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kingsfordgroup / sailfish

Rapid Mapping-based Isoform Quantification from RNA-Seq Reads
http://www.cs.cmu.edu/~ckingsf/software/sailfish
GNU General Public License v3.0
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Cannot find source file: ... external/install/src/rapmap/RapMapFileSystem.cpp #119

Open yurivict opened 2 years ago

yurivict commented 2 years ago

configure fails with the message:

CMake Error at src/CMakeLists.txt:79 (add_library):
  Cannot find source file:

    /disk-samsung/freebsd-ports/biology/sailfish/work/sailfish-0.10.1-3-g0c88dda/external/install/src/rapmap/RapMapFileSystem.cpp

  Tried extensions .c .C .c++ .cc .cpp .cxx .cu .mpp .m .M .mm .ixx .cppm .h
  .hh .h++ .hm .hpp .hxx .in .txx .f .F .for .f77 .f90 .f95 .f03 .hip .ispc

CMake Error at src/CMakeLists.txt:79 (add_library):
  No SOURCES given to target: sailfish_core

This repository doesn't contain external/install/src/rapmap/RapMapFileSystem.cpp and there are no git submodules.

LiCanhui-Huyi commented 1 year ago

@yurivict I have encountered the same problem. Whether you have solved it or not, I think my answer can help people who encounter this problem in the future. This problem is because when running "cmake ..", one of the commands is to download a github file with curl. Some networks can not connect to github smoothly. When the download fails, it will continue to run. When you run "cmake .." again, you will not run the curl command again, so you will directly report this error every time you run. resolvent: Because I forgot which file the curl command is in, I deleted and recreated the build folder. Then run "camke .." again. Then you will see the output of curl. The line above this should be his command. Then use "grep - rn The CurlCommand", and you will know which line of the file this command is in and the URL where curl downloads the file. You can download the URL manually through a network that can access github. Then replace the curl command in the file with the cp command. Of course, remember to delete the curl option. There are several similar curl commands in the process of "camke ..", which can be solved in the same way.