omarwagih / rmimp Goto Github PK

mutAA[wrongMut], is much longer than other arguments passed to sprintf

Hi

How should I input stop codons? X123* isn't working.
Also, just to make sure, indels are X, right?

Thanks!

R-MIMP would be more efficient if it would be able to load mutations from a data frame rather than a file. Sequences and sites as R objects are already included (that's great!) so it would make sense to allow this for mutations as well.

The function "subjectHIts" needs to be changed for "to"

Hi MIMP and others,

Anyone could provide an introduction about how to obtain the mutation data? I do not know which software could hold this. Thanks a lot.

Bests

I tried to install rmimp on R (version 3.6.0) but I had the following error:

install_github("omarwagih/rmimp")
Downloading GitHub repo omarwagih/rmimp@master
✔ checking for file ‘/tmp/Rtmp73qJKP/remotes295f4b06723f/omarwagih-rmimp-5bf4fc6/DESCRIPTION’ ...
─ preparing ‘rmimp’: (537ms)
✔ checking DESCRIPTION meta-information
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘rmimp_1.2.tar.gz’

Installing package into '/home/lecob/R/x86_64-pc-linux-gnu-library/3.6'
(as 'lib' is unspecified)

• installing source package ‘rmimp’ ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded from temporary location
  ** testing if installed package can be loaded from final location
  ** testing if installed package keeps a record of temporary installation path
  ERROR: hard-coded installation path: please report to the package maintainer and use ‘--no-staged-install’
• removing ‘/home/lecob/R/x86_64-pc-linux-gnu-library/3.6/rmimp’
  Error in i.p(...) :
  (converted from warning) installation of package '/tmp/Rtmp73qJKP/file295f30c4b032/rmimp_1.2.tar.gz' had non-zero exit status

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

It would be great to have a "quiet mode" in R where progress % and messages are not printed. Analysing thousands of proteins in a batch will spent a lot of energy on reporting.