Excellent! Thank you Kasper.
On Wed, Nov 20, 2013 at 3:37 PM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > 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
