[Bioc-devel] BSgenomeForge Error
Hi, I am trying to build a genome which is not listed in BSgenome but unfortunately getting following error at *R CMD check tarball* level: * installing *source* package ‘BSgenome.Ntabacum.SOLG.K326’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Error : .onLoad failed in loadNamespace() for 'BSgenome.Ntabacum.SOLG.K326', details: call: validObject(.Object) error: invalid class “RdaCollection” object: objnames slot contains duplicates Error: loading failed Execution halted ERROR: loading failed Please help me out in resolving this issue. Best, Arshi [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] VariantAnnotation: Same locus, multiple samples
The two data structures do not encode the same information. Coercion to VCF forms a rectangular matrix: position+alt by sample. There is no standard way to encode that a given cell in that matrix is absent, so coercion to VRanges simply maps each cell to an element. One could imagine using the . missing data marker for every geno field, but that's making too many assumptions. I'm not sure that's the same as an element not existing in a VRanges. On Fri, Dec 5, 2014 at 1:18 AM, Julian Gehring julian.gehr...@embl.de wrote: Hi, Assume that we have two variants from two samples at the same locus, stored in a 'VRanges' or 'VCF' object: library(VariantAnnotation) vr = VRanges(1, IRanges(c(10, 10), width = 1), ref = c(C, C), alt = c(A, G), sampleNames = c(S1, S2)) vcf = as(vr, VCF) If we convert the VCF to a VRanges, we now get each variant in each patient: vr2 = as(vcf, VRanges) length(vr) ## 2 length(vr2) ## 4 It seems that the VCF object does not store the information of the 'sampleNames' in the first conversion. Best wishes Julian ___ 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] FW: GO offspring consistency
Hi Jelle, Thank you for your patience in waiting for my answer here. It took me a lot longer to properly test and validate this than I initially expected. So if you look at amigo you can see these graph views that show you what the current terms up and downstream of a given GO term should be: http://amigo.geneontology.org/amigo/term/GO:0006915 vs it's offspring term. http://amigo.geneontology.org/amigo/term/GO:0042981 And you can see (if you click on the inferred tree view for GO:0006915) that GO:0042981 is actually listed there as an offspring term. Which just that leaves us with the mystery of why: all(subsetapt %in% setapt) Would ever return false? Now to do some more digging, if we carry your example one step further we can do this to extract the specific terms that have this surprising result: subsetapt[!subsetapt %in% setapt] And lets look closer at the very 1st result (out of 3) that we see: GO:0035602. So now we would then expect that: GO:0006915 - GO:0042981 - GO:0035602 Especially since the very latest amigo diagrams show this set of relationships for this term. http://amigo.geneontology.org/amigo/term/GO:0035602 But if we look more closely at this term we can notice something unusual about it. Specifically if you look at the Graph views you will see that it has a 'part of' rather than an 'is a' relationship to the rest of the DAG. An examination of the other two non-compliant terms indicates that they too have this kind of relationship: http://amigo.geneontology.org/amigo/term/GO:0044336 http://amigo.geneontology.org/amigo/term/GO:0044337 Also of interest is the fact that the highest level term you tested (GO:0006915), has a broader kind of relationship to the rest of the DAG). Now please hold onto those thoughts while I tell you another important fact. http://amigo.geneontology.org/amigo/term/GO:0006915 The contents of the GOBPOFFSPRING mapping are ultimately derived from the graph_path table that you can find here: http://geneontology.org/page/lead-database-schema#go-optimisations.table.graph-path And they are indeed a faithful representation of what is in that table (from GO). That is, the source files both when I made the latest GO.db package for the October release and now have the same properties for their set of relationships as you pointed out. So for our 1st example, in both places you will find that GO:0035602 is listed as having an implied link when you ask for GO:0042981 but not when you ask for GO:0006915. So the very unsatisfying answer to your question is that the terms have this relationship because that is what the data at GO say. :P But the (hopefully) more satisfying answer is that the kind of relationships that these terms have to each other creates implications for whether or not they can be transitively associated in the GO graph_path table. That is, the child term GO:0035602 is not able to be implicitly linked to GO:0006915 because that term has a 'regulates' relationship to the offspring terms and *also* because GO:0035602 has a 'part of' relationship (instead of an 'is a' relationship) to its parent terms. And those issues don't crop up between the other terms in this part of the graph. I hope this explains things better for you, Marc On 12/02/2014 04:29 AM, jelle.goe...@radboudumc.nl wrote: Hi All, When working with the GO.db package we ran into a seeming inconsistency in the GOBPOFFSPRING object. It seems there that a term's offspring may have offspring that is not offspring of the term itself. This seems inconsistent with the DAG structure of gene ontology. library(GO.db) xx - as.list(GOBPOFFSPRING) setapt - xx$GO:0006915 #apoptosis subsetapt - xx$GO:0042981 #offspring of apoptosis GO:0042981%in%setapt [1] TRUE all(subsetapt %in% setapt) [1] FALSE Is there something wrong or are we misunderstanding the GOBPOFFSPRING object? Best wishes, Jelle Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629. ___ 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
Re: [Bioc-devel] recalling methods
nice. I will play around with this. thanks Gabe!
