Closed DENGARDEN closed 1 year ago
ayaanhossain
commented
1 year ago I'm sorry, are you saying that when you install ViennaRNA from PyPI using pip install ViennaRNA on python=3.9 on your MacOS system, it works (you are able to import the library), but not when you install it a python=3.10 environment? Are you using a conda environment for this? What about `python=3.11'?
DENGARDEN
commented
1 year ago I'm working on conda environment for it, and on python=3.9, it works like a charm.
But, for python=3.10, the system logs
Collecting ViennaRNA
Using cached ViennaRNA-2.5.0a5-py3-none-any.whl
Installing collected packages: ViennaRNA
Successfully installed ViennaRNA-2.5.0a5Python 3.10.11 | packaged by conda-forge | (main, May 10 2023, 19:01:19) [Clang 14.0.6 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import ViennaRNA
Traceback (most recent call last):
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.10/site-packages/ViennaRNA/__init__.py", line 2, in <module>
import RNA
ModuleNotFoundError: No module named 'RNA'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.10/site-packages/ViennaRNA/__init__.py", line 4, in <module>
raise ImportError(' ViennaRNA / RNAlib not installed')
ImportError: ViennaRNA / RNAlib not installed
>>> About python=3.11,
Collecting ViennaRNA
Using cached ViennaRNA-2.5.0a5.tar.gz (58.0 MB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Building wheels for collected packages: ViennaRNA
Building wheel for ViennaRNA (setup.py): started
Building wheel for ViennaRNA (setup.py): still running...
Building wheel for ViennaRNA (setup.py): still running...
Building wheel for ViennaRNA (setup.py): finished with status 'error'
Running setup.py clean for ViennaRNA
Failed to build ViennaRNA
Installing collected packages: ViennaRNA
Running setup.py install for ViennaRNA: started
Running setup.py install for ViennaRNA: finished with status 'error' config.status: executing depfiles commands
config.status: executing libtool commands
configure:
======================================
ViennaRNA Package 2.5.0
======================================
Successfully configured with the following options:
Sub Packages
------------
* Kinfold : no
* RNAforester : no
* Analyse{Dists,Seqs} : no
* RNAlocmin : no
* Kinwalker : no
Extra Libraries
---------------
* Support Vector Machine : yes
* GNU Scientific Library : no
* GNU MPFR : no
* JSON : yes
Features
--------
* Use hash for NR Sampling : no
* C11 features : yes
* TTY colors : yes
* Float Precision(PF} : no
* Deprecation Warnings : no
Optimizations
-------------
* Auto Vectorization : yes
* Explicit SIMD Extension : yes
* Link Time Optimization : no
* POSIX Threads : yes
* OpenMP : no
Scripting Language Interfaces
-----------------------------
* Perl 5 : no
* Python 3.x : yes
* Python 2.x : yes
Documentation
-------------
* Reference Manual (PDF) : no
* Reference Manual (HTML) : no
* Tutorial (PDF) : no
* Tutorial (HTML) : no
* CLA (PDF) : no
Unit Tests
----------
* Executable Programs : yes
* C-Library : no
* Perl 5 Interface : no
* Python 3.x Interface : yes
* Python 2.x Interface : yes
MacOS X
-------
* Universal Binary : no
* Installer : no
* SDK : custom
Install Directories
-------------------
* Executables : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/378dd139-7851-4bf8-b80d-d54478ef695c/bin
* Libraries : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/378dd139-7851-4bf8-b80d-d54478ef695c/lib
* Header files : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/378dd139-7851-4bf8-b80d-d54478ef695c/include
* Extra Data : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/378dd139-7851-4bf8-b80d-d54478ef695c/share
* Man pages : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/378dd139-7851-4bf8-b80d-d54478ef695c/share/man
* Documentation : Not to be installed
(HTML) :
(PDF) :
* Perl5 Interface : Not to be installed
(binaries) :
(scripts) :
* Python 3.x Interface :
(binaries) : /Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages
(scripts) : /Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages
* Python 2.x Interface :
(binaries) : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/378dd139-7851-4bf8-b80d-d54478ef695c/lib/python2.7/site-packages
(scripts) : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/378dd139-7851-4bf8-b80d-d54478ef695c/lib/python2.7/site-packages
You can run 'make', 'make check', and 'make install' now!
