[Bioc-devel] Struggles with correct import .....
Dan Tenenbaum
dtenenba at fhcrc.org
Tue Dec 3 17:34:11 CET 2013
----- Original Message -----
> From: "Martin Maechler" <maechler at stat.math.ethz.ch>
> To: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
> Cc: bioc-devel at r-project.org
> Sent: Tuesday, December 3, 2013 8:13:55 AM
> Subject: Re: [Bioc-devel] Struggles with correct import .....
>
> >>>>> Kasper Daniel Hansen <kasperdanielhansen at 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 <
> > kasperdanielhansen at 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
> >> < lcollado at 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
> >>> < lcollado at 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
> >>> <hj at 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"
> >>> >>
> >>> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IRanges/R/nearest-methods.R
> >>> >> >
> >>> >> >
> >>> >> > When using devtools::check (or R CMD check) I end
> >>> up with the following >> error:
> >>> >> >
> >>> >> > Error in withCallingHandlers(expr, warning =
> >>> function(w) >> invokeRestart("muffleWarning")) : >> >
> >>> could not find function "distance" >> > Calls:
> >>> analyzeChr -> annotateNearest -> .matchGenes ->
> >>> nearestgene >> > Execution halted
> >>> >> >
> >>> >> >
> >>> >> > Note that using library("bumphunter") before the
> >>> annotateNearest call >> works. But we would like to have
> >>> it work by using the correct namespace >> imports.
> >>> >> >
> >>> >> > Thank you for your help!
> >>> >> >
> >>> >> > Best, >> > Leonardo
> >>> >> >
> >>> >> > PS Function in question is >>
> >>> https://github.com/lcolladotor/derfinder/blob/master/R/analyzeChr.R
> >>> >> >
> >>> >> > > sessionInfo() >> > R version 3.0.2 (2013-09-25)
> >>> >> > Platform: x86_64-apple-darwin10.8.0 (64-bit)
> >>> >> >
> >>> >> > locale: >> > [1]
> >>> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >>> >> >
> >>> >> > attached base packages: >> > [1] stats graphics
> >>> grDevices utils datasets methods base
> >>> >> >
> >>> >> > other attached packages: >> > [1] derfinder_0.0.34
> >>> RcppArmadillo_0.3.920.1 Rcpp_0.10.6 >> roxygen2_2.2.2
> >>> digest_0.6.3 devtools_1.3
> >>> >> >
> >>> >> > loaded via a namespace (and not attached): >> > [1]
> >>> AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0
> >>> >> biomaRt_2.18.0 Biostrings_2.30.1 biovizBase_1.10.3 >>
> >>> > [7] bitops_1.0-6 brew_1.0-6 BSgenome_1.30.0 >>
> >>> bumphunter_1.2.0 cluster_1.14.4 codetools_0.2-8 >> >
> >>> [13] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 >>
> >>> doRNG_1.5.5 evaluate_0.5.1 foreach_1.4.1 >> > [19]
> >>> GenomicFeatures_1.14.0 GenomicRanges_1.14.3 ggbio_1.10.7
> >>> >> ggplot2_0.9.3.1 grid_3.0.2 gridExtra_0.9.1 >> > [25]
> >>> gtable_0.1.2 Hmisc_3.12-2 httr_0.2 >> IRanges_1.20.5
> >>> iterators_1.0.6 itertools_0.1-1 >> > [31] labeling_0.2
> >>> lattice_0.20-24 locfit_1.5-9.1 >> MASS_7.3-29
> >>> matrixStats_0.8.12 memoise_0.1 >> > [37] munsell_0.4.2
> >>> parallel_3.0.2 pkgmaker_0.17.4 >> plyr_1.8 proto_0.3-10
> >>> qvalue_1.36.0 >> > [43] R.methodsS3_1.5.2
> >>> RColorBrewer_1.0-5 RCurl_1.95-4.1 >> registry_0.2
> >>> reshape2_1.2.2 rngtools_1.2.3 >> > [49] rpart_4.1-3
> >>> Rsamtools_1.14.1 RSQLite_0.11.4 >> rtracklayer_1.22.0
> >>> scales_0.2.3 stats4_3.0.2 >> > [55] stringr_0.6.2
> >>> tcltk_3.0.2 tools_3.0.2 >> VariantAnnotation_1.8.5
> >>> whisker_0.3-2 XML_3.95-0.2 >> > [61] xtable_1.7-1
> >>> XVector_0.2.0 zlibbioc_1.8.0
> >>> >> >
> >>> >> >
> >>> >> > Leonardo Collado Torres, PhD student >> >
> >>> Department of Biostatistics >> > Johns Hopkins
> >>> University >> > Bloomberg School of Public Health >> >
> >>> Website: http://www.biostat.jhsph.edu/~lcollado/ >> >
> >>> Blog: http://lcolladotor.github.io/
> >>> >> >
> >>> >> >
> >>> >> >
> >>> >>
> >>> >>
> >>> >
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> Bioc-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>
> >>
>
> > [[alternative HTML version deleted]]
>
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