On Fri, Dec 11, 2015 at 2:02 PM, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi, > > On 12/11/2015 12:42 PM, Krithika Bhuvaneshwar [kb...@georgetown.edu] wrote: >> >> Thank you for your email. >> >> I did fix the issue. >> >> The problem was with GenomicRanges in the DESCRIPTION/NAMESPACE file of >> the package. Initially I listed it in the "imports" section of the >> DESCRIPTION file, and it looks like the vignette was not picking it up >> when I tried to build it. >> >> So I put it in "depends" section. I also made sure import(GenomicRanges) >> was added to NAMESPACE. That seemed to fix the issue. >
I'm guessing that it was adding import(GenomicRanges) to NAMESPACE that fixed the issue. You should never have to list the package in Depends to fix symbol resolution. > > Good to know. > > I'm putting this back on the list where you originally posted this > so the other the developers know that you've addressed the issue > and they don't need to spend time trying to help you with this. > > Cheers, > H. > >> >> Thanks ! >> >> >> >> --Krithika >> >> ------------------------------------------------------------------------------ >> Ms. Krithika Bhuvaneshwar >> Bioinformatician/Data Manager >> Innovation Center for Biomedical Informatics (ICBI), >> Georgetown University Medical Center, Washington, DC >> Email: kb...@georgetown.edu <mailto:kb...@georgetown.edu> ; >> krithika...@gmail.com <mailto:krithika...@gmail.com> >> Phone: 202-687-6850; Fax: 202-687-5011 >> http://icbi.georgetown.edu/ >> >> ------------------------------------------------------------------------------- >> >> >> On Fri, Dec 11, 2015 at 3:38 PM, Hervé Pagès <hpa...@fredhutch.org >> <mailto:hpa...@fredhutch.org>> wrote: >> >> 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 [kb...@georgetown.edu >> <mailto:kb...@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]] >> >> _______________________________________________ >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> >> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M1-B514 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpa...@fredhutch.org <mailto:hpa...@fredhutch.org> >> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> >> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> >> >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel