Re: [Bioc-devel] Struggles with correct import .....
Kasper Daniel Hansen kasperdanielhan...@gmail.com on Wed, 20 Nov 2013 15:37:00 -0500 writes: Ok, I analyzed the package using codetoolsBioC and there were a number of missing imports, including what Leonardo has described. I have fixed those in bumphunter 1.3.3 Kasper Impressing and interesting. I don't see 'codetoolsBioC' to be available via biocLite(). What's the recommended way to have it among the bioconductor packages ? Martin On Wed, Nov 20, 2013 at 3:28 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: I'll have a look. Basically, issues such as this is never the end-users problem and is likely to either be caused by bumphunter not importing correctly (most likely) or IRanges not exporting correctly. Kasper On Wed, Nov 20, 2013 at 3:02 PM, Leonardo Collado Torres lcoll...@jhsph.edu wrote: Hello, Found how to solve this. Basically, the NAMESPACE of the bumphunter package is not complete (I think). I downloaded http://bioconductor.org/packages/release/bioc/src/contrib/bumphunter_1.2.0.tar.gz , changed the version to 1.2.1 and added/modified the following lines to the NAMESPACE: importFrom(IRanges, IRanges, distance, distanceToNearest, subjectHits) importMethodsFrom(GenomicRanges, seqnames, sort, strand, elementMetadata) Once bumphunter was importing IRanges::distance, I got past the error I reported. Then I found other errors related to bumphunter not importing the GenomicRanges strand and elementMetadata functions, as well as the IRanges distanceToNearest, IRanges and subjectHits functions. Best, Leo On Wed, Nov 20, 2013 at 2:46 PM, Leonardo Collado Torres lcoll...@jhsph.edu wrote: Hi Harris, Answering your question from your first email, I do not think that it would help if bumphunter exported matchGenes() or .matchGenes(). Currently by just importing annotateNearest(), R is correctly able to use annotateNearest(), then .matchGenes(), and also nearestgene(). The problem is that nearestgene() uses IRanges::distance() but that function is not being found even after importing it. So as far as I understand, everything should be working since the NAMESPACE https://github.com/lcolladotor/derfinder/blob/v0.0.34/NAMESPACEhas: importFrom(bumphunter,annotateNearest) importMethodsFrom(IRanges,distance) importFrom(IRanges,distance) That is why I am confused and do not know what is the cause of the problem. One possible explanation could be that bumphunter's NAMESPACE https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter/NAMESPACEdoesn't import the IRanges::distance method. Regarding your second email (quoted below), I do not import the IRanges::nearest method, but it doesn't seem to be causing problems. That could be because bumphunter does import the IRanges::nearest method If I comment out line 147 of https://github.com/lcolladotor/derfinder/blob/v0.0.34/R/analyzeChr.R, aka, comment out library(bumphunter) the example for analyzeChr() fails with: Error in withCallingHandlers(expr, warning = function(w) invokeRestart(muffleWarning)) : could not find function distance So yes, I get the same error in real life and not only in CMD check. Adding to the NAMESPACE the following line doesn't help either. importMethodsFrom(IRanges,nearest) Best, Leo On Wed, Nov 20, 2013 at 2:06 PM, Harris A. Jaffee h...@jhu.edu wrote: In nearestgene(), before the call to distance, there is a call to nearest. How is that getting resolved? Did you import nearest from IRanges? Can you run nearestgene under debug and step through it, seeing how nearest is resolved? Do you only get an error from CMD check and not in real life? On Nov 20, 2013, at 12:16 PM, Leonardo Collado Torres wrote: Dear BioC-devel list, I have what I hope is a simple problem. Basically, a function in my package uses bumphunter::annotateNearest. This function in turn uses IRanges::distance. I would expect that using the following roxygen2 info would work: #' @importMethodsFrom IRanges distance #' @importFrom bumphunter annotateNearest #' @importFrom IRanges distance Note that distance is a generic in IRanges with methods for Ranges
Re: [Bioc-devel] GenomicRanges: Storing 'seqlengths' as numeric
On 12/03/2013 02:29 AM, Julian Gehring wrote: Hi, Some of the chromosomes out in the world are fairly large (e.g. wheat chr 3B with 995 Mbp [1]). Currently, the 'seqlengths' of the reference sequence are stored as 'integers' which do not allow to store lengths of this size. Are there any plans of switching to 'doubles' or 64-bit integers for the 'seqlengths' slot? Or extending the slot such that a user can store it either as integer or floating-point number? But .Machine$integer.max [1] 2147483647 so we at least survive wheat chr 3B? If there is movement to support this I'd encourage exact representation as double (this is how R deals with long vectors, and I believe it is the javascript representation of integers so not completely unprecedented) rather than 64 bit integers (which do not have any support in R). I guess this would be quite a big undertaking so real use cases need to be present. And support for larger integers would seem to be useful to R generally rather than just to Bioc. Martin Best wishes Julian [1] http://www.sciencemag.org/content/322/5898/101 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] GenomicRanges: Storing 'seqlengths' as numeric
