Installation problem

[pshahnazari]

Installation problem

[lauzikaite]

Hi!
I'd try and install using the following function, which I've tested on multiple OS and R environments

# To install dependencies
install_dependencies <- function () {
  dependencies <- c("xcms",  "MSnbase", "faahKO", "igraph", "doParallel",  "foreach", "ggplot2", "viridis", "gridExtra")
  installed <- installed.packages()
  to_install <- subset(dependencies, !(dependencies %in% installed[, "Package"]))
  if (length(to_install) != 0) {
    if (!requireNamespace("BiocManager", quietly = TRUE)) {
      install.packages("BiocManager")
    }
    message("Installing packages: ", to_install, " ...")
    BiocManager::install(to_install)
  } else {
    message("All dependencies are already installed.")
  }
}
install_dependencies()

# To install development version
devtools::install_github("lauzikaite/massflowR", dependencies = FALSE)

Let me know if you encounter issues while installing it in this way.

Thanks,
Elze

[pshahnazari]

Hi Elze,
I could not install and I found this error

install_dependencies <- function () {

• dependencies <- c("xcms", "MSnbase", "faahKO", "igraph", "doParallel", "foreach", "ggplot2", "viridis", "gridExtra")
• installed <- installed.packages()
• to_install <- subset(dependencies, !(dependencies %in% installed[, "Package"]))
• if (length(to_install) != 0) {

• if (!requireNamespace("BiocManager", quietly = TRUE)) {
  

•   install.packages("BiocManager")
  

• }
  

• message("Installing packages: ", to_install, " ...")
  

• BiocManager::install(to_install)
  

• } else {

• message("All dependencies are already installed.")
  

• }
• }

install_dependencies()
All dependencies are already installed.

To install dependencies

install_dependencies <- function () {

• dependencies <- c("xcms", "MSnbase", "faahKO", "igraph", "doParallel", "foreach", "ggplot2", "viridis", "gridExtra")
• installed <- installed.packages()
• to_install <- subset(dependencies, !(dependencies %in% installed[, "massFlowR"]))
• if (length(to_install) != 0) {

• if (!requireNamespace("BiocManager", quietly = TRUE)) {
  

•   install.packages("BiocManager")
  

• }
  

• message("Installing packages: ", to_install, " ...")
  

• BiocManager::install(to_install)
  

• } else {

• message("All dependencies are already installed.")
  

• }
• }

To install dependencies

install_dependencies <- function () {

• dependencies <- c("xcms", "MSnbase", "faahKO", "igraph", "doParallel", "foreach", "ggplot2", "viridis", "gridExtra")
• installed <- installed.packages(massFlowR)
• to_install <- subset(dependencies, !(dependencies %in% installed[, "massFlowR"]))
• if (length(to_install) != 0) {

• if (!requireNamespace("BiocManager", quietly = TRUE)) {
  

•   install.packages("BiocManager")
  

• }
  

• message("Installing packages: ", to_install, "massFlowR")
  

• BiocManager::install(to_install)
  

• } else {

• message("All dependencies are already installed.")
  

• }
• }

install_dependencies()
Error in installed.packages(massFlowR) : object 'massFlowR' not found
Could you help me to install and run your package. Actually I am eager to use your package .
Thanks
Parisa

[lauzikaite]

There is an error in your code. Could you please copy and paste the code that I shared in my previous message exactly as it is and run it?

[pshahnazari]

sure, my codes: if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(" massFlowR")
The downloaded source packages are in
‘C:\Users\Win 1809 UEFI\AppData\Local\Temp\RtmpSSeXLZ\downloaded_packages’
Warning message:
package ‘ massFlowR’ is not available (for R version 3.6.3)
Error in library(massFlowR) : there is no package called ‘massFlowR’
Thank you for your attention.

[pshahnazari]

Hi again, I changed my version R to 4.0 but there is same error

[lauzikaite]

Yes, there is an error in your code. Please use my code directly as provided without modifications.