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Question: Biostrings throwing error
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gravatar for prim-and-proper
2.3 years ago by
prim-and-proper0 wrote:

I just installed package biostrings

biocLite("Biostrings")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller
  1.18.4), R version 3.2.0.
Installing package(s) ‘Biostrings’
also installing the dependencies ‘S4Vectors’, ‘IRanges’, ‘XVector’, ‘zlibbioc’

library(Biostrings)
Loading required package: S4Vectors
Loading required package: stats4
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Loading required package: IRanges
Loading required package: XVector
Warning messages:
1: package ‘S4Vectors’ was built under R version 3.2.1 
2: package ‘IRanges’ was built under R version 3.2.1 

But when I try to use it's datatypes I get the following errors. 

d <- BString("TTGAAAAACTCGN")
Error in nchar(x, type = "bytes") : 
  could not find symbol "keepNA" in environment of the generic function

 

> dna <- DNAString("TTGAAAAACTCGN")
Error in nchar(x, type = "bytes") : 
  could not find symbol "keepNA" in environment of the generic function

 

What can I do?

ADD COMMENTlink modified 2.3 years ago by James W. MacDonald45k • written 2.3 years ago by prim-and-proper0

Can you confirm that, in a new R session, library(S4Vectors) fails, and that pacakgeVersion("S4Vectors") reports version 0.6.3 installed? If that is not the installed version, please provide the full output of Jim's suggestion to biocLite("S4Vectors").

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Martin Morgan ♦♦ 20k

@Martin Morgan

I have such problem, too.

Here is my session info:

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Biostrings_2.36.4   XVector_0.8.0       IRanges_2.2.9       S4Vectors_0.6.6     BiocGenerics_0.14.0

loaded via a namespace (and not attached):
[1] zlibbioc_1.14.0 tools_3.2.0    

Can you help me for "BioStrings" package?

ADD REPLYlink written 2.0 years ago by NS10

The most reliable solution is to use a current version of R (3.2.2) and Bioconductor (3.2).

ADD REPLYlink written 2.0 years ago by Martin Morgan ♦♦ 20k
0
gravatar for James W. MacDonald
2.3 years ago by
United States
James W. MacDonald45k wrote:

Try

library(BiocInstaller)
biocLite("S4Vectors")

 

ADD COMMENTlink written 2.3 years ago by James W. MacDonald45k
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