[Bioc-devel] Struggles with correct import .....
Martin Maechler
maechler at stat.math.ethz.ch
Tue Dec 3 17:13:55 CET 2013
>>>>> 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 ?
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/
>>> >> >
>>> >> >
>>> >> >
>>> >>
>>> >>
>>> >
>>>
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>>>
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>>
>>
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