Membrane Glycolipid Mass Spectrum Simulator for polymicrobial samples
install.packages(c("MALDIquant","MALDIquantForeign"),type="source")
install.packages("MGMS2")
library("MGMS2")
or
R -e 'install.packages("MGMS2")'
install.packages(c("MALDIquant","MALDIquantForeign"),type="source")
devtools::install_github("unreno/MGMS2")
library("MGMS2")
or
R -e 'devtools::install_github("unreno/MGMS2")'
library('MGMS2')
remove.packages("MGMS2")
install.packages(c('devtools','roxygen2'))
library('devtools')
library('roxygen2')
create('MGMS2')
The "create()" function fails with "Error: Directory 'MGMS2' does not exist." after
it creates DESCRIPTION
and NAMESPACE
files and an empty R/
dir. Kinda pointless.
Could've just used a simple template for this.
Is that what its supposed to do?
Create/Edit .R
files in R/
folder with properly formated documentation above functions.
Then update NAMESPACE
and man/
from within R ...
library('devtools')
document()
Or from the bash command line ...
R -e 'library(devtools);document()'
Install from the bash command line ...
R -e 'library(devtools);document();setwd("..");install("MGMS2",upgrade=FALSE)'
Or from R with some manual checking with sample data ...
remove.packages("MGMS2")
library('devtools')
document()
setwd('..')
install('MGMS2',upgrade=FALSE)
library('MGMS2')
lsf.str("package:MGMS2")
"MGMS2" %in% rownames(installed.packages())
spectra.processed.A <- process_monospectra(
file=system.file("extdata", "listA.txt", package="MGMS2"),
mass.range=c(1000,2200))
spectra.processed.B <- process_monospectra(
file=system.file("extdata", "listB.txt", package="MGMS2"),
mass.range=c(1000,2200))
spectra.processed.C <- process_monospectra(
file=system.file("extdata", "listC.txt", package="MGMS2"),
mass.range=c(1000,2200))
spectra.mono.summary.A <- summarize_monospectra(
processed.obj=spectra.processed.A,
species='A', directory=tempdir())
spectra.mono.summary.B <- summarize_monospectra(
processed.obj=spectra.processed.B,
species='B', directory=tempdir())
spectra.mono.summary.C <- summarize_monospectra(
processed.obj=spectra.processed.C,
species='C', directory=tempdir())
mono.info=gather_summary(c(spectra.mono.summary.A, spectra.mono.summary.B, spectra.mono.summary.C))
gather_summary_file(directory=tempdir())
mixture.ratio <- list()
mixture.ratio['A']=1
mixture.ratio['B']=0.5
mixture.ratio['C']=0
sim.template <- create_insilico_mixture_template(mono.info)
insilico.spectrum <- simulate_poly_spectra(sim.template, mixture.ratio)
insilico.spectrums <- simulate_many_poly_spectra(mono.info, mixture.ratio=mixture.ratio, nsim=10 )
remove.packages("MGMS2")
ADD AUTOMATED TESTING
ADD AUTOMATED VERSIONING
Then commit and push to github repo
git commit -m "<LIST UPDATES>" -a
git push
https://xmpalantir.wu.ac.at/cransubmit/
Check for CRAN issues ...
R -e 'library(devtools);document();setwd("..");install("MGMS2",upgrade=FALSE)'
VERSION=$( awk '(/^Version/){print $2}' DESCRIPTION )
cd ..
R CMD build MGMS2
R CMD check MGMS2_${VERSION}.tar.gz
R CMD check --as-cran MGMS2_${VERSION}.tar.gz
If all is well, try to submit to CRAN
https://hilaryparker.com/2014/04/29/writing-an-r-package-from-scratch/
https://kbroman.org/pkg_primer/
https://aberdeenstudygroup.github.io/studyGroup/lessons/SG-T4-Rpackages/makingRpackages1_Intro/
https://r-pkgs.org/release.html
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