Hey I have seen the following two questions here:
Install Rmpi on Centos fails with "can't find -lmpi"
Installing Rmpi on LAM/MPI cluster
But they don't provide any concrete answer to the problem.
The following is some pertinent information:
R> system('echo "$LD_LIBRARY_PATH"')
/usr/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/java/packages/lib/amd64:/lib:/usr/lib:/usr/lib64/openmpi/lib
R> install.packages("Rmpi", configure.args="--with-Rmpi-include=/usr/include/openmpi-x86_64 --with-Rmpi-libpath=/usr/lib64/openmpi --with-Rmpi-type=OPENMPI")
This is the last part of the error message:
gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib64/openmpi -lmpi -L/usr/lib64/R/lib -lR
/usr/bin/ld: cannot find -lmpi
collect2: ld returned 1 exit status
make: *** [Rmpi.so] Error 1
Any help will be great. Thanks.
After installing openmpi-devel,
I see libmpi.so in /usr/lib64/openmpi/lib/.
$ sudo yum install openmpi-devel
$ sudo updatedb
$ locate libmpi.so
/usr/lib64/openmpi/lib/libmpi.so
/usr/lib64/openmpi/lib/libmpi.so.1
/usr/lib64/openmpi/lib/libmpi.so.1.0.2
The following should work:
install.packages(
"Rmpi",
configure.args = paste(
"--with-Rmpi-include=/usr/include/openmpi-x86_64",
"--with-Rmpi-libpath=/usr/lib64/openmpi/lib",
"--with-Rmpi-type=OPENMPI"
)
)
If may be necessary to tell the system to look for shared libraries in this directory, as well:
# echo "/usr/lib64/openmpi/lib" > /etc/ld.so.conf.d/openmpi.conf
# ldconfig
Related
I am trying to install RJulia package on windows:
Julia Version: 0.4
R Version: 3.2.1
RStudio Version: 0.99.467
You may find the relevant R code:
library(devtools)
Sys.setenv(JULIA_SRC="C:/Users/user/AppData/Local/Julia-0.4.0-rc1")
Sys.setenv(LD_LIBRARY_PATH=":/Users/user/AppData/Local/Julia-0.4.0-rc1/lib/julia")
devtools::install_github("armgong/RJulia", ref="0.4")# or ref="0.4" if using Julia v0.4
but I am getting the following error:
julia: not found
julia: not found
gcc -m32 -I"C:/PROGRA~1/R/R-32~1.1/include" -DNDEBUG -I/../../src -I/../../src/support -I/../include -I/../include/julia -D_WIN32_WINNT=0x0600 -I"d:/RCompile/r-compiling/local/local320/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Julia_R.c -o Julia_R.o
Julia_R.c:13:19: fatal error: julia.h: No such file or directory
compilation terminated.
make: *** [Julia_R.o] Error 1
Warning: running command 'make -f "Makevars.win" -f "C:/PROGRA~1/R/R-32~1.1/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-32~1.1/share/make/winshlib.mk" SHLIB="rjulia.dll" OBJECTS="Julia_R.o R_Julia.o dataframe.o embedding.o"' had status 2
ERROR: compilation failed for package 'rjulia'
Any advice is appreciated!
I re-installed the latest version of RStudio 0.99.484 and re-configured the system PATH following #rawr advice (I had two installation paths of julia v.0.4 and v.0.3.11 and I kept the stable version) and it seems to work.
I want to install netgen and try to compile the source code.
During this I got the error message:
U -L/usr/lib/x86_64-linux-gnu -ltk8.6 -ltcl8.6 -lGL -lXmu -lX11 -fopenmp -Wl,-rpath -Wl,/opt/netgen/lib
/usr/bin/ld: cannot find -lXmu
collect2: error: ld returned 1 exit status
make[2]: *** [netgen] Error 1
Maybe I have to install an additional package?
Does anyone have an idea?
