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Mesh89 / TranSurVeyor

A transposition caller.
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undefined reference to `sam_index_build' on make #1

Closed Beherith closed 5 years ago

Beherith commented 5 years ago

/TranSurVeyor/cmake-3.12.3-Linux-x86_64/bin/cmake . && make -- Configuring done -- Generating done -- Build files have been written to: /home/[redacted]/TranSurVeyor [ 6%] Linking CXX executable filter CMakeFiles/filter.dir/filter.cpp.o: In function open_samFile(char const*, bool)': filter.cpp:(.text+0x1f3c): undefined reference tosam_index_build' collect2: error: ld returned 1 exit status make[2]: [filter] Error 1 make[1]: [CMakeFiles/filter.dir/all] Error 2 make: *** [all] Error 2

Beherith commented 5 years ago

On another, also ubuntu 16.04 machine, I get the following error on cmake ., after successful compilation of build_htslib script

CMake Error: The following variables are used in this project, but they are set to NOTFOUND. Please set them or make sure they are set and tested correctly in the CMake files: HTS_LIB linked by target "filter" in directory /home/speter/oe_pgs/TranSurVeyor linked by target "add_filtering_info" in directory /home/speter/oe_pgs/TranSurVeyor linked by target "reads_categorizer" in directory /home/speter/oe_pgs/TranSurVeyor linked by target "clip_consensus_builder" in directory /home/speter/oe_pgs/TranSurVeyor linked by target "sc_categorizer" in directory /home/speter/oe_pgs/TranSurVeyor linked by target "dc_remapper" in directory /home/speter/oe_pgs/TranSurVeyor

-- Configuring incomplete, errors occurred! See also "/home/speter/oe_pgs/TranSurVeyor/CMakeFiles/CMakeOutput.log".

Mesh89 commented 5 years ago

Hi,

I updated CMakeLists.txt.

Can you try building again from scratch using the new file?

Beherith commented 5 years ago

Thanks, it now builds fine on the machine with native cmake.