I'm a TA in a statistics class, and the students are supposed to use the "asbio" package in r for multiple comparisons. Some of those who have OSX are complaining that asbio will not load. I cannot reproduce the error on my own mac.
Here are the errors one of the students is seeing:
>library(asbio)
Loading required package: tcltk
Error : .onLoad failed in loadNamespace() for 'tcltk', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/tcltk/libs/tcltk.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/library/tcltk/libs/tcltk.so, 10): Library not loaded: /opt/X11/lib/libX11.6.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/tcltk/libs/tcltk.so
Reason: image not found
Error: package ‘tcltk’ could not be loaded
> install.packages("tcltk")
Warning in install.packages :
package ‘tcltk’ is not available (for R version 3.1.1)
Here are a few things students have tried:
install tcltk2: "It works now, but I still get errors" (Sorry, I know that's a confusing answer, but it's what I have)
install xquartz: "Now it works."
I suspect that xquartz is the right answer here, but if anybody could explain what's going on and confirm, that would be awesome.
(And why the ^& would a numerical statistics package need tcl/tk anyway???)
tcl/tk needs an X11 environment to work in for graphical output and Apple no longer ships an X11 environment with their operating system. XQuartz fills that gap, but is a separate install. Said install makes the X11 libraries available (look at the missing libraries in your errors) and those libraries—in turn—make graphical operations with tcl/tk possible.
the absio package has functions that let you do animation (like anim.ci) which rely on the graphics capabilities of tcl/tk.
A student in the class posted the following instructions:
1) Install xquartz. You don't need to click it ever again after installing it.
2) Restart computer.
3) Open Rstudio (or whatever R). Run library(tcltk). Don't use require or install.packages for it. Computer should now open up xquartz on its own.
4) Run install.packages("asbio")
5) library(asbio)
6) You should be able to run pairw.anova.
(I'm still waiting to see if the student wants credit by name here, but in any case, I'm thankful to them.)
Related
I am trying to install the forecast package which depends on uroot, which apparently have been written to require a GPU?
install.packages("uroot") yields the following error. Has anyone found this issue and may suggest a work around? I am using ubuntu 16.04.
I have the file in question located here: /usr/local/cuda-8.0/ and I added to my path export PATH=/usr/local/cuda-8.0/:$PATH
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/rstudio2/R/x86_64-pc-linux-gnu-library/3.2/uroot/libs/uroot.so':
libcudart.so.8.0: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/rstudio2/R/x86_64-pc-linux-gnu-library/3.2/uroot’
Warning in install.packages :
installation of package ‘uroot’ had non-zero exit status
Just in case this is useful for someone, I stumbled with the same problem trying to install "imputeTS" with R version 3.5.1 on Fedora 27 with CUDA 10.0 correctly installed an setted in PATH.
for me it just happened that I was running install.package("imputeTS") (which depends on forecast) in a R console as root, installing the packages to the user home solved the problem. It's seems that the libraries are searched in different places according to the user running the script, it's important to note that.
I just migrated to Linux. On an Ubuntu 18.04 setup, using install.packages with dependencies set to TRUE succeeded with no complaints. (No GPU on mu box.)
install.packages("forecast", dep=TRUE)
# there are quite a few dependencies and you happened to be missing one
packageDescription()
#-----------includes this line----------
Imports: colorspace, fracdiff, ggplot2 (>= 2.2.1), graphics, lmtest,
magrittr, nnet, parallel, Rcpp (>= 0.11.0), stats,
timeDate, tseries, urca, uroot, zoo
You can try to modify file "/etc/rstudio/rserver.conf", add "LD_LIBRARY_PATH" env, like:
rsession-ld-library-path=/usr/local/cuda/lib64
Actually, When you open session of "RStudio Server" from browser, the session does't get env from the ".bashrc".
I'm running R 2.9 on a large EC2 Ubuntu instance, loaded with RAM, but without a terminal. When I load a library that has display dependencies, such as the sqldf package, I receive the following error:
library(sqldf)
...
Loading required package: tcltk
Loading Tcl/Tk interface ... Error in fun(...) : couldn't connect to display "localhost:11.0"
Error : .onLoad failed in 'loadNamespace' for 'tcltk'
Error: package 'tcltk' could not be loaded
This seems to be a general problem, and I'm wondering how others have solved it. Installing an X11 server is not a desirable solution.
