Error: could not find function "msaConvert"
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weiguo0113 • 0
@weiguo0113-7333
Last seen 5.3 years ago
United States

Hi all,

I am interested in going ahead with "msa: An R Package for Multiple Sequence Alignment". I am trying with the software manual. But "Error: could not find function "msaConvert". I can not resolve it. Could you help me? Thanks

Here is the command line that I am using:

> hemoSeq<-readAAStringSet(system.file("examples/HemoglobinAA.fasta",package="msa"))
> hemoAln<-msa(hemoSeq)
use default substitution matrix
Sequence type explicitly set to Protein
> hemoAln2 <- msaConvert(hemoAln,type="seqinr::alignment")#not work
Error: could not find function "msaConvert"

msa software error • 1.2k views
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UBodenhofer ▴ 290
@ubodenhofer-5425
Last seen 12 weeks ago
University of Applied Sciences Upper Au…

It seems to me that you have an older version of the package installed. The msaConvert() function has been added in version 1.3.3 in the devel branch. So the first release version that included this function was 1.4.0, which has been released as part of Bioconductor 3.3 on May 4, 2016. You can only install and run this version if you have at least R 3.3.0 on your system. Please enter

packageDescription("msa")$Version

I bet you see a 1.2.x number or even older. If so, I'd suggest you upgrade to R 3.3.1 and install Bioconductor 3.4 (released yesterday). If you cannot do so, a simple workaround is to download the latest package archive of the package from https://bioconductor.org/packages/release/bioc/html/msa.html, save it to your local harddisk, and install it from there. 'msa' does not rely on any new features of other packages, so it will probably install without any problems also on older R versions.

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