I am trying to install a package called sodium in R on an Ubuntu system but I'm getting an error message like the following:
install.packages("sodium", dependencies = T)
...
* installing *source* package ‘sodium’ ...
** package ‘sodium’ successfully unpacked and MD5 sums checked
Package libsodium was not found in the pkg-config search path.
Perhaps you should add the directory containing `libsodium.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libsodium' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lsodium
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libsodium was not found. Try installing:
* deb: libsodium-dev (Debian, Ubuntu, etc)
* rpm: libsodium-devel (Fedora, EPEL)
* csw: libsodium_dev (Solaris)
* brew: libsodium (OSX)
If libsodium is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libsodium.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 ‘sodium’
* removing ‘/R/x86_64-pc-linux-gnu-library/3.4/sodium’
Warning in install.packages :
installation of package ‘sodium’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmph70q7Q/downloaded_packages’
The following code didn't install it either.
install.packages("libsodium-dev", dependencies = T)
Warning in install.packages :
package ‘libsodium-dev’ is not available (for R version 3.4.4)
I also tried install_github but still get an error:
devtools::install_github("jedisct1/libsodium")
Error: Failed to install 'unknown package' from GitHub:
Timeout was reached: [api.github.com] Resolving timed out after 10000 milliseconds
Any idea on how to install this package?
I wish installing packages on an Ubuntu R was as error free as doing it on Windows R.
If someone could teach me how to avoid package installing errors in Ubuntu R, it'd be great.
You need to install libsodium-dev, some software for your computer that isn't necessarily R specific.
You can do this via your terminal in linux. Go to your terminal and execute
sudo apt install libsodium-dev
Then go back to R and install the package with the usual command
devtools::install_github("jedisct1/libsodium")
Related
I recently upgraded to R 3.5 and have been unable to install the 'tidyverse' package. Other packages are installing fine. Whenever I try to install tidyverse, I receive the following error message.
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/x86_64-linux-gnu
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/nik/anaconda3/lib/R/library/curl’
ERROR: dependency ‘curl’ is not available for package ‘httr’
* removing ‘/home/nik/anaconda3/lib/R/library/httr’
ERROR: dependency ‘httr’ is not available for package ‘rvest’
* removing ‘/home/nik/anaconda3/lib/R/library/rvest’
ERROR: dependencies ‘httr’, ‘rvest’ are not available for package ‘tidyverse’
* removing ‘/home/nik/anaconda3/lib/R/library/tidyverse’
The downloaded source packages are in
‘/tmp/RtmpHJ48Sk/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages("tidyverse") :
installation of package ‘curl’ had non-zero exit status
2: In install.packages("tidyverse") :
installation of package ‘httr’ had non-zero exit status
3: In install.packages("tidyverse") :
installation of package ‘rvest’ had non-zero exit status
4: In install.packages("tidyverse") :
installation of package ‘tidyverse’ had non-zero exit status
I have run sudo apt-get install libcurl4-openssl-dev as has been suggested on other threads for the same problem. However, this does not appear to resolve the issue (in fact, libcurl was already installed, and reinstalling it also did not work).
When I check $PATH, I do not see 'pkg-config', and PKG_CONFIG_PATH does not seem to exist. Adding /usr/bin/pkg-config to the path and setting PKG_CONFIG_PATH /home/nik/anaconda3/lib/pkgconfig/libcurl.pc also does not appear to have fixed the issue. I'm at wits end at this point, as I can't think of anything else to uninstall/reinstall, nor figure out why libcurl isn't being added to the path on its own when I install it. Any help at all would be appreciated.
try setting your path to the directory that contains libcurl and not to libcurl itself, i.e.
PKG_CONFIG_PATH=/home/nik/anaconda3/lib/pkgconfig
Trying to install R package ggiraph on my Mac OS X I ran into a problem with dependency xml2.
This seems to be a fairly common problem for users of this and other packages so after reading threads here and elsewhere I confirmed the following:
RStudio, R, and all its packages are up do date
libxml2 is installed in developer version, using homebrew
I have copied libxml-2.0.pc from homebrew folder to /usr/local/lib/pkgconfig/
I have added /usr/local/lib/pkgconfig/ to PATH and PKG_CONFIG_PATH
I still get the below error message during installation. Thankful for help!
