CLIPper installation error
55 views
Skip to first unread message
엄다훈
May 14, 2020, 2:11:00 AM5/14/20
to CLIPper-discuss
Hello. I'm Dahun
I have some problems for installation of CLIPper.
when I ran the command 'python setup.py install', some error messages came out.
running install
running bdist_egg
running egg_info
writing clipper.egg-info/PKG-INFO
writing dependency_links to clipper.egg-info/dependency_links.txt
writing entry points to clipper.egg-info/entry_points.txt
writing requirements to clipper.egg-info/requires.txt
writing top-level names to clipper.egg-info/top_level.txt
writing manifest file 'clipper.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
running build_ext
skipping 'clipper/src/readsToWiggle.c' Cython extension (up-to-date)
building 'clipper.src.peaks' extension
gcc -pthread -B /media/nepi/vol_2/Dahun/anaconda3/envs/chipseq/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/media/nepi/vol_2/Dahun/anaconda3/envs/chipseq/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 ‘int main(int, char**)’:
clipper/src/peaksmodule.cc:26:28: error: cannot convert ‘char*’ to ‘const wchar_t*’ for argument ‘1’ to ‘void Py_SetProgramName(const wchar_t*)’
Py_SetProgramName(argv[0]);
^
clipper/src/peaksmodule.cc: In function ‘PyObject* peaks_shuffle(PyObject*, PyObject*)’:
clipper/src/peaksmodule.cc:86:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for( int i = 0; i < HEIGHT.size(); i++) {
~~^~~~~~~~~~~~~~~
clipper/src/peaksmodule.cc:92:18: error: ‘PyInt_AsLong’ was not declared in this scope
long len = PyInt_AsLong(PyList_GetItem(reads, i));
^~~~~~~~~~~~
clipper/src/peaksmodule.cc:92:18: note: suggested alternative: ‘PyLong_AsLong’
long len = PyInt_AsLong(PyList_GetItem(reads, i));
^~~~~~~~~~~~
PyLong_AsLong
clipper/src/peaksmodule.cc:123:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (GENE[j] >= HEIGHT.size()) {
clipper/src/peaksmodule.cc:193:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (height_cutoff > OBS_CUTOFF.size()) {
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
clipper/src/peaksmodule.cc:202:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int cut = 0; cut < OBS_CUTOFF.size(); cut++) {
~~~~^~~~~~~~~~~~~~~~~~~
clipper/src/peaksmodule.cc:203:37: error: ‘PyInt_FromLong’ was not declared in this scope
PyList_SetItem(returnList, cut, PyInt_FromLong(OBS_CUTOFF[cut]));
^~~~~~~~~~~~~~
clipper/src/peaksmodule.cc:203:37: note: suggested alternative: ‘PyLong_FromLong’
PyList_SetItem(returnList, cut, PyInt_FromLong(OBS_CUTOFF[cut]));
^~~~~~~~~~~~~~
PyLong_FromLong
clipper/src/peaksmodule.cc: In function ‘PyObject* peaks_find_sections(PyObject*, PyObject*)’:
clipper/src/peaksmodule.cc:261:31: error: ‘PyInt_FromLong’ was not declared in this scope
PyTuple_SetItem(section, 0, PyInt_FromLong(start));
^~~~~~~~~~~~~~
clipper/src/peaksmodule.cc:261:31: note: suggested alternative: ‘PyLong_FromLong’
PyTuple_SetItem(section, 0, PyInt_FromLong(start));
^~~~~~~~~~~~~~
PyLong_FromLong
clipper/src/peaksmodule.cc:271:33: error: ‘PyInt_FromLong’ was not declared in this scope
PyTuple_SetItem(section, 0, PyInt_FromLong(start));
^~~~~~~~~~~~~~
clipper/src/peaksmodule.cc:271:33: note: suggested alternative: ‘PyLong_FromLong’
PyTuple_SetItem(section, 0, PyInt_FromLong(start));