On Fri, Dec 5, 2014 at 6:37 PM, Gabe Becker becker.g...@gene.com wrote:
Hey guys,
Surgically removed from promptClass:
classInSig - function(g, where, cl) {
cl %in% unique(unlist(findMethods(g, where)@signatures))
}
genWithClass - function(cl, where) {
allgen - getGenerics(where = where)
ok - as.logical(unlist(lapply(allgen, classInSig, cl = cl,
where = where)))
allgen[ok]
}
genWithClass(IRanges, find(classMetaName(IRanges)))
[1] ccoerce end-gaps intersect
[6] isNormal names- namespgap
pintersect
[11] psetdiff punion reduce reverse setdiff
[16] start- startthreebands union
updateObject
[21] update width- width
For semantic guessing of which ones will be useful, I've got nothing (for
now).
~G
On Fri, Dec 5, 2014 at 11:28 AM, Michael Lawrence
lawrence.mich...@gene.com wrote:
Cool. I see hypertext as being useful here, because the generics and
classes form an intricate and sometimes ambiguous web, especially when
multiple inheritance and dispatch are involved. I think we should first
build better tooling for introspecting S4 and for graph-based modeling and
analysis of S4 architecture. For example, could we statically detect
whether a dispatch ambiguity exists, knowing all of the methods and
classes? And based on that build one or more end-user UIs?
On Fri, Dec 5, 2014 at 11:05 AM, Michael Love
michaelisaiahl...@gmail.com
wrote:
On Thu, Dec 4, 2014 at 4:01 PM, Michael Lawrence
lawrence.mich...@gene.com wrote:
I think this gets at the heart of at least one of the usability issues
in Bioconductor: interface discoverability. Many simpler command line
tools
have a single-faceted interface for which it is easy to enumerate a list
of
features. There's definitely room for better ways to interrogate our
object-oriented APIs, but it's challenging. Essentially we need a way
for
the user to ask what can I do with this object?. Yes, we need better
introspection utilities, but we also need to integrate the query with
documentation. In other words, we need a more dynamic, more fluid help
system, oriented around S4.
I would be interested in working on this. A minimal goal for me is a
function that just returns a character vector of the names of the
generics defined for the object. Filtering that down to give methods
which are likely relevant using the documentation will definitely be
a bigger challenge.
On Thu, Dec 4, 2014 at 9:56 AM, Michael Love
michaelisaiahl...@gmail.com wrote:
I was thinking about a request from someone at Bioc2014 (I can't
remember at the moment)
As an end-user, if I have an object x, how can I *quickly* recall the
main methods for that? As in, without breaking my flow and going to
?myClass or help(myClass-class). Suppose x is a GRanges, how can I
remember that there is a method called narrow() which works on x?
showMethods(classes=class(x)) will print out a huge list for many
complex Bioc classes. And printTo=FALSE turns this huge list into an
unhelpful character vector, e.g.:
head(showMethods(classes=GRanges,printTo=FALSE),8)
[1] Function \.asSpace\:
[3] not an S4 generic function
[5] Function \.linkToCachedObject-\: not an S4 generic
function
[7] Function
\.replaceSEW\:
any ideas?
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[Rd] install.packages deletes PACKAGES file in local repo
Hi, running install.packages() to install a package from a local repository (i.e., starts with file:///) appears to delete the PACKAGES file that is in the src/contrib/ directory. This happens on a cluster running Scientific Linux release 6.4 (Carbon), but not on my Ubuntu local machine. Subsequent calls to install.packages() complain about src/contrib/PACKAGES not existing, although there still is a src/contrib/PACKAGES.gz file. Is this a know issue? Thank you. Bests, Renaud [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Use of tools:::httpdPort in a package for CRAN.
