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 <dtenenba@fhcrc.org> wrote:

>
>
> ----- Original Message -----
> > From: "Martin Maechler" <maechler@stat.math.ethz.ch>
> > To: "Kasper Daniel Hansen" <kasperdanielhansen@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 <kasperdanielhansen@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@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@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@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@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@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
> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>

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