I'm building release executables for RosettaCommons, I input to the terminal with the following code:
scons bin mode=release
And I got the following error:
scons: Reading SConscript files ...
Running versioning script ... Release package detected, using rosetta/main/.release.json to acquire version information...
Done. (0.0 seconds)
Number of option files updated: 0
Total 4580 options.
Finished updating ResidueProperty code
-- no changes needed
Finished updating VariantType code
-- no changes needed
scons: done reading SConscript files.
scons: Building targets ...
clang++ -o build/external/release/macos/10.16/64/x86/clang/12.0/default/libzlib.dylib -dynamiclib -install_name /Users/miotomato/Downloads/rosetta_bin_mac_2021.16.61629_bundle/main/source/build/external/release/macos/10.16/64/x86/clang/12.0/default/libzlib.dylib -stdlib=libc++ -Wl,-rpath=/Users/miotomato/Downloads/rosetta_bin_mac_2021.16.61629_bundle/main/source/build/external/release/macos/10.16/64/x86/clang/12.0/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/external/release/macos/10.16/64/x86/clang/12.0/default/dummy_zlib.os -Lexternal/lib -Lbuild/external/release/macos/10.16/64/x86/clang/12.0/default -Lexternal -L/usr/lib
ld: unknown option: -rpath=/Users/miotomato/Downloads/rosetta_bin_mac_2021.16.61629_bundle/main/source/build/external/release/macos/10.16/64/x86/clang/12.0/default
clang: error: linker command failed with exit code 1 (use -v to see invocation)
scons: *** [build/external/release/macos/10.16/64/x86/clang/12.0/default/libzlib.dylib] Error 1
scons: building terminated because of errors.
I list the version of each program:
macOS Monterey 12.0 Beta
Scons 4.2.0
Python 2.7.16
RosettaCommons 2021.16.61629
Related
I'm building a project from github (https://github.com/marsicoLab/PROmiRNA) and have the following requirements on my mac (Big Sur 11.4); gcc 9.4, cmake 3.21.1, R 4.1.0.
After using cmake, which runs without error, I use make however this gives me the below errors:
clang: error: unable to execute command: Segmentation fault: 11
clang: error: clang frontend command failed due to signal (use -v to see invocation)
Apple clang version 12.0.5 (clang-1205.0.22.9)
Target: x86_64-apple-darwin20.5.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
clang: note: diagnostic msg: Error generating preprocessed source(s).
make[2]: *** [CMakeFiles/PROmiRNA.dir/PROmiRNA.cpp.o] Error 254
make[1]: *** [CMakeFiles/PROmiRNA.dir/all] Error 2
make: *** [all] Error 2
A lot of other questions online with the same issue refer to XCode but I don't have it installed and am not a developer myself so don't think I need it..?
If anyone has any suggestions I'd really appreciate it, thanks :)
I'm trying to cross compiling ROS Melodic for aarch64 on raspberry pi 3 with toolchain that created by buildroot.
