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
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 have reproduced this error in R versions 3.2.3 and 3.4.4; running both through terminal or within RStudio GUI. My OS is Ubuntu Linux 16.04 LTS. The problem started this week.
I found that the problem does not occur on a R --vanilla session.
When I start R, I get this message:
Warning: unable to access index for repository http://www.vps.fmvz.usp.br/CRAN/src/contrib: no fue posible abrir la URL 'http://www.vps.fmvz.usp.br/CRAN/src/contrib/PACKAGES'
Next, when I try to install a package I get:
Warning in install.packages :
cannot open URL 'http://www.vps.fmvz.usp.br/CRAN/src/contrib/PACKAGES.gz': HTTP status was '403 Forbidden'
Warning in install.packages :
cannot open URL 'http://www.vps.fmvz.usp.br/CRAN/src/contrib/PACKAGES': HTTP status was '403 Forbidden'
Warning in install.packages :
unable to access index for repository http://www.vps.fmvz.usp.br/CRAN/src/contrib:
no fue posible abrir la URL 'http://www.vps.fmvz.usp.br/CRAN/src/contrib/PACKAGES'
My session info is:
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS
locale:
[1] LC_CTYPE=es_AR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=es_AR.UTF-8 LC_COLLATE=es_AR.UTF-8
[5] LC_MONETARY=es_AR.UTF-8 LC_MESSAGES=es_AR.UTF-8
[7] LC_PAPER=es_AR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_AR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
loaded via a namespace (and not attached):
[1] tools_3.2.3
The current repository is (but I have already tried with several repositories):
getOption("repos")
CRAN
"http://www.vps.fmvz.usp.br/CRAN/"
attr(,"RStudio")
[1] TRUE
I would appreciate any help.
I have the following code, basic a error message in R. Please what can i do about. I don t know what to do. error message. Please send me codes,
Hello guys i am trying to use R with Rstudio please
RcppExports.cpp:4:27: fatal error: RcppArmadillo.h: Arquivo ou diretório não encontrado compilation terminated.
/usr/lib/R/etc/Makeconf:168: recipe for target 'RcppExports.o' failed
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘geogrid’
* removing ‘/home/gabriel/R/x86_64-pc-linux-gnu-library/3.4/geogrid’
Warning in install.packages :
installation of package ‘geogrid’ had non-zero exit status
SEssion INFO
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
locale:
[1] LC_CTYPE=pt_BR.UTF-8
[2] LC_NUMERIC=C
[3] LC_TIME=pt_BR.UTF-8
[4] LC_COLLATE=pt_BR.UTF-8
[5] LC_MONETARY=pt_BR.UTF-8
[6] LC_MESSAGES=pt_BR.UTF-8
[7] LC_PAPER=pt_BR.UTF-8
[8] LC_NAME=C
[9] LC_ADDRESS=C
[10] LC_TELEPHONE=C
[11] LC_MEASUREMENT=pt_BR.UTF-8
[12] LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_0.7.6 ggplot2_3.0.0
loaded via a namespace (and not attached):
The non-zero exit status simply indicates that there was an error during the installation of the "package".
File link https://cran.r-project.org/src/contrib/geogrid_0.1.0.1.tar.gz
Try with the following command:
install.packages('FILE_PATH', repos=NULL, type = "source",dependencies = TRUE)
Doing so, all the dependencies for the package will also be downloaded.
Downloading from source will recompile the package and installs.
I am trying to install stringi package in R, but the installation never finishes. After the download and some compilation, I get the following message:
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/marcus/R/x86_64-redhat-linux-gnu-library/3.3/stringi/libs/stringi.so':
/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/marcus/R/x86_64-redhat-linux-gnu-library/3.3/stringi/libs/stringi.so)
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/marcus/R/x86_64-redhat-linux-gnu-library/3.3/stringi’
The downloaded source packages are in
‘/tmp/RtmpT5KQVP/downloaded_packages’
Warning message:
In install.packages("stringi") :
installation of package ‘stringi’ had non-zero exit status
I searched the internet and I couldn't understand what this error message means. If it helps, this is my sessionInfo():
R version 3.3.1 (2016-06-21)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
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] tools_3.3.1
I solved my problem installing gcc 4.9.2. To do so, I ran
$ sudo yum install devtoolset-3-gcc-c++
$ sudo yum install devtoolset-3-gcc-gfortran
$ scl enable devtoolset-3 bash
in the shell. The first two commands install gcc and gfortran. The last one makes gcc 4.9.2 the standard compiler in the system. After that, I opened R and ran install.packages("stringi") to have my problem solved.
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...