Hi Ben --
R has a 'y' release in x.y.z every year, but Bioconductor has a .y release
(where current devel becomes release) every 6 months.
Obviously we want to 'devel' bioc packages so that they can be released to
users of what will be the release version of R at the time of release.
When the next (typically mid-April, but no date set yet) .y releases of R and
Bioc coincide, Bioc-devel is based on R-devel.
When the next (typically mid-October) .y release of Bioc corresponds to no
change in R's y, Bioc-devel is based on release R.
So yes, now you should be using R-devel. After mid-April, you'd use R-release
for bioc devel. Then after mid-October, it would be back to R-devel.
That's not quite correct, because R has a release branch where bug fixes and
minor '.z' changes come from. So from mid-April to mid-October, technically
devel is against the R-x-y-branch of R svn repository.
This information has been added to the web site (I'm pretty sure it's already
there, but I can't find it!) at
http://bioconductor.org/developers/how-to/useDevel/
The update will propagate in the next 20 minutes or so.
Martin
________________________________________
From: Ben Ward (TGAC) [ben.w...@tgac.ac.uk]
Sent: Thursday, January 14, 2016 4:20 AM
To: Hervé Pagès; Morgan, Martin; bioc-devel@r-project.org
Subject: RE: [Bioc-devel] IRanges - PartitioningByEnd not found when package
method runs.
Hi, Herve, Martin,
Thanks! I've changed the function to use IntegerList instead of list in the
branch, although at the moment it still fails at the same place.
Should I switch entirely to a devel R and bioc whilst I work on my package? You
said 'during the current release cycle that means using the devel version on
R', does this mean it switches and sometimes release R should be used?
Many thanks,
Ben.
________________________________________
From: Hervé Pagès [hpa...@fredhutch.org]
Sent: 14 January 2016 03:28
To: Morgan, Martin; Ben Ward (TGAC); bioc-devel@r-project.org
Subject: Re: [Bioc-devel] IRanges - PartitioningByEnd not found when package
method runs.
Hi Ben, Martin,
On 01/13/2016 08:19 AM, Morgan, Martin wrote:
> Hi Ben -- nice to see you over here ;)
>
> You're using the release version of R (R-3.2.3) and presumably release
> versions of packages (my advice on placing sessionInfo() was a little too
> clever; you want your package loaded, so the versions of it's dependencies
> are apparent, so in a separate R maybe library(testRpkg); sessionInfo(); I'll
> update my support site post...).
>
> At least for Bioconductor packages, you want to be using the 'devel' version
> of Bioconductor, and during the current release cycle that means the devel
> version of R.
>
> Nonetheless, I started R-release, loaded the test package, ran the function,
> and looked at traceback()
>
>> library(testRpkg)
>> doit()
> Error in end(PartitioningByEnd(x)) :
> error in evaluating the argument 'x' in selecting a method for function
> 'end': Error: could not find function "PartitioningByEnd"
>> traceback()
> 9: end(PartitioningByEnd(x))
> 8: .unlist_NL_subscript(i, x)
> 7: fast_path_FUN(x, i)
> 6: subset_List_by_List(x, i)
> 5: object[index]
> 4: object[index]
> 3: subsetSites(dna, 1:50)
> 2: subsetSites(dna, 1:50)
> 1: doit()
>
> The suspect looks like .unlist_NL_subscript, so I went looking for it
>
>> getAnywhere(.unlist_NL_subscript)
> A single object matching '.unlist_NL_subscript' was found
> It was found in the following places
> namespace:S4Vectors
> with value
>
> function (i, x)
> {
> offsets <- c(0L, end(PartitioningByEnd(x))[-length(x)])
> i <- i + offsets
> unlist(i, use.names = FALSE)
> }
> <environment: namespace:S4Vectors>
>
> So S4Vectors wants to use PartitioningByEnd. I looked at it's NAMESPACE
> imports (actually I looked in the SVN repository...) for the packages it
> imports from...
>
>> names(getNamespaceImports("S4Vectors"))
> [1] "base" "methods" "utils" "stats" "stats4"
> [6] "BiocGenerics"
>
> and find that it does not import IRanges. So the problem is a bug in
> S4Vectors.
>
> I don't see the problem in bioc-devel, and to see why I had to be a bit
> clever -- there is no error, so no opportunity to use traceback(). Instead, I
> used the advanced-but-flexible 'trace' function to set a tracer on
> PartioningByEnd, where the tracer is the 'recover' function...
>
>> trace(IRanges::PartitioningByEnd, tracer=recover)
>
> So when PartioningByEnd is evalutated, R will get me the 'recover' prompt...
