that this will be a very rare occurence. This can
be mitigated by temporary restoring as.list() on GRanges, with a
deprecation message, and wait 1 more devel cycle to replace it with
the new behavior. I chose to disable it for now, on purpose, so I can
identify packages that break (the build report is a great tool for
that) and fix them.

I'm not using the fact that as.list() on a GRanges is not documented
as an excuse for anything. Only to help those with concerns to
relativize and relax.

H.




   > Now you should use as.list(as(gr, "GRangesList")) instead.
   > as.list() was behaving inconsistently on IRanges and
    GRanges objects,
   > which is blocking new developments. It will come back with
    a consistent
   > behavior. More generally speaking IRanges and GRanges will
    behave
   > consistently as far as their "list interpretation" is
    concerned.

    Can we please be assured to be reminded of this prominently in
    release notes?


    The changes will be announced and described on this list and in the
    NEWS files of the IRanges and GenomicRanges packages.

    H.


    Thanks!

    ~malcolm


    --     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 






___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] as.list of a GRanges

2018-02-15 Thread Hervé Pagès 

On 02/15/2018 01:57 PM, Michael Lawrence wrote:



On Thu, Feb 15, 2018 at 1:45 PM, Hervé Pagès > wrote:


On 02/15/2018 11:53 AM, Cook, Malcolm wrote:

Hi,

Can I ask, is this change under discussion in current release or
so far in Bioconductor devel only (my assumption)?


Bioconductor devel only.


   > On 02/15/2018 08:37 AM, Michael Lawrence wrote:
   > > So is as.list() no longer supported for GRanges objects?
I have found it
   > > useful in places.
   >
   > Very few places. I found a dozen of them in the entire
software repo.

However there are probably more in the wild...


What as.list() was doing on a GRanges object was not documented. Relying
on some kind of obscure undocumented feature is never a good idea.


There's just too much that is documented implicitly through inherited 
behaviors, or where we say things like "this data structure behaves as 
one would expect given base R". It's not fair to claim that those 
features are undocumented. Our documentation is not complete enough to 
use it as an excuse.


It's not fair to suggest that this is a widely used feature either.

I've identified all the places in the 1500 software packages where
this was used, and, as I said, there were very few places. BTW I
fixed most of them but my plan is to fix all of them. Some of the
code that is outside the Bioc package corpus might be affected but
it's fair to assume that this will be a very rare occurence. This can
be mitigated by temporary restoring as.list() on GRanges, with a
deprecation message, and wait 1 more devel cycle to replace it with
the new behavior. I chose to disable it for now, on purpose, so I can
identify packages that break (the build report is a great tool for
that) and fix them.

I'm not using the fact that as.list() on a GRanges is not documented
as an excuse for anything. Only to help those with concerns to
relativize and relax.

H.




   > Now you should use as.list(as(gr, "GRangesList")) instead.
   > as.list() was behaving inconsistently on IRanges and
GRanges objects,
   > which is blocking new developments. It will come back with
a consistent
   > behavior. More generally speaking IRanges and GRanges will
behave
   > consistently as far as their "list interpretation" is
concerned.

Can we please be assured to be reminded of this prominently in
release notes?


The changes will be announced and described on this list and in the
NEWS files of the IRanges and GenomicRanges packages.

H.


Thanks!

~malcolm


-- 
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 




--
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

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] as.list of a GRanges

2018-02-15 Thread Michael Lawrence 
On Thu, Feb 15, 2018 at 1:45 PM, Hervé Pagès  wrote:

> On 02/15/2018 11:53 AM, Cook, Malcolm wrote:
>
>> Hi,
>>
>> Can I ask, is this change under discussion in current release or so far
>> in Bioconductor devel only (my assumption)?
>>
>
> Bioconductor devel only.
>
>
>>   > On 02/15/2018 08:37 AM, Michael Lawrence wrote:
>>   > > So is as.list() no longer supported for GRanges objects? I have
>> found it
>>   > > useful in places.
>>   >
>>   > Very few places. I found a dozen of them in the entire software repo.
>>
>> However there are probably more in the wild...
>>
>
> What as.list() was doing on a GRanges object was not documented. Relying
> on some kind of obscure undocumented feature is never a good idea.
>
>
There's just too much that is documented implicitly through inherited
behaviors, or where we say things like "this data structure behaves as one
would expect given base R". It's not fair to claim that those features are
undocumented. Our documentation is not complete enough to use it as an
excuse.


