installation problem

[yefanglee]

Hi, I met an issue when I installed package. I run the code perl install.pl, but when installed ViennaRNA-1.8.4, errors were as follows:

make: *** [Makefile:239: all] Error 2
/usr/bin/ld: ../lib/libRNA.a(libRNA_a-subopt.o):(.bss+0xfa8): multiple definition of `Fc'; ../lib/libRNA.a(libRNA_a-fold.o):(.bss+0x10): first defined here
/usr/bin/ld: ../lib/libRNA.a(libRNA_a-subopt.o):(.bss+0xfac): multiple definition of `FcH'; ../lib/libRNA.a(libRNA_a-fold.o):(.bss+0x14): first defined here
/usr/bin/ld: ../lib/libRNA.a(libRNA_a-subopt.o):(.bss+0xfb0): multiple definition of `FcI'; ../lib/libRNA.a(libRNA_a-fold.o):(.bss+0x18): first defined here
/usr/bin/ld: ../lib/libRNA.a(libRNA_a-subopt.o):(.bss+0xfb4): multiple definition of `FcM'; ../lib/libRNA.a(libRNA_a-fold.o):(.bss+0x1c): first defined here
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:355: RNAsubopt] Error 1
make: *** [Makefile:323: install-recursive] Error 1

Can anyone give me some suggestion to solve it? Thank you!

[mschilli87]

@yefanglee: How are you trying to install miRDeep2? Which version are you trying to install? On what operating sytem are you? Where did you download miRDeep2 from? What commands have been running to install miRDeep2 that made you run into this error?

[yefanglee]

@yefanglee: How are you trying to install miRDeep2? Which version are you trying to install? On what operating sytem are you? Where did you download miRDeep2 from? What commands have been running to install miRDeep2 that made you run into this error?

Thanks for your reply. I tried to install miRDeep2 v0.1.3 downloaded from github. And the ViennaRNA v1.8.4 was downloaded automatically but it showed that RNAfold was not installed successfully. My operating system is Rocky Linux 9.2 and gcc version is 11.3.1. I run the code source ~/.bashrc, followed by perl install.pl, and then this error was written in install_error.log.

[mschilli87]

@yefanglee: Thank you for providing the information.

---

@Drmirdeep: Any idea? I could try a fresh install on the weekend if that helps.

[Drmirdeep]

I am getting actually different compiler errors for RNAfold. Seems like something has changed. What is your output of

gcc --version

[Drmirdeep]

As a current workaround please try to install the latest ViennaRNA package manually

[yefanglee]

As a current workaround please try to install the latest ViennaRNA package manually

Thank you for your reply. I have installed ViennaRNA v2.6 on the weekend and it worked:)

[Drmirdeep]

Great. I also did a bit of debugging on the ViennaRNA code.

I could get rid of the errors by deleting the files libRNA_a-subopt.o libRNA_a-fold.o in ViennaRNA-1.8.4/lib

( seems like during the compile phase something is not properly build for those object files )

and just reran make