I'm perplexed that the R.oo package installation fails on RStudio server, any idea on how I can get around it?
Installing package(s) into ‘/home/rstudio/R/library’
(as ‘lib’ is unspecified)
trying URL 'http://ftp.heanet.ie/mirrors/cran.r-project.org/src/contrib/R.oo_1.9.3.tar.gz'
Content type 'application/x-gzip' length 372217 bytes (363 Kb)
opened URL
==================================================
downloaded 363 Kb
* installing *source* package ‘R.oo’ ...
** package ‘R.oo’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Error in match(el, set, 0L) : object 'R.KEYWORDS' not found
Error : unable to load R code in package ‘R.oo’
ERROR: lazy loading failed for package ‘R.oo’
* removing ‘/home/rstudio/R/library/R.oo’
Warning in install.packages :
installation of package ‘R.oo’ had non-zero exit status
According to the author of the R.oo and R.KEYWORDS packages, there was an incompatibility between the last version of R.KEYWORDS (v1.4.2) and R.oo (the cran version 1.9.3 was incompatible, not being the last one v1.9.8). He corrected that recently.
As of last night: I can confirm this problem on two different RStudio servers, one running R.2.14.1, the other R.2.15.1, so it's not R version. One is our linux server, the other is an amazon EC2 server. And no problem installing on a local RStudio (OSX; R.2.15.0).
HOWEVER: as of an hour ago, this problem has disappeared. On both RStudio Servers, R.oo now installs fine. So, try again!
Related
I'm trying to use computer in my office for working using Rstudio because I realised that there is Rstudio installed in the computer. However, when I'm trying to install the package I need, the package is unable to install. I try so many package but the same issue happen.Even though, I'm trying to update installed package such as rlang version 1.02 to the latest one, it is also failed. I've tried to restart Rstudio as well after I installed the package, but I can't find the package that I have installed before.
Here is the error message that I receive when I try to install the very standard one such as scales package:
install.packages("scales")
also installing the dependencies ‘rlang’, ‘lifecycle’
There are binary versions available but the source versions are later:
binary source needs_compilation
rlang 1.0.2 1.0.6 TRUE
lifecycle 1.0.1 1.0.2 FALSE
scales 1.2.0 1.2.1 FALSE
Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/rlang_1.0.2.zip'
Content type 'application/zip' length 1718546 bytes (1.6 MB)
downloaded 1.6 MB
package ‘rlang’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\axk1076\AppData\Local\Temp\RtmpYjc7m3\downloaded_packages
installing the source packages ‘lifecycle’, ‘scales’
trying URL 'https://cran.rstudio.com/src/contrib/lifecycle_1.0.2.tar.gz'
Content type 'application/x-gzip' length 102178 bytes (99 KB)
downloaded 99 KB
trying URL 'https://cran.rstudio.com/src/contrib/scales_1.2.1.tar.gz'
Content type 'application/x-gzip' length 270609 bytes (264 KB)
downloaded 264 KB
'\\adf\storage\A\K\AXK1076'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* installing *source* package 'lifecycle' ...
** package 'lifecycle' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace 'rlang' 1.0.2 is being loaded, but >= 1.0.5 is required
Calls: <Anonymous> ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'lifecycle'
* removing 'C:/Program Files/R/R-4.0.3/library/lifecycle'
Warning in install.packages :
installation of package ‘lifecycle’ had non-zero exit status
'\\adf\storage\A\K\AXK1076'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
ERROR: dependency 'lifecycle' is not available for package 'scales'
* removing 'C:/Program Files/R/R-4.0.3/library/scales'
Warning in install.packages :
installation of package ‘scales’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\axk1076\AppData\Local\Temp\RtmpYjc7m3\downloaded_packages’
I don't know how Rstudio installed in this computer and I'm truly beginner in R. Is there anyone can help me? thank you in advance. Regards.
Since it is not known how R was installed in your computer, I would highly recommend you to uninstall both R and RStudio and installing the latest versions from the official websites.
