clipper displays unusual help messages and can't be used

[kerenzhou062]

After installing clipper, I got the help message from clipper -h bellow:

Usage is  [options]
file_in is a file with a list of the length of aligned reads (only the part that aligns)
Options
 -L <int>   Effective Gene Length
 -r <int>   # of iterations
 -f <int>   input file containing read lengths
 -a <float>   B-H FDR cutoff, default(.05) ... gets very slow as alpha gets smaller
 -T 1/0 default(0) print running time statistics
Output:
Significance Threshold [tab] Iterations with this observed threshold

I also noticed that when installing with setup.py, there's warnings from peaksmodule.cc. That may caused the bug.

cythoning clipper/src/readsToWiggle.pyx to clipper/src/readsToWiggle.c
/home/user/.conda/envs/clipper3/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /net/isi-dcnl/ifs/user_data/JJChen_Grp/zhoukr/home/software/clipper/clipper/src/readsToWiggle.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
building 'clipper.src.readsToWiggle' extension
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/clipper
creating build/temp.linux-x86_64-3.7/clipper/src
gcc -pthread -B /home/user/.conda/envs/clipper3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/user/.conda/envs/clipper3/include/python3.7m -c clipper/src/readsToWiggle.c -o build/temp.linux-x86_64-3.7/clipper/src/readsToWiggle.o
gcc -pthread -shared -B /home/user/.conda/envs/clipper3/compiler_compat -L/home/user/.conda/envs/clipper3/lib -Wl,-rpath=/home/user/.conda/envs/clipper3/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/clipper/src/readsToWiggle.o -o build/lib.linux-x86_64-3.7/clipper/src/readsToWiggle.cpython-37m-x86_64-linux-gnu.so
building 'clipper.src.peaks' extension
gcc -pthread -B /home/user/.conda/envs/clipper3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/user/.conda/envs/clipper3/include/python3.7m -c clipper/src/peaksmodule.cc -o build/temp.linux-x86_64-3.7/clipper/src/peaksmodule.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
clipper/src/peaksmodule.cc: In function ‘PyObject* peaks_readsToWiggle_pysam(PyObject*, PyObject*)’:
clipper/src/peaksmodule.cc:332:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  332 |   while (item = PyIter_Next(iterator)) {
      |          ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
clipper/src/peaksmodule.cc: In function ‘PyObject* PyInit_peaks()’:
clipper/src/peaksmodule.cc:513:1: warning: no return statement in function returning non-void [-Wreturn-type]
  513 | }
      | ^
g++ -pthread -shared -B /home/user/.conda/envs/clipper3/compiler_compat -L/home/user/.conda/envs/clipper3/lib -Wl,-rpath=/home/user/.conda/envs/clipper3/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/clipper/src/peaksmodule.o -o build/lib.linux-x86_64-3.7/clipper/src/peaks.cpython-37m-x86_64-linux-gnu.so

[ReutFluss]

I have the same issue! Can't use clipper. Any solution for that?

[kerenzhou062]

I have the same issue! Can't use clipper. Any solution for that?

I used clipper v1.3 instead of the latest version. It seems that the peaksmodule.cc module is available with python2 only.

[byee4]

I ended up making a docker image for CLIPper, since the student who developed this left years ago. I'm not sure if I'm able to reproduce these problems, so hopefully this helps:

docker pull brianyee/clipper:61d5456

[kerenzhou062]

I ended up making a docker image for CLIPper, since the student who developed this left years ago. I'm not sure if I'm able to reproduce these problems, so hopefully this helps:

docker pull brianyee/clipper:61d5456

Unfortunately, our slurm cluster did not support docker.