>> doit()
> Tracing IRanges::PartitioningByEnd(x) on entry
>
> Enter a frame number, or 0 to exit
>
> 1: doit()
> 2: subsetSites(dna, 1:50)
> 3: subsetSites(dna, 1:50)
> 4: object[index]
> 5: object[index]
> 6: subset_List_by_List(x, i)
> 7: fast_path_FUN(x, i)
> 8: .unlist_NL_subscript(i, x)
> 9: end(IRanges::PartitioningByEnd(x))
> 10: IRanges::PartitioningByEnd(x)
>
> Selection:
>
> This shows me the call stack (looks almost identical, so I could have
> 'guessed' that I wanted to look at .unlist_NL_subscript again) and suggests
> that the code has been fixed to explicitly indicate where PartitioningByEnd
> comes from. This is confirmed by looking at the code definition
>
>> getAnywhere(".unlist_NL_subscript")
> A single object matching '.unlist_NL_subscript' was found
> It was found in the following places
> namespace:S4Vectors
> with value
>
> function (i, x)
> {
> offsets <- c(0L, end(IRanges::PartitioningByEnd(x))[-length(x)])
> i <- i + offsets
> unlist(i, use.names = FALSE)
> }
> <environment: namespace:S4Vectors>
>
> So this is a bug in S4Vectors, but fixed in Bioc-devel where new package
> development should be occurring.
>
> I'll leave it to Herve or others to decide whether S4Vectors in release
> should be patched.
Michael fixed this in devel. Thanks Michael! I should probably backport
the fix to release.
@Ben: FWIW subsetting with an IntegerList subscript is much more
efficient than with an ordinary list:
index <- rep.int(IntegerList(index), length(object))
object[index]
It will make a big difference (e.g. 100x faster or more) if 'object' is
a DNAStringSet with tens of thousands of sequences.
Cheers,
H.
>
> Thanks for the bug report!
>
> Martin
> ________________________________________
> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ben Ward
> (TGAC) [ben.w...@tgac.ac.uk]
> Sent: Wednesday, January 13, 2016 10:57 AM
> To: bioc-devel@r-project.org
> Subject: [Bioc-devel] IRanges - PartitioningByEnd not found when package
> method runs.
>
> Hi All,
>
> I am having an issue with an un-exported method in a package I am developing,
> the package imports Biostrings and IRanges.
>
> I have created a minimal, reproducible example, (many many thanks to Martin
> Morgan for telling me how to do this) in this repo branch:
> https://github.com/Ward9250/testRpkg/tree/PartByEnd
>
> The method, as you will see from the branch, is called subsetSites, and is
> supposed to cut a DNAString set down to only the sites/base positions
> indicated by a provided vector of integers. It does this by indexing the
> DNAStringSet with re.int.
>
> If I try to run this however, it seems to fail, indicating that it cannot
> find the PartitioningByEnd function. This puzzles me as I know the function
> is part of IRanges, which is imported in the package, and I would assume
> Biostrings would import any IRanges functionality it needed for the
> DNAStringSet indexing operator.
>
> Below is an example run of what I see, and my session info.
>
> If anyone can see what my issue is or knows how to solve this it would be a
> big help.
>
> Many Thanks,
> Ben W.
>
>
> bward@n78620:/tmp$ git clone g...@github.com:ward9250/testRpkg.git -b
> PartByEnd
> Cloning into 'testRpkg'...
> remote: Counting objects: 18, done.
> remote: Compressing objects: 100% (10/10), done.
> remote: Total 18 (delta 1), reused 18 (delta 1), pack-reused 0
> Receiving objects: 100% (18/18), done.
> Resolving deltas: 100% (1/1), done.
> Checking connectivity... done.
> bward@n78620:/tmp$ cd testRpkg
> bward@n78620:/tmp/testRpkg$ R CMD INSTALL .
> * installing to library
> �/usr/users/TGAC_ga002/bward/R/x86_64-pc-linux-gnu-library/3.2�
> * installing *source* package �testRpkg� ...
> ** R
> ** preparing package for lazy loading
> ** help
> No man pages found in package �testRpkg�
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> * DONE (testRpkg)
> bward@n78620:/tmp/testRpkg$ R --vanilla -e "sessionInfo(); testRpkg::doit()"
> R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
> Copyright (C) 2015 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>> sessionInfo(); testRpkg::doit()
> R version 3.2.3 (2015-12-10)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 14.04.3 LTS
>
> locale:
> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
> Error in end(PartitioningByEnd(x)) :
> error in evaluating the argument 'x' in selecting a method for function
> 'end': Error: could not find function "PartitioningByEnd"
> Calls: <Anonymous> ... subset_List_by_List -> fast_path_FUN ->
> .unlist_NL_subscript -> end
> Execution halted
>
>
>
> [[alternative HTML version deleted]]
>
>
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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
This email message may contain legally privileged and/or confidential
information. If you are not the intended recipient(s), or the employee or
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delete this email message from your computer. Thank you.
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