Hello,
I wrote a function to show the help/index page of a package in a
browser (and want to include this in an update for a CRAN package). I
asked in R-help how to obtain the 00Index.html file, Duncan Murdoch
suggested to inspect (see
http://r.789695.n4.nabble.com/Obtain-00Index-html-tt4697661.html)
tools:::httpd (thank you therefore!). So I came up with:
help.index - function (pkg, browser = NA, encodeIfNeeded = FALSE) {
pkg - as.character(substitute(pkg))
hport - tools:::httpdPort
if (!pkg %in% rownames(installed.packages()))
stop(paste(Package, pkg, not found.))
if (hport == 0) {
cat(Starting dynamic help.\n)
t - try(startDynamicHelp(), silent = TRUE)
if (class(t) == try-error)
stop(Could not start dynamic help.)
hport - tools:::httpdPort
}
if (!is.na(browser)) {
if (tolower(browser) == rstudio)
options(browser = function (x) .Call(rs_browseURL, url))
else
options(browser = browser)
}
url - paste0(http://127.0.0.1:;, hport, /library/, pkg,
/html/00Index.html)
browseURL(url, encodeIfNeeded = encodeIfNeeded)
invisible(NULL)
}
(also at https://github.com/setempler/miscset/blob/master/R/help.index.R)
I tried to avoid `:::` so I used the 00Index.html file from the
library on my disk (like
/home/user.foo/R/lib.bar/package.baz/html/00Index.html). It does show
the index, but the link to the help pages are not accessible.
Nevertheless, my implementation now works, but R CMD check --as-cran
gives a warning, and the R help also says to avoid `:::`. Also
get(httpd, as.environment(package:tools)) didn't help.
My question: do I have another possibility to achieve my goal without
referencing by `:::` (concerning a submission to CRAN), if so, please
tell me!
Thank you in advance,
Sven.
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Re: [Rd] Use of tools:::httpdPort in a package for CRAN.
On 05/12/2014 11:24 AM, Sven E. Templer wrote:
Hello,
I wrote a function to show the help/index page of a package in a
browser (and want to include this in an update for a CRAN package). I
asked in R-help how to obtain the 00Index.html file, Duncan Murdoch
suggested to inspect (see
http://r.789695.n4.nabble.com/Obtain-00Index-html-tt4697661.html)
tools:::httpd (thank you therefore!). So I came up with:
help.index - function (pkg, browser = NA, encodeIfNeeded = FALSE) {
pkg - as.character(substitute(pkg))
hport - tools:::httpdPort
I don't see any way to get it other than this, but it seems like a
reasonable thing to want to do. I think the way I'd do it is to modify
the exported function startDynamicHelp() so that it doesn't give an
error if the help system is already running, it just returns the active
port number.
So the code above would become
hport - startDynamicHelp()
(or some variation using try().)
I think a change like this could make it into 3.1.3 and later versions.
Duncan Murdoch
if (!pkg %in% rownames(installed.packages()))
stop(paste(Package, pkg, not found.))
if (hport == 0) {
cat(Starting dynamic help.\n)
t - try(startDynamicHelp(), silent = TRUE)
if (class(t) == try-error)
stop(Could not start dynamic help.)
hport - tools:::httpdPort
}
if (!is.na(browser)) {
if (tolower(browser) == rstudio)
options(browser = function (x) .Call(rs_browseURL, url))
else
options(browser = browser)
}
url - paste0(http://127.0.0.1:;, hport, /library/, pkg,
/html/00Index.html)
browseURL(url, encodeIfNeeded = encodeIfNeeded)
invisible(NULL)
}
(also at https://github.com/setempler/miscset/blob/master/R/help.index.R)
I tried to avoid `:::` so I used the 00Index.html file from the
library on my disk (like
/home/user.foo/R/lib.bar/package.baz/html/00Index.html). It does show
the index, but the link to the help pages are not accessible.
Nevertheless, my implementation now works, but R CMD check --as-cran
gives a warning, and the R help also says to avoid `:::`. Also
get(httpd, as.environment(package:tools)) didn't help.
My question: do I have another possibility to achieve my goal without
referencing by `:::` (concerning a submission to CRAN), if so, please
tell me!