I followed the document http://wiki.ros.org/ROS/CrossCompiling/RaspberryPi/Cross-Compile%20ROS%20for%20the%20RaspberryPi, the source of ROS I try to build comes from:
rosinstall_generator ros_comm --rosdistro melodic --deps --tar > melodic-ros_comm.rosinstall
wstool init -j8 src melodic-ros_comm.rosinstall
And I got the error messages like these:
[100%] Linking CXX shared library /home/developer/ros_pi/ros_catkin_ws/devel_isolated/class_loader/lib/libclass_loader.so
/home/developer/buildroot-2020.02.1/output/host/lib/gcc/aarch64-buildroot-linux-gnu/8.4.0/../../../../aarch64-buildroot-linux-gnu/bin/ld: /home/developer/buildroot-2020.02.1/output/host/aarch64-buildroot-linux-gnu/sysroot/usr/lib/libboost_thread.so: error adding symbols: file in wrong format
collect2: error: ld returned 1 exit status
CMakeFiles/class_loader.dir/build.make:180: recipe for target '/home/developer/ros_pi/ros_catkin_ws/devel_isolated/class_loader/lib/libclass_loader.so' failed
make[2]: *** [/home/developer/ros_pi/ros_catkin_ws/devel_isolated/class_loader/lib/libclass_loader.so] Error 1
CMakeFiles/Makefile2:195: recipe for target 'CMakeFiles/class_loader.dir/all' failed
make[1]: *** [CMakeFiles/class_loader.dir/all] Error 2
Makefile:140: recipe for target 'all' failed
make: *** [all] Error 2
<== Failed to process package 'class_loader':
Command '['/home/developer/ros_pi/ros_catkin_ws/install_isolated/env.sh', 'make', '-j8', '-l8']' returned non-zero exit status 2
Reproduce this error by running:
==> cd /home/developer/ros_pi/ros_catkin_ws/build_isolated/class_loader && /home/developer/ros_pi/ros_catkin_ws/install_isolated/env.sh make -j8 -l8
Command failed, exiting.
This is my toolchain.cmake:
set(CMAKE_SYSTEM_NAME Linux)
set(CMAKE_SYSTEM_VERSION 1)
set(CMAKE_LIBRARY_ARCHITECTURE aarch64)
set( CMAKE_CXX_IMPLICIT_INCLUDE_DIRECTORIES "/home/developer/buildroot-2020.02.1/output/host/aarch64-buildroot-linux-gnu/sysroot/usr/include/")
set( CMAKE_C_COMPILER aarch64-linux-gcc)
set( CMAKE_CXX_COMPILER aarch64-linux-g++)
set(CMAKE_FIND_ROOT_PATH "/home/developer/buildroot-2020.02.1/output/host/aarch64-buildroot-linux-gnu/sysroot")
set(CMAKE_FIND_ROOT_PATH_MODE_PROGRAM NEVER)
set(CMAKE_FIND_ROOT_PATH_MODE_LIBRARY ONLY)
set(CMAKE_FIND_ROOT_PATH_MODE_INCLUDE ONLY)
include_directories(/home/developer/buildroot-2020.02.1/output/host/aarch64-buildroot-linux-gnu/sysroot/usr/include/)
I guess the problem comes from boost?
The version of boost which I used is 1.65.1
All the steps I tried is contained in Dockerfile as link as below:
https://github.com/i-am-neet/cc-ros/blob/master/Dockerfile
Thank you for your patience
When I try to build Artery on Ubuntu 16.04. the following happens after invoking
$ cmake --build /home/hardt/Veins/artery-master/build
[ 23%] Linking CXX shared library libartery.so
/usr/bin/ld: /usr/local/lib/libvanetza_btp.a(data_request.cpp.o): relocation R_X86_64_32 against `.bss' can not be used when making a shared
object; recompile with -fPIC
/usr/local/lib/libvanetza_btp.a: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
src/artery/CMakeFiles/artery.dir/build.make:954: recipe for target'src/artery/libartery.so' failed
make[2]: *** [src/artery/libartery.so] Error 1
CMakeFiles/Makefile2:229: recipe for target 'src/artery/CMakeFiles/artery.dir/all' failed
make[1]: *** [src/artery/CMakeFiles/artery.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2
As I am not all that familiar with building source on Unix systems I am not quite sure how to deal with this error.
I am using cmake version 3.9.3, boost 1.65.1 and crypto++ 5.6.4 the geographiclib built without error as well.
As one can read in the comments, the problem is solved.
The path to the vanetza directory VANETZA_DIR in the cmake configuration was wrong. Correcting this via ccmake solved the problem.
