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When attempting to install tidyverse in R studio on fedora tidyverse's dependencies wont install
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Closed 2 days ago.
I am on Fedora 37 and am failing to install tidyverse.
When I first tried install.packages("tidyverse") I got a list of warning saying that said R was unable to resolve the installation of curl, openssl, googlesheets4 among others. More specifically "In install.package("{insert package name}"): installation had non-zero exit status"
And then I tried install.packages(c("tidyverse","ids", "httr", "gargle" ,"rvest", "covr"), dependencies = TRUE), only to be given the same errors and then some.
The dependencies had dependencies, so is there a way to perhaps allow the installation of sub-dependencies as well?
But more importantly, I do have curl and openssl installed so, this is perhaps more a problem of R not being to find them (unless R's curl is something other than the system curl).
How can I either set all dependency requests to TRUE or check that R can access system tools and if not make them available to R?
Doing this in Jupyter and the full text from the editor reads:
Installing packages into ‘/home/rijan/R/x86_64-redhat-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
also installing the dependencies ‘googledrive’, ‘googlesheets4’, ‘openssl’, ‘curl’, ‘jpeg’, ‘aws.ec2metadata’, ‘sodium’
Warning message in install.packages(c("tidyverse", "ids", "httr", "gargle", "rvest", :
“installation of package ‘openssl’ had non-zero exit status”
Warning message in install.packages(c("tidyverse", "ids", "httr", "gargle", "rvest", :
“installation of package ‘curl’ had non-zero exit status”
Warning message in install.packages(c("tidyverse", "ids", "httr", "gargle", "rvest", :
“installation of package ‘jpeg’ had non-zero exit status”
Warning message in install.packages(c("tidyverse", "ids", "httr", "gargle", "rvest", :
“installation of package ‘sodium’ had non-zero exit status”
Warning message in install.packages(c("tidyverse", "ids", "httr", "gargle", "rvest", :
“installation of package ‘aws.ec2metadata’ had non-zero exit status”
Warning message in install.packages(c("tidyverse", "ids", "httr", "gargle", "rvest", :
“installation of package ‘ids’ had non-zero exit status”
Warning message in install.packages(c("tidyverse", "ids", "httr", "gargle", "rvest", :
“installation of package ‘httr’ had non-zero exit status”
Warning message in install.packages(c("tidyverse", "ids", "httr", "gargle", "rvest", :
“installation of package ‘gargle’ had non-zero exit status”
Warning message in install.packages(c("tidyverse", "ids", "httr", "gargle", "rvest", :
“installation of package ‘rvest’ had non-zero exit status”
Warning message in install.packages(c("tidyverse", "ids", "httr", "gargle", "rvest", :
“installation of package ‘covr’ had non-zero exit status”
Warning message in install.packages(c("tidyverse", "ids", "httr", "gargle", "rvest", :
“installation of package ‘googledrive’ had non-zero exit status”
Warning message in install.packages(c("tidyverse", "ids", "httr", "gargle", "rvest", :
“installation of package ‘googlesheets4’ had non-zero exit status”
Warning message in install.packages(c("tidyverse", "ids", "httr", "gargle", "rvest", :
“installation of package ‘tidyverse’ had non-zero exit status”
When switching from Jupyter notebooks to R in terminal, and using the commands install.packages("curl", verbose = TRUE, dependencies = TRUE) I am gettting the following error message:
Installing package into ‘/home/rijan/R/x86_64-redhat-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
system (cmd0): /usr/lib64/R/bin/R CMD INSTALL
--- Please select a CRAN mirror for use in this session ---
also installing the dependency ‘webutils’
trying URL 'https://cloud.r-project.org/src/contrib/webutils_1.1.tar.gz'
Content type 'application/x-gzip' length 24751 bytes (24 KB)
==================================================
downloaded 24 KB
trying URL 'https://cloud.r-project.org/src/contrib/curl_4.3.3.tar.gz'
Content type 'application/x-gzip' length 670416 bytes (654 KB)
==================================================
downloaded 654 KB
foundpkgs: webutils, curl, /tmp/RtmpojeCdr/downloaded_packages/webutils_1.1.tar.gz, /tmp/RtmpojeCdr/downloaded_packages/curl_4.3.3.tar.gz
files: /tmp/RtmpojeCdr/downloaded_packages/webutils_1.1.tar.gz,
/tmp/RtmpojeCdr/downloaded_packages/curl_4.3.3.tar.gz
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
Package 'libcurl', required by 'virtual:world', not found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
Package 'libcurl', required by 'virtual:world', not found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
* deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
* rpm: libcurl-devel (Fedora, CentOS, RHEL)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/rijan/R/x86_64-redhat-linux-gnu-library/4.2/curl’
ERROR: dependency ‘curl’ is not available for package ‘webutils’
* removing ‘/home/rijan/R/x86_64-redhat-linux-gnu-library/4.2/webutils’
The downloaded source packages are in
‘/tmp/RtmpojeCdr/downloaded_packages’
Warning messages:
1: In install.packages("curl", verbose = TRUE, dependencies = TRUE) :
installation of package ‘curl’ had non-zero exit status
2: In install.packages("curl", verbose = TRUE, dependencies = TRUE) :
installation of package ‘webutils’ had non-zero exit status
Trying sudo dnf install libcurl-devel solved the issue for curl.
