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SpatialTranscriptomicsResearch / st_pipeline

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.
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"cdistance.o" missing when building pipeline #113

Closed fatimasnc closed 3 years ago

fatimasnc commented 4 years ago

Hi!

I am trying to install the ST pipeline and when I type the "python setup.py build" command I get the following error:

"gcc -pthread -B /home/sfatima/miniconda3/envs/ST/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/sfatima/miniconda3/envs/ST/include/python3.7m -c stpipeline/common/cdistance.c -o build/temp.linux-x86_64-3.7/stpipeline/common/cdistance.o gcc: error: stpipeline/common/cdistance.c: No such file or directory error: command 'gcc' failed with exit status 1"

I tried to find such file and could only come across "cdistance.pyx" in that location. Could it be that "cdistance.c" is accidentally missing after some update? I checked the GitHub repository itself and it's also not there.

Thanks a lot for your help!

Best, Fátima

JSheng2023 commented 4 years ago

I think Cython will generate cdistnace.c from cdistance.pyx. Have you properly installed Cython?