MSqRob installation · Issue #1 · statOmics/MSqRob (original) (raw)

We had some issues to install MSqRob on a windows comuter.
Here is the procedure we used to make it work.
It may help somebody else.

install.packages("devtools") library(devtools)

source("https://bioconductor.org/biocLite.R") biocLite("Biobase") biocLite("limma") biocLite("MSnbase") biocLite("preprocessCore") biocLite("vsn")

install.packages("lme4") install.packages("htmltools") install.packages("httpuv") install.packages("xtable") install.packages("DT") install.packages("shinyjs")

devtools::install_github("ludgergoeminne/MSqRob") library(MSqRob)

shiny::runApp(system.file("App-MSqRob", package="MSqRob"))

Here are our session data:

session info:

Session info ---------------------------------------------------------------------------------------------------------------------- setting value
version R version 3.3.1 (2016-06-21) system x86_64, mingw32
ui RStudio (0.99.903)
language (EN)
collate French_France.1252
tz Europe/Paris
date 2017-01-20

Packages -------------------------------------------------------------------------------------------------------------------------- package * version date source
devtools * 1.12.0 2016-06-24 CRAN (R 3.3.2)
digest 0.6.11 2017-01-03 CRAN (R 3.3.2)
lattice 0.20-34 2016-09-06 CRAN (R 3.3.2)
lme4 * 1.1-12 2016-04-16 CRAN (R 3.3.2)
MASS 7.3-45 2016-04-21 CRAN (R 3.3.1)
Matrix * 1.2-7.1 2016-09-01 CRAN (R 3.3.2)
memoise 1.0.0 2016-01-29 CRAN (R 3.3.2)
minqa 1.2.4 2014-10-09 CRAN (R 3.3.2)
MSqRob * 0.6.2 2017-01-17 Github (ludgergoeminne/MSqRob@47285d0) nlme 3.1-128 2016-05-10 CRAN (R 3.3.1)
nloptr 1.0.4 2014-08-04 CRAN (R 3.3.2)
Rcpp 0.12.9 2017-01-14 CRAN (R 3.3.2)
withr 1.0.2 2016-06-20 CRAN (R 3.3.2)

Warning: Error in renderPlot: Please provide a protein groups file or untick the box "Remove proteins that are only identified by modified peptides".

Warning: Error in check_expAnn: Make sure that exactly one column in the experiment annotation has elements equal to the mass spec run names in the data. Maybe one of the following columns has an error in at least one of its elements: run.