I want to compile hsphase package (R package available in CRAN).
I used this command in R install.packages("hsphase").
I have got the following errors:
g++ -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o hsphase.so FastDist.o MAF.o Ohd.o TypeConversion.o block.o block4Phase.o co.o diag.o hsp.o main.o memory.o oh.o swDetect.o [1] 0 -L/usr/lib64/R/lib -lRlapack -L/usr/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/usr/lib64/R/lib -lR
g++: error: [1]: No such file or directory
g++: error: 0: No such file or directory
/usr/share/R/make/shlib.mk:6: recipe for target 'hsphase.so' failed
make: *** [hsphase.so] Error 1
ERROR: compilation failed for package ‘hsphase’
* removing ‘/home/mhf/R/x86_64-redhat-linux-gnu-library/3.3/hsphase’
The downloaded source packages are in
‘/tmp/RtmpYukJQa/downloaded_packages’
Warning message:
In install.packages("hsphase") :
installation of package ‘hsphase’ had non-zero exit status
I am using fedora 24.
The g++ version:
gcc version 6.1.1 20160621 (Red Hat 6.1.1-3) (GCC)
Please check the link flag:
what is this:
[1] 0
I comment this line in the scr/Makevars file:
#PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS)
Now, I can compile the package.
Related
This is likely an error installing PCRE2 (which I did using "sudo port install pcre2"), but when I "make" sample code for RInside, I get:
$ make rinside_sample0
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include -I/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RInside/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include rinside_sample0.cpp -L/usr/local/lib -F/Library/Frameworks/R.framework/.. -framework R -L/usr/local/lib -lpcre2-8 -llzma -lbz2 -lz -licucore -ldl -lm -liconv -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RInside/lib/libRInside.a -o rinside_sample0
In file included from rinside_sample0.cpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RInside/include/RInside.h:26:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RInside/include/RInsideCommon.h:38:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data'
[-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
ld: library not found for -lpcre2-8
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [rinside_sample0] Error 1
$
Thank you for the comment, Dirk. You got me pointed in the correct direction. I had two old versions of code: pcre2 and Rcpp.
I followed the directions for installing the latest version of "pcre2" here: https://izziswift.com/how-to-install-pcre-development-headers-on-mac-osx/.
I downloaded "pcre" version 10.39, cd'd to that directory, ran:
./configure
make
make install
After that, the examples in RInside compiled, but I got a runtime error:
$ ./rinside_sample0
Error: function 'Rcpp_precious_remove' not provided by package 'Rcpp'
Execution halted
$
Some searching showed that error arose from running an older version (1.0.6) of "Rcpp". I went into RStudio, typed "install.packages("Rcpp")" to update to version 1.0.7 and now everything runs!
Hopefully going through these steps will help anyone else who encounters these problems.
I'm new on R version 3.6.3 (2020-02-29). I'm working on a Linux Mint 19.3 Tricia. I tried to install the package statmod with this code line:
install.package("statmod")
When I compiled this line R return this error:
error:
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o statmod.so gaussq2.o init.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld : ne peut trouver -lgfortran
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'statmod.so' failed
make: *** [statmod.so] Error 1
ERROR: compilation failed for package ‘statmod’
* removing ‘/home/etudiant/R/x86_64-pc-linux-gnu-library/3.6/statmod’
Warning in install.packages :
installation of package ‘statmod’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp8yGctp/downloaded_packages’
More informations:
gfortran compile basic function and when I wrote gfortran -v in my terminal, I got this answer :
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 7.5.0-3ubuntu1~18.04' --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-7 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04)
I don't know how to solve this error. If someone has an idea that can really help me.
Thank you very much by advance.
I am attempting to install rJava on Suse SLES 12. I have installed JDK 7 (7u51), fixed my JAVA_HOME, run sudo R CMD javareconf and installed the package suggested here: rJava won't install on openSUSE 13.2.
gcc -std=gnu99 -o libjri.so Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o -shared -L/usr/java/jdk1.7.0_51/jre/lib/amd64/server -ljvm -Wl,--export-dynamic -fopenmp -L/usr/lib64/R/lib -lR -lpcre -llzma -lz -lrt -ldl -lm -licuuc -licui18n
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lpcre
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -llzma
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status
Makefile.all:38: recipe for target 'libjri.so' failed
make[2]: *** [libjri.so] Error 1
make[2]: Leaving directory '/tmp/RtmptpO8Z9/R.INSTALL7e795f7a8704/rJava/jri/src'
Makefile.all:21: recipe for target 'src/JRI.jar' failed
make[1]: *** [src/JRI.jar] Error 2
make[1]: Leaving directory '/tmp/RtmptpO8Z9/R.INSTALL7e795f7a8704/rJava/jri'
Makevars:14: recipe for target 'jri' failed
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’
* removing ‘/opt/node_apps/acas-2016-02-03-13-07-09/r_libs/rJava’
I have attempted to update zypper install libpcre1 and zypper install liblzma5, but updating them did not change the error message.