^~~~~~~~~~~~~~
PyLong_FromLong
clipper/src/peaksmodule.cc:281:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < sections.size(); i++) {
~~^~~~~~~~~~~~~~~~~
clipper/src/peaksmodule.cc: In function ‘PyObject* peaks_readsToWiggle_pysam(PyObject*, PyObject*)’:
clipper/src/peaksmodule.cc:329:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
while (item = PyIter_Next(iterator)) {
~~~~~^~~~~~~~~~~~~~~~~~~~~~~
clipper/src/peaksmodule.cc:390:34: error: ‘PyInt_FromLong’ was not declared in this scope
PyTuple_SetItem(read_loc, 0, PyInt_FromLong(read_start));
^~~~~~~~~~~~~~
clipper/src/peaksmodule.cc:390:34: note: suggested alternative: ‘PyLong_FromLong’
PyTuple_SetItem(read_loc, 0, PyInt_FromLong(read_start));
^~~~~~~~~~~~~~
PyLong_FromLong
clipper/src/peaksmodule.cc:421:25: error: ‘PyInt_AsLong’ was not declared in this scope
long incremented = PyInt_AsLong(jxnCount);
^~~~~~~~~~~~
clipper/src/peaksmodule.cc:421:25: note: suggested alternative: ‘PyLong_AsLong’
long incremented = PyInt_AsLong(jxnCount);
^~~~~~~~~~~~
PyLong_AsLong
clipper/src/peaksmodule.cc:455:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < lengths.size(); i++) {
~~^~~~~~~~~~~~~~~~
clipper/src/peaksmodule.cc:456:35: error: ‘PyInt_FromLong’ was not declared in this scope
PyList_SetItem(retLengths, i, PyInt_FromLong(lengths[i]));
^~~~~~~~~~~~~~
clipper/src/peaksmodule.cc:456:35: note: suggested alternative: ‘PyLong_FromLong’
PyList_SetItem(retLengths, i, PyInt_FromLong(lengths[i]));
^~~~~~~~~~~~~~
PyLong_FromLong
clipper/src/peaksmodule.cc:464:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < wiggle.size(); i++) {
~~^~~~~~~~~~~~~~~
clipper/src/peaksmodule.cc:468:36: error: ‘PyInt_FromLong’ was not declared in this scope
PyList_SetItem(retWiggle, i, PyInt_FromLong(wiggle[i]));
^~~~~~~~~~~~~~
clipper/src/peaksmodule.cc:468:36: note: suggested alternative: ‘PyLong_FromLong’
PyList_SetItem(retWiggle, i, PyInt_FromLong(wiggle[i]));
^~~~~~~~~~~~~~
PyLong_FromLong
clipper/src/peaksmodule.cc:471:38: error: ‘PyInt_FromLong’ was not declared in this scope
PyList_SetItem(retPos_counts, i, PyInt_FromLong(pos_counts[i]));
^~~~~~~~~~~~~~
clipper/src/peaksmodule.cc:471:38: note: suggested alternative: ‘PyLong_FromLong’
PyList_SetItem(retPos_counts, i, PyInt_FromLong(pos_counts[i]));
^~~~~~~~~~~~~~
PyLong_FromLong
clipper/src/peaksmodule.cc: In function ‘PyObject* initpeaks()’:
clipper/src/peaksmodule.cc:501:3: error: ‘Py_InitModule’ was not declared in this scope
Py_InitModule("peaks", peaks_methods);
^~~~~~~~~~~~~
clipper/src/peaksmodule.cc:501:3: note: suggested alternative: ‘Py_Initialize’
Py_InitModule("peaks", peaks_methods);
^~~~~~~~~~~~~
Py_Initialize
clipper/src/peaksmodule.cc:502:1: warning: no return statement in function returning non-void [-Wreturn-type]
}
^
error: command 'gcc' failed with exit status 1
python version is 3.7.6
gcc version is 7.5.0
Thank you.
Sol Katzman
May 14, 2020, 11:36:09 AM5/14/20
to CLIPper-discuss
You should always search postings. There are previous posts about install errors where you will find your problem answered.
In any case: Python 3 is not supported by Clipper. Use Python 2.
Reply all
Reply to author
Forward
Message has been deleted
0 new messages