Installing R 3.5.0 with --enable-R-shlib - r

I am trying to install R 3.5.0 from source with the flag --enable-R-shlib under Linux Mint. Configuring and installing it without the flag works fine, but RStudio requires the flag to be set. However, when running
./configure --enable-R-shlib
make
I get the error
/usr/bin/ld: CommandLineArgs.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
CommandLineArgs.o: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
Makefile:177: recipe for target 'libR.so' failed
make[3]: *** [libR.so] Error 1
make[3]: Leaving directory '/home/hps/Downloads/R-3.5.0/src/main'
Makefile:135: recipe for target 'R' failed
make[2]: *** [R] Error 2
make[2]: Leaving directory '/home/hps/Downloads/R-3.5.0/src/main'
Makefile:28: recipe for target 'R' failed
make[1]: *** [R] Error 1
make[1]: Leaving directory '/home/hps/Downloads/R-3.5.0/src'
Makefile:60: recipe for target 'R' failed
make: *** [R] Error 1
I tried setting the -fPIC flag as mentioned in the error message following the advice from [1]
CC="gcc -fPIC" ./configure --enable-R-shlib
to no avail, I still get the same error message.
[1] Passing a gcc flag through makefile

After adding these PPAs for Ubuntu, I was able to update R to 3.5.0 for my Linux Mint 17.3 Rosa.
sudo add-apt-repository ppa:marutter/rrutter3.5
sudo add-apt-repository ppa:marutter/c2d4u
sudo apt-get update
Ref: https://cran.r-project.org/bin/linux/ubuntu/
Edit: To compile from source, follow the suggestion here
sudo apt-get update
sudo apt-get build-dep r-base
wget https://cran.r-project.org/src/base/R-3/R-3.5.0.tar.gz
tar -xvf R-3.5.0.tar.gz
cd R-3.5.0
./configure --enable-R-shlib
make

Just in case someone else runs into this problem.
The issue is the object files ".o" are already compiled without the -fpic option.
The proper solution is to remove the object files from the first build and recomplile:
make clean
./configure --enable-R-shlib
make -j 4
sudo make install
The -j 4 tells make to spawn four compile processes at a time. Adjust the number to match the number of processor cores.

Related

recipe for target 'runtime_ccall.o' failed in installing julia (llvm?)

I just downloaded and installed the latest version of linux mint, mate. I want to install julia again but I get an strange error during the installation of v1.3.0
(... lots of output)
/home/usr/julia/usr/include/llvm/Support/MathExtras.h:545:38: required from here
/home/usr/julia/usr/include/llvm/Support/MathExtras.h:189:16: error: ‘static_assert’ was not declared in this scope
Makefile:165: recipe for target 'runtime_ccall.o' failed
make[1]: *** [runtime_ccall.o] Error 1
Makefile:75: recipe for target 'julia-src-release' failed
make: *** [julia-src-release] Error 2
This is somehow strange, but it appears to be related to LLVM. In trying to update LLVM I typed
sudo apt-get update -y
sudo apt-get install -y llvm
But the error keeps showing... any idea what am I missing?

R: Compiling issue

I want to compile the R source code on my own.
In order to this, I have installed all the required packages and two more with these commands
sudo apt-get build-dep r-recommended
sudo apt install libicu-dev gobjc-5
Then, I run the usual commands to configure with two additional options
./configure --enable-R-shlib --with-ICU
Until now everything ok, but when I tried to compile with the make command and at a certain point I got these error messages
make[2]: Entering directory '/home/myuser/Downloads/R-3.2.3/src/library/Recommended'
begin installing recommended package MASS
Error in untar2(tarfile, files, list, exdir, restore_times) :
incomplete block on file
Makefile:51: recipe for target 'MASS.ts' failed
make[2]: *** [MASS.ts] Error 1
make[2]: Leaving directory '/home/myuser/Downloads/R-3.2.3/src/library/Recommended'
Makefile:39: recipe for target 'recommended-packages' failed
make[1]: *** [recommended-packages] Error 2
make[1]: Leaving directory '/home/myuser/Downloads/R-3.2.3/src/library/Recommended'
Makefile:77: recipe for target 'stamp-recommended' failed
make: *** [stamp-recommended] Error 2
I have searched online but I haven't been able to figure it out what causes that error.
Thanks in advance.
OS: Ubuntu 15.10 64bit
Briefly:
You probably need apt-get build-dep r-base to get build-dependencies, not apt-get build-dep r-recommended
Your error is from also trying to build recommended packages for which you need an additional download step as explained in the documention
So add --without-recommended-packages to the configure call.

/usr/bin/ld: cannot find -lXmu

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

WKHTMLTOPDF with Patched QT Ubuntu 14.04 Errors during compiling

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!

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I try to install SimpleDB::Class from cpan as sudo cpan SimpleDB::Class. it needs a dependency Memcached::libmemcached. so i try to install it, but it have the following errors.
CCLD clients/memstat
CC tests/atomsmasher.o
CCLD tests/atomsmasher
CXX tests/tests_hashplus-hash_plus.o
./config/depcomp: line 611: exec: g++: not found
make[2]: *** [tests/tests_hashplus-hash_plus.o] Error 127
make[2]: Leaving directory `/home/vanitha/.cpan/build/Memcached-libmemcached-0.4406- Oq4Z_m/src/libmemcached'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/vanitha/.cpan/build/Memcached-libmemcached-0.4406- Oq4Z_m/src/libmemcached'
make: *** [install] Error 2
Unable to build libmemcached: Error running cd src/libmemcached && make install
Aborted.
No 'Makefile' created TIMB/Memcached-libmemcached-0.4406.tar.gz
/usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK
Running make test
Make had some problems, won't test
Running make install
Make had some problems, won't install
could not read metadata file. Falling back to other methods to determine prerequisites
exec: g++: not found - this is the error
Try this first of all: sudo apt-get install g++

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