First install R from: https://cran.r-project.org/bin/windows/base/
Install RStudio from: https://www.rstudio.com/products/rstudio/download/
Maybe they were installed in the wrong settings for your computer. Also to prevent bigger issues in the future (especially for beginners), that's the best option.
I've had a problem for a while now in which I can't load the stringi package until I install it clean. This seems to work as long as I'm in a single R session. Then, some time later, maybe when I create a new session or probably after a longer delay, I have to install it again.
This all broke this morning for some reason. Now, if I can install it straight away, and load it, but it's not recognized by ggplot2. Specifically when I try to install ggplot2 I get:
> library(stringi)
> install.packages("ggplot2")
Installing package into ‘/home/bensmith/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/ggplot2_3.0.0.tar.gz'
Content type 'application/x-gzip' length 2847050 bytes (2.7 MB)
==================================================
downloaded 2.7 MB
* installing *source* package ‘ggplot2’ ...
** package ‘ggplot2’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/bensmith/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/libs/Rcpp.so':
/home/bensmith/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/libs/Rcpp.so: undefined symbol: R_ContinueUnwind
ERROR: lazy loading failed for package ‘ggplot2’
* removing ‘/home/bensmith/R/x86_64-pc-linux-gnu-library/3.4/ggplot2’
* restoring previous ‘/home/bensmith/R/x86_64-pc-linux-gnu-library/3.4/ggplot2’
Warning in install.packages :
installation of package ‘ggplot2’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpEStEk4/downloaded_packages’
As you can see, stringi loads successfully into the environment, but I get this error when installing ggplot2.
Elsewhere this problem has been reported as fixed by installing stringi, but here, that doesn't help. But I suspect something is wrong with the stringi installation because of the previous problems I have had having to continually reinstall it.
I have tried installing stringi and ggplot2 using
install.packages("stringi", type = "source")
install.packages("ggplot2", type = "source")
Once again, stringi installs but ggplot2 does not.
Seems to be installing Rcpp again that fixed the problem.
Thanks to commenter at https://community.rstudio.com/t/stringi-installation-not-recognized-consequently-ggplot-wont-install/11590
I need to install the "plm" package. After installing it, the "sandwich" package was missing.
> library(plm)
Error: package or namespace load failed for ‘plm’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘sandwich
Tried to install the "sandwich" package, returned with this:
Installing package into ‘library_path’
(as ‘lib’ is unspecified)
also installing the dependency ‘zoo’
There is a binary version available but the source version is later:
binary source needs_compilation
sandwich 2.3-4 2.4-0 FALSE
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/zoo_1.8-0.zip'
Content type 'application/zip' length 901864 bytes (880 KB)
downloaded 880 KB
package ‘zoo’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\directory\downloaded_packages
installing the source package ‘sandwich’
trying URL 'https://cran.rstudio.com/src/contrib/sandwich_2.4-0.tar.gz'
Content type 'application/x-gzip' length 1280592 bytes (1.2 MB)
downloaded 1.2 MB
'\\directory\My Documents'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* installing *source* package 'sandwich' ...
** package 'sandwich' successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
Warning in file(con, "w") :
cannot open file '\\library_path/sandwich/doc/index.html': No such file or directory
Error in file(con, "w") : cannot open the connection
ERROR: installing vignettes failed
* removing '\\library_path/sandwich'
Warning in install.packages :
running command '"C:/R-34~1.1/bin/x64/R" CMD INSTALL -l "\\library_path" C:\directory/downloaded_packages/sandwich_2.4-0.tar.gz' had status 1
Warning in install.packages :
installation of package ‘sandwich’ had non-zero exit status
The downloaded source packages are in
‘C:\directory\downloaded_packages’
Had tried:
Reinstall R and RStudio directly to C (not in C:\Program Files)
Using this command to install all the dependencies:
install.packages("sandwich", dependencies=TRUE)
Still, the "non-zero exit status" appeared. Do you have any suggestions?