>
>>   > Now you should use as.list(as(gr, "GRangesList")) instead.
>>   > as.list() was behaving inconsistently on IRanges and GRanges objects,
>>   > which is blocking new developments. It will come back with a
>> consistent
>>   > behavior. More generally speaking IRanges and GRanges will behave
>>   > consistently as far as their "list interpretation" is concerned.
>>
>> Can we please be assured to be reminded of this prominently in release
>> notes?
>>
>
> The changes will be announced and described on this list and in the
> NEWS files of the IRanges and GenomicRanges packages.
>
> H.
>
>
>> Thanks!
>>
>> ~malcolm
>>
>>
> --
> 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
>
>

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] as.list of a GRanges

2018-02-15 Thread Hervé Pagès 

On 02/15/2018 11:53 AM, Cook, Malcolm wrote:

Hi,

Can I ask, is this change under discussion in current release or so far in 
Bioconductor devel only (my assumption)?


Bioconductor devel only.



  > On 02/15/2018 08:37 AM, Michael Lawrence wrote:
  > > So is as.list() no longer supported for GRanges objects? I have found it
  > > useful in places.
  >
  > Very few places. I found a dozen of them in the entire software repo.

However there are probably more in the wild...


What as.list() was doing on a GRanges object was not documented. Relying
on some kind of obscure undocumented feature is never a good idea.



  > Now you should use as.list(as(gr, "GRangesList")) instead.
  > as.list() was behaving inconsistently on IRanges and GRanges objects,
  > which is blocking new developments. It will come back with a consistent
  > behavior. More generally speaking IRanges and GRanges will behave
  > consistently as far as their "list interpretation" is concerned.

Can we please be assured to be reminded of this prominently in release notes?


The changes will be announced and described on this list and in the
NEWS files of the IRanges and GenomicRanges packages.

H.



Thanks!

~malcolm



--
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

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] as.list of a GRanges

2018-02-15 Thread Michael Lawrence 
On Thu, Feb 15, 2018 at 11:53 AM, Cook, Malcolm  wrote:

> Hi,
>
> Can I ask, is this change under discussion in current release or so far in
> Bioconductor devel only (my assumption)?
>
>  > On 02/15/2018 08:37 AM, Michael Lawrence wrote:
>  > > So is as.list() no longer supported for GRanges objects? I have found
> it
>  > > useful in places.
>  >
>  > Very few places. I found a dozen of them in the entire software repo.
>
> However there are probably more in the wild...
>
>
Yes, this is what I meant. The Bioc package corpus is not very
representative for some of these entry points. Please keep that in mind
when making refactoring decisions.


>  > Now you should use as.list(as(gr, "GRangesList")) instead.
>  > as.list() was behaving inconsistently on IRanges and GRanges objects,
>  > which is blocking new developments. It will come back with a consistent
>  > behavior. More generally speaking IRanges and GRanges will behave
>  > consistently as far as their "list interpretation" is concerned.
>
>
Please be careful with these changes in behavior. Given the amount of code
that now depends on this software, consistency with existing behavior needs
to be weighted heavily.


> Can we please be assured to be reminded of this prominently in release
> notes?
>
> Thanks!
>
> ~malcolm
>

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] as.list of a GRanges

2018-02-15 Thread Cook, Malcolm 
Hi,

Can I ask, is this change under discussion in current release or so far in 
Bioconductor devel only (my assumption)?

 > On 02/15/2018 08:37 AM, Michael Lawrence wrote:
 > > So is as.list() no longer supported for GRanges objects? I have found it
 > > useful in places.
 > 
 > Very few places. I found a dozen of them in the entire software repo.

However there are probably more in the wild...

 > Now you should use as.list(as(gr, "GRangesList")) instead.
 > as.list() was behaving inconsistently on IRanges and GRanges objects,
 > which is blocking new developments. It will come back with a consistent
 > behavior. More generally speaking IRanges and GRanges will behave
 > consistently as far as their "list interpretation" is concerned.