I am trying to build from the bigloo scheme's latest source 3.8a on a Linux Mint 12 (lisa), which is Ubuntu 11 (Oneric) derivative:
Here is my "configure":
./configure --enable-pthread --enable-fthread --enable-ssl --enable-sqlite --enable-web --enable-multimedia --enable-mail --enable-calendar --enable-pkgcomp --enable-pkglib --enable-gstreamer --enable-text --enable-srfi1 --enable-srfi27 --enable-crypto --enable-openpgp --enable-phone --enable-alsa --enable-mpg123 --enable-csv --jvm=yes
** Configuration summary **
Release features:
release number.............. 3.8a
supported backends.......... native:yes JVM:yes
default backend............. native
additional APIs............. pthread fthread sqlite web multimedia mail calendar pkgcomp pkglib text srfi1 srfi27 packrat crypto openpgp phone mpg123 csv
native threads support...... yes
openssl support............. no
sqlite support.............. sqltiny + sqlite
dynamic libraries support... yes
Bee configuration:
bee support................. partial
emacs....................... emacs
emacs brand................. emacs23
Implementation details:
tuning...................... standard
cc.......................... gcc
gc.......................... custom (bigloogc-3.8a, v731)
Java version................ 1.3
bignum support.............. gmp (5.0.1)
Directories where Bigloo will be installed:
binaries.................... /usr/local/bin
libraries................... /usr/local/lib
files directory............. bigloo/3.8a
standard zip................ /usr/local/lib/bigloo/3.8a
standard dll................ /usr/local/lib/bigloo/3.8a
manual pages................ /usr/local/man/man1
info documentation.......... /usr/local/info
lisp files..................
temporary build dir......... /tmp
The "make" succeeds; however "make test" fails for pthread
*** pthread **********
make[2]: Entering directory `/home/liew/Downloads/bigloo3.8a/api/pthread/recette'
/home/liew/Downloads/bigloo3.8a/bin/bigloo -c -call/cc -O3 -fcfa-arithmetic -q recette.scm -o recette.o
/home/liew/Downloads/bigloo3.8a/bin/bigloo -O3 -fcfa-arithmetic -q recette.o -o recette
/usr/bin/ld: recette: hidden symbol `pthread_atfork' in /usr/lib/i386-linux-gnu/libpthread_nonshared.a(pthread_atfork.oS) is referenced by DSO
/usr/bin/ld: final link failed: Bad value
collect2: ld returned 1 exit status
make[2]: *** [recette] Error 1
make[2]: Leaving directory `/home/liew/Downloads/bigloo3.8a/api/pthread/recette'
make[1]: *** [c-test] Error 1
make[1]: Leaving directory `/home/liew/Downloads/bigloo3.8a'
make: *** [test] Error 2
According to this excellent post about this pthread issue, we need to rearrange the command line parameters while linking pthread library. However, I was unable to find the required Makefile code - probably because it relies on the Makefile default that links the library in a certain way.
Any help will be appreciated.
The problem is probably fixed in newer versions of bigloo.
I'm trying to create a project as a shared library in OS X using CMake 2.8 and gcc 4.6 (from macports). When CMake gets to the point of linking my library into a .dylib, I get the following error from gcc:
g++ -dynamiclib -headerpad_max_install_names -o libmycoollibrary.dylib etc...
g++: error: unrecognized option '-h'
make[2]: *** [libnrtCore.dylib] Error 1
make[1]: *** [CMakeFiles/nrtCore.dir/all] Error 2
make: *** [all] Error 2
This -headerpad_max_install_names seems to be the problem, but I've never seen it before. Does anyone know how to either get CMake to not include this option, or to get GCC to accept this option?
You can re-build cmake to fix this -- it's apparently generating code for the XCode / Darwin version of g++ (a special version of 4.2), which accepts a number of non-standard linker flags.
Just change the Modules/Platform/Darwin*.cmake files and re-build. The culprit lines look like this:
SET(CMAKE_CXX_LINK_FLAGS "-Wl,-search_paths_first -headerpad_max_install_names")