I am using Windows 7 (64 bit), R 3.4.1 and RStudio 1.0.153
I think i found a temporary answer for my problem. I previously had problems related to the privilege in writing the library folder in R. Tried to work around by turning off anti-virus live update, change the security of the R folder, etc. I thought it was worked, since I did not find anymore issues on "unable to move temporary installation....". But when I restart my computer, the problem came again.
Since I am working in a university provided laptop, I need to wait until the IT grants me access as an admin. While waiting for it, I created a new library in C:/ (in my case, I named it as "R library local"). Downloaded all the package to that library
install.packages("plm", dependencies = TRUE, lib = "C:/R library local")
And load the package from the library
library("plm", lib="C:/R library local")
It works well :)
Dunno if I still need the admin access for the library in R folder or not.
I am trying to install the package RWeka. I installed the java version 8, but i am keep getting this error. Can anybody help?
> install.packages('RWeka')
There is a binary version available but the source version is later:
binary source needs_compilation
RWeka 0.4-26 0.4-33 FALSE
installing the source package ‘RWeka’
trying URL 'https://cran.rstudio.com/src/contrib/RWeka_0.4-33.tar.gz'
Content type 'application/x-gzip' length 415763 bytes (406 KB)
==================================================
downloaded 406 KB
* installing *source* package ‘RWeka’ ...
** package ‘RWeka’ successfully unpacked and MD5 sums checked
Need at least Java version 1.7/7.0.
ERROR: configuration failed for package ‘RWeka’
* removing ``‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RWeka’
Warning in install.packages :
installation of package ‘RWeka’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/sh/6qsjq6gn0ysf4h1cv9nctzfr0000gn/T/RtmpCVEaSY/downloaded_packages’``
From experience, I believe there is a difference between Java and Java Offline.
Try installing the x86/x64 offline version from http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html (A handy link to keep hold of)
If you have the newest Java, just open a terminal and run
sudo R CMD javareconf
Then in a R-session,
install.packages("rJava",type='source')
install.packages("RWeka")
Ref: https://justrocketscience.com/post/install-rweka-mac
I'm having problems installing the package car in R.
There are previous posts on the topic, including this one and this other one.
I have followed the suggestions I've come across so far without success. I am using R Version 3.2.2. and RStudio.
This is the message I get:
install.packages("car")
Installing package into ‘C:/Users/.../Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/car_2.1-3.zip'
Content type 'application/zip' length 1447213 bytes (1.4 MB)
downloaded 1.4 MB
package ‘car’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\...\AppData\Local\Temp\Rtmpc3xr5i\downloaded_packages
If I check I get,
?car
No documentation for ‘car’ in specified packages and libraries:
you could try ‘??car’
I tried installing it from R with Install packages from local zip drives, and looking for the zip in C:\Users\...\AppData\Local\Temp\Rtmpc3xr5i\downloaded_packages, but this is the result:
library(car)
Error in library.dynam(lib, package, package.lib) :
DLL ‘SparseM’ not found: maybe not installed for this architecture?
In addition: Warning message:
package ‘car’ was built under R version 3.2.5
Error: package or namespace load failed for ‘car’
I did try installing SparseM even before posting the OP without success:
> install.packages("SparseM")
Installing package into ‘C:/Users/.../Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/SparseM_1.7.zip'
Content type 'application/zip' length 795531 bytes (776 KB)
downloaded 776 KB
package ‘SparseM’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\...\AppData\Local\Temp\Rtmpc3xr5i\downloaded_packages
> ?SparseM
No documentation for ‘SparseM’ in specified packages and libraries:
you could try ‘??SparseM’
Follow up:
After a comment regarding R version 3.2.3 I thought it would be an easy fix to just download this version, install, and erase 3.2.2. The problem then is that RStudio did not seem to work. I un-installed and re-installed R-studio, and now I get this when opening R studio:
Without knowing what version of the car package you're using, it's hard to know exactly what the source of the problem is. It seems likely, however, that you haven't installed the proper version of the pbkrtest, on which the Rcmdr package depends.
Is there a compelling reason not to upgrade everything to their current versions, including R, all packages, and RStudio?
Best,
John