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About r : Warning-in-installpackages-installation-of-package-‘tidyverse-had-non-zero-exit-status

Question Detail

I am using this site for reference:
http://r4ds.had.co.nz/introduction.html
but I am unable to install the tidyverse package. Using dependencies = TRUE did not help. What else can I do?

 installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
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
No package 'libcurl' 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
No package 'libcurl' 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)
 * csw: libcurl_dev (Solaris)
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/akriti/R/x86_64-pc-linux-gnu-library/3.2/curl’
Warning in install.packages :
  installation of package ‘curl’ had non-zero exit status
* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
Using PKG_CFLAGS=
Using PKG_LIBS=-lssl -lcrypto
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because openssl was not found. Try installing:
 * deb: libssl-dev (Debian, Ubuntu, etc)
 * rpm: openssl-devel (Fedora, CentOS, RHEL)
 * csw: libssl_dev (Solaris)
 * brew: [email protected] (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.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 ‘openssl’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/openssl’
Warning in install.packages :
  installation of package ‘openssl’ had non-zero exit status
* installing *source* package ‘evaluate’ ...
** package ‘evaluate’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (evaluate)
* installing *source* package ‘highr’ ...
** package ‘highr’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (highr)
* installing *source* package ‘markdown’ ...
** package ‘markdown’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rbase64.c -o Rbase64.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rmarkdown.c -o Rmarkdown.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c autolink.c -o autolink.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c buffer.c -o buffer.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c houdini_href_e.c -o houdini_href_e.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c houdini_html_e.c -o houdini_html_e.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c html.c -o html.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c html_smartypants.c -o html_smartypants.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c markdown.c -o markdown.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stack.c -o stack.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o markdown.so Rbase64.o Rinit.o Rmarkdown.o autolink.o buffer.o houdini_href_e.o houdini_html_e.o html.o html_smartypants.o markdown.o stack.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/markdown/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (markdown)
* installing *source* package ‘yaml’ ...
** package ‘yaml’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c api.c -o api.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dumper.c -o dumper.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c emitter.c -o emitter.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c implicit.c -o implicit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c loader.c -o loader.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c parser.c -o parser.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c r-ext.c -o r-ext.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c reader.c -o reader.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c scanner.c -o scanner.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c writer.c -o writer.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o yaml.so api.o dumper.o emitter.o implicit.o loader.o parser.o r-ext.o reader.o scanner.o writer.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/yaml/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (yaml)
* installing *source* package ‘htmltools’ ...
** package ‘htmltools’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c template.cpp -o template.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o htmltools.so RcppExports.o template.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/htmltools/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (htmltools)
* installing *source* package ‘base64enc’ ...
** package ‘base64enc’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c base64.c -o base64.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c uriencode.c -o uriencode.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utf8.c -o utf8.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o base64enc.so base64.o uriencode.o utf8.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/base64enc/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (base64enc)
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lxml2
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
 * deb: libxml2-dev (Debian, Ubuntu, etc)
 * rpm: libxml2-devel (Fedora, CentOS, RHEL)
 * csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.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 ‘xml2’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/xml2’
Warning in install.packages :
  installation of package ‘xml2’ had non-zero exit status
* installing *source* package ‘caTools’ ...
** package ‘caTools’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Gif2R.cpp -o Gif2R.o
g++ -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c GifTools.cpp -o GifTools.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c runfunc.c -o runfunc.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o caTools.so Gif2R.o GifTools.o runfunc.o -L/usr/lib/R/lib -lR
installing to /home/akriti/R/x86_64-pc-linux-gnu-library/3.2/caTools/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (caTools)
* installing *source* package ‘rprojroot’ ...
** package ‘rprojroot’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rprojroot)
ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/httr’
Warning in install.packages :
  installation of package ‘httr’ had non-zero exit status
* installing *source* package ‘knitr’ ...
** package ‘knitr’ successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (knitr)
ERROR: dependencies ‘xml2’, ‘httr’ are not available for package ‘rvest’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/rvest’
Warning in install.packages :
  installation of package ‘rvest’ had non-zero exit status
* installing *source* package ‘rmarkdown’ ...
** package ‘rmarkdown’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rmarkdown)
ERROR: dependencies ‘httr’, ‘rvest’, ‘xml2’ are not available for package ‘tidyverse’
* removing ‘/home/akriti/R/x86_64-pc-linux-gnu-library/3.2/tidyverse’
Warning in install.packages :
 *installation of package ‘tidyverse’ had non-zero exit status

Question Answer

You find the answer in your error message:

------------------------ ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
....
....

Copy and paste the following to your Terminal and than try installing tidyverse again. Should solve the problem.

# Required for many packages
sudo apt-get install -y libxml2-dev libcurl4-openssl-dev libssl-dev

The problem occurred because tidyverse has system dependencies (i.e., libcurl4-openssl-dev, libssl-dev, libxml2-dev). I wrote a blog post that explains the solution in more details.

try this , it helped me out

sudo apt-get install -y libxml2-dev libcurl4-openssl-dev libssl-dev

A strategy I have found successful is to install R and R-Studio through anaconda (https://www.anaconda.com/). Create a separate environment for R and use the anaconda navigator to install R-Studio.

(Two great things about this approach: i) dependencies are automatically taken care of in the background ii) your working environment is sandboxed against accidents … unless you’re looking for trouble 🙂 )

I had the same issue with RStudio on Ubuntu 20.04 but switched to using R and R – Studio through anaconda.Tidyverse can be loaded without issues.

library(tidyverse)
── Attaching packages ─────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.1 ──
✓ ggplot2 3.3.5 ✓ purrr 0.3.4
✓ tibble 3.1.2 ✓ dplyr 1.0.7
✓ tidyr 1.1.3 ✓ stringr 1.4.0
✓ readr 1.4.0 ✓ forcats 0.5.1
── Conflicts ────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
x dplyr::filter() masks stats::filter()
x dplyr::lag() masks stats::lag()

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