The following system dependencies were required for tidyverse to be installed (fedora specific installation commands):
sudo dnf install openssl-devel
sudo dnf install libcurl-devel
sudo dnf install libsodium-devel
sudo dnf install openssl-devel
Not sure why but my Jupyter was not giving out the full error message even with verbose = TRUe with install.packages("curl", verbose = TRUE, dependencies = TRUE) but R in the terminal was a bit more clear.
Unsure if there is a way to automatically fetch system dependencies for a R package.
I'm trying to install geojsonio in Colab using:
install.packages("geojsonio")
library(geojsonio)
However, the following error arises:
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
also installing the dependencies ‘triebeard’, ‘geometries’, ‘jsonify’, ‘rapidjsonr’, ‘sfheaders’, ‘urltools’, ‘httpcode’, ‘protolite’, ‘lazyeval’, ‘geojsonsf’, ‘rgeos’, ‘crul’, ‘maptools’, ‘V8’, ‘geojson’, ‘jqr’
Warning message in install.packages("geojsonio"):
“installation of package ‘protolite’ had non-zero exit status”
Warning message in install.packages("geojsonio"):
“installation of package ‘jqr’ had non-zero exit status”
Warning message in install.packages("geojsonio"):
“installation of package ‘geojson’ had non-zero exit status”
Warning message in install.packages("geojsonio"):
“installation of package ‘geojsonio’ had non-zero exit status”
Error in library(geojsonio): there is no package called ‘geojsonio’
Traceback:
1. library(geojsonio)
Any idea why it's happening?
Thanks!
I have problems installing RVAideMemoire packages. It gives me errors saying "car" is not available. When I try to install "car", then I have the following errors
Can somebody help me? thanks a lot
ERROR: configuration failed for package ‘rgl’
* removing ‘/home/anna/R/x86_64-pc-linux-gnu-library/3.6/rgl’
ERROR: dependency ‘curl’ is not available for package ‘rio’
* removing ‘/home/anna/R/x86_64-pc-linux-gnu-library/3.6/rio’
ERROR: dependency ‘rio’ is not available for package ‘car’
* removing ‘/home/anna/R/x86_64-pc-linux-gnu-library/3.6/car’
ERROR: dependency ‘car’ is not available for package ‘alr4’
* removing ‘/home/anna/R/x86_64-pc-linux-gnu-library/3.6/alr4’
The downloaded source packages are in
‘/tmp/Rtmpet3m65/downloaded_packages’
Warning messages:
1: In install.packages("car", dep = T) :
installation of package ‘curl’ had non-zero exit status
2: In install.packages("car", dep = T) :
installation of package ‘rgl’ had non-zero exit status
3: In install.packages("car", dep = T) :
installation of package ‘rio’ had non-zero exit status
4: In install.packages("car", dep = T) :
installation of package ‘car’ had non-zero exit status
5: In install.packages("car", dep = T) :
installation of package ‘alr4’ had non-zero exit status
I had used this to try to install the car package:
install.packages("car", dependencies=TRUE, INSTALL_opts = c('--no-lock'))
but received this error:
ERROR: dependency ‘openxlsx’ is not available for package ‘rio’
* removing ‘/home/dan-laptop/R/x86_64-pc-linux-gnu-library/3.2/rio’
Warning in install.packages :
installation of package ‘rio’ had non-zero exit status
ERROR: dependency ‘rio’ is not available for package ‘car’
* removing ‘/home/dan-laptop/R/x86_64-pc-linux-gnu-library/3.2/car’
Warning in install.packages :
installation of package ‘car’ had non-zero exit status
ERROR: dependency ‘car’ is not available for package ‘alr4’
* removing ‘/home/dan-laptop/R/x86_64-pc-linux-gnu-library/3.2/alr4’
Warning in install.packages :
installation of package ‘alr4’ had non-zero exit status
I tried installing the dependencies individually with no luck. Any help would be greatly appreciated. Thanks.
I'm trying to install basic packages in R but having a lot of trouble. I've tried several solutions but am having trouble getting to the bottom of it. I've added dependencies = TRUE, made sure my R was updated, tried to manually install packages, all to no avail.
Error message: also installing the dependencies ‘rlang’, ‘utf8’, ‘pillar’, ‘tibble’, ‘testthat’, ‘covr’
Warning message in install.packages("readr", dependencies = TRUE):
“installation of package ‘rlang’ had non-zero exit status”Warning message in install.packages("readr", dependencies = TRUE):
“installation of package ‘utf8’ had non-zero exit status”Warning message in install.packages("readr", dependencies = TRUE):
“installation of package ‘covr’ had non-zero exit status”Warning message in install.packages("readr", dependencies = TRUE):
“installation of package ‘pillar’ had non-zero exit status”Warning message in install.packages("readr", dependencies = TRUE):
“installation of package ‘testthat’ had non-zero exit status”Warning message in install.packages("readr", dependencies = TRUE):
“installation of package ‘tibble’ had non-zero exit status”Warning message in install.packages("readr", dependencies = TRUE):
“installation of package ‘readr’ had non-zero exit status”Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
also installing the dependencies ‘utf8’, ‘pillar’, ‘bit’, ‘glue’, ‘purrr’, ‘rlang’, ‘tibble’, ‘bit64’, ‘covr’, ‘dbplyr’, ‘dtplyr’, ‘ggplot2’, ‘Lahman’, ‘microbenchmark’, ‘nycflights13’, ‘RMySQL’, ‘RPostgreSQL’, ‘RSQLite’, ‘testthat’