Use the virtual framebuffer X11 server -- we do the same to build packages requiring X11 for R builds in headless chroots. Taking e.g. pars of the Build-Depends from rggobi:
xvfb xauth xfonts-base
After installing these you can use the xvfb-run command. If you start R via e.g.
xvfb-run R --no-save
you should now be able to use routines and commands requiring X11 as e.g. some of the plotting devices, or the tcl/tk initialization which also insists on having X11.
The same trick is useful for web servers.
Dirk's suggestion indeed works well, if you have control over the server & can run xvfb.
If not, read on...
in newer versions of R (>= 2.10 & maybe earlier), this is no longer an error, it's a warning:
> library(tcltk)
Loading Tcl/Tk interface ... done
Warning message:
In fun(libname, pkgname) : no DISPLAY variable so Tk is not available
You can now suppress this warning, and the subsequent package loading message via:
> suppressPackageStartupMessages(suppressWarnings(library(tcltk)))
Often you will see this message due to loading a package like qvalue which depends on tcltk; if you're after silent operation, you should silently load tcltk first, then the package of interest:
> suppressPackageStartupMessages(suppressWarnings(library(tcltk)))
> library(qvalue)
Mark
resurrected due to: http://dev.list.galaxyproject.org/wrapping-qvalue-in-Galaxy-td4655164.html
I'm trying to install the package nloptr on Mac OS High Sierra in order to use many nice packages like lme4, and I'm using RStudio inside Anaconda, with R 3.4.2. I have also installed NLopt (downloaded from the NLopt website, not the development version. I have also installed Xcode command line tool. But I still can't install nloptr, and get this
Error: package or namespace load failed for ‘nloptr’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/lambda/anaconda3/lib/R/library/nloptr/libs/nloptr.so':
dlopen(/Users/lambda/anaconda3/lib/R/library/nloptr/libs/nloptr.so, 6): Symbol not found: _nlopt_add_equality_mconstraint
Referenced from: /Users/lambda/anaconda3/lib/R/library/nloptr/libs/nloptr.so
Expected in: flat namespace
in /Users/lambda/anaconda3/lib/R/library/nloptr/libs/nloptr.so
I already searched online for what to do, and did add the path where NLopt was installed to LD_LIBRARY_PATH in the /etc/ldpaths file, but I still get the same error. Yes, I have the same problem as in Trouble installing nloptr package on R 3.3.0, but I didn't find a solution that works there since the person who asked that question resolved it himself and I don't know what he meant when he said "installed as a root". Can anyone help?
Also, I got something like this when installing NLopt with CMake, and this happened to many different functions:
In file included from f77api.c:103:
./f77funcs.h:57:14: warning: 'nlopt_minimize_constrained' is deprecated
[-Wdeprecated-declarations]
*info = nlopt_minimize_constrained((nlopt_algorithm) *algorithm,
^
./nlopt.h:348:35: note: 'nlopt_minimize_constrained' has been explicitly marked
deprecated here
int maxeval, double maxtime) NLOPT_DEPRECATED;
^
./nlopt.h:320:43: note: expanded from macro 'NLOPT_DEPRECATED'
# define NLOPT_DEPRECATED __attribute__((deprecated))
^
Would this be why the library isn't loaded?
BTW, I have installed Rcpp and updated it. Rcpp works on my computer.
Update: I changed the default C and C++ compiler to clang4 downloaded from R project. I tried the installation again, and got a different error:
Error: package or namespace load failed for ‘nloptr’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Users/lambda/anaconda3/lib/R/library/nloptr/libs/nloptr.so':
dlopen(/Users/lambda/anaconda3/lib/R/library/nloptr/libs/nloptr.so, 6): Library not loaded: #rpath/libnlopt.0.dylib
Referenced from: /Users/lambda/anaconda3/lib/R/library/nloptr/libs/nloptr.so
Reason: image not found
Error: loading failed
I have tried to tell R where the library is by Sys.geteng(DYLD_LIBRARY_PATH = "/usr/local/lib"), but it didn't work. It actually appears that R does know where the shared library is, according to the messages I got from installation, but it just can't load it. Please help!