/Library/Developer/CommandLineTools/usr/bin/make all-recursive
Making all in src
Making all in ViennaRNA
Making all in static
/Library/Developer/CommandLineTools/usr/bin/make all-am
make[5]: Nothing to be done for `all-am'.
CC fold_compound.lo
CC dist_vars.lo
CC part_func.lo
CC part_func_wrappers.lo
CC pf_fold.lo
CC pf_multifold.lo
CC treedist.lo
CC inverse.lo
CC ProfileDist.lo
CC RNAstruct.lo
CC mfe.lo
CC mfe_window.lo
CC mfe_wrappers.lo
CC mfe_window_wrappers.lo
CC fold.lo
CC stringdist.lo
CC subopt.lo
CC subopt_zuker.lo
CC Lfold.lo
CC cofold.lo
CC part_func_co.lo
CC ProfileAln.lo
CC duplex.lo
CC alifold.lo
CC alipfold.lo
CC LPfold.lo
CC part_func_up.lo
CC ribo.lo
CC MEA.lo
CC mm.lo
CC 2Dfold.lo
CC 2Dpfold.lo
CC plex_functions.lo
CC ali_plex.lo
CC c_plex.lo
CC plex.lo
CC snofold.lo
CC snoop.lo
CC gquad.lo
CC perturbation_fold.lo
CC centroid.lo
CC model.lo
CC dp_matrices.lo
CC boltzmann_sampling.lo
CC bs_wrappers.lo
CC equilibrium_probs.lo
CXX ../libsvm-3.25/svm.lo
../libsvm-3.25/svm.cpp:53:2: warning: 'vsprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead. [-Wdeprecated-declarations]
vsprintf(buf,fmt,ap);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:207:1: note: 'vsprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use vsnprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
#define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
^
1 warning generated.
CC ../json/json.lo
CC alphabet.lo
CC sequence.lo
CC unstructured_domains.lo
CC grammar.lo
CC heat_capacity.lo
CC zscore.lo
CC libRNA_concentrations_la-concentrations.lo
CXX ../dlib-19.22/dlib/all/libRNA_concentrations_la-source.lo
CXX libRNA_concentrations_la-wrap_dlib.lo
CXXLD libRNA_concentrations.la
CC constraints/constraints.lo
CC constraints/SHAPE.lo
CC constraints/hard.lo
CC constraints/soft.lo
CC constraints/ligand.lo
CCLD libRNA_constraints.la
CC datastructures/basic_datastructures.lo
CC datastructures/lists.lo
CC datastructures/char_stream.lo
CC datastructures/stream_output.lo
CC datastructures/hash_tables.lo
datastructures/hash_tables.c:339:7: warning: assigning to 'unsigned char *' from 'char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
k = ((vrna_ht_entry_db_t *)x)->structure;
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
datastructures/hash_tables.c:340:39: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign]
len = length = (unsigned int)strlen(k);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/string.h:82:28: note: passing argument to parameter '__s' here
size_t strlen(const char *__s);
^
2 warnings generated.
CC datastructures/heap.lo
CCLD libRNA_datastructures.la
CC utils/utils.lo
CC utils/string_utils.lo
CC utils/structure_utils.lo
CC utils/structure_tree.lo
CC utils/msa_utils.lo
CC utils/higher_order_functions.lo
CC utils/cpu.lo
CC utils/units.lo
CC io/io_utils.lo
CC io/file_formats.lo
CC io/file_formats_msa.lo
CC search/BoyerMoore.lo
CC commands.lo
CC combinatorics.lo
CC utils/svm_utils.lo
CCLD libRNA_utils.la
CC plotting/alignments.lo
CC plotting/layouts.lo
CC plotting/probabilities.lo
CC plotting/structures.lo
CC plotting/plot_utils.lo
CC plotting/naview.lo
CC plotting/RNApuzzler/RNApuzzler.lo
In file included from plotting/RNApuzzler/RNApuzzler.c:20:
In file included from plotting/RNApuzzler/includes/resolveIntersections.inc:15:
plotting/RNApuzzler/includes/handleAncestorIntersections.inc:64:11: warning: 10 enumeration values not handled in switch: 'noIntersection', 'LxL', 'LxS'... [-Wswitch]
switch (it) {
^~
plotting/RNApuzzler/includes/handleAncestorIntersections.inc:64:11: note: add missing switch cases
switch (it) {
^
1 warning generated.
