System command error - can't install

[artgolden]

The downloaded source packages are in
    ‘/tmp/RtmpjdbjHB/downloaded_packages’
✔  checking for file ‘/tmp/RtmpjdbjHB/remotescfd390643de/BMILAB-scNPF-742ec64/DESCRIPTION’ ...
─  preparing ‘scNPF’:
✔  checking DESCRIPTION meta-information ...
   Warning in file(con, "r") :
     cannot open file 'man': No such file or directory
    ERROR
   computing Rd index failed:cannot open the connection
Error in (function (command = NULL, args = character(), error_on_status = TRUE,  : 
  System command error

This error occurs on a fresh R install (3.5.1, 3.6, 3.6) on three separate computers, running Ubuntu 18.04, 16.04, Windows 8.1 respectively. To reproduce:

install R

install.packages("devtools") # with all dependencies
install.packages("BiocManager")
BiocManager::install(c("AnnotationDbi", "GO.db", "impute", "preprocessCore"))
devtools::install_github("BMILAB/scNPF")

Any help appreciated!

Further reading on the internet suggested that this can be devtools issue with function install_github(). However other packages are installing just fine.

> devtools::install_github("r-lib/remotes")
Downloading GitHub repo r-lib/remotes@master
✔  checking for file ‘/tmp/RtmpGYWxMe/remotes24c444e1d84a/r-lib-remotes-ba2f034/DESCRIPTION’ ...
─  preparing ‘remotes’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘remotes_2.0.4.9000.tar.gz’

* installing *source* package ‘remotes’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (remotes)
> 

[nikou123456]

Hi,

Thanks for contacting. I think this is an issue in R rather than in devtools. Maybe you can install it locally.

• According to the "DESCRIPTION" file of scNPF, installing all dependencies.

  Depends: R (>= 3.1.0), igraph, WGCNA, foreach, doParallel, Matrix, plyr, methods
  Suggests: gplots, RColorBrewer
  Such as 
  >BiocManager::install(c("impute","preprocessCore","GO.db"))

• Download Zip

• Unzip this file and rename this file.

  >unzip scNPF-master.zip
  >mv scNPF-master   scNPF
  >zip -r scNPF.zip scNPF

• Install it locally

  >install.packages("C:/Users/yec/Downloads/scNPF/scNPF.zip", repos = NULL, type = "win.binary")
  >library(scNPF)
  #loading example data
  > load(system.file("data","yan.Rdata",package = "scNPF"))
  > exp.data <- yan$data
  > dim(exp.data)
  [1] 17916    90
  >##Using String network to smooth expression values.
  >load(system.file("data","string.Rdata",package = "scNPF"))
  >string.data <- scNPF.pro(x=exp.data, network=string,nThreads=8)

[BMILAB]

The downloaded source packages are in
  ‘/tmp/RtmpjdbjHB/downloaded_packages’
✔  checking for file ‘/tmp/RtmpjdbjHB/remotescfd390643de/BMILAB-scNPF-742ec64/DESCRIPTION’ ...
─  preparing ‘scNPF’:
✔  checking DESCRIPTION meta-information ...
   Warning in file(con, "r") :
     cannot open file 'man': No such file or directory
    ERROR
   computing Rd index failed:cannot open the connection
Error in (function (command = NULL, args = character(), error_on_status = TRUE,  : 
  System command error

This error occurs on a fresh R install (3.5.1, 3.6, 3.6) on three separate computers, running Ubuntu 18.04, 16.04, Windows 8.1 respectively. To reproduce:

install R

install.packages("devtools") # with all dependencies
install.packages("BiocManager")
BiocManager::install(c("AnnotationDbi", "GO.db", "impute", "preprocessCore"))
devtools::install_github("BMILAB/scNPF")

Any help appreciated!

Further reading on the internet suggested that this can be devtools issue with function install_github(). However other packages are installing just fine.

> devtools::install_github("r-lib/remotes")
Downloading GitHub repo r-lib/remotes@master
✔  checking for file ‘/tmp/RtmpGYWxMe/remotes24c444e1d84a/r-lib-remotes-ba2f034/DESCRIPTION’ ...
─  preparing ‘remotes’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘remotes_2.0.4.9000.tar.gz’

* installing *source* package ‘remotes’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (remotes)
> 

Thanks for your contacting. I have fixed the problem and updated the scNPF package，you can try to install it again

install.packages("devtools")
library(devtools)
install_github("BMILAB/scNPF")
library(scNPF)

if you use the R version 3.6， you may encounter the following problems

install_github("BMILAB/scNPF")
* installing *source* package ‘scNPF’ ... 
** using staged installation 
** R 
** data 
*** moving datasets to lazyload DB 
** byte-compile and prepare package for lazy loading 
Error: (converted from warning) package ‘foreach’ was built under R version 3.6.2 
Execution halted
ERROR: lazy loading failed for package ‘scNPF’ * removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/scNPF’ 
Error: Failed to install 'scNPF' from GitHub:   (converted from warning) installation of package ‘/var/folders/sc/7

You can set Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS=TRUE) to fix it

install.packages("devtools")
library(devtools)
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS=TRUE) 
install_github("BMILAB/scNPF")
library(scNPF)