I tried to install the package RcppParallel on a cluster but encountered the error below.
Content type 'application/x-gzip' length 1967672 bytes (1.9 MB)
==================================================
downloaded 1.9 MB
* installing *source* package ‘RcppParallel’ ...
** package ‘RcppParallel’ successfully unpacked and MD5 sums checked
Rscript execution error: No such file or directory
ERROR: configuration failed for package ‘RcppParallel’
* removing ‘/moto/home/yz4247/rpackages/RcppParallel’
The downloaded source packages are in
‘/tmp/RtmpvW3tlA/downloaded_packages’
Warning message:
In install.packages("RcppParallel") :
installation of package ‘RcppParallel’ had non-zero exit status
Because it is on a cluster, I installed the package in my personal library. The GCC version is 11.2.0.
How should I get rid of the error? Thanks!
Related
I am having a lot of OS issues with the new version of RStudio. I am working on a Mac.
It does not recognize the packages that I had to reinstall. The current problem I am dealing with is that source('filename.R') is not working.
I get the following:
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
trying URL 'https://cran.mirrors.hoobly.com/src/contrib/rmarkdown_2.19.tar.gz'
Content type 'application/x-gzip' length 3243575 bytes (3.1 MB)
==================================================
downloaded 3.1 MB
* installing *source* package ‘rmarkdown’ ...
** package ‘rmarkdown’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rmarkdown)
The downloaded source packages are in
‘/private/var/folders/yk/spk56bkn22n8w43h0mr6x59xtb6t8m/T/RtmpTD79O7/downloaded_packages’
Error in eval(ei, envir) : object 'xfun' not found
I have re installed various libraries including xfun
I was having a lot of trouble knitting a markdown file so I tried to run the code from an r-script.
But I have the same error.
I am confused why it is trying to install rmarkdown and dplyr when I use source() in the script file.
Both dplyr and rmarkdown have already been installed as well as xfun.
So I think there is a problem with a path name where to find the various packages but I don't know how to fix this.
I want to use the RSQLite package, but when I try to use the library, I get this error:
Error: package or namespace load failed for ‘RSQLite’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘blob’
Is there a way to fix this?
I've tried updating the RSQLite Library which did not change anything, and
I tried installing the blob package, but it did not work.
It said "Warning in install.packages
installation of package ‘blob’ had non-zero exit status"
I tried to install the RSQLite package using:
install.packages("RSQLite")
and this was the output:
Installing package into C:/Users/malik/OneDrive/Documents/R/win-library/3.4
(as lib is unspecified)
also installing the dependencies ellipsis, rlang, vctrs, blob
There are binary versions available but the source versions are later:
binary source needs_compilation
ellipsis 0.1.0 0.2.0.1 TRUE
rlang 0.3.4 0.4.0 TRUE
vctrs 0.1.0 0.2.0 TRUE
blob 1.1.1 1.2.0 FALSE
RSQLite 2.1.1 2.1.2 TRUE
Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/ellipsis_0.1.0.zip'
Content type 'application/zip' length 30847 bytes (30 KB)
downloaded 30 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/rlang_0.3.4.zip'
Content type 'application/zip' length 1080437 bytes (1.0 MB)
downloaded 1.0 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/vctrs_0.1.0.zip'
Content type 'application/zip' length 499748 bytes (488 KB)
downloaded 488 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/RSQLite_2.1.1.zip'
Content type 'application/zip' length 2097863 bytes (2.0 MB)
downloaded 2.0 MB
package ‘ellipsis’ successfully unpacked and MD5 sums checked
package ‘rlang’ successfully unpacked and MD5 sums checked
package ‘vctrs’ successfully unpacked and MD5 sums checked
package ‘RSQLite’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\malik\AppData\Local\Temp\RtmpOsEBnR\downloaded_packages
installing the source package �blob�
trying URL 'https://cran.rstudio.com/src/contrib/blob_1.2.0.tar.gz'
Content type 'application/x-gzip' length 9355 bytes
downloaded 9355 bytes
* installing *source* package 'blob' ...
