date:20160215

Re: [Bioc-devel] dimnames of multidimensional assays in SummarizedExperiment

2016-02-15 Thread Hervé Pagès


Hi Pete,

I'll look into this. Thanks!

H.

On 02/10/2016 12:33 PM, Peter Hickey wrote:

The assays slot in a SummarizedExperiment object supports elements
with up to 4 dimensions [*]

library(SummarizedExperiment)
makeSE <- function(n) {
   assay <- array(1:2^n,
  dim = rep(2, n),
  dimnames = split(letters[1:(2 * n)], seq_len(n)))
   SummarizedExperiment(assay)
}
x <- makeSE(4)

However, the "higher-order" dimnames of the assays aren't preserved
when calling the `assays` or `assay` getters:


dimnames(assay(x, withDimnames = TRUE))

[[1]]
[1] "a" "e"

[[2]]
[1] "b" "f"

[[3]]
NULL

[[4]]
NULL

This is despite the data still being available in the assays slot:


dimnames(x@assays[[1]])

1`
[1] "a" "e"

2`
[1] "b" "f"

3`
[1] "c" "g"

4`
[1] "d" "h"

The following patch fixes this by only touching the rownames and
colnames and not touching the "higher-order" dimnames. Seem
reasonable?

Index: R/SummarizedExperiment-class.R
===
   --- R/SummarizedExperiment-class.R (revision 113505)
+++ R/SummarizedExperiment-class.R (working copy)
@@ -174,7 +174,10 @@
{
   assays <- as(x@assays, "SimpleList")
   if (withDimnames)
 -endoapply(assays, "dimnames<-", dimnames(x))
   + endoapply(assays, function(assay) {
 +dimnames(assay)[1:2] <- dimnames(x)
 +assay
 +})
   else
 assays
})

[*] In fact, the assay elements can have more than 4 dimensions when
constructed, although subsetting with `[` isn't supported (possibly
things other than subsetting break as well in this case).

# No error
y <- makeSE(5)
y

# Error
y[1, ]

Perhaps there should be a check in the constructor that all assay
elements have < 5 dimensions?

Cheers,
Pete

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--
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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Re: [Bioc-devel] package citation and version is not updated

2016-02-15 Thread Dan Tenenbaum

OK, I looked into this a bit. The citation is there now and I will continue to 
look into this.
Dan


- Original Message -
> From: "Michael Love" 
> To: "Dan Tenenbaum" 
> Cc: "bioc-devel" 
> Sent: Monday, February 15, 2016 7:36:14 AM
> Subject: Re: [Bioc-devel] package citation and version is not updated

> hi Dan,
> 
> I'm having the same issue with tximport:
> 
> http://bioconductor.org/packages/devel/bioc/html/tximport.html
> 
> The CITATION file has been in there since the package was added to devel
> last week
> 
> https://github.com/Bioconductor-mirror/tximport/blob/master/inst/CITATION
> 
> citation("tximport") works
> 
> thanks,
> Mike
> 
> On Fri, Jan 29, 2016 at 5:56 PM, Dan Tenenbaum 
> wrote:
> 
>> This is fixed now. Thanks for the report.
>> Dan
>>
>>
>> - Original Message -
>> > From: "Ludwig Geistlinger" 
>> > To: "bioc-devel" 
>> > Sent: Friday, January 29, 2016 2:06:37 AM
>> > Subject: [Bioc-devel] package citation and version is not updated
>>
>> > Dear Dan,
>> >
>> > For some reason the citation on my package's landing page
>> >
>> > http://bioconductor.org/packages/EnrichmentBrowser.html
>> >
>> > is not displayed in agreement with my inst/CITATION file.
>> >
>> > Furthermore, the version number is also not up to date here, although
>> > displayed correctly at the bottom of the page (--> Package Archives).
>> >
>> > How to resolve this?
>> >
>> > Thx,
>> > Ludwig
>> >
>> > --
>> > Dipl.-Bioinf. Ludwig Geistlinger
>> >
>> > Lehr- und Forschungseinheit für Bioinformatik
>> > Institut für Informatik
>> > Ludwig-Maximilians-Universität München
>> > Amalienstrasse 17, 2. Stock, Büro A201
>> > 80333 München
>> >
>> > Tel.: 089-2180-4067
>> > eMail: ludwig.geistlin...@bio.ifi.lmu.de
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] BiocGenerics attaches when methods package is imported

2016-02-15 Thread Andreas Kapouranis

Hi Michael,

Thanks for the reply.