I know that on Ubuntu there is a liblzma-dev that could help (https://github.com/s-u/rJava/issues/8), but I can't find a similar package for Suse.
Does anyone know what I am missing?
Please install the following RPM packages
xz-devel
pcre-devel
pcre-devel-static
zlib-devel
and try again. I'm not quite sure right now, but if that didn't help, please make sure that these packages are installed aswell:
xz
libpcre1
liblzma5
I am trying to install RCurl in R 3.2.0 in RHEL 5.
install.packages("RCurl")
At the end it failed because
gcc -std=gnu99 -shared -L/home/gowthan/Downloads/R-3.2.0/lib -L/usr/local/lib64 -o RCurl.so base64.o curl.o curlInit.o curl_base64.o enums.o json.o memoryManagement.o myUTF8.o -L/local/p4clients/pkgbuild-5R4zB/workspace/build/Curl/Curl-7.18.1.155.6782/RHEL5_64/DEV.STD.PTHREAD/build/private/curl/install/lib -lcurl -L/opt/brazil-pkg-cache/packages/Fbopenssl/Fbopenssl-0.0.4.504.7765/RHEL5_64/DEV.STD.PTHREAD/build/lib -lfbopenssl -L/local/p4clients/pkgbuild-5R4zB/workspace/build/Curl/Curl-7.18.1.155.6782/RHEL5_64/DEV.STD.PTHREAD/build/private/tmp/brazil-path/[Openssl]lib.libfarm/lib -L/local/p4clients/pkgbuild-k5Vrj/workspace/build/Libxml2/Libxml2-2.7.8.334.176/RHEL5_64/DEV.STD.PTHREAD/build/private/libxml2/install/lib -lxml2 -lz -lm -L/home/gowthan/Downloads/R-3.2.0/lib -lR
/usr/bin/ld: cannot find -lfbopenssl
collect2: ld returned 1 exit status
make: *** [RCurl.so] Error 1
ERROR: compilation failed for package \u2018RCurl\u2019
The line it fails is : /usr/bin/ld: cannot find -lfbopenssl. But, I have openssl at /usr/bin/openssl. How do I make 'ld' use it?
Regarding openssl-devel, yum install openssl-devel says that I already have the latest package. But "where openssl-devel" says that its not found! Is something wrong here?
Is fbopenssl same as openssl?
I am having problems installing the Package packfor form source in Mac OS X Yosemite in the R software. I know that the package depends on fortran compiler, so I installed the gfortran available in CRAN but it does not affect anything. Bellow I am reproducing the error log.
please if anyone has any advice on this would be much appreciated.
Thanks in advance
install.packages("~/Downloads/packfor_0.0-8.tar", repos =
NULL,type="source")
installing source package ‘packfor’ ...
** libs clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c forward.c -o forward.o forward.c:411:3: warning: implicit declaration of function 'dgesvd_' is invalid in C99 [-Wimplicit-function-declaration]
F77_CALL(dgesvd)(&jobu, &jobvt,&size, &size,A, &size,
D,U,&size,V,&size,&work1, &lwork,&error); ^
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:82:22:
note: expanded from macro 'F77_CALL'
define F77_CALL(x) x ## _
^ :8:1: note: expanded from here dgesvd_ ^ forward.c:421:43: warning: data argument not used by
format string [-Wformat-extra-args]
fprintf(stderr, "error in dinvG: ", error);
~~~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Resources/include/R_ext/Error.h:51:15:
note: expanded from macro 'error'
define error Rf_error
^ 2 warnings generated. clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o packfor.so forward.o -L/Library/Frameworks/R.framework/Resources/lib
-lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation Warning message: In install.packages("~/Downloads/packfor_0.0-8.tar", repos = NULL, :
installation of package ‘/Users/rafael/Downloads/packfor_0.0-8.tar’
had non-zero exit status ld: warning: directory not found for option
'-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2' ld: library not
found for -lquadmath clang: error: linker command failed with exit
code 1 (use -v to see invocation) make: *** [packfor.so] Error 1
ERROR: compilation failed for package ‘packfor’
* removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/packfor’
>