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Installation failed: error in running command #1722

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nick-youngblut opened this issue Feb 27, 2018 · 6 comments

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@nick-youngblut
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@nick-youngblut nick-youngblut commented Feb 27, 2018

There's not much of an error report, so I'm not sure what's going wrong. I do have internet connectivity, so that should not be the problem.

> devtools::install_github("tidyverse/dplyr")
Downloading GitHub repo tidyverse/dplyr@master
from URL https://api.github.com/repos/tidyverse/dplyr/zipball/master
Installation failed: error in running command
> devtools::install_github("r-lib/devtools")
Downloading GitHub repo r-lib/devtools@master
from URL https://api.github.com/repos/r-lib/devtools/zipball/master
Installation failed: error in running command
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /ebio/abt3_projects/software/miniconda3/envs/ga_R_install/lib/R/lib/libRblas.so
LAPACK: /ebio/abt3_projects/software/miniconda3/envs/ga_R_install/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_3.4.1
@jimhester

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@jimhester jimhester commented Feb 27, 2018

Is it possible R is not on your PATH?

@nsgrantham

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@nsgrantham nsgrantham commented Mar 2, 2018

I have been experiencing the same error, as have others:

The proposed solutions from these issues is to set options(unzip = "internal") before installing from github:

library(devtools)
options(unzip = "internal")
devtools::install_github("tidyverse/dplyr")

or to run sudo apt-get install unzip. However, this alone did not solve my problem.

After a little more digging, the problem arises from the fact that, in my case, the conda-provided R install (conda install -c r r-base) sets TAR=/bin/gtar within R (Sys.getenv["TAR"]) which does not exist on a vanilla Ubuntu 16.04 install (it should be TAR=/bin/tar according to #379).

The following worked for me:

sudo apt-get install unzip
export TAR=/bin/tar
# run R code here

Instead of export TAR=/bin/tar you could also create a symlink with sudo ln -s /bin/tar /bin/gtar, but exporting the environmental variable is preferred.

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@jimhester jimhester commented Mar 9, 2018

So this (at least in your case) seems like a conda bug then, do you think you could open an issue at https://github.com/conda/conda/issues?

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@jimhester jimhester commented Mar 9, 2018

This same behavior is also mentioned at #379 (comment)

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@rvernica rvernica commented May 14, 2018

I ran into the same issue and it was indeed conda-forge/r-devtools-feedstock#4 It would be nice for devtools to give a better error message than just error in running command.

nickschurch added a commit to bartongroup/RoSA that referenced this issue Sep 25, 2018
Added tar tot he install to avoid this conda issue: r-lib/devtools#1722
nickschurch added a commit to bartongroup/RoSA that referenced this issue Sep 25, 2018
Updated instructions to deal with a conda/R interplay issue. See r-lib/devtools#1722
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@lock lock bot commented Nov 10, 2018

This old issue has been automatically locked. If you believe you have found a related problem, please file a new issue (with reprex) and link to this issue. https://reprex.tidyverse.org/

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