I created a minimal reproducible package with the issue. As it seems the
warning comes because I have a 'data' folder where I have stored some
example data, and one of the data is stored in GRanges format.
If I delete the GRanges example data and keep any other data, I get no
warning.

So the issue is only when I import the 'methods' package and I have data
locally stored as GRanges objects in the 'data' folder.

You can download and install the simple example package by typing:

devtools::install_github("andreaskapou/simplePackage")


Or you can see the code in the following link, which just contains a simple
function to call the methods::is() function and create a GRanges object.
https://github.com/andreaskapou/simplePackage

Thanks,
Andreas

--
Chantriolnt - Andreas Kapourani
PhD Candidate in Data Science,
School of Informatics,
University of Edinburgh

e-mail  : c.a.kapour...@sms.ed.ac.uk  
   : kapouranis.andr...@gmail.com

On Mon, Feb 15, 2016 at 4:22 PM, Michael Lawrence  wrote:

> It would be helpful to have a reproducible example, i.e., your actual
> package or a skeleton of it that reproduces the issue. Btw, you might
> be able to debug this behavior by:
>
> debug(tools::undoc)
> tools::undoc(dir=yourPackageDir)
>
>
>
> On Mon, Feb 15, 2016 at 7:52 AM, Andreas Kapouranis
>  wrote:
> > Hi,
> >
> > I am developing a package for Bioconductor, and I have a weird issue when
> > importing the 'methods' package. Before I add the 'methods' package in
> > Imoprts in the DESCRIPTION file, I pass the CMD check without any
> warnings.
> >
> > However, when I add the 'methods' package in the Imports field, I get a
> > warning during CMD check. (I need the methods package since I use the
> > methods::is() function, and if I call it just as is(), when running the
> > package from Rscript will fail since by default it does not load the
> > 'methods' package.)
> >
> > I read a similar issue here:
> > https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html
> > and I updated all my packages from Bioconductor including IRanges and
> > GenomicRanges.
> >
> > This is the warning that I get, which is exactly the same as the previous
> > issue in Bioc-Devel, and I understand that for some reason the
> BiocGenerics
> > is attached only when the 'methods' package is imported.
> >
> > * checking for missing documentation entries ... WARNING
> >
> > Attaching package: ‘BiocGenerics’
> >
> > The following objects are masked from ‘package:parallel’:
> >
> > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
> > clusterExport, clusterMap, parApply, parCapply, parLapply,
> > parLapplyLB, parRapply, parSapply, parSapplyLB
> >
> > The following objects are masked from ‘package:stats’:
> >
> > IQR, mad, xtabs
> >
> > The following objects are masked from ‘package:base’:
> >
> > Filter, Find, Map, Position, Reduce, anyDuplicated, append,
> > as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
> > eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
> > lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
> > pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
> > tapply, union, unique, unlist, unsplit
> >
> > All user-level objects in a package should have documentation entries.
> > See chapter ‘Writing R documentation files’ in the ‘Writing R
> > Extensions’ manual.
> >
> >
> >
> > My DESCRIPTION file when I add the 'methods' package is the following:
> > ...
> > Depends: R (>= 3.2.0)
> > LazyData: TRUE
> > RoxygenNote: 5.0.1
> > Imports: GenomicRanges,
> > IRanges,
> > assertthat,
> > S4Vectors,
> > graphics,
> > data.table,
> > methods
> > Suggests: knitr,
> > rmarkdown,
> > testthat
> > VignetteBuilder: knitr
> >
> >
> >
> > Regards,
> > Andreas
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] BiocGenerics attaches when methods package is imported

2016-02-15 Thread Andreas Kapouranis

Hi Joris,

Apologies for not including the NAMESPACE file, but I have included the
methods package also there, although I have used:

importFrom(methods,is)

since I just need the is() function for the time being.