Hi, Agreed with Martin that until someone comes up with a chromosome that is longer than .Machine$integer.max I don't see the need for switching to double or int64 to represent the seqlengths. Furthermore, since the seqlengths are used in many range operations like checking the validity of the ranges in a GRanges object, trimming them, computing coverage, handling circularity, etc... it would not make much sense to make the switch for the seqlengths without also making it for Ranges objects. That would be a serious undertaking though and probably with many backward compatibility issues. H. On 12/03/2013 10:07 AM, Martin Morgan wrote: On 12/03/2013 02:29 AM, Julian Gehring wrote: Hi, Some of the chromosomes out in the world are fairly large (e.g. wheat chr 3B with 995 Mbp [1]). Currently, the 'seqlengths' of the reference sequence are stored as 'integers' which do not allow to store lengths of this size. Are there any plans of switching to 'doubles' or 64-bit integers for the 'seqlengths' slot? Or extending the slot such that a user can store it either as integer or floating-point number? But .Machine$integer.max [1] 2147483647 so we at least survive wheat chr 3B? If there is movement to support this I'd encourage exact representation as double (this is how R deals with long vectors, and I believe it is the javascript representation of integers so not completely unprecedented) rather than 64 bit integers (which do not have any support in R). I guess this would be quite a big undertaking so real use cases need to be present. And support for larger integers would seem to be useful to R generally rather than just to Bioc. Martin Best wishes Julian [1] http://www.sciencemag.org/content/322/5898/101 ___ 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...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Conflict between BiocStyle and the verbatim package
Hej Martin!
I’d like to have multi-line comments in my vignette and the easiest way I know
is to use the “comment” environment from the verbatim package - i.e.
\begin{comment}…\end{comment}. However, when I do this, i.e. load the verbatim
package after having “sourced” the BiocStyle package, generating the pdf just
fails without any error message.
Here’s a tiny .Rnw example of how to reproduce the error:
\documentclass[11pt,a4paper]{article}
% Bioc style
style, eval=TRUE, echo=FALSE, results=tex=
BiocStyle::latex()
@
\usepackage{verbatim}
\begin{document}
Some text
\begin{comment}
some comments not to be seen by the user
\end{comment}
Some more text
\end{document}
The generated pdf stops after the text “Some text”. I tried to track it down,
but I’m out of my depth in latex style file. Do you have any idea what is
happening? And do you have any suggestion of how I could go around this other
than using % on every comment line?
Cheers,
Nico
---
Nicolas Delhomme
Nathaniel Street Lab
Department of Plant Physiology
Umeå Plant Science Center
Tel: +46 90 786 7989
Email: nicolas.delho...@umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
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Re: [Bioc-devel] Conflict between BiocStyle and the verbatim package
On 12/03/2013 12:30 PM, Nicolas Delhomme wrote:
Hej Martin!
I’d like to have multi-line comments in my vignette and the easiest way I know
is to use the “comment” environment from the verbatim package - i.e.
\begin{comment}…\end{comment}. However, when I do this, i.e. load the verbatim
package after having “sourced” the BiocStyle package, generating the pdf just
fails without any error message.
Here’s a tiny .Rnw example of how to reproduce the error:
\documentclass[11pt,a4paper]{article}
% Bioc style
style, eval=TRUE, echo=FALSE, results=tex=
BiocStyle::latex()
@
\usepackage{verbatim}
\begin{document}
Some text
\begin{comment}
some comments not to be seen by the user
\end{comment}
Some more text
\end{document}
The generated pdf stops after the text “Some text”. I tried to track it down,
but I’m out of my depth in latex style file. Do you have any idea what is
happening? And do you have any suggestion of how I could go around this other
than using % on every comment line?
If I take your file and
R CMD Sweave Nico.Rnw
pdflatex Nico.tex
I get
! Undefined control sequence.
\f@ncyolh -\thetitle
\strut
l.15 \end{document}
?
which is because the vignette needs to have a title, e.g., in the preamble
\usepackage{verbatim}
\title{My amazing document}
\begin{document}
If I add this, then things seem to work fine.