Can we please be assured to be reminded of this prominently in release notes?

Thanks!

~malcolm
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] as.list of a GRanges

2018-02-15 Thread Hervé Pagès 

On 02/15/2018 08:37 AM, Michael Lawrence wrote:
So is as.list() no longer supported for GRanges objects? I have found it 
useful in places.


Very few places. I found a dozen of them in the entire software repo.
Now you should use as.list(as(gr, "GRangesList")) instead.
as.list() was behaving inconsistently on IRanges and GRanges objects,
which is blocking new developments. It will come back with a consistent
behavior. More generally speaking IRanges and GRanges will behave
consistently as far as their "list interpretation" is concerned.

I'll send more details later.

H.



On Thu, Feb 15, 2018 at 8:30 AM, Hervé Pagès > wrote:


Hi Bernat,

Use as(gr, "GRangesList") instead of as.list() on your GRanges objects.

Most of the times (e.g. for passing to lapply() or mclapply()), you
don't need an ordinary list, but, if you really want one, you can call
as.list() on the GRangesList object returned by as(gr, "GRangesList").

Hope this helps,
H.


On 02/15/2018 12:05 AM, Bernat Gel wrote:

Hi,

I'm having an error in the devel version of my package
karyoploteR due to an error when converting a GRanges into a
list of GRanges with "as.list".

This used to be possible and it was working a few weeks ago.

Am I suposed to use a different approach or is there a problem
somewhere?

Thanks!

Bernat

Here's an example

rr <- GRanges(seqnames = c("chr1", "chr2"), ranges =
IRanges(start=c(1, 2), end=c(11, 12)))
as.list(rr)

And the error message

Error in (function (classes, fdef, mtable)  :
    unable to find an inherited method for function
'getListElement' for signature '"GRanges"'


and the sessionInfo

  > sessionInfo()
R Under development (unstable) (2018-02-14 r74250)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS:
/software/debian-8/general/R-Bioc-Devel/current/lib/R/lib/libRblas.so
LAPACK:
/software/debian-8/general/R-Bioc-Devel/current/lib/R/lib/libRlapack.so

locale:
   [1] LC_CTYPE=en_US.UTF-8  LC_NUMERIC=C LC_TIME=C
LC_COLLATE=en_US.utf8
   [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
LC_PAPER=es_ES.UTF-8  LC_NAME=C
   [9] LC_ADDRESS=C  LC_TELEPHONE=C
LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats graphics  grDevices utils
datasets methods   base

other attached packages:
[1] GenomicRanges_1.31.20 GenomeInfoDb_1.15.5 IRanges_2.13.26
S4Vectors_0.17.32 BiocGenerics_0.25.3

loaded via a namespace (and not attached):
[1] zlibbioc_1.25.0    compiler_3.5.0 XVector_0.19.8
tools_3.5.0    GenomeInfoDbData_1.1.0
[6] RCurl_1.95-4.10    bitops_1.0-6




-- 
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 


___
Bioc-devel@r-project.org  mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel






--
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

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] as.list of a GRanges

2018-02-15 Thread Michael Lawrence 
So is as.list() no longer supported for GRanges objects? I have found it
useful in places.

On Thu, Feb 15, 2018 at 8:30 AM, Hervé Pagès  wrote:

