Compilation error on Ubuntu

[SzilviaKiriakov]

Hi, Thank you for the great software, I quite like ControlFREEC, especially for its easy to use and understand output.

While trying to install it on Ubuntu 18.04.6 LTS using the latest release (FREEC-11.6), I faced an issue. After unzipping the archive, I tried to run make inside the /src directory. This is the output I get even if I run make clean before running make:

make -f Makefile.freec init make[1]: Entering directory 'FREEC-11.6/src' make[1]: Nothing to be done for 'init'. make[1]: Leaving directory 'FREEC-11.6/src' make -f Makefile.freec depend make[1]: Entering directory 'FREEC-11.6/src' make[1]: Leaving directory 'FREEC-11.6/src' make -f Makefile.freec all make[1]: Entering directory 'FREEC-11.6/src' g++ -m64 -O3 -g -o freec main.o ConfigFile.o Chameleon.o GenomeDensity.o Help.o myFunc.o KernelVector.o ChrDensity.o ChrCopyNumber.o GenomeCopyNumber.o chisquaredistr.o ap.o igammaf.o gammafunc.o normaldistr.o ablasf.o ablas.o ortfac.o sblas.o rotations.o reflections.o linreg.o hblas.o descriptivestatistics.o creflections.o blas.o bdsvd.o svd.o ialglib.o EntryCNV.o SNPinGenome.o SNPatChr.o SNPposition.o binomialdistr.o ibetaf.o ThreadPool.o BAFpileup.o SeekSubclones.o -lpthread /usr/bin/ld: main.o: unable to initialize decompress status for section .debug_info /usr/bin/ld: main.o: unable to initialize decompress status for section .debug_info /usr/bin/ld: main.o: unable to initialize decompress status for section .debug_info /usr/bin/ld: main.o: unable to initialize decompress status for section .debug_info main.o: file not recognized: File format not recognized collect2: error: ld returned 1 exit status make[1]: [Makefile.freec:31: freec] Error 1 make[1]: Leaving directory 'FREEC-11.6/src' make: [Makefile:17: all] Error 2

Do you have any recommendations on how to install it on Ubuntu?

[valeu]

I have never seen such an issue. Usually with any Linux OS things are quite smooth.. Did you google the error?

[SzilviaKiriakov]

I did google the error, the solution for

main.o: file not recognized: File format not recognized

is make clean which doesn't work for FREEC-11.6.

[valeu]

Dear Szilvia, did you solve the issue? Can you compile any other C++ program?

[SzilviaKiriakov]

Dear Professor Boeva,

ControlFREEC installation issue is still unsolved. I can compile other C++ programs (test and production code as well) without any problems.

Let me know if you have any suggestions for ControlFREEC. Thank you, Szilvia

[SzilviaKiriakov]

Update: FREEC can be compiled if conda is deactivated. Once compiled, it runs within the active conda environment fine.

[yifanhu1]

Update: FREEC can be compiled if conda is deactivated. Once compiled, it runs within the active conda environment fine.

My problem solved.