Thank you in advance,
Sven.
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Re: [Rd] Use of tools:::httpdPort in a package for CRAN.
Perhaps I missed something, but isn't this just a one-liner function?
help.index = function (pkg) help(package = (pkg), help_type = html)
Regards,
Yihui
--
Yihui Xie xieyi...@gmail.com
Web: http://yihui.name
On Fri, Dec 5, 2014 at 10:24 AM, Sven E. Templer sven.temp...@gmail.com wrote:
Hello,
I wrote a function to show the help/index page of a package in a
browser (and want to include this in an update for a CRAN package). I
asked in R-help how to obtain the 00Index.html file, Duncan Murdoch
suggested to inspect (see
http://r.789695.n4.nabble.com/Obtain-00Index-html-tt4697661.html)
tools:::httpd (thank you therefore!). So I came up with:
help.index - function (pkg, browser = NA, encodeIfNeeded = FALSE) {
pkg - as.character(substitute(pkg))
hport - tools:::httpdPort
if (!pkg %in% rownames(installed.packages()))
stop(paste(Package, pkg, not found.))
if (hport == 0) {
cat(Starting dynamic help.\n)
t - try(startDynamicHelp(), silent = TRUE)
if (class(t) == try-error)
stop(Could not start dynamic help.)
hport - tools:::httpdPort
}
if (!is.na(browser)) {
if (tolower(browser) == rstudio)
options(browser = function (x) .Call(rs_browseURL, url))
else
options(browser = browser)
}
url - paste0(http://127.0.0.1:;, hport, /library/, pkg,
/html/00Index.html)
browseURL(url, encodeIfNeeded = encodeIfNeeded)
invisible(NULL)
}
(also at https://github.com/setempler/miscset/blob/master/R/help.index.R)
I tried to avoid `:::` so I used the 00Index.html file from the
library on my disk (like
/home/user.foo/R/lib.bar/package.baz/html/00Index.html). It does show
the index, but the link to the help pages are not accessible.
Nevertheless, my implementation now works, but R CMD check --as-cran
gives a warning, and the R help also says to avoid `:::`. Also
get(httpd, as.environment(package:tools)) didn't help.
My question: do I have another possibility to achieve my goal without
referencing by `:::` (concerning a submission to CRAN), if so, please
tell me!
Thank you in advance,
Sven.
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Re: [Rd] install.packages deletes PACKAGES file in local repo
Can you post exact code, i have not seen this behavior, and I work with local repositories quite extensively on my current project. ~G On Fri, Dec 5, 2014 at 7:45 AM, Renaud Gaujoux ren...@mancala.cbio.uct.ac.za wrote: Hi, running install.packages() to install a package from a local repository (i.e., starts with file:///) appears to delete the PACKAGES file that is in the src/contrib/ directory. This happens on a cluster running Scientific Linux release 6.4 (Carbon), but not on my Ubuntu local machine. Subsequent calls to install.packages() complain about src/contrib/PACKAGES not existing, although there still is a src/contrib/PACKAGES.gz file. Is this a know issue? Thank you. Bests, Renaud [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Gabriel Becker Graduate Student Statistics Department University of California, Davis [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R CMD check --as-cran and (a)spell checking
Does anyone know if it is possible to add a dictionary file of known words that becomes part of the *built* package to tell 'R CMD check --as-cran' not to report these words as misspelled. I want this dictionary to come with the *.tar.gz such that it will be available regardless where the package is checked. For instance, currently I get: * using log directory 'T:/R/_R-3.1.2patched/matrixStats.Rcheck' * using R version 3.1.2 Patched (2014-12-03 r67101) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'matrixStats/DESCRIPTION' ... OK * this is package 'matrixStats' version '0.12.0' * checking CRAN incoming feasibility ... NOTE Maintainer: 'Henrik Bengtsson henr...@braju.com' Possibly mis-spelled words in DESCRIPTION: rowMedians (18:74) rowRanks (18:92) rowSds (18:111) * checking package namespace information ... OK ... Thanks Henrik __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] does parLapplyLB do load-balancing?