> Hi Bernat,
>
> Use as(gr, "GRangesList") instead of as.list() on your GRanges objects.
>
> Most of the times (e.g. for passing to lapply() or mclapply()), you
> don't need an ordinary list, but, if you really want one, you can call
> as.list() on the GRangesList object returned by as(gr, "GRangesList").
>
> Hope this helps,
> H.
>
>
> On 02/15/2018 12:05 AM, Bernat Gel wrote:
>
>> Hi,
>>
>> I'm having an error in the devel version of my package karyoploteR due to
>> an error when converting a GRanges into a list of GRanges with "as.list".
>>
>> This used to be possible and it was working a few weeks ago.
>>
>> Am I suposed to use a different approach or is there a problem somewhere?
>>
>> Thanks!
>>
>> Bernat
>>
>> Here's an example
>>
>> rr <- GRanges(seqnames = c("chr1", "chr2"), ranges = IRanges(start=c(1,
>> 2), end=c(11, 12)))
>> as.list(rr)
>>
>> And the error message
>>
>> Error in (function (classes, fdef, mtable)  :
>>unable to find an inherited method for function 'getListElement' for
>> signature '"GRanges"'
>>
>>
>> and the sessionInfo
>>
>>  > sessionInfo()
>> R Under development (unstable) (2018-02-14 r74250)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Debian GNU/Linux 8 (jessie)
>>
>> Matrix products: default
>> BLAS: /software/debian-8/general/R-Bioc-Devel/current/lib/R/lib/li
>> bRblas.so
>> LAPACK: /software/debian-8/general/R-Bioc-Devel/current/lib/R/lib/li
>> bRlapack.so
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8  LC_NUMERIC=C LC_TIME=C
>> LC_COLLATE=en_US.utf8
>>   [5] LC_MONETARY=en_US.utf8LC_MESSAGES=en_US.utf8
>> LC_PAPER=es_ES.UTF-8  LC_NAME=C
>>   [9] LC_ADDRESS=C  LC_TELEPHONE=C LC_MEASUREMENT=en_US.utf8
>> LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel  stats4stats graphics  grDevices utils datasets
>> methods   base
>>
>> other attached packages:
>> [1] GenomicRanges_1.31.20 GenomeInfoDb_1.15.5 IRanges_2.13.26
>> S4Vectors_0.17.32 BiocGenerics_0.25.3
>>
>> loaded via a namespace (and not attached):
>> [1] zlibbioc_1.25.0compiler_3.5.0 XVector_0.19.8
>> tools_3.5.0GenomeInfoDbData_1.1.0
>> [6] RCurl_1.95-4.10bitops_1.0-6
>>
>>
>>
>>
> --
> 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
>
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] as.list of a GRanges

2018-02-15 Thread Hervé Pagès 

Hi Bernat,

Use as(gr, "GRangesList") instead of as.list() on your GRanges objects.

Most of the times (e.g. for passing to lapply() or mclapply()), you
don't need an ordinary list, but, if you really want one, you can call
as.list() on the GRangesList object returned by as(gr, "GRangesList").

Hope this helps,
H.

On 02/15/2018 12:05 AM, Bernat Gel wrote:

Hi,

I'm having an error in the devel version of my package karyoploteR due 
to an error when converting a GRanges into a list of GRanges with 
"as.list".


This used to be possible and it was working a few weeks ago.

Am I suposed to use a different approach or is there a problem somewhere?

Thanks!

Bernat

Here's an example

rr <- GRanges(seqnames = c("chr1", "chr2"), ranges = IRanges(start=c(1, 
2), end=c(11, 12)))

as.list(rr)

And the error message

Error in (function (classes, fdef, mtable)  :
   unable to find an inherited method for function 'getListElement' for 
signature '"GRanges"'



and the sessionInfo

 > sessionInfo()
R Under development (unstable) (2018-02-14 r74250)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS: /software/debian-8/general/R-Bioc-Devel/current/lib/R/lib/libRblas.so
LAPACK: 
/software/debian-8/general/R-Bioc-Devel/current/lib/R/lib/libRlapack.so


locale:
  [1] LC_CTYPE=en_US.UTF-8  LC_NUMERIC=C LC_TIME=C 
LC_COLLATE=en_US.utf8
  [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8 
LC_PAPER=es_ES.UTF-8  LC_NAME=C
  [9] LC_ADDRESS=C  LC_TELEPHONE=C LC_MEASUREMENT=en_US.utf8 
LC_IDENTIFICATION=C


attached base packages:
[1] parallel  stats4    stats graphics  grDevices utils datasets 
methods   base


other attached packages:
[1] GenomicRanges_1.31.20 GenomeInfoDb_1.15.5 IRanges_2.13.26 
S4Vectors_0.17.32 BiocGenerics_0.25.3


loaded via a namespace (and not attached):
[1] zlibbioc_1.25.0    compiler_3.5.0 XVector_0.19.8 
tools_3.5.0    GenomeInfoDbData_1.1.0

