Hello, I am working on creating a package, and have come across an issue.
I have some R code in the "R" folder that works just fine when I test it. The code contains a function accepts a GRangesList as input. I call the function from my Rmarkdown file in the "vignette" folder. When I test the "code chunk" from the Rmd file, the function works just fine. But when I try to "knitPDF", it gives this error Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : subscript contains invalid names Calls: <Anonymous> ... [ -> normalizeSingleBracketSubscript -> NSBS -> NSBS The code is like this: data("grl") run.cin.chr(grl.seg = grl) #grl is the GRangesList input Any help on how to fix this issue is much appreciated. This is my session Info. > session_info() Session info ----------------------------------------------------------------------------------------- setting value version R version 3.2.2 (2015-08-14) system x86_64, darwin13.4.0 ui RStudio (0.99.489) language (EN) collate en_US.UTF-8 tz America/New_York date 2015-12-10 Packages --------------------------------------------------------------------------------------------- package * version date source acepack 1.3-3.3 2014-11-24 CRAN (R 3.2.0) affxparser 1.42.0 2015-10-14 Bioconductor affyio 1.40.0 2015-10-14 Bioconductor AnnotationDbi * 1.32.2 2015-12-09 Bioconductor AnnotationHub * 2.2.2 2015-11-08 Bioconductor Biobase * 2.30.0 2015-10-14 Bioconductor BiocGenerics * 0.16.1 2015-11-06 Bioconductor BiocInstaller 1.20.1 2015-11-18 Bioconductor BiocParallel 1.4.0 2015-10-14 Bioconductor biomaRt 2.26.1 2015-11-23 Bioconductor Biostrings * 2.38.2 2015-11-21 Bioconductor biovizBase * 1.18.0 2015-10-14 Bioconductor bit 1.1-12 2014-04-09 CRAN (R 3.2.0) bitops 1.0-6 2013-08-17 CRAN (R 3.2.0) BSgenome 1.38.0 2015-10-14 Bioconductor caTools 1.17.1 2014-09-10 CRAN (R 3.2.0) CINdex * 0.99.4 2015-12-10 Bioconductor cluster 2.0.3 2015-07-21 CRAN (R 3.2.2) codetools 0.2-14 2015-07-15 CRAN (R 3.2.2) colorspace 1.2-6 2015-03-11 CRAN (R 3.2.0) DBI * 0.3.1 2014-09-24 CRAN (R 3.2.0) devtools * 1.9.1 2015-09-11 CRAN (R 3.2.0) dichromat 2.0-0 2013-01-24 CRAN (R 3.2.0) digest 0.6.8 2014-12-31 CRAN (R 3.2.0) ff 2.2-13 2014-04-09 CRAN (R 3.2.0) foreach 1.4.3 2015-10-13 CRAN (R 3.2.0) foreign 0.8-66 2015-08-19 CRAN (R 3.2.0) Formula 1.2-1 2015-04-07 CRAN (R 3.2.0) futile.logger 1.4.1 2015-04-20 CRAN (R 3.2.0) futile.options 1.0.0 2010-04-06 CRAN (R 3.2.0) gdata 2.17.0 2015-07-04 CRAN (R 3.2.0) GenomeInfoDb * 1.6.1 2015-11-03 Bioconductor GenomicAlignments 1.6.1 2015-10-22 Bioconductor GenomicFeatures * 1.22.6 2015-12-03 Bioconductor GenomicRanges * 1.22.1 2015-11-06 Bioconductor