Question: devtools Installation error in R (version 3.5.3)?
0
gravatar for Dineshkumar K
15 months ago by
Kasaragod, Kerala, India
Dineshkumar K40 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 15 months ago by RamRS27k • written 15 months ago by Dineshkumar K40
2

Maybe try first successfully installing: httr and usethis ?

ADD REPLYlink written 15 months ago by zx87549.3k

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 15 months ago by Dineshkumar K40

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 15 months ago by zx87549.3k
1

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

ADD REPLYlink written 15 months ago by Arup Ghosh2.5k

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 15 months ago by Dineshkumar K40

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 15 months ago • written 15 months ago by Arup Ghosh2.5k

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

ADD REPLYlink written 15 months ago by Dineshkumar K40

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

ADD REPLYlink written 15 months ago by Arup Ghosh2.5k

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 15 months ago • written 15 months ago by Dineshkumar K40

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

ADD REPLYlink written 15 months ago by russhh5.4k

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 15 months ago by Dineshkumar K40
0
gravatar for Ashastry
15 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 15 months ago by zx87549.3k • written 15 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 15 months ago by Dineshkumar K40

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

ADD REPLYlink written 15 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 15 months ago • written 15 months ago by Dineshkumar K40

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

BiocManager::install("devtools")

ADD REPLYlink written 15 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 7 months ago by genomax85k • written 15 months ago by Dineshkumar K40
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 15 months ago by Arup Ghosh2.5k

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 15 months ago by Dineshkumar K40

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 7 months ago by lessismore880
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