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.
Related
So probably this is some odd setting I've added, but removing my .Renviron/.Rprofile/~/.R/Makevars don't seem to help. Grateful for any suggestions on how to debug.
BiocManager::install("DropletUtils") leads to this error (normal output up to this point omitted):
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘DropletUtils’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/alan/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-DropletUtils/00new/DropletUtils/libs/DropletUtils.so':
/home/alan/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-DropletUtils/00new/DropletUtils/libs/DropletUtils.so: undefined symbol: __ubsan_vptr_type_cache
Error: loading failed
Execution halted
sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] BiocManager_1.30.12 compiler_4.0.5 tools_4.0.5
[4] parallel_4.0.5
I have upgraded Ubuntu from 18.04 to 20.04 and now some of my R packages fail to compile/load. One example is shown below:
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'myPackage' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/site-library/00LOCK-my_package/00new/myPackage/libs/myPackage.so':
/usr/local/lib/R/site-library/00LOCK-my_package/00new/myPackge/libs/myPackage.so: undefined symbol: dgesvx_
Error: loading failed
Execution halted
ERROR: loading failed
This dgesvx_ looks like a LAPACK problem (https://www.netlib.org/lapack/explore-html/d7/d3b/group__double_g_esolve_ga9d90ccf6e340cacd08b7bbbb502ceb21.html#ga9d90ccf6e340cacd08b7bbbb502ceb21).
And I have latest LAPACK version available in Ubuntu 20.04 installed (3.9.0-1build1).
What can I do here to resolve the problem?
My sessionInfo():
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
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=en_US.UTF-8 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 methods base
loaded via a namespace (and not attached):
[1] compiler_4.0.2 tools_4.0.2
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 am trying to install locfit R package, but not able to install on Red Hat Enterprise Linux Server 7.4 (Maipo). It works fine on my local machine. I get the following error.
lf_adap.c(132) (col. 34): internal error: 04010026_1450
icc: error #10014: problem during multi-file optimization compilation (code 4)
make: *** [locfit.so] Error 4
ERROR: compilation failed for package 'locfit'
* removing '/home/a/ahwani/R/x86_64-pc-linux-gnu-library/3.6/locfit'
The downloaded source packages are in
'/tmp/Rtmp9zRFVC/downloaded_packages'
Warning message:
In install.packages("locfit") :
installation of package 'locfit' had non-zero exit status
sessionInfo():
version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.4 (Maipo)
Matrix products: default
BLAS/LAPACK: /apps/intel/2019/compilers_and_libraries_2019.1.144/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so
locale:
[1] LC_CTYPE=C 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_3.6.0
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