I upgraded to 2.15 (I have 2.14.x and 2.13.x in my local directory). Then, I got error messages that proto had no Namespace, re-install. That simply won't work. I remove.packages("proto") for all local and main libraries. I've even tried running as root (I know), and I still get this when I attempt to install.
Selection: 50 trying URL
'http://cran.stat.auckland.ac.nz/src/contrib/proto_0.3-9.2.tar.gz'
Content type 'application/x-gzip' length 536813 bytes (524 Kb) opened
URL
================================================== downloaded 524 Kb
Loading required package: plyr
Attaching package: ‘reshape’
The following object(s) are masked from ‘package:plyr’:
rename, round_any
Loading required package: proto Error: package ‘proto’ could not be
loaded In addition: Warning message: In library(pkg, character.only =
TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no
package called ‘proto’ Execution halted
The downloaded source packages are in
‘/tmp/RtmpaUy8i4/downloaded_packages’ Updating HTML index of packages
in '.Library' Making packages.html ... done Warning message: In
install.packages("proto") : installation of package ‘proto’ had
non-zero exit status
Well, yeah, proto doesn't yet exist, I'm trying to install it.
ubuntu 10.04. 2.13.x and 2.14.x installed, with ggplot2, without incident.
sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets grid methods base
other attached packages:
[1] reshape_0.8.4 plyr_1.6
loaded via a namespace (and not attached):
[1] tools_2.15.0
I'm going back to 2.14.2 and see if things
There appears to be a conflict with .Rprofile, in that I was able to uninstall/install 2.15 without incident after I moved it.
My suggestion would be to run:
update.packages("proto", checkBuilt = TRUE)
Related
I'm having problem installing "Rcurl" in Rstudio on opensuse 15.2. I have installed Rstudio from the OS repository, I have been searching for similar questions and answers, and found this other question which I think it's the closest one to mine but in Ubuntu. Following some suggestions I didn't get to solve the problem in my case. Here is the error I get:
Error: package or namespace load failed for ‘RCurl’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/alcides/R/x86_64-suse-linux-gnu-library/3.5/RCurl/libs/RCurl.so':
libicui18n.so.58: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/username/R/x86_64-suse-linux-gnu-library/3.5/RCurl’
Warning in install.packages :
installation of package ‘RCurl’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpKXseTK/downloaded_packages’
This is my session info
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE Leap 15.2
Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0
Thanks
I reproduced the error and at first I couldn't install RCurl. The way I solved is by installing:
sudo zypper install libcurl-devel
And then from R
install.packages ("RCurl")
Among the packages available for Leap 15.2 is also R-RCurl-1.95_4.11-lp152.6.7.x86_64.rpm, but it is for R 4.0.2, not 3.5 like the one you use.
I want to use Feature Selection with the Caret R Package, but I can't install it on my linux machine. I've tried various things, I've also used dependencies=TRUE inside install.packages with no results. Any help?
Here is the log:
Warning: dependency 'car' is not available
trying URL 'http://cran.rstudio.com/src/contrib/caret_6.0-52.tar.gz'
Content type 'application/x-gzip' length 3665293 bytes (3.5 Mb)
opened URL
==================================================
downloaded 3.5 Mb
ERROR: dependency 'car' is not available for package 'caret'
* removing '/usr/lib64/R/library/caret'
The downloaded source packages are in
'/tmp/RtmpKfvgyR/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("caret") :
installation of package âcaretâ had non-zero exit status
>
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
UPDATE:
I've upgraded R to version 3.2.1 and now I can install caret package. Just sudo yum install R and it was solved.
I am unable to install packages from CRAN after upgrading R from 3.1.3 to 3.2.1.
The error message is that the shared object internet.so cannot be loaded.
install.packages("randomForest")
Installing package into ‘/gs/project/feb-684-aa/BIF/R/R-3.2.1/library’ (as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Error in url("http://cran.r-project.org/CRAN_mirrors.csv") :
internet routines cannot be loaded
In addition: Warning message:
In url("http://cran.r-project.org/CRAN_mirrors.csv") :
unable to load shared object '/software/areas/ircm/tools/R-3.2.1/lib64/R/modules//internet.so':
/software/areas/ircm/tools/R-3.2.1/lib64/R/modules//internet.so: undefined symbol: curl_multi_wait
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: CentOS release 6.5 (Final)
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] nvimcom_0.9-8
loaded via a namespace (and not attached):
[1] tools_3.2.1
[blancha#lg-1r17-n04 BIF]$ ls /software/areas/ircm/tools/R-3.2.1/lib64/R/modules//internet.so -l
-rwxrwxr-x 1 blancha feb-684-01 275221 Jul 12 09:47 /software/areas/ircm/tools/R-3.2.1/lib64/R/modules//internet.so
The following post appears to address a similar issue.
Error in install.packages: internet routines cannot be loaded using StatET while it works in R console
Fixed!
Thank you #David Robinson for your suggestions. They put me on the right track.
I just added the following command to my .bash_profile, and the problem was solved:
export LD_LIBRARY_PATH=$TOOLS/curl-7.43.0/lib:$LD_LIBRARY_PATH
I am unable to install e1071 on my ubuntu machine.
I tried using:
sudo apt-get install r-cran-e1071
gives an error message:
Warning messages:
1: In open.connection(con, "r") :
unable to connect to 'cran.r-project.org' on port 80.
2: E: Unable to locate package r-cran-e1071
and
install.packages("e1071", dep = TRUE, type = "source")
gives an error message:
package ‘e1071’ is not available (for R version 2.15.2)
sessionInfo() gives:
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_IN LC_NUMERIC=C LC_TIME=en_IN
[4] LC_COLLATE=en_IN LC_MONETARY=en_IN LC_MESSAGES=en_IN
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tcltk_2.15.2 tools_2.15.2
The package e1071 depends on package class. The package class depends on R (≥ 3.0.0). Hence, you should update to a more recent R version.
Like #SvenHohenstein already said, the package needs a different version of R. What you can do is get an old version of the package from its archives, but you'll probably have to install older versions of other packages. In addition, you'll have to build the old version of the package from source as no binary versions are archived. Simply updating to a new R version is much easier...
I'm running RStudio Server and am unable to install the zoo package. The error message I get is as follows:
Installing package(s) into ‘/home/tsajid/R/library’
(as ‘lib’ is unspecified)
trying URL 'http://mirrors.nics.utk.edu/cran/src/contrib/zoo_1.7-9.tar.gz'
Content type 'application/x-gzip' length 807084 bytes (788 Kb)
opened URL
==================================================
downloaded 788 Kb
** installing source package ‘zoo’ ...
** package ‘zoo’ successfully unpacked and MD5 sums checked
** libs
sh: make: command not found
ERROR: compilation failed for package ‘zoo’
** removing ‘/home/tsajid/R/library/zoo’
Warning in install.packages :
installation of package ‘zoo’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpsKlJWz/downloaded_packages’
I tried installing the package archive file but I get an identical error message.
Session info:
R version 2.15.1 (2012-06-22)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] svMisc_0.9-65
loaded via a namespace (and not attached):
[1] tools_2.15.1
It states it pretty clearly:
sh: make: command not found
So please do install the Red Hat equivalent of the Debian / Ubuntu command
sudo apt-get install r-base-dev
which via its dependence on build-essential also installs make, gcc etc pp