Never mind, I reinstalled Anaconda, and installed the standalone R and RStudio (not within Anaconda), and those packages all installed successfully. Maybe it's a bad idea to use the RStudio inside Anaconda.
Edit: For those who run into similar scenarios: I switched to Microsoft R Open (MRO), since I'm dealing a lot with linear algebra recently. Then when I tried to install nloptr in MRO, I got a similar error message that shared library failed to load because image not found. I reinstalled the CRAN R 3.4.3 and nloptr installed totally fine there. So I found where nloptr was installed in CRAN R 3.4.3 by .libPaths(), copied the nloptr folder to where MRO stores packages, and used the utility RSwitch to change the default version of R to MRO. Then I loaded nloptr in MRO, installed packages that depend on it, and used those packages; they worked fine. I don't know what's wrong with MRO that caused the error, but at least this worked.
I'm running R 2.9 on a large EC2 Ubuntu instance, loaded with RAM, but without a terminal. When I load a library that has display dependencies, such as the sqldf package, I receive the following error:
library(sqldf)
...
Loading required package: tcltk
Loading Tcl/Tk interface ... Error in fun(...) : couldn't connect to display "localhost:11.0"
Error : .onLoad failed in 'loadNamespace' for 'tcltk'
Error: package 'tcltk' could not be loaded
This seems to be a general problem, and I'm wondering how others have solved it. Installing an X11 server is not a desirable solution.
Use the virtual framebuffer X11 server -- we do the same to build packages requiring X11 for R builds in headless chroots. Taking e.g. pars of the Build-Depends from rggobi:
xvfb xauth xfonts-base
After installing these you can use the xvfb-run command. If you start R via e.g.
xvfb-run R --no-save
you should now be able to use routines and commands requiring X11 as e.g. some of the plotting devices, or the tcl/tk initialization which also insists on having X11.
The same trick is useful for web servers.
Dirk's suggestion indeed works well, if you have control over the server & can run xvfb.
If not, read on...
in newer versions of R (>= 2.10 & maybe earlier), this is no longer an error, it's a warning:
> library(tcltk)
Loading Tcl/Tk interface ... done
Warning message:
In fun(libname, pkgname) : no DISPLAY variable so Tk is not available
You can now suppress this warning, and the subsequent package loading message via:
> suppressPackageStartupMessages(suppressWarnings(library(tcltk)))
Often you will see this message due to loading a package like qvalue which depends on tcltk; if you're after silent operation, you should silently load tcltk first, then the package of interest:
> suppressPackageStartupMessages(suppressWarnings(library(tcltk)))
> library(qvalue)
Mark
resurrected due to: http://dev.list.galaxyproject.org/wrapping-qvalue-in-Galaxy-td4655164.html
I'm trying to install the R package ggplot2, though the error that I am getting seems unrelated to that specific package. I am running on Mac OSX 10.6.8. The error message is at the bottom of this message. What happened was:
I opened up R and typed install.packages("ggplot2"). After typing this, an X11 window opened saying that I should update to the latest version of X11. I clicked through and updated X11. The install went through fine, ending with a big green check mark.
Then, I thought, "let me check if R is up to date as well, as the ggplot documentation suggests updating R before installing ggplot". So I opened up R, and clicked "check for updates". Lo and behold! an update appeared. I downloaded and installed the update. The install went through fine, ending with a big green check mark.
When I opened R, I typed install.packages("ggplot2") and I got the message below:
> install.packages("ggplot2");
--- Please select a CRAN mirror for use in this session ---
Error: .onLoad failed in loadNamespace() for 'tcltk', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object
'/Library/Frameworks/R.framework/Versions/3.0/Resources/library/tcltk/libs/tcltk.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/tcltk/libs/tcltk.so, 10):
Library not loaded: /usr/X11/lib/libfreetype.6.dylib
Referenced from: /usr/local/lib/libtk8.6.dylib
Reason: Incompatible library version: libtk8.6.dylib requires version 14.0.0 or later, but libfreetype.6.dylib provides version 13.0.0
Your help is greatly appreciated. Thanks.
Try installing the latest version of XQuartz. It worked for me.