I am working on a server to which I don't have admin rights.
I linked R to MKL for fast linear algebra using a Conda environment following these steps:
Conda install r-essentials with MKL
The linking of R to MKL was successful, the output for R InfoSession() under the activated environment is as follows:
R version 3.6.3 (2020-02-29) Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS/LAPACK:
/userInfo/miniconda3/envs/R_mkl/lib/libmkl_rt.so
locale: [1] C
attached base packages: [1] stats graphics grDevices utils
datasets methods base
loaded via a namespace (and not attached): [1] compiler_3.6.3
My goal is to install and use the R tgp package under this environment.
When trying to install the tgp package with R CMD INSTALL, the installation fails with the following error
libopenblas.so.0: cannot open shared object file: No such file or
directory
This installation succeeds when using the 'regular' R version that is not linked to MKL.
This error concerns OpenBlas while I want to use MKL.
I hope anyone knows how to fix these dependencies knowing I do not have admin rights.
Related
I have recently installed the arm64 version of R from the Mac nightly builds page. It's working great! Except - for packages that require compilation. For example, if I try and install xfun which is required for blogdown, I get the following error
ld: warning: ignoring file /usr/local/opt/llvm/lib/libc++.dylib, building for macOS-arm64 but attempting to link with file built for macOS-x86_64
ld: in '/usr/local/opt/llvm/lib/libunwind.dylib', building for macOS-arm64 but attempting to link with file built for macOS-x86_64
So..... how to fix this in order to keep things trucking?
For reference, here is my sessionInfo()
> sessionInfo()
R version 4.1.0 alpha (2021-04-26 r80229)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.2.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
loaded via a namespace (and not attached):
[1] compiler_4.1.0 tools_4.1.0 parallel_4.1.0
OK. This was due to setting some MAKEVARS from an older R installation.
I feel ashamed.
But, if anyone else is having this problem, look at ~/.R/Makevars
Now to solve gfortran issues.
New job gave me a fresh Windows laptop where I am struggling (to say the very least) to set up a fresh R environment. Specifically, when developing a package, the commmand Install and Restart exits abruptly due to permission issues on a specific .dll file.
==> Rcmd.exe INSTALL --no-multiarch --with-keep.source --install-tests curl
* installing to library 'C:/R/R-Library'
* installing *source* package 'curl' ...
ERROR: cannot remove earlier installation, is it in use?
* removing 'C:/R/R-Library/curl'
* restoring previous 'C:/R/R-Library/curl'
Warning in file.copy(lp, dirname(pkgdir), recursive = TRUE, copy.date = TRUE) :
problem copying C:\R\R-Library\00LOCK-curl\curl\libs\x64\curl.dll to C:\R\R-Library\curl\libs\x64\curl.dll: Permission denied
Exited with status 1.
As a first attempt to ameliorate the issue, I've moved both my R installation and library at C:/. This obviously seems not to be enough.
> .libPaths()
[1] "C:/R/R-Library" "C:/R/R-4.0.3/library"
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252 LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C
[5] LC_TIME=Italian_Italy.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.0.3 tools_4.0.3
I am kind of lost as to where to look next. As a last shot in the dark I've tried to run RStudio with Admin right with no luck.
As it didn't work, I reinstalled. But without success.
What do I miss?
install.packages('C:/gurobi800/win64/R/gurobi_8.0-0.zip', repos=NULL)
# package ‘gurobi’ successfully unpacked and MD5 sums checked
Sys.getenv()
# ...
# GRB_LICENSE_FILE C:\gurobi800\gurobi.lic
# GUROBI_HOME C:\gurobi800\win64
# ...
library("gurobi")
Error: package or namespace load failed for ‘gurobi’: package ‘gurobi’
was installed by an R version with different internals; it needs to be
reinstalled for use with this R version
From the DESCRIPTION in Gurobi's R folder:
Depends: slam (>= 0.1-9)
URL: http://www.gurobi.com
Built: R 3.4.0; x86_64-w64-mingw32; 2018-04-21 00:42:28 UTC; windows
SessionInfo:
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=German_Switzerland.1252 LC_CTYPE=German_Switzerland.1252 LC_MONETARY=German_Switzerland.1252
[4] LC_NUMERIC=C LC_TIME=German_Switzerland.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] slam_0.1-44
loaded via a namespace (and not attached):
[1] compiler_3.5.1 imsbasics_1.9.7 tools_3.5.1 yaml_2.1.19
It looks like you'll either need to go back to R 3.4.4 or get Gurobi >= 8.0.1; because a lot was changed under the hood in R moving from 3.4.4 to 3.5.0, binaries compiled for R versions < 3.5.0 will not work with R >= 3.5.0, so your Gurobi 8.0.0 will not work with your current installation of R.
Other Gurobi users have had this issue; see here, and more informatively, here:
The current Gurobi release 8.0.1 ships a R package for R 3.5.X
If you'd prefer to go to an older version of R rather than a newer version of Gurobi, you can get R 3.4.4 for Windows here.
I have recently updated both R (version 3.4.1) and RStudio (version 1.0.143) and I am now unable to install packages from Rstudio.
If I install a package in R directly using install.packages() it works fine.
If I try and install a package in Rstudio using either install.packages() or using the package install menu I get the error below. I have tried a few different packages, and have uninstalled and reinstalled both R and RStudio.
To get the error:
Run:
install.packages("lme4")
Output:
Installing package into ‘E:/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
also installing the dependencies ‘minqa’, ‘nloptr’, ‘RcppEigen’
Warning in install.packages :
lzma decoding result 10
Error in install.packages : error reading from connection
I am working off my personal computer, below is some of my system info:
Output from options("repos")
$repos
CRAN CRANextra
"https://cran.stat.auckland.ac.nz/" "http://www.stats.ox.ac.uk/pub/RWin"
attr(,"RStudio")
[1] TRUE
Output from sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_New Zealand.1252 LC_CTYPE=English_New Zealand.1252
LC_MONETARY=English_New Zealand.1252
[4] LC_NUMERIC=C LC_TIME=English_New Zealand.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.4.1 tools_3.4.1
This certainly is an issue with your connection:the proxies you are using and repositories configured in your RStudio. I was getting the same error when I was connected to US VPN from India.I disconnected VPN and restarted RStudio and it worked like a charm!
I had the same issue when I tried to install caret.
The best solution is to restart R studio.
Now the install.packages() works fine.
Just restart the R studio it works for me.
I had the same issue after I misspelled a package name when trying to install it. I restarted R Studio and then it worked.
Kindly select appropriate CRAN mirror in R Studio through following option:
Tools>>>Packages>>>CRAN Mirror(Select appropriate CRAN depending on your location).
A simple solution would be to download manually the zip folder of the package and install it with the command :
install.packages('package.zip', lib='destination_directory',repos = NULL)
Package zip : the path to the zip file of the package
Destination_directory: where the packages are installed by default like C:/Users/unknown/Documents/R/win-library/3.3
Hope it helps
I've run into a problem with getting tcltk to run properly on r-gui. It's a required package for one of the packages (aplpack) I'd like to work with.
Preliminary Stuff
13" Macbook Air
OSX Yosemite - Version 10.10.5
R Version 3.2.3
R.app GUI 1.66 (6956) x86_64-apple-darwin14.5.0
r and r-gui were installed via homebrew
I installed aplpack in order to use the bagplot function. Upon loading the package I received the following output:
Loading required package: tcltk 2015-12-23 09:44:11.134 R[6529:31353]
-[NSApplication _setup:]: unrecognized selector sent to instance 0x60800011b3f0 2015-12-23 09:44:11.135 R[6529:31353] ***
run_REngineRmainloop: exception -[NSApplication _setup:]: unrecognized
selector sent to instance 0x60800011b3f0 caught during REPL iteration.
Update to the latest GUI version and consider reporting this properly
(see FAQ) if it persists and is not known. Consider saving your work
soon in case this develops into a problem.
The session became unresponsive and I had to force quit.
To try and solve the problem, I checked to see if tcltk was installed:
> capabilities()["tcltk"]
tcltk
TRUE
It was also available via the package manager but trying to load it, both through the gui and using library("tcltk") caused R to become unresponsive and resulted in an identical error:
2015-12-23 09:49:24.370 R[6571:33844] -[NSApplication _setup:]:
unrecognized selector sent to instance 0x608000108f70 2015-12-23
09:49:24.370 R[6571:33844] *** run_REngineRmainloop: exception
-[NSApplication _setup:]: unrecognized selector sent to instance 0x608000108f70 caught during REPL iteration. Update to the latest GUI
version and consider reporting this properly (see FAQ) if it persists
and is not known. Consider saving your work soon in case this develops
into a problem.
Some googling led me to do the following:
uninstall r-gui via homebrew
uninstall r via homebrew
download and install the most recent version of xquartz
installed homebrew/dupes/tcl-tk (which I thought was supposed to fix the issue)
ran brew update
ran brew upgrade
ran brew doctor
installed r via homebrew
installed r-gui via homebrew
After taking the above steps, I'm still running into the same issue as before.
Here is the output of sessionInfo():
sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-apple-darwin14.5.0 (64-bit) Running under: OS X 10.10.5
(Yosemite)
locale: [1]
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] stats graphics grDevices utils
datasets methods base
Following the advice in the Mac OSX FAQ (to attempt to replicate the issue), I opened the r in terminal and was able to not only load tcltk, but also aplpack:
R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree" Copyright (C)
2015 The R Foundation for Statistical Computing Platform:
x86_64-apple-darwin14.5.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY. You are
welcome to redistribute it under certain conditions. Type 'license()'
or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors. Type
'contributors()' for more information and 'citation()' on how to cite
R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help. Type 'q()' to
quit R.
sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-apple-darwin14.5.0 (64-bit) Running under: OS X 10.10.5
(Yosemite)
locale: [1]
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] stats graphics grDevices utils
datasets methods base
library("aplpack") Loading required package: tcltk
sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-apple-darwin14.5.0 (64-bit) Running under: OS X 10.10.5
(Yosemite)
locale: [1]
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] tcltk stats graphics grDevices
utils datasets methods [8] base
other attached packages: [1] aplpack_1.3.0
I believe that the issue with loading tcltk is interfering with loading aplpack and that something in R.app/r-gui is not playing nicely with tcltk.
To my understanding
install.packages("tcltk")
Returns
package ‘tcltk’ is not available (for R version 3.2.3)
A work around would be to use the previous version of R which is compatible with tcltk.