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grenaud / schmutzi

Maximum a posteriori estimate of contamination for ancient samples
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Schmutzi compilation issue #14

Closed ywakiyama closed 3 years ago

ywakiyama commented 3 years ago

Hello, I'm trying to install schmutzi and I am getting the following error:

make -C src/ /usr/bin/g++ -o endoCaller ../lib/libgab//libgab.a ../lib/libgab//ReconsReferenceBAM.o endoCaller.o miscfunc.o ../lib/libgab/gzstream/libgzstream.a ../lib/bamtools//build/src/utils/CMakeFiles/BamTools-utils.dir/*cpp.o ../lib/bamtools//build/src/api/libbamtools.a -lpthread -lm -lz ld: archive has no table of contents file '../lib/libgab//libgab.a' for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make[1]: *** [endoCaller] Error 1 make: *** [src/endoCaller] Error 2

Could you please help me to fix this issue?

Thank you, Yoshiki

grenaud commented 3 years ago

Dear Yoshiki, Thank you for your interest in our method! Can you try going in the root directory and do: rm -rfv lib/bamtools/* rm -rfv lib/libgab/* make can you also temm me your OS+CPU type? please do a uname -a and lsb_release -a

ywakiyama commented 3 years ago

Thank you for your quick response. After removing bamtools and libgab, the installation went well! test running went well, too.

OS+CPU type is here. (base) yoshikiwakiyama@Yoshikis-MacBook-Pro ~ % uname -a Darwin Yoshikis-MacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64 (base) yoshikiwakiyama@Yoshikis-MacBook-Pro ~ % sw_vers ProductName: Mac OS X ProductVersion: 10.15.7 BuildVersion: 19H2

Thank you.

grenaud commented 3 years ago

perfect! can I close the issue?

On Tue, Mar 9, 2021 at 6:35 PM ywakiyama notifications@github.com wrote:

Thank you for your quick response. After removing bamtools and libgab, the installation went well! test running went well, too.

OS+CPU type is here. (base) yoshikiwakiyama@Yoshikis-MacBook-Pro ~ % uname -a Darwin Yoshikis-MacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64 (base) yoshikiwakiyama@Yoshikis-MacBook-Pro ~ % sw_vers ProductName: Mac OS X ProductVersion: 10.15.7 BuildVersion: 19H2

Thank you.

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ywakiyama commented 3 years ago

Yes!