I have worked now for some time on an R project in my office's desktop computer, but need to carry the scripts with me while on travel. I copied everything into my laptop and did some changes to the code. Alas, when trying to compile (following the exact same procedure I was using in my desktop computer), the following error:
$ R CMD INSTALL --no-multiarch --with-keep.source coala
* installing to library ‘/home/my_pc/R/x86_64-pc-linux-gnu-library/3.3’
* installing *source* package ‘coala’ ...
** libs
make: Nothing to be done for `all'.
installing to /home/my_pc/R/x86_64-pc-linux-gnu-library/3.3/coala/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/my_pc/R/x86_64-pc-linux-gnu-library/3.3/coala/libs/coala.so':
/home/my_pc/R/x86_64-pc-linux-gnu-library/3.3/coala/libs/coala.so: undefined symbol: _ZSt24__throw_out_of_range_fmtPKcz
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/my_pc/R/x86_64-pc-linux-gnu-library/3.3/coala’
* restoring previous ‘/home/my_pc/R/x86_64-pc-linux-gnu-library/3.3/coala’
Both computers have the same Ubuntu but different R version. Also, I have to mention that I am working in two libraries at the same time and that the accompanying library update without problems, which makes this error message more puzzling. I have checked answers that may be related to this question, but can't figure out how to apply their solutions:
R: error installing packages UBUNTU - Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object
Got message unable to load shared object stats.so when R starts
Is there a way to solve this problem? Which may be the cause? What is the undefined symbol _ZSt24__throw_out_of_range_fmtPKcz?
I had a similar issue with rgdal on Ubuntu. Re-installing the package was enough to getting it working again.
$ sudo R
> install.packages("rgdal")
> quit()
$ exit
What is .libPaths() giving you as the output?
I encountered the same problem using the latest update today (R 3.3.1 for MacOS X). My R installation seemed to crash after updating it. My solution was simply to remove the lib directories from the file system and reinstall R:
rm -rf /Users/johann/Library/R/3.3/library
sudo rm -rf Library/Frameworks/R.framework/Versions/3.3/Resources/library
Hope this helps...
The problem is the linkage with your g++ stdlib. Different versions of Ubuntu have different versions of g++ stdlib. You cant always copy binaries from one to the other.
You may fix this by recompiling R for the laptop, or using the Ubuntu R packages. e.g. http://packages.ubuntu.com/xenial/r-base
For Mac / Linux
Press command + space
Type terminal and press enter to open terminal. In terminal paste this open /Library/Frameworks/R.framework/Resources/library and press enter. A finder window should open with a lot of folders
Each folder matches an installed R package.
Delete them all, close RStudio, reopen RStudio and install the packages you need with install.packages("dplyr") etc
After I did this, the issue went away
Related
A while back, I created a fork of the RDCOMClient package to keep it working with R 3.6 (https://github.com/dkyleward/RDCOMClient). People are now running into issues again because it won't work with R 4.0. The problem doesn't seem as easy to fix, and I'm hoping for some help.
If I flip Rstudio back to R 3.6 (and rtools35), I can use the package after installing with devtools::install_github(). When I try in R 4.0 (and rtools40), the package builds and I can connect over COM to an application. The first line of code below works, and xl is a COM pointer; however, trying to do anything with it (like set Excel to visible) will crash R.
xl <- RDCOMClient::COMCreate("Excel.Application")
xl[["Visible"]] <- TRUE
Again, the above works in R 3.6.
Is there is a way to continue building with the previous rtools? I came across https://github.com/r-windows/rtools-backports#readme, which talks about using rtools35 to keep building packages, so I have hope, but I don't understand how to make it happen.
Alternatively, if there are minor changes I can make to the R or cpp code that will solve my problem, I'm all ears. I'm a cpp novice, though.
This was a quick fix :
install.packages("RDCOMClient", repos = "http://www.omegahat.net/R")
Install R-4.0.0
Install Rtools35
Edit $R_HOME/etc/x64/Makeconf (for R-4.0.0-x64)
Rcmd INSTALL RDCOMClient
Rik's answer was incredibly helpful and got a version working; however, after spending a day on it, I was able to improve on it. I want to put that here in case I have to do it again. The main improvement is being able to build a working package for both 32- and 64-bit architectures. By default, R installs both, and this makes things easier when installing dependent packages.
The first two steps are the same:
Install R-4.0.0 (https://cran.r-project.org/bin/windows/base/old/4.0.0/R-4.0.0-win.exe)
Install Rtools35 (https://cran.r-project.org/bin/windows/Rtools/Rtools35.exe) in directory c:\Rtools
If (like me) you had already installed rtools40, a system environment variable named RTOOLS40_HOME is created. The first step is to change that to:
C:\rtools
If you don't have rtools40 installed, then create the RTOOLS40_HOME system environment variable.
Two changes are still needed in the make files. These are found in your R installation directory.
In etc\x64\Makeconf, add underscores to match the rtools35 directory structure by setting these values:
MINGW_PREFIX = /mingw_$(WIN)
BINPREF ?= "$(RTOOLS40_ROOT)/mingw_64/bin/"
Do the same in etc\i386\Makeconf:
MINGW_PREFIX = /mingw_$(WIN)
BINPREF ?= "$(RTOOLS40_ROOT)/mingw_32/bin/"
Do not set BINPREF as an environment variable, or this will overwrite the makefile changes (like RTOOLS40_HOME does). With these complete, finish off with the same steps that Rik outlined:
Open windows command prompt and change to the directory that contains the RDCOMClient subdirectory and type:
R CMD INSTALL RDCOMClient –-build RDCOMClient.zip
This installs RDCOMClient in the local installation of R-4.0.0 and additionally creates the file RDCOMClient_0.94-0.zip that can be installed on other systems using the following command:
install.packages("RDCOMClient_0.94-0.zip", repos = NULL, type = "win.binary")
I can confirm that the procedure delineated in the answer above leads in the right direction but a few extra steps may be required. I can also confirm that the procedure below produces a Windows binary file that can be installed and will run under R-4.0.0:
Install R-4.0.0 (https://cran.r-project.org/bin/windows/base/old/4.0.0/R-4.0.0-win.exe)
Install Rtools35 (https://cran.r-project.org/bin/windows/Rtools/Rtools35.exe) in directory c:\Rtools
Edit $R_HOME/etc/x64/Makeconf (for R-4.0.0-x64) by changing
## The rtools40 installer sets RTOOLS40_HOME, default to standard install path
RTOOLS40_HOME ?= c:/rtools40
to
## The rtools40 installer sets RTOOLS40_HOME, default to standard install path
RTOOLS40_HOME ?= c:/rtools
Download RDCOMClient-master.zip from https://github.com/omegahat/RDCOMClient (click the green Clone button and select download zip)
Unpack to a directory named RDCOMClient
Ensure that the following PATH variables are set:
C:\Program Files\R\R-4.0.0\bin\x64 (assuming this is the location where R is installed)
C:\Rtools\bin
C:\Rtools\mingw_64\bin
Add environment variable BINPREF with the following value (the final slash is important):
C:/Rtools/mingw_64/bin/
Open windows command prompt and change to the directory that contains the RDCOMClient subdirectory and type:
R CMD INSTALL RDCOMClient –-build RDCOMClient.zip
This installs RDCOMClient in the local installation of R-4.0.0 and additionally creates the file RDCOMClient_0.94-0.zip that can be installed on other systems using the following command:
install.packages("RDCOMClient_0.94-0.zip", repos = NULL, type = "win.binary")
I am using R 4.1.2 and I found RDCOMClient will crash the R Session and the above solutions were not working.
Then, I further check with the source owner and found out the solution.
https://github.com/omegahat/RDCOMClient/issues/36
Duncantl gave the solution and it works.
dir.create("MyTemp")
remotes::install_github("BSchamberger/RDCOMClient", ref = "main", lib = "MyTemp")
If that is successful, we can then load the newly installed package with
library("RDCOMClient", lib.loc = "MyTemp")
I am the author of https://github.com/akoyabio/rtree. Until recently, I was able to develop the package in RStudio on Windows with no problems. I was able to check and install the package without any error.
Something has changed and I can no longer build the package. In RStudio, "Install and restart" (with --debug) gives the output
==> Rcmd.exe INSTALL --no-multiarch --with-keep.source --debug rtree
Loading C:\Users\kjohnson\Documents\Rprofile.site
processing 'rtree'
a directory
* installing to library 'C:/Program Files/R/Library'
* build_help_types=html
* DBG: 'R CMD INSTALL' now doing do_install()
* created lock directory 'C:/Program Files/R/Library/00LOCK-rtree'
* installing *source* package 'rtree' ...
** backing up earlier installation
** libs
about to run R CMD SHLIB -o rtree.dll RcppExports.cpp rtree.cpp --debug
ERROR: compilation failed for package 'rtree'
* removing 'C:/Program Files/R/Library/rtree'
* restoring previous 'C:/Program Files/R/Library/rtree'
In R CMD INSTALL
Exited with status 1.
I'm looking for help troubleshooting this error. How can I get more details about the failure?
I do have RTools installed, at C:\RTools, and my PATH includes both
C:\Rtools\bin and C:\Program Files\R\R-3.5.3\bin.
Note: I see the same error if I create a new Rcpp project in RStudio and try to build it. Thank you for any suggestions...
I never really found out how to get more visibility into the failure. I did find the cause - it was an anti-virus program called Minerva's Shield. Turning it off allowed me to build again.
I am trying to load a .dll file using python cffi library, but whiele I am trying to load it I am getting following error:-
*** OSError: cannot load library C:\WINDOWS\libzsfc.dll: error 0xc1
I am using this
from cffi import FFI
ffi = FFI()
lib = ffi.dlopen("libzsfc.dll")
but this giving me error, I tried a lot to resolve this, but it remains same, please let me know if anyone faced same issue.
