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/NAMESPACE > doesn'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