ggplot2 1.0.1 2015-03-17 CRAN (R 3.2.0) GO.db * 3.2.2 2015-11-12 Bioconductor gplots 2.17.0 2015-05-02 CRAN (R 3.2.0) graph 1.48.0 2015-10-14 Bioconductor gridExtra 2.0.0 2015-07-14 CRAN (R 3.2.0) gtable 0.1.2 2012-12-05 CRAN (R 3.2.0) gtools 3.5.0 2015-05-29 CRAN (R 3.2.0) Hmisc 3.17-0 2015-09-21 CRAN (R 3.2.0) Homo.sapiens * 1.3.1 2015-12-09 Bioconductor htmltools 0.2.6 2014-09-08 CRAN (R 3.2.0) httpuv 1.3.3 2015-08-04 CRAN (R 3.2.0) httr 1.0.0 2015-06-25 CRAN (R 3.2.0) interactiveDisplayBase 1.8.0 2015-10-14 Bioconductor IRanges * 2.4.5 2015-12-08 Bioconductor iterators 1.0.8 2015-10-13 CRAN (R 3.2.0) KernSmooth 2.23-15 2015-06-29 CRAN (R 3.2.2) knitr * 1.11 2015-08-14 CRAN (R 3.2.2) lambda.r 1.1.7 2015-03-20 CRAN (R 3.2.0) lattice 0.20-33 2015-07-14 CRAN (R 3.2.2) latticeExtra 0.6-26 2013-08-15 CRAN (R 3.2.0) magrittr 1.5 2014-11-22 CRAN (R 3.2.0) MASS 7.3-45 2015-11-10 CRAN (R 3.2.2) memoise 0.2.1 2014-04-22 CRAN (R 3.2.0) mime 0.4 2015-09-03 CRAN (R 3.2.0) munsell 0.4.2 2013-07-11 CRAN (R 3.2.0) nnet 7.3-11 2015-08-30 CRAN (R 3.2.0) oligo * 1.34.0 2015-10-14 Bioconductor oligoClasses * 1.32.0 2015-10-14 Bioconductor org.Hs.eg.db * 3.2.3 2015-12-09 Bioconductor OrganismDbi * 1.12.0 2015-10-14 Bioconductor pd.genomewidesnp.6 * 3.14.1 2015-11-30 Bioconductor plyr 1.8.3 2015-06-12 CRAN (R 3.2.0) preprocessCore 1.32.0 2015-10-14 Bioconductor proto 0.3-10 2012-12-22 CRAN (R 3.2.0) R6 2.1.1 2015-08-19 CRAN (R 3.2.0) RBGL 1.46.0 2015-10-14 Bioconductor RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.2.0) Rcpp 0.12.2 2015-11-15 CRAN (R 3.2.2) RCurl 1.95-4.7 2015-06-30 CRAN (R 3.2.0) reshape2 1.4.1 2014-12-06 CRAN (R 3.2.0) rmarkdown 0.8.1 2015-10-10 CRAN (R 3.2.2) rpart 4.1-10 2015-06-29 CRAN (R 3.2.2) Rsamtools 1.22.0 2015-10-14 Bioconductor RSQLite * 1.0.0 2014-10-25 CRAN (R 3.2.0) rtracklayer * 1.30.1 2015-10-22 Bioconductor S4Vectors * 0.8.4 2015-12-08 Bioconductor scales 0.3.0 2015-08-25 CRAN (R 3.2.0) shiny 0.12.2 2015-08-05 CRAN (R 3.2.0) som 0.3-5 2010-04-07 CRAN (R 3.2.0) stringi 1.0-1 2015-10-22 CRAN (R 3.2.0) stringr 1.0.0 2015-04-30 CRAN (R 3.2.0) SummarizedExperiment 1.0.1 2015-11-06 Bioconductor survival 2.38-3 2015-07-02 CRAN (R 3.2.2) TxDb.Hsapiens.UCSC.hg18.knownGene * 3.2.2 2015-12-09 Bioconductor TxDb.Hsapiens.UCSC.hg19.knownGene * 3.2.2 2015-12-09 Bioconductor VariantAnnotation 1.16.4 2015-12-09 Bioconductor XML 3.98-1.3 2015-06-30 CRAN (R 3.2.0) xtable 1.8-0 2015-11-02 CRAN (R 3.2.0) XVector * 0.10.0 2015-10-14 Bioconductor yaml 2.1.13 2014-06-12 CRAN (R 3.2.0) zlibbioc 1.16.0 2015-10-14 Bioconductor Thanks, --Krithika [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel