When I try to build my package I get this weird issue about Glib:
/usr/bin/ld: main_window.o: undefined reference to symbol 'ceilf##GLIBC_2.2.5'
/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/libm.so: error adding symbols: DSO missing from command line
I have Glib in the required build packages and have added a bunch of PPAs that had Glib packages in them. I can't seem to make this error go away. Any ideas?
Setting _LDADD in automake fixed it but the paths are not dynamic.
Related
I am on Apple M1. I tried to install a special package (Vienna RNA Package, precompiled binary package, https://www.tbi.univie.ac.at/RNA/#pack_macosx).
Installation is finished, but when I type the following
$ RNAduplex
I get the following:
dyld: Library not loaded: /usr/local/opt/mpfr/lib/libmpfr.4.dylib
Referenced from: /usr/local/bin/RNAfold
Reason: image not found
Abort trap: 6
Mpfr is installed via homebrew, but only the most recent version (4.1.0). I guess I need to install the previous version (3.1.6), but I don't get it work.
I tried to install it from https://www.mpfr.org/mpfr-3.1.6/ downloaded from https://www.mpfr.org/mpfr-3.1.6/.
When I do
./configure
I get
configure: error: gmp.h can't be found, or is unusable.
even though gmp is already installed via homebrew (present at /opt/homebrew/Cellar/gmp/).
Any advice on this?
Looking forward to any comments!
Best,
Stefanie
The config.log file may give more information about the error, but I suppose that gmp.h isn't in the include search path. You can try something similar, by compiling:
#include <gmp.h>
int main (void) { return 0; }
You will probably get an error as well.
So you may need to add the directory where gmp.h has been installed to the CPATH or C_INCLUDE_PATH environment variable. You will need to do something similar for the library. Another solution is to use the --with-gmp=... configure option with the GMP installation directory. See the INSTALL file for more information.
I have added a package Relief.jl to my environment. I have also checked if it's available by typing stand it's listed under available packages for the environment. However when I type using Relief I get the following error,
ERROR: ArgumentError: Package Relief [e59a39ae-ffc4-11ea-35a5-2b2996f35250] is required but does not seem to be installed:
- Run Pkg.instantiate() to install all recorded dependencies.
Any ideas what I should do to resolve this?
You need to run the command: ] build "name of package" in the terminal. This should fix the problem.
(Without the speech marks. That is just to highlight its a name)
Recently we have downgraded R(latest) to 3.3.0 to RHEL.
Which requires to install xlsx and other rJava dependent packages, though I have deep dived into every possible duplicate and tried all options.
Details:
Command Executed
R CMD javareconf
Error:
.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/lib64/R/lib64/R/lib/libR.a(CommandLineArgs.o): could not read symbols: Bad value
collect2: ld returned 1 exit status
make[2]: *** [libjri.so] Error 1
make[2]: Leaving directory /tmp/RtmpH1WhQR/R.INSTALL4a1266bbb309/rJava/jri/src'
`
Net search: I searched and found following link
https://github.com/BVLC/caffe/issues/2171 suggests to use
export CXXFLAGS=-fPIC
but no luck also I do not see CMakeCache.txt in the R folder, still not clear which piece I am missing and any help will be highly appreciated.
NOTE: This might seem to be a duplicate, but seriously I have already tried all the related/relevant posts on stackoverflow.
I resolved this, by manually placing the rJava folder(which I had in a different environment while we used R latest version), while entering into R add this following command before installing rJava dependant libraries:
.libPaths("/usr/lib64/R/library")
Change the path to the path where R is installed.
Hope this helps.
I am working on an R package containing Fortran source files. The structure of the Fortran code is rather complex, with many dependencies, therefore I have a Makefile in the src folder for the compilation of the shared library.
So far I have been compiling this package on my machine running Ubuntu 14.04, without any problems. I am now trying to compile it on Windows using Rtools, and I am running into a problem when linking the objects to produce the shared library. More precisely, the linker does not find the functions REXIT, RWARN and RCHKUSR, as I get the following error messages:
undefined reference to `rchkusr_'
undefined reference to `rexit_'
undefined reference to `rwarn_'
These functions are supposed to be in the shared library R.dll (libR.so under Linux). I checked this library with Dependencies Walker and I could find these functions. I have tried to link with -I C:/Program\ Files/R/R-3.1.1/bin/i386/R.dll to make explicit the reference to the shared library. I have tried to recompile with -fno-underscoring to make sure the underscores were not the problem. Nothing helped.
Any ideas where the problem could come from? Any suggestions would be more than welcome!
Under Linux I did not have to do anything special, the linker found the functions without specifying anything in the Makefile.
I am using R version 3.1.1 and Rtools version 3.1.
Many thanks for your help.
After fiddling with the Makefile, I finally found the solution to my problem: The flags I was trying to pass to the linker were wrong. Only the path of the shared library R.dll should be specified, using -L, and the name of the library should be specified using the flag -lR at the end of the command. In short, I specified
gfortran -shared *.o -o myLib.dll -L C:/Program\ Files/R/R-3.1.1/bin/i386 -lR
to create myLib.dll and it worked! I guess I got confused because under Linux there is no need to specify anything, the linker finds the shared library on its own.
Probably not the best and most portable solution I can get (I now have two Makefiles to deal with, Makefile for Linux and Makefile.win for Windows...), but good enough for now.
During installing rJava package, I got the following error messages:
checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this.
ERROR: configuration failed for package ‘rJava’
May I know what is the cause for this failure and how to fix this issue? Thanks.
If it installed but does not work try first : remove.package("rJava") and the install.package("rJava"). Some times helps. If still ahvgin problem post more data. But unless it's not necessary.
EDIT : see also java path if it's correctly set up. Sometimes its messed up.