Regards,
Andreas

--
Chantriolnt - Andreas Kapourani
PhD Candidate in Data Science,
School of Informatics,
University of Edinburgh

e-mail  : c.a.kapour...@sms.ed.ac.uk  
   : kapouranis.andr...@gmail.com

On Mon, Feb 15, 2016 at 4:16 PM, Joris Meys  wrote:

> Hi Andreas,
>
> for a good understanding: just mentioning the methods package in the
> DESCRIPTION file isn't doing a thing if you don't also add
>
> import(methods)
>
> to the NAMESPACE file.
>
> So it looks like the warning occurs when the package indicates that the
> methods package is imported when it actually isn't. Do you still get that
> warning if you update the NAMESPACE file?
>
> Cheers
> Joris
>
> On Mon, Feb 15, 2016 at 4:52 PM, Andreas Kapouranis <
> kapouranis.andr...@gmail.com> wrote:
>
>> Hi,
>>
>> I am developing a package for Bioconductor, and I have a weird issue when
>> importing the 'methods' package. Before I add the 'methods' package in
>> Imoprts in the DESCRIPTION file, I pass the CMD check without any
>> warnings.
>>
>> However, when I add the 'methods' package in the Imports field, I get a
>> warning during CMD check. (I need the methods package since I use the
>> methods::is() function, and if I call it just as is(), when running the
>> package from Rscript will fail since by default it does not load the
>> 'methods' package.)
>>
>> I read a similar issue here:
>> https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html
>> and I updated all my packages from Bioconductor including IRanges and
>> GenomicRanges.
>>
>> This is the warning that I get, which is exactly the same as the previous
>> issue in Bioc-Devel, and I understand that for some reason the
>> BiocGenerics
>> is attached only when the 'methods' package is imported.
>>
>> * checking for missing documentation entries ... WARNING
>>
>> Attaching package: ‘BiocGenerics’
>>
>> The following objects are masked from ‘package:parallel’:
>>
>> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
>> clusterExport, clusterMap, parApply, parCapply, parLapply,
>> parLapplyLB, parRapply, parSapply, parSapplyLB
>>
>> The following objects are masked from ‘package:stats’:
>>
>> IQR, mad, xtabs
>>
>> The following objects are masked from ‘package:base’:
>>
>> Filter, Find, Map, Position, Reduce, anyDuplicated, append,
>> as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
>> eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
>> lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
>> pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
>> tapply, union, unique, unlist, unsplit
>>
>> All user-level objects in a package should have documentation entries.
>> See chapter ‘Writing R documentation files’ in the ‘Writing R
>> Extensions’ manual.
>>
>>
>>
>> My DESCRIPTION file when I add the 'methods' package is the following:
>> ...
>> Depends: R (>= 3.2.0)
>> LazyData: TRUE
>> RoxygenNote: 5.0.1
>> Imports: GenomicRanges,
>> IRanges,
>> assertthat,
>> S4Vectors,
>> graphics,
>> data.table,
>> methods
>> Suggests: knitr,
>> rmarkdown,
>> testthat
>> VignetteBuilder: knitr
>>
>>
>>
>> Regards,
>> Andreas
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
>
> --
> Joris Meys
> Statistical consultant
>
> Ghent University
> Faculty of Bioscience Engineering
> Department of Mathematical Modelling, Statistics and Bio-Informatics
>
> tel : +32 9 264 59 87
> joris.m...@ugent.be
> ---
> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>

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Re: [Bioc-devel] BiocGenerics attaches when methods package is imported

2016-02-15 Thread Michael Lawrence

It would be helpful to have a reproducible example, i.e., your actual
package or a skeleton of it that reproduces the issue. Btw, you might
be able to debug this behavior by:

debug(tools::undoc)
tools::undoc(dir=yourPackageDir)