The undefined control sequence doesn't sound like what you saw, so maybe more
details are needed? I'm using
$ R --vanilla --slave -e R.version.string
[1] R Under development (unstable) (2013-12-01 r64371)
$ pdflatex --version
pdfTeX 3.1415926-1.40.10-2.2 (TeX Live 2009/Debian)
Martin
Cheers,
Nico
---
Nicolas Delhomme
Nathaniel Street Lab
Department of Plant Physiology
Umeå Plant Science Center
Tel: +46 90 786 7989
Email: nicolas.delho...@umu.se
SLU - Umeå universitet
Umeå S-901 87 Sweden
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Struggles with correct import .....
It is super super super useful for NAMESPACE issues. I don't really use the other stuff. Kasper On Tue, Dec 3, 2013 at 11:34 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: - Original Message - From: Martin Maechler maech...@stat.math.ethz.ch To: Kasper Daniel Hansen kasperdanielhan...@gmail.com Cc: bioc-devel@r-project.org Sent: Tuesday, December 3, 2013 8:13:55 AM Subject: Re: [Bioc-devel] Struggles with correct import . Kasper Daniel Hansen kasperdanielhan...@gmail.com on Wed, 20 Nov 2013 15:37:00 -0500 writes: Ok, I analyzed the package using codetoolsBioC and there were a number of missing imports, including what Leonardo has described. I have fixed those in bumphunter 1.3.3 Kasper Impressing and interesting. I don't see 'codetoolsBioC' to be available via biocLite(). What's the recommended way to have it among the bioconductor packages ? Check it out from svn: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/codetoolsBioC/ (username/password: readonly) The package has some issues and needs some attention; this is why it has not been released. It's still useful though. Dan Martin On Wed, Nov 20, 2013 at 3:28 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: I'll have a look. Basically, issues such as this is never the end-users problem and is likely to either be caused by bumphunter not importing correctly (most likely) or IRanges not exporting correctly. Kasper On Wed, Nov 20, 2013 at 3:02 PM, Leonardo Collado Torres lcoll...@jhsph.edu wrote: Hello, Found how to solve this. Basically, the NAMESPACE of the bumphunter package is not complete (I think). I downloaded http://bioconductor.org/packages/release/bioc/src/contrib/bumphunter_1.2.0.tar.gz , changed the version to 1.2.1 and added/modified the following lines to the NAMESPACE: importFrom(IRanges, IRanges, distance, distanceToNearest, subjectHits) importMethodsFrom(GenomicRanges, seqnames, sort, strand, elementMetadata) Once bumphunter was importing IRanges::distance, I got past the error I reported. Then I found other errors related to bumphunter not importing the GenomicRanges strand and elementMetadata functions, as well as the IRanges distanceToNearest, IRanges and subjectHits functions. Best, Leo On Wed, Nov 20, 2013 at 2:46 PM, Leonardo Collado Torres lcoll...@jhsph.edu wrote: Hi Harris, Answering your question from your first email, I do not think that it would help if bumphunter exported matchGenes() or .matchGenes(). Currently by just importing annotateNearest(), R is correctly able to use annotateNearest(), then .matchGenes(), and also nearestgene(). The problem is that nearestgene() uses IRanges::distance() but that function is not being found even after importing it. So as far as I understand, everything should be working since the NAMESPACE https://github.com/lcolladotor/derfinder/blob/v0.0.34/NAMESPACE has: importFrom(bumphunter,annotateNearest) importMethodsFrom(IRanges,distance) importFrom(IRanges,distance) That is why I am confused and do not know what is the cause of the problem. One possible explanation could be that bumphunter's NAMESPACE https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bumphunter/NAMESPACEdoesn't import the IRanges::distance method. Regarding your second email (quoted below), I do not import the IRanges::nearest method, but it doesn't seem to be causing problems. That could be because bumphunter does import the IRanges::nearest method If I comment out line 147 of https://github.com/lcolladotor/derfinder/blob/v0.0.34/R/analyzeChr.R, aka, comment out library(bumphunter) the example for analyzeChr() fails with: Error in withCallingHandlers(expr, warning = function(w) invokeRestart(muffleWarning)) : could not find function distance So yes, I get the same error in real life and not only in CMD check. Adding to the NAMESPACE the following line doesn't help either. importMethodsFrom(IRanges,nearest) Best, Leo On Wed, Nov 20, 2013 at 2:06 PM, Harris A. Jaffee h...@jhu.edu wrote: In nearestgene(), before the call to distance, there is a