CC plotting/RNApuzzler/RNAturtle.lo
CCLD libRNA_plotting.la
CC params/io.lo
CC params/default.lo
CC params/params.lo
CC params/convert.lo
CCLD libRNA_params.la
CC eval.lo
CC eval_wrappers.lo
CCLD libRNA_eval.la
CC loops/external.lo
CC loops/external_bt.lo
CC loops/external_pf.lo
CC loops/hairpin.lo
CC loops/hairpin_bt.lo
CC loops/hairpin_pf.lo
CC loops/internal.lo
CC loops/internal_bt.lo
CC loops/internal_pf.lo
CC loops/multibranch.lo
CC loops/multibranch_bt.lo
CC loops/multibranch_pf.lo
CCLD libRNA_loops.la
CC move_set.lo
CC landscape/move.lo
CC landscape/findpath.lo
CC landscape/neighbor.lo
CC landscape/walk.lo
CCLD libRNA_landscape.la
CXXLD libRNA_conv.la
CXXLD libRNA.la
CC special_const.lo
CC ugly_bt.lo
CCLD libRNA_special_const.la
GEN libRNA.a
Making all in bin
CC RNAfold_cmdl.o
CC RNAfold.o
CC input_id_helpers.lo
CC parallel_helpers.lo
CC ../cthreadpool/thpool.lo
CCLD libhelpers.la
CCLD RNAfold
CC RNAeval_cmdl.o
CC RNAeval.o
CCLD RNAeval
CC RNAheat_cmdl.o
CC RNAheat.o
CCLD RNAheat
CC RNApdist_cmdl.o
CC RNApdist.o
CCLD RNApdist
CC RNAdistance_cmdl.o
CC RNAdistance.o
CCLD RNAdistance
CC RNAinverse_cmdl.o
CC RNAinverse.o
CCLD RNAinverse
CC RNAplot_cmdl.o
CC RNAplot.o
CCLD RNAplot
CC RNAsubopt_cmdl.o
CC RNAsubopt.o
CCLD RNAsubopt
CC RNALfold_cmdl.o
CC RNALfold.o
CCLD RNALfold
CC RNAcofold_cmdl.o
CC RNAcofold.o
CCLD RNAcofold
CC RNApaln_cmdl.o
CC RNApaln.o
CCLD RNApaln
CC RNAduplex_cmdl.o
CC RNAduplex.o
CCLD RNAduplex
CC RNAalifold_cmdl.o
CC RNAalifold.o
RNAalifold.c:1072:7: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro]
THREADSAFE_FILE_OUTPUT({
^~~~~~~~~~~~~~~~~~~~~~~~
./parallel_helpers.h:27:7: note: expanded from macro 'THREADSAFE_FILE_OUTPUT'
(a); \
^
RNAalifold.c:1072:30: note: '{' token is here
THREADSAFE_FILE_OUTPUT({
^
./parallel_helpers.h:27:8: note: expanded from macro 'THREADSAFE_FILE_OUTPUT'
(a); \
^
RNAalifold.c:1080:7: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro]
});
^
./parallel_helpers.h:27:8: note: expanded from macro 'THREADSAFE_FILE_OUTPUT'
(a); \
^
RNAalifold.c:1072:7: note: ')' token is here
THREADSAFE_FILE_OUTPUT({
^~~~~~~~~~~~~~~~~~~~~~~~
./parallel_helpers.h:27:9: note: expanded from macro 'THREADSAFE_FILE_OUTPUT'
(a); \
^
RNAalifold.c:1072:7: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro]
THREADSAFE_FILE_OUTPUT({
^~~~~~~~~~~~~~~~~~~~~~~~
./parallel_helpers.h:30:7: note: expanded from macro 'THREADSAFE_FILE_OUTPUT'
(a); \
^
RNAalifold.c:1072:30: note: '{' token is here
THREADSAFE_FILE_OUTPUT({
^
./parallel_helpers.h:30:8: note: expanded from macro 'THREADSAFE_FILE_OUTPUT'
(a); \
^
RNAalifold.c:1080:7: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro]
});
^
./parallel_helpers.h:30:8: note: expanded from macro 'THREADSAFE_FILE_OUTPUT'
(a); \
^
RNAalifold.c:1072:7: note: ')' token is here
THREADSAFE_FILE_OUTPUT({
^~~~~~~~~~~~~~~~~~~~~~~~
./parallel_helpers.h:30:9: note: expanded from macro 'THREADSAFE_FILE_OUTPUT'
(a); \
^
4 warnings generated.