You can check, depending on your specific OS, if you are not missing the missing the non-versioned named (i.e. libXmu.so).
Check for ls /usr/lib/libXmu*.*, and if not found, type:
ln -s /usr/lib/libXmu.so libXmu.so.6
ln -s /usr/lib/libXuu.so libXmuu.so.1
If you don't have any libXmu*.* files, then you need to install first libxmu-dev:
sudo apt-get install libxmu-dev
I am trying to compile the wkhtmltopdf with patched qt using these instructions and when i get to the make && make install it gives me an error has anyone else done this on Ubuntu 14.04? I can't figure out what to do from here.
these are the instructions i am following i know they are not for 14.04 but i hoped they would have worked https://gist.github.com/Zauberfisch/8773593
This is the error i get:
cd src/lib/ && make -f Makefile make[1]: Entering directory /temp/wkhtmltopdf/src/lib' rm -f libwkhtmltox.so.0.12.1 libwkhtmltox.so libwkhtmltox.so.0 libwkhtmltox.so.0.12 g++ -Wl,-O1 -Wl,-rpath,/temp/wkqt/lib -shared -Wl,-soname,libwkhtmltox.so.0 -o libwkhtmltox.so.0.12.1 ../../build/loadsettings.o ../../build/multipageloader.o ../../build/tempfile.o ../../build/converter.o ../../build/websettings.o ../../build/reflect.o ../../build/utilities.o ../../build/pdfsettings.o ../../build/pdfconverter.o ../../build/outline.o ../../build/tocstylesheet.o ../../build/imagesettings.o ../../build/imageconverter.o ../../build/pdf_c_bindings.o ../../build/image_c_bindings.o ../../build/moc_multipageloader_p.o ../../build/moc_converter_p.o ../../build/moc_pdfconverter_p.o ../../build/moc_imageconverter_p.o ../../build/moc_pdf_c_bindings_p.o ../../build/moc_image_c_bindings_p.o ../../build/moc_converter.o ../../build/moc_multipageloader.o ../../build/moc_utilities.o ../../build/moc_pdfconverter.o ../../build/moc_imageconverter.o ../../build/qrc_wkhtmltopdf.o -L/temp/wkqt/lib -lQtWebKit -lQtSvg -L/temp/wkqt/lib -L/usr/X11R6/lib -lQtXmlPatterns -lQtGui -lQtNetwork -lQtCore -lpthread /usr/bin/ld: ../../build/qrc_wkhtmltopdf.o: relocation R_X86_64_32 against.rodata' can not be used when making a shared object; recompile with -fPIC ../../build/qrc_wkhtmltopdf.o: error adding symbols: Bad value collect2: error: ld returned 1 exit status make[1]: * [../../bin/libwkhtmltox.so.0.12.1] Error 1 make[1]: Leaving directory `/temp/wkhtmltopdf/src/lib' make: * [sub-src-lib-make_default-ordered] Error 2
I downloaded a binary from their site that already had the QT build and that fixed the issue for me. Thanks!
I cannot get Rcpp to work on Windows 8.1. When I run the following minimal example, I get an error.
> library(Rcpp)
> evalCpp("1 + 1")
g++ -m64 -I"C:/R/R-31~1.0/include" -DNDEBUG -I"C:/R/R-3.1.0/library/Rcpp/include" -
I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c file11dc2120723d.cpp -o
file11dc2120723d.o g++: not found make: *** [file11dc2120723d.o] Error 127 Warning message: running
command 'make -f "C:/R/R-31~1.0/etc/x64/Makeconf" -f "C:/R/R-31~1.0/share/make/winshlib.mk"
SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="sourceCpp_97232.dll" WIN=64 TCLBIN=64
OBJECTS="file11dc2120723d.o"' had status 2
Error in sourceCpp(code = code, env = env, rebuild = rebuild, showOutput = showOutput, :
Error 1 occurred building shared library.