> install.packages("ggiraph")
Installing package into ‘/usr/local/lib/R/3.5/site-library’
(as ‘lib’ is unspecified)
also installing the dependency ‘xml2’
trying URL 'https://cran.rstudio.com/src/contrib/xml2_1.2.0.tar.gz'
Content type 'application/x-gzip' length 251614 bytes (245 KB)
==================================================
downloaded 245 KB
trying URL 'https://cran.rstudio.com/src/contrib/ggiraph_0.6.0.tar.gz'
Content type 'application/x-gzip' length 208710 bytes (203 KB)
==================================================
downloaded 203 KB
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/libxml2
Using PKG_LIBS=-L/usr/lib -lxml2 -lz -lpthread -licucore -lm
------------------------- 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 ‘/usr/local/lib/R/3.5/site-library/xml2’
Warning in install.packages :
installation of package ‘xml2’ had non-zero exit status
ERROR: dependency ‘xml2’ is not available for package ‘ggiraph’
* removing ‘/usr/local/lib/R/3.5/site-library/ggiraph’
Warning in install.packages :
installation of package ‘ggiraph’ had non-zero exit status
This is a recurrent problem I have on macOS with Homebrew and libxml2. The includes of libxml2 are located in a subdirectory /path/to/includes/libxml2/libxml/ which can't be found by compilers.
I successfully installed xml2 in R doing two things:
Create symlink [...]/include/libxml pointing to [...]/include/libxml2/libxml
Add the include folder path to INCLUDE_DIR
Do point 1 in a terminal. Although filepath may be different on your installation, the shell command on my mac was:
Bash > ln -s /usr/local/Cellar/libxml2/2.9.9_2/include/libxml2/libxml /usr/local/Cellar/libxml2/2.9.9_2/include/libxml`
Do point 2 in RStudio's R Terminal. The command on my mac was:
R > Sys.setenv(INCLUDE_DIR = paste("/usr/local/Cellar/libxml2/2.9.9_2/include", Sys.getenv("INCLUDE_DIR"), sep = ":"))`
Then install xml2 and ultimately ggiraph:
R > install.packages(c("xml2", "ggiraph"))
I just installed ubunutu 18.04 and I successfully install R version 3.5.1. I am having problems installing R packages such as plotly. It seems that the packages curl and httr are not available. The full error message:
> install.packages("plotly")
Installing package into ‘/home/lualeperez/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
also installing the dependencies ‘curl’, ‘openssl’, ‘httr’
trying URL 'https://cloud.r-project.org/src/contrib/curl_3.2.tar.gz'
Content type 'application/x-gzip' length 367047 bytes (358 KB)
==================================================
downloaded 358 KB
trying URL 'https://cloud.r-project.org/src/contrib/openssl_1.0.2.tar.gz'
Content type 'application/x-gzip' length 1194883 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
trying URL 'https://cloud.r-project.org/src/contrib/httr_1.3.1.tar.gz'
Content type 'application/x-gzip' length 147593 bytes (144 KB)
==================================================
downloaded 144 KB
trying URL 'https://cloud.r-project.org/src/contrib/plotly_4.8.0.tar.gz'
Content type 'application/x-gzip' length 1860673 bytes (1.8 MB)
==================================================
downloaded 1.8 MB
* 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/lualeperez/R/x86_64-pc-linux-gnu-library/3.5/curl’
* installing *source* package ‘openssl’ ...
** package ‘openssl’ successfully unpacked and MD5 sums checked
Using PKG_CFLAGS=
------------------------- 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: openssl#1.1 (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/lualeperez/R/x86_64-pc-linux-gnu-library/3.5/openssl’
ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
* removing ‘/home/lualeperez/R/x86_64-pc-linux-gnu-library/3.5/httr’
ERROR: dependency ‘httr’ is not available for package ‘plotly’
* removing ‘/home/lualeperez/R/x86_64-pc-linux-gnu-library/3.5/plotly’
The downloaded source packages are in
‘/tmp/RtmpNTZBPJ/downloaded_packages’
Warning messages:
1: In install.packages("plotly") :
installation of package ‘curl’ had non-zero exit status
2: In install.packages("plotly") :
installation of package ‘openssl’ had non-zero exit status
3: In install.packages("plotly") :
installation of package ‘httr’ had non-zero exit status
4: In install.packages("plotly") :
installation of package ‘plotly’ had non-zero exit status
I tried to solve the problem by installing libcurl4 by doing
sudo apt-get install libcurl4
but the systems then removes all the r-base dependencies.
I haven't tried to solve the problem with the httr package.
Does any one have any hint on how to solve this problem?
Just ran into the same issue, this is the solution I found:
Since just installing libcurl4-openssl-dev removes all the r-base packages what I did was
sudo apt-get install libcurl4-openssl-dev r-base
and afterwards
R -q -e "install.packages(c('curl'))"
and it worked.
Only caveat is that it upgrades your R version, but if you are already using the latest one then its not an issue.
You are attempting to compile from source. That sometimes has so-called build dependencies. You are missing them, and you are overlooking the (somewhat clear) error messages to that extend because you are getting swamped by multiple installations.
So first tip, so it one package at a time.
Second tip: realize that many (if not all) of these are available within Ubuntu. So just do
sudo apt install r-cran-curl
to install e.g. curl. Ditto for the others.
Third tip: There are over 3000 CRAN packages for Ubuntu at Michael's PPA. Read the top of
this README and then go this PPA (provided you want 3.5 which you do).
Fedora 36:
dnf install cmake
dnf install openssl-devel
dnf install libcurl-devel.x86_64
I try to install R quantmod
When I try:
install.packages('quantmod')
I see:
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
also installing the dependency ‘curl’
trying URL 'https://cloud.r-project.org/src/contrib/curl_3.1.tar.gz'
Content type 'application/x-gzip' length 366086 bytes (357 KB)
==================================================
downloaded 357 KB
trying URL 'https://cloud.r-project.org/src/contrib/quantmod_0.4-
12.tar.gz'
Content type 'application/x-gzip' length 140216 bytes (136 KB)
==================================================
downloaded 136 KB
* 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=
------------------------- 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 ‘/usr/local/lib/R/site-library/curl’
Warning in install.packages :
installation of package ‘curl’ had non-zero exit status
ERROR: dependency ‘curl’ is not available for package ‘quantmod’
* removing ‘/usr/local/lib/R/site-library/quantmod’
Warning in install.packages :
installation of package ‘quantmod’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpeR1Cmy/downloaded_packages’ Using PKG_LIBS=-lcurl
And I can't run this library.
When I try:
install.packages("quantmod", repos="https://github.com/joshuaulrich/quantmod")
I see:
Warning in install.packages :
package ‘quantmod’ is not available (for R version 3.4.4)
But R version 3.4.4 is the latest!!
What is the problem?
P.S. My R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Linux Mint 17.2 Rafaela
It looks like you need to install curl for your system. Open a terminal and run:
sudo apt-get update
sudo apt-get install curl libcurl4-openssl-dev libssl-dev
Then try again in R to install your package:
install.packages('quantmod')
If this doesn't work edit your question and post any additional error messages.
I am trying to install RMySQL on Mac running OSX Sierra ver 10.12.2
I have reviewed the comments and suggestions provided for OSX Mavericks for a homebrew install of MySQL. I had already installed MySQL with the MySQL/Oracle installer, so I attempted to replace the homebrew paths with the specific paths for my install per the following commands within R-Studio (R version 3.3.1 "Bug in Your Hair"):
Sys.setenv(PKG_CPPFLAGS = "-I//usr/local/mysql-5.7.17-macos10.12-x86_64/include/")
Sys.setenv(PKG_LIBS="-L/usr/local/mysql-5.7.17-macos10.12-x86_64/lib/ -lmysqlclient")
I then attempted to install/build the RMySQL package as follows
install.packages("RMySQL", type="source")
I got the following error message
trying URL 'https://cran.rstudio.com/src/contrib/RMySQL_0.10.9.tar.gz'
Content type 'application/x-gzip' length 54012 bytes (52 KB)
==================================================
downloaded 52 KB
* installing *source* package ‘RMySQL’ ...
** package ‘RMySQL’ successfully unpacked and MD5 sums checked
Using PKG_CFLAGS=-I/usr/local/opt/mariadb-connector-c/include/mariadb
Using PKG_LIBS=-L/usr/local/opt/{openssl/lib,mariadb-connector- c/lib/mariadb} -lmysqlclient -lssl -lcrypto -lz
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libmysqlclient was not found. Try installing:
* deb: libmariadb-client-lgpl-dev (Debian, Ubuntu 16.04)
libmariadbclient-dev (Ubuntu 14.04)
* rpm: mariadb-devel | mysql-devel (Fedora, CentOS, RHEL)
* csw: mysql56_dev (Solaris)
* brew: mariadb-connector-c (OSX)
If libmysqlclient is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libmysqlclient.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 ‘RMySQL’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RMySQL’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RMySQL’
Warning in install.packages :
installation of package ‘RMySQL’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/6h/29_3qxmn0sd0n7zh7qr65txm0000gp/T/RtmpjmKIr5/downloaded_packages’
I think the installation is overwriting the environment variables that I set but I am not sure.
I am not that familiar with using HomeBrew as I have installed all of the software on my Mac using standard install packages. I would prefer not to uninstall MySQL and reinstall via HomeBrew if possible since I already have several databases that are in use. I have some limited experience using Linux, but not enough to understand the underlying build process and environment variables being used to build RMySQL, so I don't know how to modify any of the other examples I have found for installing RMySQL that I have found on the site.