CCLD RNAalifold
CC RNAplfold_cmdl.o
CC RNAplfold.o
CCLD RNAplfold
CC RNAup_cmdl.o
CC RNAup.o
CCLD RNAup
CC RNAaliduplex_cmdl.o
CC RNAaliduplex.o
CCLD RNAaliduplex
CC RNALalifold_cmdl.o
CC RNALalifold.o
CCLD RNALalifold
CC RNA2Dfold_cmdl.o
CC RNA2Dfold.o
CCLD RNA2Dfold
CC RNAparconv_cmdl.o
CC RNAparconv.o
CCLD RNAparconv
CC RNAPKplex_cmdl.o
CC RNAPKplex.o
CCLD RNAPKplex
CC RNAplex_cmdl.o
CC RNAplex.o
RNAplex.c:2083:46: warning: 'sscanf' may overflow; destination buffer in argument 3 has size 255, but the corresponding specifier may require size 256 [-Wfortify-source]
if (sscanf(names[0], "%255[^/]/%lld-%lld", bla, &begin, &end) == 3) /* initialize location_flag; */
^
RNAplex.c:2099:48: warning: 'sscanf' may overflow; destination buffer in argument 3 has size 255, but the corresponding specifier may require size 256 [-Wfortify-source]
if (sscanf(names[i], "%255[^/]/%lld-%lld", bla, &begin, &end) == 3) {
^
2 warnings generated.
CCLD RNAplex
CC RNAsnoop_cmdl.o
CC RNAsnoop.o
CCLD RNAsnoop
CC RNApvmin_cmdl.o
CC RNApvmin.o
CCLD RNApvmin
CC RNAdos_cmdl.o
CC RNAdos.o
CCLD RNAdos
CC RNAmultifold_cmdl.o
CC RNAmultifold.o
CCLD RNAmultifold
Making all in Utils
CC b2ct.o
CCLD b2ct
CC popt.o
CCLD popt
CC ct2db_cmdl.o
CC ct2db.o
CCLD ct2db
make[3]: Nothing to be done for `all-am'.
Making all in man
make[2]: Nothing to be done for `all'.
Making all in misc
make[2]: Nothing to be done for `all'.
Making all in doc
Making all in CLA
make[3]: Nothing to be done for `all'.
make[3]: Nothing to be done for `all-am'.
Making all in RNA-Tutorial
make[2]: Nothing to be done for `all'.
Making all in interfaces
Making all in Python
CXX _RNA_la-RNA_wrap.lo
RNA_wrap.cpp:4693:11: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
sprintf(msg, "attempt to assign sequence of size %lu to extended slice of size %lu", (unsigned long)is.size(), (unsigned long)replacecount);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
#define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
^
RNA_wrap.cpp:4709:9: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
sprintf(msg, "attempt to assign sequence of size %lu to extended slice of size %lu", (unsigned long)is.size(), (unsigned long)replacecount);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
#define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
^
RNA_wrap.cpp:5049:2: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
sprintf(msg, "in sequence element %d ", (int)_index);
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
#define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
^
3 warnings generated.
CXXLD _RNA.la
GEN RNA/__init__.py
GEN RNA/_RNANone
GEN RNA/__pycache__/__init__.cpython-311.pyc
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named '_RNA'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/ViennaRNA-2.5.0/interfaces/Python/RNA/__init__.py", line 11, in <module>
from . import _RNA
ImportError: cannot import name '_RNA' from partially initialized module 'RNA' (most likely due to a circular import) (/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/ViennaRNA-2.5.0/interfaces/Python/RNA/__init__.py)
make[3]: *** [RNA/__pycache__/__init__.cpython-311.pyc] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/setup.py", line 110, in <module>
setup(
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/__init__.py", line 87, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/dist.py", line 1208, in run_command
super().run_command(command)
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/wheel/bdist_wheel.py", line 360, in run
self.run_command("install")
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/dist.py", line 1208, in run_command
super().run_command(command)
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/setup.py", line 107, in run
self.compile_and_install_ViennaRNA()
File "/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/setup.py", line 98, in compile_and_install_ViennaRNA
subprocess.check_call('make', cwd=src_path, shell=True)
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'make' returned non-zero exit status 2.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for ViennaRNA
error: subprocess-exited-with-error
× Running setup.py install for ViennaRNA did not run successfully.
