R version for the tool - Githubissues

simonzzc034 commented 6 years ago

Hey, does mr.mosaic require a particular R version or R version after certain release? I am asking because when I tried to make the code, got the following error:

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : namespace ‘proto’ 0.3-10 is already loaded, but >= 1.0.0 is required

PBmitshu commented 6 years ago

Latest R version 3.4.3 works well with all dependencies need for this tool

PamelaMehanna commented 6 years ago

Mine works with R/3.3.3

simonzzc034 commented 6 years ago

Thank you everyone. I was using an old version R but now I am on R3.4.1, and run into another error while 'make' the code:

install_github("asifrim/mrmosaic",ref="master",subdir="mrmosaic") Downloading GitHub repo asifrim/mrmosaic@master from URL https://api.github.com/repos/asifrim/mrmosaic/zipball/master Installing mrmosaic '/home/karvai/anaconda/envs/r-env/lib/R/bin/R' --no-site-file --no-environ \ --no-save --no-restore --quiet CMD INSTALL \ '/tmp/Rtmp9ztqnS/devtools37be750ec863/asifrim-mrmosaic-969c39a/mrmosaic' \ --library='/home/zzhang/R/x86_64-pc-linux-gnu-library/3.4' --install-tests

installing source package ‘mrmosaic’ ... R preparing package for lazy loading Error in .stop(output, "parse error:") : parse error: usage: PROGRAM [-h] [--child CHILD] [--dad DAD] [--mum MUM] [--denovo DENOVO] [--prefix PREFIX] [--outputdir OUTPUTDIR] PROGRAM: error: unrecognized arguments: nextArg/tmp/Rtmp9ztqnS/devtools37be750ec863/asifrim-mrmosaic-969c39a/mrmosaicnextArg--library=/home/zzhang/R/x86_64-pc-linux-gnu-library/3.4nextArg--install-tests Error : unable to load R code in package ‘mrmosaic’ ERROR: lazy loading failed for package ‘mrmosaic’

Any of you seen this before. It looks like an argparse error, not necessarily R version issue to me? Thanks!

Zhancheng

simonzzc034 commented 6 years ago

Also may I ask how recently did you guys install this tool?

dwalinybalin commented 6 years ago

As I answered in a previous post, perform the following steps:

Move the "plot_denovos.R" and "plot_mrm.R" files located in the R folder inside the mrmosaic R package folder to the scripts folder in the package folder.
In the install_package.R file, change the line:

install_github("asifrim/mrmosaic",ref="master",subdir="mrmosaic")

for

install.packages("mrmosaic", repos=NULL, type="source")

Run make

simonzzc034 commented 6 years ago

That works. Thank you so much Marcos!

ik3rp3r3 commented 6 years ago

Hi,

My R version is 3.4.4 and I've followed the steps you said but I am still getting the exact same error as simonzzc034. Does anyone know why?

Thanks!

asifrim / mrmosaic

R version for the tool #6