Entering edit mode
4.3 years ago
leonmcswain
▴
10
I am running into some issues installing STAR aligner. I attempted to follow others solutions. Ive re-installed gcc thinking this was the issue while compiling but I am still getting an error:
leonfoymcswain@Leons-MBP ~ % cd ~/Desktop/Bio_Packages/STAR/source
leonfoymcswain@Leons-MBP source % make STARforMacStatic CXX=/usr/local/Cellar/gcc/8.2.0/bin/g++-8
/usr/local/Cellar/gcc/8.2.0/bin/g++-8 -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Mon Jul 20 22:06:48 EDT 2020 :/Users/leonfoymcswain/Desktop/Bio_Packages/STAR/source"' -D'COMPILE_FOR_MAC' -pipe -Wall -Wextra soloInputFeatureUMI.cpp
make: /usr/local/Cellar/gcc/8.2.0/bin/g++-8: No such file or directory
make: *** [soloInputFeatureUMI.o] Error 1
leonfoymcswain@Leons-MBP source % STAR
zsh: permission denied: STAR
leonfoymcswain@Leons-MBP source %
This was the second time I tried this so it doesn't show the entire output from the first attempt (looked like it basically finished compiling and then gave an error). Even if I set the PATH to the STAR unix executable file I still get permission denied. I have also tried sudo chmod to give permissions and again permission denied. Clearly a novice, any help would be great.
what do you get when you type
which g++-8on your machine? Also, where did you obtain the file? Did you get it from github? https://github.com/alexdobin/STARI've looked into the makefile in the github and see that it simply uses the g++ on your machine. So if your
which g++come back with something sensible, using the github version should work.When I type which g++ I get usr/bin/g++ if I type which g++-8 I don't get anything. I used git clone to clone STAR through the terminal onto a file on my desktop (running this on mac). When I check the path (I realize the way I've done it below is not efficient) I find the gcc version is 10.1.0 and I think I need version 8.2.0? How would I install a specific version of gcc? Assuming this needs to be done through homebrew.
leonfoymcswain@Leons-MBP gcc % ls 10.1.0 leonfoymcswain@Leons-MBP gcc % cd 10.1.0 leonfoymcswain@Leons-MBP 10.1.0 % cd bin leonfoymcswain@Leons-MBP bin % ls
c++-10 gfortran-10 cpp-10 lto-dump-10 g++-10 x86_64-apple-darwin19-c++-10 gcc-10 x86_64-apple-darwin19-g++-10 gcc-ar-10 x86_64-apple-darwin19-gcc-10 gcc-nm-10 x86_64-apple-darwin19-gcc-10.1.0 gcc-ranlib-10 x86_64-apple-darwin19-gcc-ar-10 gcov-10 x86_64-apple-darwin19-gcc-nm-10 gcov-dump-10 x86_64-apple-darwin19-gcc-ranlib-10 gcov-tool-10 x86_64-apple-darwin19-gfortran-10 gfortran leonfoymcswain@Leons-MBP bin %
I found a solution. I uninstalled all gcc compilers other than gcc@8 and then changed the make directory to match the gcc@8 and it worked.
This came at the end when compiling was finished and I am not sure if its significant or not.
Parameters_openReadsFiles.cpp: In member function 'void Parameters::openReadsFiles()': Parameters_openReadsFiles.cpp:25:20: warning: variable 'imate' might be clobbered by 'longjmp' or 'vfork' [-Wclobbered] for (uint imate=0;imate<readfilesnames.size();imate++) {="" open="" readin="" files="" ^~~~~<="" p="">
ld: warning: direct access in function 'operator new(unsigned long, std::nothrow_t const&) [clone .cold.0]' from file '/usr/local/Cellar/gcc@8/8.4.0_1/lib/gcc/8/gcc/x86_64-apple-darwin19/8.4.0/../../../libstdc++.a(new_opnt.o)' to global weak symbol 'operator new(unsigned long, std::nothrow_t const&)' from file '/usr/local/Cellar/gcc@8/8.4.0_1/lib/gcc/8/gcc/x86_64-apple-darwin19/8.4.0/../../../libstdc++.a(new_opnt.o)' means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
actually, using gcc 10.1.0 is ok, so you don't need to remove your gcc installation.
As for your last question. Maybe you can do a make clean or to clean the directory and redo the compilation. This should ensure that all your files are compiled by the same compiler. Should worth a try anyway.
How do I remove the compiled files to "clean"? When I delete the STAR file and reinstall followed by compiling it shows compiled files like the files were never deleted.
rm *.oin your build directory usually does the trick (unless there are some underlying structure)