I think you have to first register the dll in windows then load will work fine.
To register the same use command regsvr32 <complete dll path>
Use Regsvr32.exe from the %SystemRoot%\Syswow64 folder. For example, type the following commands to register the DLL: cd \windows\syswow64 regsvr32 c:\filename.dll
Old question, but I just had the same issue. Fixed:
Super easy - reinstall tessaract. Head over to https://github.com/UB-Mannheim/tesseract/wiki. Get their installer. It'll have you uninstall the old version. Worked immediately for me.
I've made an R package with Rcpp, to use the methods of a library I programmed in c++.
I've R running on the last version:
R version 3.2.5 (2016-04-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04 LTS
I'm executing the following instruction to install my package:
> install.packages("mypackage", repos = NULL)
The package compiles well, I have the .o files of my source code, but in the linking phase I got the error:
* installing *source* package ‘rbdd’ ...
** libs
make: No se hace nada para 'all'.
installing to /home/sergio/R/x86_64-pc-linux-gnu-library/3.2/mypackage/libs
** R
** preparing package for lazy loading
** help
Warning: /home/sergio/R/mypackage/man/mypackage-package.Rd:27: All text must be in a section
Warning: /home/sergio/R/mypackage/man/mypackage-package.Rd:28: All text must be in a section
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/sergio/R/x86_64-pc-linux-gnu-library/3.2/mypackage/libs/mypackage.so':
/home/sergio/R/x86_64-pc-linux-gnu-library/3.2/mypackage/libs/mypackage.so: undefined symbol: _ZN4cudd12defaultErrorENSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEE
Error: loading failed
Ejecución interrumpida
ERROR: loading failed
mypackge.so is created in the src folder of my package.
I've got a Makevars file (in src, too) with the following content:
PKG_CPPFLAGS=-I./buddy-2.5/src -I./cudd-3.0.0/cudd -I./cudd-3.0.0/mtr -I./cudd-3.0.0/cplusplus -I./cudd-3.0.0/dddmp -I./cudd-3.0.0/util -I./cudd-3.0.0 -isystem /usr/include/c++/v1 -std=c++11
PKG_LIBS=-lc++ -L/lib
and my NAMESPACE file has the lines:
useDynLib(mypackage)
exportPattern("^[[:alpha:]]+")
importFrom(Rcpp, evalCpp)
Someone knows how to solve this problem?
I am a little concerned about
PKG_LIBS=-lc++ -L/lib
Did you really mean /lib? If it is your library, a more common place would be /usr/local/lib which is also search by default.
But, and that is a BIG but, you also need to understand what you need to do for ldconfig for the proper setup of libfoo.so, libfoo.so.$MAJOR and so on. I taught myself that many moons ago from a Linux HOWTO.
If and when that is setup right, you can link it to R via Rcpp. Otherwise maybe stick with system libraries, or package-local static libraries. That approach will also make your package more portable.
The problem was I am consumming external libs, and I must compile it and execute ldconfig before compile my R library.
I'm new to Macs (and quite new to Django) and I'm setting up an existing Django/MySQL site that uses Mercurial as a site package, on a new Macbook Pro.
All was going well during installation - no error messages. I installed the default versions of most packages from macports.
However when I try runserver, localhost shows the following error message:
ImportError at /
.../lib/python2.6/site-packages/mercurial/osutil.so: no appropriate 64-bit architecture (see "man python" for running in 32-bit mode)
Please could anyone advise? I've tried typing the following at the terminal:
defaults write com.apple.versioner.python Prefer-32-Bit -bool yes
but it didn't help.
I've gotten a similar error and a combination of two things helped me install Mercurial for OS X Lion. I'm running OS X 10.7.3.
First, there is a bug on line 455 of the setup.py script (at least for Mercurial 2.2.1, the version I tried). The line
version = runcmd(['/usr/bin/xcodebuild', '-version'], {})[0].splitlines()
should be replaced with
version = runcmd(['/usr/bin/xcodebuild', '-version'], {})[0]
Second, after I installed Mercurial (either by easy_install, Mac OS X binary installer, and compilation), I kept getting the following error message:
ImportError: dlopen(/Library/Python/2.7/site-packages/mercurial/osutil.so, 2): no suitable image found. Did find: /Library/Python/2.7/site-packages/mercurial/osutil.so: mach-o, but wrong architecture
However, after seeing this post, I noticed that
defaults read com.apple.versioner.python Prefer-32-Bit
outputs 1 on my system. However, running this command
defaults write com.apple.versioner.python Prefer-32-Bit -bool no
and then recompiling / installing mercurial resulted in a working executable for me at the end.
If everything from my comment checks out, try setting that Prefer-32-bit in an user environment variable instead of at the command line.
Edit this file: ~/.MacOSX/environment.plist
See:
http://developer.apple.com/mac/library/documentation/MacOSX/Conceptual/BPRuntimeConfig/Articles/EnvironmentVars.html#//apple_ref/doc/uid/20002093-113982