Hey,
prokAligned3 <- msaConvert(prokAligned, type="phangorn::phyDat")
Keep trying this code. keep getting the error could not find "msaconvert"
have upgraded everything,running latest version of R
Well, as obvious from your sessionInfo() results, you are using R 3.2.4 which is more than two years old. Since Bioconductor binds releases to the latest R version, you only have Bioconductor 3.3, which includes 'msa' version 1.2.1. The msaConvert() function has been introduced in 'msa' version 1.3.3. In order to use msaConvert(), you need to install a newer version of R (ideally R 3.5.0 or 3.5.1), otherwise you will not have access to the latest features.
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
I have seen such error messages in the past, and the reason was always that the users read the manual of a newer version than they actually used. So, if you have the latest version, this is a new issue that I will be glad to go into. Please provide a minimal example that produces that error along with the result of
sessionInfo(), otherwise I do not have sufficient information to analyze the issue.This was the command:- prokAligned2 <- msaConvert(prokAligned, type="seqinr::alignment")
Error: could not find function "msaConvert"
sessionInfo()
R version 3.2.4 (2016-03-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel stats graphics
[5] grDevices utils datasets methods
[9] base
other attached packages:
[1] seqinr_3.4-5 msa_1.2.1
[3] Biostrings_2.38.4 XVector_0.10.0
[5] IRanges_2.4.8 S4Vectors_0.8.11
[7] BiocGenerics_0.16.1
loaded via a namespace (and not attached):
[1] MASS_7.3-50 zlibbioc_1.16.0
[3] tools_3.2.4 yaml_2.1.19
[5] Rcpp_0.12.17 ade4_1.7-10
>
i use this to install msa
source("https://bioconductor.org/biocLite.R") biocLite("msa")and always get version 1.2.1