[byee4]

Can you use singularity? Eg. singularity pull docker://brianyee/clipper:61d5456 SECURE: MESSAGE FROM Keren Zhou ON 2/10/22, 4:33 PM I ended up making a docker image for CLIPper, since the student who developed this left years ago. I'm not sure if I'm able to reproduce these problems, so hopefully this helps: docker pull brianyee/clipper:61d5456 Unfortunately, our slurm cluster did not support docker. — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/YeoLab/clipper/issues/103*issuecomment-1035678160__;Iw!!LLK065n_VXAQ!1yHlt7Fepy0ZMhBIhquwASAljI99GidKyFtbGi8lE1yqmW3fHJLnRjDuRSwF90xggnI$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AB7TJP3KSUA4ZEWEC4NRIKLU2RKLVANCNFSM5N35KTLQ__;!!LLK065n_VXAQ!1yHlt7Fepy0ZMhBIhquwASAljI99GidKyFtbGi8lE1yqmW3fHJLnRjDuRSwF2IpDEIk$>. You are receiving this because you commented.Message ID: ***@***.***>

[y9c]

This is because peaksmodule.cc is not complied correctly, The easiest solution is to compile this c code by yourself and replace the one within the package path.

You are using the python3.7 in a conda env, so you can compile the code by:

g++ -fPIC -shared -O3 -Wall -I/home/user/.conda/include/python3.7 -o peaks.cpython-37m-x86_64-linux-gnu.so peaksmodule.cc

Then check the path of clipper package, and move the peaks.cpython-37m-x86_64-linux-gnu.so into this path.

python -c "import clipper;print(clipper.__file__)"

The warning message is not relative to this problem, but it can be fixed by this patch: #104

---

Relative issues that can also fix in this way:
#82 #101

[yuanjianwen-gif]

I got the same error. Could you clarify the “path of clipper package”？ Thanks for your time！

This is because peaksmodule.cc is not complied correctly, The easiest solution is to compile this c code by yourself and replace the one within the package path.

You are using the python3.7 in a conda env, so you can compile the code by:

g++ -fPIC -shared -O3 -Wall -I/home/user/.conda/include/python3.7 -o peaks.cpython-37m-x86_64-linux-gnu.so peaksmodule.cc

Then check the path of clipper package, and move the peaks.cpython-37m-x86_64-linux-gnu.so into this path.

python -c "import clipper;print(clipper.__file__)"

The warning message is not relative to this problem, but it can be fixed by this patch: #104

Relative issues that can also fix in this way: #82 #101

[y9c]

run python -c "import clipper;print(clipper.__file__)" in the command line to find out.

[yuanjianwen-gif]

Thanks for the reply, but unfortunately I still failed to install it. I gave it up after a long time trying.

[luasauluas]

This is because peaksmodule.cc is not complied correctly, The easiest solution is to compile this c code by yourself and replace the one within the package path.

You are using the python3.7 in a conda env, so you can compile the code by:

g++ -fPIC -shared -O3 -Wall -I/home/user/.conda/include/python3.7 -o peaks.cpython-37m-x86_64-linux-gnu.so peaksmodule.cc

Then check the path of clipper package, and move the peaks.cpython-37m-x86_64-linux-gnu.so into this path.

python -c "import clipper;print(clipper.__file__)"

The warning message is not relative to this problem, but it can be fixed by this patch: #104

Relative issues that can also fix in this way: #82 #101

I fixed this issue as you mentioned. However, I had to move the output file peaks.cpython-37m-x86_64-linux-gnu.so to the directory /home/user/.conda/envs/clipper3/lib/python3.7/site-packages/clipper/src instead of the directory that I obtained with python -c "import clipper;print(clipper.file)"

Furthermore, before moving the peaks.cpython-37m-x86_64-linux-gnu.so to the mentioned folder, I deleted the peaks.cpython-37m-x86_64-linux-gnu.so file that was stored in this folder previously. I hope this can solve the issue for other people, I spent half a day trying to solve this.

[QizeZ]

If you encounter the warning message, it might be the problem with the peaksmodule.cc code; Revise your code as this link below:
7a9e5a5
Then, you can compile it smoothly!