Looking at parLapplyLB, one sees that it takes in X and then passes splitList(X, length(cl)) to clusterApplyLB, which then calls dynamicClusterApply. Thus while dynamicClusterApply does handle tasks in a load-balancing fashion, sending out individual tasks as previous tasks complete, parLapplyLB preempts that by splitting up the tasks in advance into as many groups of tasks as there are cluster processes. This seems to defeat the purpose of load-balancing and of the manner in which dynamicClusterApply is coded. This question basically repeats a question posed in 2013 -- see http://r.789695.n4.nabble.com/parLapplyLB-Load-balancing-tt4671848.html I'm reposting because there doesn't seem to have been any response to the previous posting, and it looks like the issue is still present in R 3.1 so it seems asking again if this is the intended behavior of parLapplyLB. I'm using R 3.1.1 and the 3.1.1 version of the parallel package under Ubuntu 14.04, but the code appears to be the same in R-devel. Chris -- Chris Paciorek Statistical Computing Consultant Statistical Computing Facility, Econometrics Laboratory, Berkeley Research Computing Office: 495 Evans Hall Email: pacio...@stat.berkeley.edu Mailing Address:Voice: 510-842-6670 Department of StatisticsFax: 510-642-7892 367 Evans Hall Skype: cjpaciorek University of California, Berkeley WWW: www.stat.berkeley.edu/~paciorek Berkeley, CA 94720 USA Permanent forward: pacio...@alumni.cmu.edu __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] install.packages deletes PACKAGES file in local repo
Hi,
I was only doing install.packages('pkgname'), with the local repo being
defined in the default repos option.
After retrying it just now, this issue mysteriously suddenly disappeared,
and things work as expected whether on the front node or in a job on a
node. Really no idea of what happened.
Closing the thread.
Thanks.
On 6 December 2014 at 02:23, Gabriel Becker gmbec...@ucdavis.edu wrote:
Can you post exact code, i have not seen this behavior, and I work with
local repositories quite extensively on my current project.
~G
On Fri, Dec 5, 2014 at 7:45 AM, Renaud Gaujoux
ren...@mancala.cbio.uct.ac.za wrote:
Hi,
running install.packages() to install a package from a local repository
(i.e., starts with file:///) appears to delete the PACKAGES file that is
in
the src/contrib/ directory.
This happens on a cluster running Scientific Linux release 6.4 (Carbon),
but not on my Ubuntu local machine.
Subsequent calls to install.packages() complain about src/contrib/PACKAGES
not existing, although there still is a src/contrib/PACKAGES.gz file.
Is this a know issue?
Thank you.
Bests,
Renaud
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Graduate Student
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University of California, Davis
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Re: [Rd] does parLapplyLB do load-balancing?
Hello, In such cases, try the Rhpc package. The following is the result of the benchmark. http://prs.ism.ac.jp/~nakama/Rhpc/#benchmark # but tuning is not finished... 2014-12-06 10:36 GMT+09:00 Chris Paciorek pacio...@stat.berkeley.edu: Looking at parLapplyLB, one sees that it takes in X and then passes splitList(X, length(cl)) to clusterApplyLB, which then calls dynamicClusterApply. Thus while dynamicClusterApply does handle tasks in a load-balancing fashion, sending out individual tasks as previous tasks complete, parLapplyLB preempts that by splitting up the tasks in advance into as many groups of tasks as there are cluster processes. This seems to defeat the purpose of load-balancing and of the manner in which dynamicClusterApply is coded. This question basically repeats a question posed in 2013 -- see http://r.789695.n4.nabble.com/parLapplyLB-Load-balancing-tt4671848.html I'm reposting because there doesn't seem to have been any response to the previous posting, and it looks like the issue is still present in R 3.1 so it seems asking again if this is the intended behavior of parLapplyLB. I'm using R 3.1.1 and the 3.1.1 version of the parallel package under Ubuntu 14.04, but the code appears to be the same in R-devel. Chris -- Chris Paciorek Statistical Computing Consultant Statistical Computing Facility, Econometrics Laboratory, Berkeley Research Computing Office: 495 Evans Hall Email: pacio...@stat.berkeley.edu Mailing Address:Voice: 510-842-6670 Department of StatisticsFax: 510-642-7892 367 Evans Hall Skype: cjpaciorek University of California, Berkeley WWW: www.stat.berkeley.edu/~paciorek Berkeley, CA 94720 USA Permanent forward: pacio...@alumni.cmu.edu __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Best Regards, -- Eiji NAKAMA nakama (a) ki.rim.or.jp \u4e2d\u9593\u6804\u6cbb nakama (a) ki.rim.or.jp __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
