I'm running an error similar to R, biocLite, error installing DESeq2 with the difference that I have the libxml2-dev and libcurl4-openssl-dev properly installed...
But I keep getting the same ERROR message in R:
------------------------- 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=...'
Running on a Ubuntu 17.10 OS. Trying to install it in miniconda env.
Of note, libcurl4-openssl-dev properly installed.
Tried:
export PKG_CONFIG_PATH=/home/cpat/miniconda3/lib/pkgconfig/libcurl.pc
Didn't help.
libcurl.pc files found in
/home/cpat/miniconda3/lib/pkgconfig/libcurl.pc
and
/usr/lib/x86_64-linux-gnu/pkgconfig/libcurl.pc
I really don't know how to proceed further.
Installed it outside of conda and everything worked perfectly.
Related
I am getting the following error at an Ubuntu 22.04, when trying to install rsvg at Rstudio.
--------------------------- [ANTICONF] --------------------------------
Configuration failed to find the librsvg-2.0 library. Try installing:
deb: librsvg2-dev (Debian,Ubuntu, etc)
rpm: librsvg2-devel (Fedora, EPEL)
csw: librsvg_dev, sunx11_devel (Solaris)
brew: librsvg (OSX)
If librsvg-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a librsvg-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=...'
This problem is similar to this post, but involving a different context/error message.
The point is:
The library librsvg2-dev is already installed and updated;
From here, I understood how to check this 'PKG_CONFIG_PATH'...
The pkg-config --libs librsvg-2.0 returns:
-lrsvg-2 -lm -lgio-2.0 -lgdk_pixbuf-2.0 -lgobject-2.0 -lglib-2.0 -lcairo
Which I do not understand completely but sounds ok, as it does not return 'not fond' as in that post.
The which pkg-config returns
/usr/bin/pkg-config
I am not able to understand this part of the error message:
If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD
The R+RStudio is running with a conda environment. Maybe it is related to it. How to meet system dependencies when a conda environment is used? I understand the conda install x sudo apt-get issues, and I should opt for conda install librsvg2-dev when I have conda environments, but it returns
PackagesNotFoundError: The following packages are not available from
current channels:
I made a search at anaconda page, and I have already installed at the conda environment:
conda install -c conda-forge r-rsvg
conda install -c conda-forge librsvg
Still without success in installing rsvg...
Perhaps the question is Ubuntu related... but not sure... How can I solve it? How must I proceed to
set INCLUDE_DIR and LIB_DIR manually
As the message appears incomplete?
Any help is appreciated.
install.packages('xml2')
For example, if I try to install the above package, I get this error message:
------------------------- 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=...'
--------------------------------------------------------------------
I think I need to fix the path. How do I do that? I have the latest version of Linux Mint.
You have two basic choices:
First, you follow the advice of the error message you quoted and do
sudo apt install libxml2-dev
as your distribution is in fact a Debian/Ubuntu derivative.
Second, you could just install the existing binary from the distro
sudo apt install r-cran-xml2
Also, the r-sig-debian list is a good place to lurk and learn and ask questions.
so i want to install rvest package in my rstudio but wasn't able to as it said to install some packages on my system first ,i used this -->
sudo apt-get install libssl-dev
this got executed but after this also the error was -->
------------------------- 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=...'
--------------------------------------------------------------------
and
------------------------- 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=...'
--------------------------------------------------------------------
so i tried installing then using -->
sudo apt-get install libcurl4-openssl-dev
sudo apt-get install libssl-dev
but these are not working the error is -->
Reading package lists... Done
Building dependency tree
Reading state information... Done
Suggested packages:
libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev libssl-dev
The following NEW packages will be installed:
libcurl4-openssl-dev
0 upgraded, 1 newly installed, 0 to remove and 31 not upgraded.
Need to get 318 kB of archives.
After this operation, 1,508 kB of additional disk space will be used.
Ign:1 http://in.archive.ubuntu.com/ubuntu disco-updates/main amd64 libcurl4-openssl-dev amd64 7.64.0-2ubuntu1.2
Err:1 http://security.ubuntu.com/ubuntu disco-updates/main amd64 libcurl4-openssl-dev amd64 7.64.0-2ubuntu1.2
404 Not Found [IP: 2403:8940:ffff::f 80]
E: Failed to fetch http://security.ubuntu.com/ubuntu/pool/main/c/curl/libcurl4-openssl-dev_7.64.0-2ubuntu1.2_amd64.deb 404 Not Found [IP: 2403:8940:ffff::f 80]
E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?
then i tried using both of these too -->
sudo apt-get update
sudo apt-get install libcurl4-openssl-dev --fix-missing
how can this problem be solved ?
You simply have a networking problem. It failed to connect to security,ubuntu.com.
Also not that a number of key packages are already in the distro so just do
sudo apt install r-cran-rvest
which works for me on 19.10 and may well too for you on 19.04 (which you should upgrade from).
I'm trying to install V8 rpackage on Ubuntu 18.04.1 LTS.
The version of R used is R 3.5.1.
I proceeded as follows:
I installed libv8 by typing : sudo apt-get install -y libv8-3.14-dev
I type this command to install in R : install.packages("V8")
Then, I received this error:
package ‘V8’ correctement décompressé et sommes MD5 vérifiées
Using PKG_CFLAGS=-I/usr/include/v8-3.14
Using PKG_LIBS=-lv8
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because was not found. Try installing:
deb: libv8-3.14-dev (formerly: libv8-dev) (Debian, Ubuntu)
rpm: v8-314-devel (formerly: v8-devel) (Fedora, EPEL)
brew: v8#3.15 (OSX) -- NOT regular v8! Tap from homebrew/versions
csw: libv8_dev (Solaris)
To use a custom libv8, set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
ERROR: configuration failed for package ‘V8’
removing ‘/opt/Anaconda/Anaconda3-5.1.0/envs/mro_env/lib/R/library/V8’
restoring previous ‘/opt/Anaconda/Anaconda3-5.1.0/envs/mro_env/lib/R/library/V8’
Warning message:
In install.packages("/home/ben/Bureau/miniCRAN/src/contrib/V8_1.5.tar.gz", :
l'installation du package ‘/home/ben/Bureau/miniCRAN/src/contrib/V8_1.5.tar.gz’ a eu un statut de sortie non nul
Then, I check if i have installed libv8 correctly by typing:
(mro_env) root#ben-Aspire-E5-575G:/opt/Anaconda/Anaconda3-5.1.0# find /lib* /usr/lib* -name 'libv8'
/usr/lib/libv8.so
/usr/lib/libv8.so.3.14.5
And
(mro_env) root#ben-Aspire-E5-575G:/opt/Anaconda/Anaconda3-5.1.0# ldconfig -p | grep libv8
libv8.so.3.14.5 (libc6,x86-64) => /usr/lib/libv8.so.3.14.5
libv8.so (libc6,x86-64) => /usr/lib/libv8.so
but when I verify if libv8.pc exists in /usr/lib/pkgconfig/ I didn't find it.
I'm stuck and I do not know how I can solve this problem.
Try this in R from Jeroem Ooms:
# For Linux: download libv8 during installation
Sys.setenv(DOWNLOAD_STATIC_LIBV8=1)
install.packages("V8")
I have created an EC2 instance in AWS(with Ubuntu), installed r studio server, but when I am trying to install the plotly package it gives an error related to OpenSSL:
------------------------- 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=...'
-------------------------------------------------------------------
Also, I have tried to install devtools but no luck. Please help as this is the only part where I am stuck?
Thanks!
As the error message tells you, you need to install (the development files for) libcurl:
sudo apt-get install libcurl4-openssl-dev
There might be more such error messages down the road.
An interesting alternative to manual installation is to use binary packages, since their dependencies are handled automatically. See http://dirk.eddelbuettel.com/blog/2017/12/22/#014_finding_binary_deb_packages for details.
In Ubuntu 18.04 and later open the terminal and type:
sudo apt install r-cran-plotly
In earlier Ubuntu releases than Ubuntu 18.04 plotly can be installed with the following commands:
sudo R -e "install.packages('ggplot2', repos = 'http://cran.us.r-project.org')"
sudo R -e "install.packages('plotly', repos = 'http://cran.us.r-project.org')"