Question: Error: could not find function "msaConvert"
0
gravatar for singh24s
17 months ago by
singh24s0
singh24s0 wrote:

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

msa • 259 views
ADD COMMENTlink modified 17 months ago by UBodenhofer250 • written 17 months ago by singh24s0

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.

ADD REPLYlink written 17 months ago by UBodenhofer250

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    

ADD REPLYlink written 17 months ago by singh24s0

i use this to install msa

source("https://bioconductor.org/biocLite.R")
biocLite("msa")

 

and always get version 1.2.1

ADD REPLYlink written 17 months ago by singh24s0
Answer: Error: could not find function "msaConvert"
0
gravatar for UBodenhofer
17 months ago by
UBodenhofer250
Johannes Kepler University, Linz, Austria
UBodenhofer250 wrote:

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.

ADD COMMENTlink written 17 months ago by UBodenhofer250
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