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
Related
I am trying to install fable running the command install.packages("fable"), as it says in https://cran.r-project.org/web/packages/fable/readme/README.html
however i am getting the following:
It says clearly that it is because i don't have llapack, lblas and lgfortran in my computer. But i am not sure how to procede here. I'm using Ubuntu 20.04.3 LTS
I'll appreciate any guidence.
To install from sources, you will need a GNU Fortran compiler installed. On Ubuntu this can be done with sudo apt install gfortran.
Alternatively, you can install a precompiled binary from the RStudio Package Manager - some guidance on how this can be done can be found here: https://packagemanager.rstudio.com/client/#/repos/1/overview
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()
Conda was used to install R in my centos 7 sysytem. conda install r
the version of installed r is r-3.4.1.
However, when I use r, there have a error output. "/usr/local/bin/miniconda3/lib64/R/bin/exec/R: error while loading shared libraries: libtinfow.so.6: cannot open shared object file: No such file or directory"
Some tests have been used according to search by google use the keyword "libtinfow.so.6".
Only two information can be found. They have no help to me.
enter image description here
I had the same problem on a recent centos installation. But I think this has nothing to do with centos, but rather to misconfiguration related to different R packages version. To solve the problem, I just uninstall all the R related packages and gxx and gcc packages using "conda uninstall ". Than I installed R using "conda install -c r r", which force to install gcc and gxx within the same process.
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
I have RHEL 6.5 Server with an installation of R (3.1.1) & RStudioServer (0.98.1062)
I have postgresql-9.3 installed and handling a large database. In order to connect R to PostgreSQL, I have in the past used the RPostgreSQL (still do on my CentOS 7 Workstation). However, attempting to compile under RHEL 6.5 I get an error
In file included from RS-PQescape.c:7:
RS-PostgreSQL.h:23:26: error: libpq-fe.h: No such file or directory
The file is located on my system here:
/usr/pgsql-9.3/include/libpq-fe.h
Libpq is part of the Postgres installation, but RPostgreSQL cannot find it:
[root#server /]# yum list libpq*
Loaded plugins: product-id, refresh-packagekit, security, subscription-manager
Installed Packages
libpqxx.x86_64 1:4.0.1-1.rhel6 #pgdg93
libpqxx-debuginfo.x86_64 1:4.0.1-1.rhel6 #pgdg93
libpqxx-devel.x86_64 1:4.0.1-1.rhel6 #pgdg93
Is there any way to tell RPostgreSQL where to look (symbolic links?) or some other workaround? This should be simple, but I've wasted several hours on this already...
Followup info because I just had the same problem.
Installing yum install postgresql-devel resolves the error too.
I ended up looking into the RPostgreSQL configure file in the tarball, searched for the file name the script couldn't find and decided it was easiest to create an environmental variable:
export PG_INCDIR=/usr/pgsql-9.3/include/
Worked like a charm after that.
If you have sudo rights, you could also try:
yum install postgresql-devel