Cannot intall fatal error: jansson.h: No such file or directory

[dxyzx0]

CCMpred/src/ccmpred.c:17:0:
/path/DGraphDTA/CCMpred/include/meta.h:2:10: fatal error: jansson.h: No such file or directory
 #include "jansson.h"
          ^~~~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/ccmpred.dir/src/ccmpred.c.o] Error 1
make[1]: *** [CMakeFiles/ccmpred.dir/all] Error 2
make: *** [all] Error 2

But I have installed both jasson 2.13.1 and jansson-devel
And

cmake version 3.18.2
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)

[dxyzx0]

When executing cmake .
I got the following log:

-- MsgPack was not found. Make sure MSGPACK_LIBRARY and MSGPACK_INCLUDE_DIR are set.                                                                                                                                                                                                       
 -- Configuring done
 -- Generating done
 -- Build files have been written to: /path/CCMpred

But I have installed msgpack through yum install msgpack

[croth1]

Hi @DingXiangYuanZhiXing,
Can you give some extra information about the distribution you are using? If you are using yum to satisfy the dependencies, you will want to install jansson-devel and msgpack-devel.

[dxyzx0]

sorry, I don’t quite get your question. I’m using centos 7. Is that what you need?

…

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--------------原始邮件-------------- 发件人："Christian Roth "<notifications@github.com&gt;; 发送时间：2020年9月12日(星期六) 晚上6:21 收件人："soedinglab/CCMpred" <CCMpred@noreply.github.com&gt;; 抄送："DingXiangYuanZhiXing "<151120093@smail.nju.edu.cn&gt;;"Mention "<mention@noreply.github.com&gt;; 主题：Re: [soedinglab/CCMpred] Cannot intall fatal error: jansson.h: No such file or directory (#31) ----------------------------------- Hi @DingXiangYuanZhiXing, Can you give some extra information about the distribution you are using? If you are using yum to satisfy the dependencies, you will want to install jansson-devel and msgpack-devel. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[croth1]

Yes, thanks. You will need to install msgpack-devel and jansson-devel with yum.
If you are still getting errors after installing these two libraries, please start from fresh, post the cmake and make command you are using and the full output and I might be able to help you debug it.

[dxyzx0]

After I delete the whole folder and start with git clone again, I solved the bug. But I got the following warning

make
Scanning dependencies of target conjugrad
[  5%] Building C object lib/libconjugrad/CMakeFiles/conjugrad.dir/src/conjugrad.c.o
[ 10%] Building C object lib/libconjugrad/CMakeFiles/conjugrad.dir/src/debug.c.o
[ 15%] Building C object lib/libconjugrad/CMakeFiles/conjugrad.dir/src/arithmetic_ansi.c.o
[ 21%] Building C object lib/libconjugrad/CMakeFiles/conjugrad.dir/src/conjugrad_cuda.c.o
[ 26%] Building CUDA object lib/libconjugrad/CMakeFiles/conjugrad.dir/src/conjugrad_kernels.cu.o
[ 31%] Linking CUDA static library libconjugrad.a
[ 31%] Built target conjugrad
Scanning dependencies of target ccmpred
[ 36%] Building C object CMakeFiles/ccmpred.dir/src/ccmpred.c.o
[ 42%] Building C object CMakeFiles/ccmpred.dir/src/sequence.c.o
[ 47%] Building C object CMakeFiles/ccmpred.dir/src/util.c.o
[ 52%] Building C object CMakeFiles/ccmpred.dir/src/io.c.o
[ 57%] Building C object CMakeFiles/ccmpred.dir/src/evaluate_cpu.c.o
[ 63%] Building C object CMakeFiles/ccmpred.dir/src/parseopt.c.o
[ 68%] Building C object CMakeFiles/ccmpred.dir/src/reweighting.c.o
[ 73%] Building C object CMakeFiles/ccmpred.dir/src/numdif.c.o
[ 78%] Building C object CMakeFiles/ccmpred.dir/src/meta.c.o
[ 84%] Building C object CMakeFiles/ccmpred.dir/src/evaluate_cpu_omp.c.o
[ 89%] Building C object CMakeFiles/ccmpred.dir/src/evaluate_cuda.c.o
[ 94%] Building CUDA object CMakeFiles/ccmpred.dir/src/evaluate_cuda_kernels.cu.o
In file included from /path/CCMpred/src/evaluate_cuda_kernels.cu:3:0:
/usr/local/cuda-10.2/targets/x86_64-linux/include/math_functions.h:54:2: warning: #warning "math_functions.h is an internal header file and must not be used directly.  This file will be removed in a future CUDA release.  Please use cuda_runtime_api.h or cuda_runtime.h instead." [-Wcpp]
 #warning "math_functions.h is an internal header file and must not be used directly.  This file will be removed in a future CUDA release.  Please use cuda_runtime_api.h or cuda_runtime.h instead."
  ^
In file included from /path/CCMpred/src/evaluate_cuda_kernels.cu:3:0:
/usr/local/cuda-10.2/targets/x86_64-linux/include/math_functions.h:54:2: warning: #warning "math_functions.h is an internal header file and must not be used directly.  This file will be removed in a future CUDA release.  Please use cuda_runtime_api.h or cuda_runtime.h instead." [-Wcpp]
 #warning "math_functions.h is an internal header file and must not be used directly.  This file will be removed in a future CUDA release.  Please use cuda_runtime_api.h or cuda_runtime.h instead."
  ^
[100%] Linking CUDA executable bin/ccmpred
[100%] Built target ccmpred

Will the warning prevent me from using CUDA? Thank you very much!

[dxyzx0]

By the way, can I remove the folder after make?? Or I need to put bin folder somewhere else so the program can find it? Thank you very much!!

[croth1]

Will the warning prevent me from using CUDA? Thank you very much!

It's just a warning. I don't think this will cause any problems.

By the way, can I remove the folder after make?? Or I need to put bin folder somewhere else so the program can find it?

You have two options:

• either you keep the folder and start ccmpred out of this folder.
• you use make install to install it into a folder of your choice. (See also this for how to set the folder). If you go with this option you can delete the build folder.