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 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
