[Bioc-devel] Error in NSBS
Hi Krithika,
NSBS() is the internal helper defined in the S4Vectors package that
takes care of checking and normalizing the supplied subscript when
one tries to subset a Vector derivative (e.g. an Rle, Hits, IRanges,
GRanges, GRangesList, etc...). For example:
> IRanges(1:26, 50, names=letters)[LETTERS]
Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
subscript contains invalid names
It's just saying that the subscript 'i' contains names that are not
valid.
So it seems that in your case a subsetting operation that happens
in run.cin.chr() works just fine when you run run.cin.chr()
interactively but not in the context of knitPDF.
It's hard to know why without having more details.
Could you please run R CMD Stangle on your Rmarkdown file? That will
produce a .R file. Then start R and source this .R file with
source("file_produced_by_R_CMD_Stangle.R" , echo=TRUE).
Then please report the full output you get as well as the output of
sessionInfo() (call this after the source() command terminates).
Please use sessionInfo(), not session_info().
Thanks,
H.
On 12/10/2015 09:27 PM, Krithika Bhuvaneshwar [kb472 at georgetown.edu] wrote:
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]]
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