Question: devtools Installation error in R (version 3.5.3)?
0
gravatar for Dineshkumar K
7 months ago by
Kasaragod, Kerala, India
Dineshkumar K30 wrote:

I am trying to install devtools in R (R version=3.5.3, OS= Ubuntu 18.04.2 LTS) by using following commands,

install.packages("devtools")
install.packages("devtools")
devtools::install_github("r-lib/devtools")

Its getting downloaded but shows error like this,

> ERROR: dependencies ‘httr’, ‘usethis’ are not available for package ‘devtools’
* removing ‘/home/ga/R/x86_64-pc-linux-gnu-library/3.5/devtools’
Warning in install.packages :
  installation of package ‘devtools’ had non-zero exit status
> The downloaded source packages are in
    ‘/tmp/RtmpP6MtMf/downloaded_packages’

when I try to call the package as follows,

library(devtools)

> Error in library(devtools) : there is no package called ‘devtools’

Therefore, please help me to fix this issue.

ADD COMMENTlink modified 7 months ago by RamRS24k • written 7 months ago by Dineshkumar K30
2

Maybe try first successfully installing: httr and usethis ?

ADD REPLYlink written 7 months ago by zx87548.4k

Dear zx8754, When I try to install httr, I am getting error as follows,

ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’ * removing ‘/home/ga/R/x86_64-pc-linux-gnu-library/3.5/httr’ Warning in install.packages : installation of package ‘httr’ had non-zero exit status The downloaded source packages are in ‘/tmp/RtmpP6MtMf/downloaded_packages’

ADD REPLYlink written 7 months ago by Dineshkumar K30

Now, maybe try first successfully installing: curl and openssl? Error is saying, it can't install packageX because it needs packageY and packageZ to be installed first.

ADD REPLYlink written 7 months ago by zx87548.4k
1

Try installing using install.packages("devtools", dependencies=TRUE) .

ADD REPLYlink written 7 months ago by arup1.9k

Dear arup, I tried your command as well and got same error

ERROR: dependencies ‘httr’, ‘usethis’ are not available for package ‘devtools’ * removing ‘/home/ga/R/x86_64-pc-linux-gnu-library/3.5/devtools’ Warning in install.packages : installation of package ‘devtools’ had non-zero exit status The downloaded source packages are in ‘/tmp/RtmpP6MtMf/downloaded_packages’

ADD REPLYlink written 7 months ago by Dineshkumar K30

Not sure why it is not able to get "httr" and "usethis " from CRAN mirror. Can you try with the ETHZ CRAN mirror install.packages('devtools',dependencies=TRUE, repos='https://stat.ethz.ch/CRAN/') ?

ADD REPLYlink modified 7 months ago • written 7 months ago by arup1.9k

Dear arup, Thank you for your help. But still it is showing the same error.

ADD REPLYlink written 7 months ago by Dineshkumar K30

Can you share sessionInfo() . Have you tried unloading all the packages/starting a fresh session?

ADD REPLYlink written 7 months ago by arup1.9k

The fresh session info as follows,

sessionInfo() R version 3.5.3 (2019-03-11) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.2 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1 locale: [1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C LC_TIME=en_IN.UTF-8
[4] LC_COLLATE=en_IN.UTF-8 LC_MONETARY=en_IN.UTF-8 LC_MESSAGES=en_IN.UTF-8
[7] LC_PAPER=en_IN.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] BiocManager_1.30.4 compiler_3.5.3 tools_3.5.3 yaml_2.2.0

ADD REPLYlink modified 7 months ago • written 7 months ago by Dineshkumar K30

Is there a particular reason why you need the github version of devtools, rather than the cran version?

ADD REPLYlink written 7 months ago by russhh4.8k

There is no particular reason to install github version of devtools. However, I am getting error, when I tried with cran version as well.

ADD REPLYlink written 7 months ago by Dineshkumar K30
0
gravatar for Ashastry
7 months ago by
Ashastry60
Ashastry60 wrote:

Can you try it with a different CRAN mirror? Also may be try this

source("https://bioconductor.org/biocLite.R")

biocLite("devtools")
ADD COMMENTlink modified 7 months ago by zx87548.4k • written 7 months ago by Ashastry60

Dear Ashastry, Initially the problem started with biocLite only, I could manage to install BiocManager. But I could not install biocLite. I could not fix it, whether problem with my OS or R version.

ADD REPLYlink written 7 months ago by Dineshkumar K30

What error did you receive when you tried to install biocLite?

ADD REPLYlink written 7 months ago by Ashastry60

The error, which I am getting as follows,

Bioconductor version 3.8 (BiocInstaller 1.32.1), ?biocLite for help Warning message:'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN package instead.

ADD REPLYlink modified 7 months ago • written 7 months ago by Dineshkumar K30

As suggested by Arup, start a new session and then do this -

BiocManager::install("devtools")

ADD REPLYlink written 7 months ago by Ashastry60

Dear Ashastry, I am getting error like this, after following the command on new session

    iocManager::install("devtools")

> ERROR: configuration failed for package ‘openssl’
* removing ‘/home/ga/R/x86_64-pc-linux-gnu-library/3.5/openssl’
ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
* removing ‘/home/ga/R/x86_64-pc-linux-gnu-library/3.5/httr’
ERROR: dependency ‘httr’ is not available for package ‘gh’
* removing ‘/home/ga/R/x86_64-pc-linux-gnu-library/3.5/gh’
ERROR: dependencies ‘curl’, ‘gh’ are not available for package ‘usethis’
* removing ‘/home/ga/R/x86_64-pc-linux-gnu-library/3.5/usethis’
ERROR: dependencies ‘httr’, ‘usethis’ are not available for package ‘devtools’
* removing ‘/home/ga/R/x86_64-pc-linux-gnu-library/3.5/devtools’

The downloaded source packages are in
    ‘/tmp/RtmpfcKBZE/downloaded_packages’
installation path not writeable, unable to update packages: cluster, foreign, MASS, survival
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘curl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘openssl’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘httr’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘gh’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘usethis’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘devtools’ had non-zero exit status
ADD REPLYlink modified 2 days ago by genomax74k • written 7 months ago by Dineshkumar K30
3

Before installing OpenSSL package install the OpenSSL library in the system. For Ubuntu, the command is sudo apt-get install -y libssl-dev.

Ref: https://github.com/jeroen/openssl

ADD REPLYlink written 7 months ago by arup1.9k

Thank you arup, openssl package has been successfully installed by following your instruction. However, I could not install curl httr usethis and devtools I am getting the same error, when I try to install the above packages

ADD REPLYlink written 7 months ago by Dineshkumar K30

Thank you so much! this installation worked for me only when upgrading from 16.10 to 18.04.3 thanks to this guide > https://www.linuxbabe.com/ubuntu/upgrade-ubuntu-16-10-17-04-to-ubuntu-18-04

ADD REPLYlink written 2 days ago by lessismore710
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