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