The two first entries in my path are:
PATH=c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;
R is installed in a directory C:\R\R-3.1.0
Rtools is in the directory C:\R\Rtools
Some additional information:
> library(devtools)
> find_rtools(T)
Scanning path...
ls : c:\Rtools\bin\ls.exe
Scanning registry...
Found c:/Rtools for 3.1
VERSION.txt
Rtools version 3.1.0.1942
[1] TRUE
> has_devel()
"C:/R/R-31~1.0/bin/x64/R" --vanilla CMD SHLIB foo.c
gcc -m64 -I"C:/R/R-31~1.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include"
O2 -Wall -std=gnu99 -mtune=core2 -c foo.c -o foo.o
gcc: not found
make: *** [foo.o] Error 127
Warning message:
running command 'make -f "C:/R/R-31~1.0/etc/x64/Makeconf" -f "C:/R/R-31~1.0/share/make/winshlib.mk"
SHLIB="foo.dll" WIN=64 TCLBIN=64 OBJECTS="foo.o"' had status 2
Error: Command failed (1)
> system('g++ -v')
Warning message:
running command 'g++ -v' had status 127
Unsure if you have solved your problem but it appears you don't have gcc or g++ installed. For windows you can get these tools with MinGW.
Install MinGW which you can donwload from here. The homepage for information is here
Once you have it installed MinGW, you can open the 'MinGW Installation Manager' and install the bin and dev for 'mingw32-gcc-g++'.
You must then update your PATH environmental variable to include 'C:\MinGW\bin' and 'C:\MinGW\msys\1.0\bin'.
Restart your R session, couldn't hurt to also reinstall 'Rcpp', and tryrequire(Rcpp); evalCpp("1 + 1") again.
I had this problem while trying to call C-code directly. Switching from the function system() to system2() solved it immediately.
I got that fix by installing RTools and adding RBuildTools to the path:
Sys.setenv("PATH" = paste(Sys.getenv("PATH"),
"C:\\RBuildTools\\3.4\\bin",
"C:\\RBuildTools\\3.4\\mingw_32",
"C:\\RBuildTools\\3.4\\mingw_64", sep = ";"))
I don't understand these things clearly but #cdeterman solutions was not working for building my package while its example evalCpp("1 + 1") did.
I am unable to build sqlcipher on Windows with following these steps.
install Win32 OpenSSL v0.9.8m
install TclTk
rename MINGWPATH/bin/tclsh84.exe to tclsh.exe
cd sqlcipher
$ ./configure --disable-tcl --disable-amalgamation
CFLAGS="-DSQLITE_HAS_CODEC -I../OpenSSL/include /c/Windows/System32/libeay32.dll"
$ make
$ make dll
$ make install
At the link stage, gcc gives this error:
libtool: link: gcc -g -O2 -DSQLITE_OS_WIN=1 -I. -I./src -I./ext/rtree -D_HAVE_SQ
LITE_CONFIG_H -DBUILD_sqlite -DNDEBUG -DSQLITE_THREADSAFE=1 -DSQLITE_OMIT_LOAD_E
XTENSION=1 -DHAVE_READLINE=0 -o .libs/sqlite3.exe ./src/shell.c ./.libs/libsqli
te3.a -lpthread -L/usr/local/lib
./.libs/libsqlite3.a(func.o): In function `sqlite3RegisterBuiltinFunctions':
c:\sqlcipher/./src/func.c:1439: **undefined reference to `sqlcipher_exportFunc**'
collect2: ld çıkış durumu 1 ile döndü
make: *** [sqlite3.exe] Error 1
You forget to define SQLITE_TEMP_STORE as document has specified.
I can confirm it's working smoothly on Ubuntu 12.04 LTS , with latest source on github:
In short for dynamic linking:
./configure --enable-tempstore=yes CFLAGS="-DSQLITE_HAS_CODEC -DSQLITE_TEMP_STORE=2" LDFLAGS="-lcrypto"