** package 'blob' successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace 'vctrs' 0.1.0 is being loaded, but >= 0.2.0 is required
ERROR: lazy loading failed for package 'blob'
* removing 'C:/Users/malik/OneDrive/Documents/R/win-library/3.4/blob'
In R CMD INSTALL
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-34~1.3/bin/x64/R" CMD INSTALL -l "C:\Users\malik\OneDrive\Documents\R\win-library\3.4" C:\Users\malik\AppData\Local\Temp\RtmpOsEBnR/downloaded_packages/blob_1.2.0.tar.gz' had status 1
Warning in install.packages :
installation of package ‘blob’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\malik\AppData\Local\Temp\RtmpOsEBnR\downloaded_packages’
When I try to use the RSQLite Library, I get this error:
I wanted to use the library, but it won't let me.
Try this..
library(remotes)
install_github("cran/blob")
install_github("cran/RSQLite")
It worked for me.........
On a Mac with Sierra OS and the latest versions of xcode command line tools and r/rstudio, when trying to install rcpp I get the following error. Is this a path problem? Any help would be greatly appreciated!
> install.packages("Rcpp", type = "source")
trying URL 'https://cran.rstudio.com/src/contrib/Rcpp_0.12.12.tar.gz'
Content type 'application/x-gzip' length 2421289 bytes (2.3 MB)
==================================================
downloaded 2.3 MB
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
sh: mv: command not found
** libs
sh: make: command not found
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp’
sh: rm: command not found
Warning in install.packages :
installation of package ‘Rcpp’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/hn/zpnk2qsx19x1y974vym8wr7r0000gn/T/RtmptRz4Oe/downloaded_packages’
I have R version 3.2.2 and am working on Windows 10. I am trying to install library(plyr), but could not install 'Rcpp' dependency (see warning in bold fonts). Install message and warnings below. Any suggestions?
Thanks!
utils:::menuInstallPkgs()
also installing the dependency ‘Rcpp’
trying URL >'https://mirrors.nics.utk.edu/cran/bin/windows/contrib/3.2/Rcpp_0.12.1.zip'
Content type 'application/zip' length 3189850 bytes (3.0 MB)
downloaded 3.0 MB
trying URL
'https://mirrors.nics.utk.edu/cran/bin/windows/contrib/3.2/plyr_1.8.3.zip'
Content type 'application/zip' length 1114768 bytes (1.1 MB)
downloaded 1.1 MB
package ‘Rcpp’ successfully unpacked and MD5 sums checked
Warning: unable to move temporary installation > >‘C:\Users\xxx\Documents\R\win-library\3.2\file2e0437cc54d8\Rcpp’ to
‘C:\Users\xxx\Documents\R\win-library\3.2\Rcpp’
package ‘plyr’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mydejesus\AppData\Local\Temp\Rtmp0yK2yD\downloaded_packages
library(plyr)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck =
vI[[j]]) :
there is no package called ‘Rcpp’
Error: package or namespace load failed for ‘plyr’
Looks like it's a permissions setting in Windows. I changed the permission on the folder to share with everyone and it installed successfully.
I am trying to install predictionet but having troubles. Clearly there are no windows binaries available so I have been trying to install by building from source.
I have Rtools installed from here.
So far I have tried to use this command:
> install.packages("C:/Users/Blah/predictionet_1.10.0.tar.gz", repos = NULL, type="source")
But I am receiving this error message:
Installing package into ‘C:/Users/Blah/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
* installing *source* package 'predictionet' ...
** libs
*** arch - i386
Warning: running command 'make -f "C:/PROGRA~1/R/R-31~1.0/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-31~1.0/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="predictionet.dll" OBJECTS="foo_mrmr.o mrnet_adapted.o mrnet_adapted2.o mrnet_ensemble_standalone.o"' had status 309
ERROR: compilation failed for package 'predictionet'
* removing 'C:/Users/Blah/Documents/R/win-library/3.1/predictionet'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-31~1.0/bin/x64/R" CMD INSTALL -l "C:\Users\Blah\Documents\R\win-library\3.1" "C:/Users/Blah/Desktop/predictionet_1.10.0.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘C:/Users/Blah/Desktop/predictionet_1.10.0.tar.gz’ had non-zero exit status
I am new to R so have no idea how to go about troubleshooting this, any help would be much obliged!
Note: I am using Rstudio
You may try :
source("http://bioconductor.org/biocLite.R")
biocLite("predictionet")