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devtools::install_github("databio/GenomicDistributions") does not work #2101

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DzLGasoline opened this issue Sep 4, 2019 · 2 comments
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@DzLGasoline
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I tried to install an R package "GenomicDistributions" with only provided way by the devs:
devtools::install_github("databio/GenomicDistributions")

And it only returns this error message:

Downloading GitHub repo databio/GenomicDistributions@master
sh: /usr/local/bin/gtar: No such file or directory
sh: /usr/local/bin/gtar: No such file or directory
Error: Failed to install 'GenomicDistributions' from GitHub:
error in running command
In addition: Warning messages:
1: In system(cmd) : error in running command
2: In utils::untar(tarfile, ...) :
‘/usr/local/bin/gtar -xf '/tmp/RtmphcCAry/filea6967cdf34f3.tar.gz' -C '/tmp/RtmphcCAry/remotesa696220d7d91'’ returned error code 127

I tried almost everything I could, i.e. running R with sudo... etc.

I installed R through anaconda, and I guess it might be a cause of this problem, but I'm not sure.

My R session information is stated below.

─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 3.6.1 (2019-07-05)
os macOS Mojave 10.14.6
system x86_64, darwin13.4.0
ui unknown
language (EN)
collate ko_KR.UTF-8
ctype ko_KR.UTF-8
tz Asia/Seoul
date 2019-09-04

─ Packages ───────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.1)
backports 1.1.4 2019-04-10 [1] CRAN (R 3.6.1)
callr 3.3.1 2019-07-18 [1] CRAN (R 3.6.1)
cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.1)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.1)
curl 4.0 2019-07-22 [1] CRAN (R 3.6.1)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.1)
devtools 2.1.0 2019-07-06 [1] CRAN (R 3.6.1)
digest 0.6.20 2019-07-04 [1] CRAN (R 3.6.1)
fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.1)
glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.1)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.1)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.1)
pkgbuild 1.0.5 2019-08-26 [1] CRAN (R 3.6.1)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.1)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.1)
processx 3.4.1 2019-07-18 [1] CRAN (R 3.6.1)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.1)
R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.1)
Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.6.1)
remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.1)
rlang 0.4.0 2019-06-25 [1] CRAN (R 3.6.1)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.1)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.1)
testthat 2.2.1 2019-07-25 [1] CRAN (R 3.6.1)
usethis 1.5.1 2019-07-04 [1] CRAN (R 3.6.1)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.1)

[1] /Users/spark_2/miniconda3/lib/R/library

I really appreciate any helps or advices. Thank you in advance.

@jimhester
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I installed R through anaconda, and I guess it might be a cause of this problem

Yes that is the problem. If you are using conda you need to use conda to install all of the packages. See https://whattheyforgot.org/set-up-an-r-dev-environment.html#what-about-conda for our advice.

@lock
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lock bot commented Mar 10, 2020

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/

@lock lock bot locked and limited conversation to collaborators Mar 10, 2020
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