On Mon, Feb 15, 2016 at 7:52 AM, Andreas Kapouranis
 wrote:
> Hi,
>
> I am developing a package for Bioconductor, and I have a weird issue when
> importing the 'methods' package. Before I add the 'methods' package in
> Imoprts in the DESCRIPTION file, I pass the CMD check without any warnings.
>
> However, when I add the 'methods' package in the Imports field, I get a
> warning during CMD check. (I need the methods package since I use the
> methods::is() function, and if I call it just as is(), when running the
> package from Rscript will fail since by default it does not load the
> 'methods' package.)
>
> I read a similar issue here:
> https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html
> and I updated all my packages from Bioconductor including IRanges and
> GenomicRanges.
>
> This is the warning that I get, which is exactly the same as the previous
> issue in Bioc-Devel, and I understand that for some reason the BiocGenerics
> is attached only when the 'methods' package is imported.
>
> * checking for missing documentation entries ... WARNING
>
> Attaching package: ‘BiocGenerics’
>
> The following objects are masked from ‘package:parallel’:
>
> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
> clusterExport, clusterMap, parApply, parCapply, parLapply,
> parLapplyLB, parRapply, parSapply, parSapplyLB
>
> The following objects are masked from ‘package:stats’:
>
> IQR, mad, xtabs
>
> The following objects are masked from ‘package:base’:
>
> Filter, Find, Map, Position, Reduce, anyDuplicated, append,
> as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
> eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
> lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
> pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
> tapply, union, unique, unlist, unsplit
>
> All user-level objects in a package should have documentation entries.
> See chapter ‘Writing R documentation files’ in the ‘Writing R
> Extensions’ manual.
>
>
>
> My DESCRIPTION file when I add the 'methods' package is the following:
> ...
> Depends: R (>= 3.2.0)
> LazyData: TRUE
> RoxygenNote: 5.0.1
> Imports: GenomicRanges,
> IRanges,
> assertthat,
> S4Vectors,
> graphics,
> data.table,
> methods
> Suggests: knitr,
> rmarkdown,
> testthat
> VignetteBuilder: knitr
>
>
>
> Regards,
> Andreas
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] BiocGenerics attaches when methods package is imported

2016-02-15 Thread Joris Meys

Hi Andreas,

for a good understanding: just mentioning the methods package in the
DESCRIPTION file isn't doing a thing if you don't also add

import(methods)

to the NAMESPACE file.

So it looks like the warning occurs when the package indicates that the
methods package is imported when it actually isn't. Do you still get that
warning if you update the NAMESPACE file?

Cheers
Joris

On Mon, Feb 15, 2016 at 4:52 PM, Andreas Kapouranis <
kapouranis.andr...@gmail.com> wrote:

> Hi,
>
> I am developing a package for Bioconductor, and I have a weird issue when
> importing the 'methods' package. Before I add the 'methods' package in
> Imoprts in the DESCRIPTION file, I pass the CMD check without any warnings.
>
> However, when I add the 'methods' package in the Imports field, I get a
> warning during CMD check. (I need the methods package since I use the
> methods::is() function, and if I call it just as is(), when running the
> package from Rscript will fail since by default it does not load the
> 'methods' package.)
>
> I read a similar issue here:
> https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html
> and I updated all my packages from Bioconductor including IRanges and
> GenomicRanges.
>
> This is the warning that I get, which is exactly the same as the previous
> issue in Bioc-Devel, and I understand that for some reason the BiocGenerics
> is attached only when the 'methods' package is imported.
>
> * checking for missing documentation entries ... WARNING
>
> Attaching package: ‘BiocGenerics’
>
> The following objects are masked from ‘package:parallel’:
>
> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
> clusterExport, clusterMap, parApply, parCapply, parLapply,
> parLapplyLB, parRapply, parSapply, parSapplyLB
>
> The following objects are masked from ‘package:stats’:
>
> IQR, mad, xtabs
>
> The following objects are masked from ‘package:base’:
>
> Filter, Find, Map, Position, Reduce, anyDuplicated, append,
> as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
> eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
> lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
> pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
> tapply, union, unique, unlist, unsplit
>
> All user-level objects in a package should have documentation entries.
> See chapter ‘Writing R documentation files’ in the ‘Writing R
> Extensions’ manual.
>
>
>
> My DESCRIPTION file when I add the 'methods' package is the following:
> ...
> Depends: R (>= 3.2.0)
> LazyData: TRUE
> RoxygenNote: 5.0.1
> Imports: GenomicRanges,
> IRanges,
> assertthat,
> S4Vectors,
> graphics,
> data.table,
> methods
> Suggests: knitr,
> rmarkdown,
> testthat
> VignetteBuilder: knitr
>
>
>
> Regards,
> Andreas
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel




-- 
Joris Meys
Statistical consultant

Ghent University
Faculty of Bioscience Engineering
Department of Mathematical Modelling, Statistics and Bio-Informatics

tel : +32 9 264 59 87
joris.m...@ugent.be
---
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php

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[Bioc-devel] BiocGenerics attaches when methods package is imported

2016-02-15 Thread Andreas Kapouranis

Hi,

I am developing a package for Bioconductor, and I have a weird issue when
importing the 'methods' package. Before I add the 'methods' package in
Imoprts in the DESCRIPTION file, I pass the CMD check without any warnings.

However, when I add the 'methods' package in the Imports field, I get a
warning during CMD check. (I need the methods package since I use the
methods::is() function, and if I call it just as is(), when running the
package from Rscript will fail since by default it does not load the
'methods' package.)

I read a similar issue here:
https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html
and I updated all my packages from Bioconductor including IRanges and
GenomicRanges.

This is the warning that I get, which is exactly the same as the previous
issue in Bioc-Devel, and I understand that for some reason the BiocGenerics
is attached only when the 'methods' package is imported.

* checking for missing documentation entries ... WARNING

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, xtabs

The following objects are masked from ‘package:base’:

Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unlist, unsplit

All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.



My DESCRIPTION file when I add the 'methods' package is the following:
...
Depends: R (>= 3.2.0)
LazyData: TRUE
RoxygenNote: 5.0.1
Imports: GenomicRanges,
IRanges,
assertthat,
S4Vectors,
graphics,
data.table,
methods
Suggests: knitr,
rmarkdown,
testthat
VignetteBuilder: knitr



Regards,
Andreas

[[alternative HTML version deleted]]

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Re: [Bioc-devel] package citation and version is not updated

2016-02-15 Thread Michael Love

hi Dan,

I'm having the same issue with tximport:

http://bioconductor.org/packages/devel/bioc/html/tximport.html

The CITATION file has been in there since the package was added to devel
last week

https://github.com/Bioconductor-mirror/tximport/blob/master/inst/CITATION

citation("tximport") works

thanks,
Mike

On Fri, Jan 29, 2016 at 5:56 PM, Dan Tenenbaum 
wrote:

> This is fixed now. Thanks for the report.
> Dan
>
>
> - Original Message -
> > From: "Ludwig Geistlinger" 
> > To: "bioc-devel" 
> > Sent: Friday, January 29, 2016 2:06:37 AM
> > Subject: [Bioc-devel] package citation and version is not updated
>
> > Dear Dan,
> >
> > For some reason the citation on my package's landing page
> >
> > http://bioconductor.org/packages/EnrichmentBrowser.html
> >
> > is not displayed in agreement with my inst/CITATION file.
> >
> > Furthermore, the version number is also not up to date here, although
> > displayed correctly at the bottom of the page (--> Package Archives).
> >
> > How to resolve this?
> >
> > Thx,
> > Ludwig
> >
> > --
> > Dipl.-Bioinf. Ludwig Geistlinger
> >
> > Lehr- und Forschungseinheit für Bioinformatik
> > Institut für Informatik
> > Ludwig-Maximilians-Universität München
> > Amalienstrasse 17, 2. Stock, Büro A201
> > 80333 München
> >
> > Tel.: 089-2180-4067
> > eMail: ludwig.geistlin...@bio.ifi.lmu.de
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] Close connections continuously in fasta.index in Biostrings

2016-02-15 Thread Thomas Lin Pedersen

Hi (mostly Hervé)

I’m running into problems trying to run fasta.index() from Biostrings on a list 
of 4700 files, as the limit on open files are reached. Is it possible to 
continuously open and close the connections in the C code to circumvent this? I 
expect this problem also arises with readXStringSet..? I know dealing with such 
a high number of files in one chunk is probably an edge case, so I can 
understand if this is not something you wish to change the code for...

with best wishes

Thomas Lin Pedersen
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