[6] RCurl_1.95-4.10    bitops_1.0-6





--
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

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] os X Build Error and Java

2018-02-15 Thread Shepherd, Lori 
Java 8 is installed on the Bioconductor build machines

merida2:~ biocbuild$ java -version
java version "1.8.0_111"
Java(TM) SE Runtime Environment (build 1.8.0_111-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.111-b14, mixed mode)

The CRAN binaries for R3.5 are not yet available for some of the dependency 
packages.  When CRAN releases those binaries the ERRORs should be rectified.  
If the package is building OK for malbec2 and tokay2, you can ignore the ERROR 
on merida2 for now.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Mattia Chiesa 

Sent: Thursday, February 15, 2018 4:34:06 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] os X Build Error and Java

Dear all,
I am the maintainer of the DaMiRseq package. For several days, my package is in 
ERROR status, only for merida2 (OS X 10.11.6 El Capitan / x86_64) in the devel 
release. I tried to trace the error back and I found out that the problem was 
due to the RWeka/Rwekajars packages.
I contacted the RWeka author and he kindly suggested to update the java version 
(java 8) in mer​ida2 (OS X 10.11.6 El Capitan / x86_64).
Could it be feasible?

Thanks in advance,
Mattia

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] os X Build Error and Java

2018-02-15 Thread Mattia Chiesa 
Dear all,
I am the maintainer of the DaMiRseq package. For several days, my package is in 
ERROR status, only for merida2 (OS X 10.11.6 El Capitan / x86_64) in the devel 
release. I tried to trace the error back and I found out that the problem was 
due to the RWeka/Rwekajars packages.
I contacted the RWeka author and he kindly suggested to update the java version 
(java 8) in mer​ida2 (OS X 10.11.6 El Capitan / x86_64).
Could it be feasible?

Thanks in advance,
Mattia

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] as.list of a GRanges

2018-02-15 Thread Bernat Gel 

Hi,

I'm having an error in the devel version of my package karyoploteR due 
to an error when converting a GRanges into a list of GRanges with "as.list".


This used to be possible and it was working a few weeks ago.

Am I suposed to use a different approach or is there a problem somewhere?

Thanks!

Bernat

Here's an example

rr <- GRanges(seqnames = c("chr1", "chr2"), ranges = IRanges(start=c(1, 
2), end=c(11, 12)))

as.list(rr)

And the error message

Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function 'getListElement' for 
signature '"GRanges"'



and the sessionInfo

> sessionInfo()
R Under development (unstable) (2018-02-14 r74250)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS: /software/debian-8/general/R-Bioc-Devel/current/lib/R/lib/libRblas.so
LAPACK: 
/software/debian-8/general/R-Bioc-Devel/current/lib/R/lib/libRlapack.so


locale:
 [1] LC_CTYPE=en_US.UTF-8  LC_NUMERIC=C LC_TIME=C 
LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8 
LC_PAPER=es_ES.UTF-8  LC_NAME=C
 [9] LC_ADDRESS=C  LC_TELEPHONE=C LC_MEASUREMENT=en_US.utf8 
LC_IDENTIFICATION=C


attached base packages:
[1] parallel  stats4    stats graphics  grDevices utils datasets  
methods   base


other attached packages:
[1] GenomicRanges_1.31.20 GenomeInfoDb_1.15.5 IRanges_2.13.26   
S4Vectors_0.17.32 BiocGenerics_0.25.3


loaded via a namespace (and not attached):
[1] zlibbioc_1.25.0    compiler_3.5.0 XVector_0.19.8 
tools_3.5.0    GenomeInfoDbData_1.1.0

[6] RCurl_1.95-4.10    bitops_1.0-6



--

*Bernat Gel Moreno*
Bioinformatician

Hereditary Cancer Program
Program of Predictive and Personalized Medicine of Cancer (PMPPC)
Germans Trias i Pujol Research Institute (IGTP)

Campus Can Ruti
Carretera de Can Ruti, Camí de les Escoles s/n
08916 Badalona, Barcelona, Spain

Tel: (+34) 93 554 3068
Fax: (+34) 93 497 8654
08916 Badalona, Barcelona, Spain
b...@igtp.cat 
www.germanstrias.org 









___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel