I need to install plotly package for R(3.3.1) in a Redhat server 5.11. It requires curl to be installed first. I downloaded the package from https://cran.r-project.org/web/packages/curl/index.html.
When I try to install the package, it gives below error:
version.c: In function 'R_curl_version':
version.c:15: error: 'curl_version_info_data' has no member named 'libssh_version'
version.c:15: error: 'curl_version_info_data' has no member named 'libssh_version'
make: *** [version.o] Error 1
ERROR: compilation failed for package 'curl'
Has anyone had the same issue before?
Thanks in advance for any suggestion.
You need to install the development version of the curl library before installing the package. Try yum install curl-devel.
One note though - whenever you run into a similar error it is typically because a development version of a library is not installed on your redhat system.
Thanks Jim for your reply.
I found the solution is to use a lower version curl package which has not included the definition for "libssh_version" in the file version.c, e.g. curl_0.9.6.tar.gz with the command:
sudo R CMD INSTALL curl_0.9.6.tar.gz
I've also tried "yum install curl-devel", but it shows the message:
This system is receiving updates from RHN Classic or RHN Satellite.
Setting up Install Process
Package curl-devel-7.15.5-17.el5_9.x86_64 already installed and latest version
Package curl-devel-7.15.5-17.el5_9.i386 already installed and latest version
Nothing to do
Related
When I tried to install r package "osmdata" (or any other package) with command
install.packages("osmdata")
it failed with error
"GLIBCXX_3.4.29' not found (required by /home...R/x86_64-unknown-linux-gnu-library/4.2/00LOCK-osmdata/00new/osmdata/libs/osmdata.so)
host system is debian, r is installed using package manager Guix.
The error means: osmdata.so was compiled with g++ version 11.1.0 (ABI mapping of GLIBCXX to g++ version is documented here), but the version of libstdc++.so.6 installed on the system is older, and doesn't provide GLIBCXX_3.4.29.
You need to get a version of osmdata.so appropriate for your system, or you need to build it from source, or you need to update your libstdc++.so.6.
P.S. Your question has nothing to do with glibc.
I solved it by installing package r-guix-install from Guix package manager and using this command
guix.install::guix.install("osmdata")
I am trying to install package SBCK from R build using Rscript build.R -c -v -i in windows command prompt following the steps given here. However, I ended up with package SBCK being not installed because of following error/warning InstallationWarning: package 'SBCK' is in use and will not be installed. I have no package with name SBCK installed on my system, so I do not understand why I am getting this warning message and thus not to be able to install the R package.
I know that similar question have been asked before here but solution there does not work in my case.
I am using R version 4.2.0 on Windows 10.
Once 'build.R' is run, "SBCK_0.5.0.tar.gz" is created in the 'SBCK-R' folder.
You can now install it via the package archive file option or pointing to that file in the install.packages command. I faced the same issue and this solved it.
Following this question, I am trying to install the package (running R64 as admin on Windows):
devtools::install_github("markhwhiteii/processr")
or
devtools::install_github("cardiomoon/processR")
However, I get the error message:
Error: Failed to install 'processr' from GitHub:
(converted from warning) cannot remove prior installation of package 'digest'
no matter which update option I select. Running the command .libPaths() I found the packages installation folder C:/Program Files/R/R-3.6.2/library and manually deleted the digest package and reinstalled it with package.install("digest"). But I still get the same error! I would appreciate it if you could help me understand what is the problem and how I can resolve it.
The simplest solution is to say no when install_github asks if it should replace digest.
If it still fails for some reason (and I can't see why; neither package requires a specific version of digest and you've reinstalled it in any case), then the problem is that devtools itself uses digest, so it can't be removed as long as devtools is loaded. So you can't use install_github.
You have a couple of options:
Clone the repo, then from the command line, run R CMD INSTALL . in that directory. Note that you'll need to insert the path to your R executable.
Install from the GitHub archive of the master branch: install.packages("https://github.com/markhwhiteii/processr/archive/master.tar.gz")
The steps to install the markhwhiteii/processr package:
install.packages("devtools")
library(devtools)
install.packages("https://github.com/markhwhiteii/processr/archive/master.tar.gz")
for testing the instalation:
library(processr)
processr::model1
Sent a PR on the GitHub repo.
and if you want to run R in the Jupyter environment just follow the instructions to install and regsiter the kernel:
install.packages('IRkernel')
IRkernel::installspec()
I am trying to install XLConnectJars to R and I keep getting the following error despite having Java DK and rJava installed?
Error: Package as namespace load failed for 'XLConnectJars'
.onLoad failed om LoadNamespace() for 'rJava', details:
call: library.dynam("rJava",pkgname,libname)
error: DLL 'rJava' not found: maybe not installed for this architecture?
Any help greatly appreciated!
XLConnectJars is a support package used by XLConnect, a platform-independent interface to Microsoft Excel. In order for XLConnectJars to install correctly, one must also install the rJava package.
The error noted in the OP indicates that rJava did not install correctly.
error: DLL 'rJava' not found: maybe not installed for this architecture?
Many people encounter problems installing rJava because it cannot access the Java Runtime from the operating system. Solutions to the "unable to access Java runtime" problem vary by operating system.
Windows
People often have 32-bit Java installed and then use 64-bit R. The 64-bit version of R requires the 64-bit version of Java.
Solution: Install the 64-bit version of the Java Runtime for Windows from the Java Download web page.
MacOS
Details to configure rJava on MacOS are covered in another SO answer I posted, Unable to load rJava in RStudio, which I am reposting here for convenience.
There is a very specific sequence of steps that must be taken to get rJava to work on a Macbook, as documented in rJava Issues #86.
Download and install Java from Oracle
Uninstall any previously installed version of rJava
Add JAVA_HOME to your .bashrc
Close & restart terminal, R and RStudio sessions so they pick up the updated JAVA_HOME
Use install.packages() to install rJava
See the URL link above for additional details on each step.
Ubuntu Linux
Use the Advanced Packaging Tool to install Java, then reconfigure Java support in R.
sudo apt-get install openjdk-8-jdk # openjdk-9-jdk has some installation issues
sudo R CMD javareconf
Once these steps are completed, install the XLConnectJars package with install.packages("XLConnectJars").
NOTE: some of this content is adapted from an article I previously posted on my Github site, Common Problems with Java and the xlsx Package.
I have CentOS 7 (3.10.0-123.el7.x86_64) and I seem not be able to install R and then get Rstudio server working.
This is what I did:
rpm -Uvh http://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
yum install R
Then I got this error:
Transaction check error:
file /usr/lib/systemd/system/blk-availability.service from install of device-mapper-7:1.02.107-5.el7_2.1.x86_64 conflicts with file from package lvm2-7:2.02.105-14.el7.x86_64
file /usr/sbin/blkdeactivate from install of device-mapper-7:1.02.107-5.el7_2.1.x86_64 conflicts with file from package lvm2-7:2.02.105-14.el7.x86_64
file /usr/share/man/man8/blkdeactivate.8.gz from install of device-mapper-7:1.02.107-5.el7_2.1.x86_64 conflicts with file from package lvm2-7:2.02.105-14.el7.x86_64
I am not sure what it is. There is nothing from whereis R because it didn't install.
If I install Rstudio Server, it would fail to start the service and said ERROR unable to find installation of R in the system
Can someone tell me how to install R properly on Centos 7?
That is not related to R. Your log shows a conflict between "device-mapper" and "lvm2", and these packages are used to operate with devices such as hard disks and partitions (before someone downvotes me, YES this is a crude simplification).
You should try to update your system with yum before installing R.
I resolved this problem by updating lvm2 firstly, then install R.
This idea was from: https://bugzilla.redhat.com/show_bug.cgi?id=1294128