Attempts to install package lme4 result in:
cpp -o external.o
In file included from external.cpp:8:0:
predModule.h:12:23: fatal error: RcppEigen.h: No such file or directory
compilation terminated.
/usr/lib64/R/etc/Makeconf:139: recipe for target 'external.o' failed
make: *** [external.o] Error 1
ERROR: compilation failed for package ‘lme4’
The system is Fedora Core 23
R is 3.3.1
Searches do not produce references to resolve the RccpEigen reference. Is there a workaround.
Related
I am using this code to download ape on R version 3.6.0:
install.packages("ape", dependencies = T)
and I am finding the following errors:
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [ape.so] Error 1
ERROR: compilation failed for package ‘ape’
I have attempted to download using the terminal too and this has also failed. I have checked the R version and APE is compatible with Rv3.6. Any ideas why this package cannot be downloaded?
check your R version, because i intalled 1 min ago and i'm not have problem.
I'm using RStudio on Ubuntu 18 and I'm trying to install the htslib package from the Bioconductor repo, but I'm stuck now.
This is what I get:
* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.7" && make -f "/usr/lib/R/etc/Makeconf" -f "Makefile.Rhtslib"
make[1]: Entering directory '/tmp/RtmpbL8Yil/R.INSTALL1664f5019f4/Rhtslib/src/htslib-1.7'
Makefile.Rhtslib:128: warning: overriding recipe for target '.c.o'
/usr/lib/R/etc/Makeconf:168: warning: ignoring old recipe for target '.c.o'
...
cram/cram_io.c:61:10: fatal error: lzma.h: No such file or directory
#include <lzma.h>
^~~~~~~~
compilation terminated.
Makefile.Rhtslib:128: recipe for target 'cram/cram_io.o' failed
make[1]: Leaving directory '/tmp/RtmpbL8Yil/R.INSTALL1664f5019f4/Rhtslib/src/htslib-1.7'
Makevars.common:24: recipe for target 'htslib' failed
make[1]: *** [cram/cram_io.o] Error 1
make: *** [htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/home/thiago/R/x86_64-pc-linux-gnu-library/4.1/Rhtslib’
The downloaded source packages are in
‘/tmp/RtmpL0DYph/downloaded_packages’
Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages:
spatial
Warning message:
In .inet_warning(msg) :
installation of package ‘Rhtslib’ had non-zero exit status
What can I do in order to properly install the package?
EDIT: My OS is 10.15.4 and R is 4.0.0 and Xcode 11.4.1
I tried to install an archived package "OC" (Optimal Classification). I downloaded the file from here (oc_1.01.tar.gz) first and store it on my desktop. I have tried to install this through install.packages("oc_1.01.tar.gz", repo=NULL, type="source") or install_version("oc", version = "1.01", repos = "https://cran.r-project.org/") and it always failed with warnings as:
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [oc.so] Error 1
ERROR: compilation failed for package ‘oc’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/oc’
Error: Failed to install 'unknown package' from URL:
(converted from warning) installation of package ‘/var/folders/yv/gzy_ljk971d4jnlntnfvht_40000gn/T//Rtmpr8pJmf/remotes1e1745dfa9dc/oc’ had non-zero exit status
I have tried several solutions similar to this to download gcc or gcc#8 through Homebrew and made changes on the file Makeconf. However, as long as I made changes (even I restored the original codes), installation still fails and returns warnings as:
R clang: error: no such file or directory: 'SHLIB_LIBADD'
R clang: error: no such file or directory: '='
If I changed CC, CXX (including all CXX related such as CXX17), and FLIBS to gcc-8 or gcc-9, the returned warnings become:
R gcc-8: error: no such file or directory: 'SHLIB_LIBADD'
R gcc-8: error: no such file or directory: '='
I appreciate any help.
I've been trying to troubleshoot installation of rJava in R (3.4.2) on my Mac OS Sierra 10.12.6. I've followed the advice I've found about OpenMP issues (http://thecoatlessprofessor.com/programming/openmp-in-r-on-os-x/). The error I'm getting now, though, identifies the library not found as '-lomp' instead of '-fopenmp.' I'm not sure how to proceed from here.
Here's what it looks like when it hits the error:
ld: library not found for -lomp
clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [libjri.jnilib] Error 1
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/y_/0bm1vdx95dn4m8x_xtctp2gh0000gn/T/RtmpfslTnc/downloaded_packages’
I had the same issue, and fixed it by creating a link to the library (libomp.dylib) in a directory where it can be found (/usr/local/lib/), as explained here.
Take a look here for full description of how to compile most recent Java inside OSX.
Note that you need clang with omp support - it is not available directly from Apple: http://www.owsiak.org/r-3-4-rjava-macos-and-even-more-mess/
You need to:
get clang from llvm page
configure R to use JDK of your choice
compile rJava from sources
When trying to install the pcalg package, I am getting the following error:
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [pcalg.so] Error 1
ERROR: compilation failed for package ‘pcalg’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/pcalg’
The downloaded source packages are in
‘/private/var/folders/54/nwpr9hkn49b1m4h3hjmwph6r0000gn/T/RtmpREqD5T/downloaded_packages’
Warning message:
In install.packages("pcalg") :
installation of package ‘pcalg’ had non-zero exit status
I'm assuming this is because the gfortan package now in gcc, but I don't know how to point it to the right place. Does anybody know how to fix this?