I'm trying to build Pardiso 5 on Mac 10.12.6 through Julia but am having issues.
I added the Pardiso package through Julia, then I followed the Pardiso manual (p.33/69) and set LD_LIBRARY_PATH=~/.julia/v0.6/Pardiso/deps/libpardiso500-MACOS-X86-64.dylib from my .bash_profile. Then I run Pkg.build("Pardiso") and get the following error
INFO: Building Pardiso
found library but it failed to load due to:
could not load library "~/.julia/v0.6/Pardiso/deps/libpardiso500-MACOS-X86-64.dylib"
dlopen(~/.julia/v0.6/Pardiso/deps/libpardiso500-MACOS-X86-64.dylib, 9): Library not loaded: /usr/local/lib/libgfortran.3.dylib
Referenced from: ~/.julia/v0.6/Pardiso/deps/libpardiso500-MACOS-X86-64.dylib
Reason: image not foundfound library but it failed to load due to:
could not load library "libpardiso500-MACOS-X86-64.dylib"
dlopen(libpardiso500-MACOS-X86-64.dylib, 9): Library not loaded: /usr/local/lib/libgfortran.3.dylib
Referenced from: ~/.julia/v0.6/Pardiso/deps/libpardiso500-MACOS-X86-64.dylib
Reason: image not founddid not find libpardiso, assuming PARDISO 5.0 is not installed
did not find MKLROOT key, assuming MKL is not installed
WARNING: no Pardiso library managed to load
The Julia documentation didn't seem to indicate that I had to do any gcc stuff from terminal myself, so I haven't done any manual linking against BLAS/LAPACK, etc.
Any advice? Thanks!
Related
I am trying to use the Pardiso package in Julia together with the Pardiso library. However, I can’t build the package. When I look into the build log, I see this message:
Looking in “C:\Users\Rodrigo.julia\packages\Pardiso\yZsYO\deps” for libraries
found “C:\Users\Rodrigo.julia\packages\Pardiso\yZsYO\deps\libpardiso600-WIN-X86-64.dll”, attempting to load it…
failed to load due to:
did not find libpardiso, assuming PARDISO 5/6 is not installed
I don't know if I need anything else besides the pardiso.lic and libpardiso600-WIN-X86-64.dll files.
Thanks
While loading rJava package, I receive this error:
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: inDL(x, as.logical(local), as.logical(now), ...)
error: unable to load shared object 'C:/Users/ankitagarwal5/Documents/R/win-library/3.2/rJava/libs/x64/rJava.dll':
LoadLibrary failure: %1 is not a valid Win32 application.
In addition: Warning message:
package ‘rJava’ was built under R version 3.2.3
Error: package or namespace load failed for ‘rJava’
I referred various posts on StackOverflow and tried to make changes accordingly, but nothing worked. These are the various steps I followed to resolve the issue:
if (Sys.getenv("JAVA_HOME")!="")
Sys.setenv(JAVA_HOME="")
library(rJava)
This didn't work.
Then I tried this:
options(java.home="C:\\Program Files\\Java\\jre1.8.0_91\\")
library(rJava)
This didn't work either.
My jvm.dll is at this location in my Windows 7 64 bit OS - C:\Program Files (x86)\Java\jre1.8.0_91\bin\client
I also added C:\Program Files (x86)\Java\jre1.8.0_91\bin\client to my PATH variable in my Environment variables and restarted RStudio and tried to install and load rJava again. That also didn't work.
I would really appreciate if someone could please help me resolve this issue.
Thanks guys!
This worked for me -
This error is often resolved by installing a Java version (i.e. 64-bit Java or 32-bit Java) that fits to the type of R version that you are using (i.e. 64-bit R or 32-bit R). This problem can easily effect Windows 7 users, since they might have installed a version of Java that is different than the version of R they are using.
Note that it is necessary to ‘manually download and install’ the 64 bit version of JAVA. By default, the download page gives a 32 bit version .
You can pick the exact version of Java you wish to install from this link. If you might (for some reason) work on both versions of R, you can install both version of Java (Installing the “Java Runtime Environment” is probably good enough for your needs).
(Source: Uwe Ligges)
Other possible solutions is trying to re-install rJava.
If that doesn’t work, you could also manually set the directory of your Java location by setting it before loading the library:
Sys.setenv(JAVA_HOME='C:\\Program Files\\Java\\jre7') # for 64-bit version
Sys.setenv(JAVA_HOME='C:\\Program Files (x86)\\Java\\jre7') # for 32-bit version
library(rJava)
Refer this link - http://www.r-bloggers.com/how-to-load-the-rjava-package-after-the-error-java_home-cannot-be-determined-from-the-registry/
I encountered the same problem. Be sure to check the file path for Java. To solve the error I needed to download 64bit Java version. However the following code in R did not work as the folder was incorrect for the latest version for Java:
Sys.setenv(JAVA_HOME='C:\\Program Files\\Java\\jre7') # for 64-bit version
Instead I changed the name to:
Sys.setenv(JAVA_HOME='C:\\Program Files\\Java\\jre1.8.0_144')
Hope that helps
I have noticed in different fresh installations of R, RStudio and rJava in WIndows, that what fixes the error is:
Uninstall R
Reinstall R but only selecting one architecture. Example, x64, or x86, but not both. That tends to confuse R or RStudio when they are compiling.
In my case, I fixed the message
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: inDL(x, as.logical(local), as.logical(now), ...)
error: unable to load shared object 'C:/Users/ankitagarwal5/Documents/R/win-library/3.2/rJava/libs/x64/rJava.dll':
LoadLibrary failure: %1 is not a valid Win32 application.
Following steps 1 and 2 above.
I tried what the other have said to not avail. For me the solution was to eliminate the old folders and shortcuts of R version 32 bit on my computer that remained there even after uninstalling.
This happened to me when Java was updated to a 32-bit, but R required a 64-bit version.
The solution:
Simply download the 64-bit version of Java
install it.
Restart RStudio
Everything should work
Where to download 64-bit java:
I guess your OS architecture and R architecture are not matching. If they are matching, the following might be the problem
It worked for me after i added the R library path to the environment variables list on my windows 7.
So,
Add 'C:/Users/Rohan-PC/Documents/R/win-library/3.1' this path to the Path variables list under System variables list(not to be confused with the PATH variable under User variables). Restart R and try loading the library. It works!!!!!
If you have both 64-bit R and 32-bit R versions installed, try from each one.
For me it worked on R 64bits but not R 32bits.
But of course that depends on your java version (64-bit Java vs 32-bit Java).
I have been using cairo_pdf(...) to ggplot pdf's that contain unicode for phonetic (IPA) characters (like "\u025B"). This worked great until today when I updated RStudio to 1.1.456 and R to 3.5.1 (running on OS X 10.13.5). Now, when I call cairo_pdf(...) I get a message saying "failed to load cairo DLL". I have done install.packages("Cairo") and now library("Cairo") spits out a series of messages:
Error: package or namespace load failed for ‘Cairo’:
.onLoad failed in loadNamespace() for 'Cairo', details:
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Cairo/libs/Cairo.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Cairo/libs/Cairo.so, 6): Library not loaded: /opt/X11/lib/libfreetype.6.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Cairo/libs/Cairo.so
Reason: Incompatible library version: Cairo.so requires version 19.0.0 or later, but libfreetype.6.dylib provides version 17.0.0
I'm not sure whether I should try to work out what has changed in Cairo or R, or learn a different way to put unicode characters in plots. I did try .png outputs but the quality was inadequate.
tx
The most recent version of the system cairo package in the Mac http://r.research.att.com/libs/ directory is: http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
You might get some information and possibly even some success with the suggested method at the bottom the the libs page. Open Terminal.app and paste these two lines (all of them) into the Unix console:
curl -O http://r.research.att.com/libs/cairo-1.14.2-darwin.13-x86_64.tar.gz
sudo tar fvxz gmp-4.2.4-darwin8-bin4.tar.gz -C /
I edited your tags since the other possibility of a system issue is whether Rstudio honors or recognizes the location of the cairo lib.
On my Rstudio installation it seems to. I was able to load, update, run: detach("package:Cairo", unload=TRUE), and reload the (R) Cairo package from the R console. But I'm not a particularly knowledgeable user of Rstudio. I'm still using the CRAN distributed R.app.
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.
While loading rJava package, I receive this error:
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: inDL(x, as.logical(local), as.logical(now), ...)
error: unable to load shared object 'C:/Users/ankitagarwal5/Documents/R/win-library/3.2/rJava/libs/x64/rJava.dll':
LoadLibrary failure: %1 is not a valid Win32 application.
In addition: Warning message:
package ‘rJava’ was built under R version 3.2.3
Error: package or namespace load failed for ‘rJava’
I referred various posts on StackOverflow and tried to make changes accordingly, but nothing worked. These are the various steps I followed to resolve the issue:
if (Sys.getenv("JAVA_HOME")!="")
Sys.setenv(JAVA_HOME="")
library(rJava)
This didn't work.
Then I tried this:
options(java.home="C:\\Program Files\\Java\\jre1.8.0_91\\")
library(rJava)
This didn't work either.
My jvm.dll is at this location in my Windows 7 64 bit OS - C:\Program Files (x86)\Java\jre1.8.0_91\bin\client
I also added C:\Program Files (x86)\Java\jre1.8.0_91\bin\client to my PATH variable in my Environment variables and restarted RStudio and tried to install and load rJava again. That also didn't work.
I would really appreciate if someone could please help me resolve this issue.
Thanks guys!
This worked for me -
This error is often resolved by installing a Java version (i.e. 64-bit Java or 32-bit Java) that fits to the type of R version that you are using (i.e. 64-bit R or 32-bit R). This problem can easily effect Windows 7 users, since they might have installed a version of Java that is different than the version of R they are using.
Note that it is necessary to ‘manually download and install’ the 64 bit version of JAVA. By default, the download page gives a 32 bit version .
You can pick the exact version of Java you wish to install from this link. If you might (for some reason) work on both versions of R, you can install both version of Java (Installing the “Java Runtime Environment” is probably good enough for your needs).
(Source: Uwe Ligges)
Other possible solutions is trying to re-install rJava.
If that doesn’t work, you could also manually set the directory of your Java location by setting it before loading the library:
Sys.setenv(JAVA_HOME='C:\\Program Files\\Java\\jre7') # for 64-bit version
Sys.setenv(JAVA_HOME='C:\\Program Files (x86)\\Java\\jre7') # for 32-bit version
library(rJava)
Refer this link - http://www.r-bloggers.com/how-to-load-the-rjava-package-after-the-error-java_home-cannot-be-determined-from-the-registry/
I encountered the same problem. Be sure to check the file path for Java. To solve the error I needed to download 64bit Java version. However the following code in R did not work as the folder was incorrect for the latest version for Java:
Sys.setenv(JAVA_HOME='C:\\Program Files\\Java\\jre7') # for 64-bit version
Instead I changed the name to:
Sys.setenv(JAVA_HOME='C:\\Program Files\\Java\\jre1.8.0_144')
Hope that helps
I have noticed in different fresh installations of R, RStudio and rJava in WIndows, that what fixes the error is:
Uninstall R
Reinstall R but only selecting one architecture. Example, x64, or x86, but not both. That tends to confuse R or RStudio when they are compiling.
In my case, I fixed the message
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: inDL(x, as.logical(local), as.logical(now), ...)
error: unable to load shared object 'C:/Users/ankitagarwal5/Documents/R/win-library/3.2/rJava/libs/x64/rJava.dll':
LoadLibrary failure: %1 is not a valid Win32 application.
Following steps 1 and 2 above.
I tried what the other have said to not avail. For me the solution was to eliminate the old folders and shortcuts of R version 32 bit on my computer that remained there even after uninstalling.
This happened to me when Java was updated to a 32-bit, but R required a 64-bit version.
The solution:
Simply download the 64-bit version of Java
install it.
Restart RStudio
Everything should work
Where to download 64-bit java:
I guess your OS architecture and R architecture are not matching. If they are matching, the following might be the problem
It worked for me after i added the R library path to the environment variables list on my windows 7.
So,
Add 'C:/Users/Rohan-PC/Documents/R/win-library/3.1' this path to the Path variables list under System variables list(not to be confused with the PATH variable under User variables). Restart R and try loading the library. It works!!!!!
If you have both 64-bit R and 32-bit R versions installed, try from each one.
For me it worked on R 64bits but not R 32bits.
But of course that depends on your java version (64-bit Java vs 32-bit Java).