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
-----------------------------------------------------------------------------------------
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
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