The statement m[, 1L] <- map[m[, 1L]] seems pretty likely to cause Error in map[m[, 1L]] : object of type 'closure' is not subsettable This occurs with nearest(select="all") when there is no overlap. Slightly sanitized real-life example: > library(TxDb.Hsapiens.UCSC.hg19.knownGene) Loading required package: GenomicFeatures Loading required package: BiocGenerics ... > TT <- transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, by="gene") > tt <- TT[[1]] > tt GRanges with 2 ranges and 2 metadata columns: seqnames ranges strand | tx_id tx_name <rle> <iranges> <rle> | <integer> <character> [1] chr19 [58858172, 58864865] - | 68796 uc002qsd.4 [2] chr19 [58859832, 58874214] - | 68797 uc002qsf.2 --- seqlengths: chr1 chr2 ... chrUn_gl000249 249250621 243199373 ... 38502 > q <- GRanges(IRanges(1,1), seqnames="chr19", strand="*") > nearest(q, tt) [1] 1 > nearest(q, tt, select="all") Error in map[m[, 1L]] : object of type 'closure' is not subsettable > sessionInfo() R version 2.15.1 Patched (2012-07-01 r59713) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 [2] GenomicFeatures_1.10.0 [3] AnnotationDbi_1.20.2 [4] Biobase_2.18.0 [5] GenomicRanges_1.10.2 [6] IRanges_1.16.3 [7] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] biomaRt_2.14.0 Biostrings_2.26.2 bitops_1.0-4.1 BSgenome_1.26.1 [5] DBI_0.2-5 parallel_2.15.1 RCurl_1.95-1.1 Rsamtools_1.10.1 [9] RSQLite_0.11.2 rtracklayer_1.18.0 stats4_2.15.1 tools_2.15.1 [13] XML_3.95-0.1 zlibbioc_1.4.0

Thanks for the bug report. Now fixed in 1.11.6 devel and 1.10.3 in release. Valerie On 10/25/2012 12:09 PM, Harris A. Jaffee wrote: > The statement > > m[, 1L] <- map[m[, 1L]] > > seems pretty likely to cause > > Error in map[m[, 1L]] : object of type 'closure' is not subsettable > > This occurs with nearest(select="all") when there is no overlap. > > Slightly sanitized real-life example: > >> library(TxDb.Hsapiens.UCSC.hg19.knownGene) > Loading required package: GenomicFeatures > Loading required package: BiocGenerics > ... >> TT <- transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, by="gene") >> tt <- TT[[1]] >> tt > GRanges with 2 ranges and 2 metadata columns: > seqnames ranges strand | tx_id tx_name > <rle> <iranges> <rle> | <integer> <character> > [1] chr19 [58858172, 58864865] - | 68796 uc002qsd.4 > [2] chr19 [58859832, 58874214] - | 68797 uc002qsf.2 > --- > seqlengths: > chr1 chr2 ... chrUn_gl000249 > 249250621 243199373 ... 38502 > >> q <- GRanges(IRanges(1,1), seqnames="chr19", strand="*") >> nearest(q, tt) > [1] 1 >> nearest(q, tt, select="all") > Error in map[m[, 1L]] : object of type 'closure' is not subsettable > >> sessionInfo() > R version 2.15.1 Patched (2012-07-01 r59713) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C > [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 > [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 > [2] GenomicFeatures_1.10.0 > [3] AnnotationDbi_1.20.2 > [4] Biobase_2.18.0 > [5] GenomicRanges_1.10.2 > [6] IRanges_1.16.3 > [7] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] biomaRt_2.14.0 Biostrings_2.26.2 bitops_1.0-4.1 BSgenome_1.26.1 > [5] DBI_0.2-5 parallel_2.15.1 RCurl_1.95-1.1 Rsamtools_1.10.1 > [9] RSQLite_0.11.2 rtracklayer_1.18.0 stats4_2.15.1 tools_2.15.1 > [13] XML_3.95-0.1 zlibbioc_1.4.0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor