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