│ exit code: 1
╰─> [473 lines of output]
running install
/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking for stdio.h... yes
checking for stdlib.h... yes
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./configure: line 19003: #include: command not found
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checking whether C compiler accepts -flto... yes
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checking whether C compiler accepts -ffat-lto-objects... yes
checking whether C++ compiler accepts -ffat-lto-objects... yes
configure: WARNING: Trying to re-set ar/ranlib/nm to compiler specific wrappers
configure: WARNING: Building for OS X
checking whether the linker supports Link time Optimization (LTO)... no
configure: WARNING: Your linker does not support Link Time Optimizaton! Disabling LTO support!
configure: WARNING: Your compiler/linker combination does not support link-time optimization (LTO)
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configure: WARNING: "Can't find libgsl. Falling back to default implementation."
checking whether gcc is Clang... yes
checking whether pthreads work with "-pthread" and "-lpthread"... yes
checking whether Clang needs flag to prevent "argument unused" warning when linking with -pthread... no
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checking whether more special flags are required for pthreads... no
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checking compiler support for AVX 512 instructions... no
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configure: WARNING:
==========================
Failed to find mpfr.h!
You probably need to install the mpfr-devel package or similar
==========================
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checking for ./interfaces/Python2/RNA_wrap.cpp... yes
checking for ./interfaces/Python2/RNA.py... yes
checking for python2... /Library/Frameworks/Python.framework/Versions/2.7/bin/python2
checking for Python2 include path... /Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
checking for /Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/Python.h... yes
checking for Python2 ldflags... -bundle -undefined dynamic_lookup
checking for Python2 extension linker... gcc -bundle -undefined dynamic_lookup -arch x86_64 -g
checking for directory to install Python2 scripts in... ${prefix}/lib/python2.7/site-packages
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checking for Python2 module extension... .so
checking for ./interfaces/Python/Makefile.am... yes
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checking for Python3 include path... /Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/include/python3.11
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checking for Python3 ldflags... -bundle -undefined dynamic_lookup
checking for Python3 extension linker... clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib -L/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib -Wl,-rpath,/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib -L/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib
checking for directory to install Python3 scripts in... /Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages
checking for directory to install architecture dependent python3 things in... /Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages
checking for Python3 module extension... None
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configure: WARNING: check not found -- will not build C-library Unit tests
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checking whether g++ supports C++11 features with -std=c++11... yes
checking for ./src/dlib-19.22/dlib/all/source.cpp... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating packaging/macosx/Makefile
config.status: creating packaging/macosx/Distribution.xml
config.status: creating packaging/macosx/resources/welcome.txt
config.status: creating interfaces/Python2/Makefile
config.status: creating interfaces/Python2/version.i
config.status: creating interfaces/Python/Makefile
config.status: creating interfaces/Python/version.i
config.status: creating tests/Makefile
config.status: creating tests/RNApath.py
config.status: creating tests/RNAHelpers.pm
config.status: creating tests/test-env.sh
config.status: creating src/ViennaRNA/static/templates_postscript.h
config.status: creating src/ViennaRNA/static/templates_svg.h
config.status: creating src/ViennaRNA/static/energy_parameter_sets.h
config.status: creating src/ViennaRNA/vrna_config.h
config.status: creating misc/Makefile
config.status: creating interfaces/Makefile
config.status: creating Makefile
config.status: creating RNAlib2.pc
config.status: creating src/Utils/Makefile
config.status: creating src/bin/Makefile
config.status: creating src/Makefile
config.status: creating src/ViennaRNA/Makefile
config.status: creating src/ViennaRNA/static/Makefile
config.status: creating man/Makefile
config.status: creating doc/Makefile
config.status: creating doc/CLA/Makefile
config.status: creating RNA-Tutorial/Makefile
config.status: creating man/cmdlopt.sh
config.status: creating examples/Makefile
config.status: creating packaging/viennarna.spec
config.status: creating packaging/PKGBUILD
config.status: creating packaging/win_installer_archlinux_i686.nsi
config.status: creating packaging/win_installer_archlinux_x86_64.nsi
config.status: creating packaging/win_installer_fedora_i686.nsi
config.status: creating packaging/win_installer_fedora_x86_64.nsi
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
configure:
======================================
ViennaRNA Package 2.5.0
======================================
Successfully configured with the following options:
Sub Packages
------------
* Kinfold : no
* RNAforester : no
* Analyse{Dists,Seqs} : no
* RNAlocmin : no
* Kinwalker : no
Extra Libraries
---------------
* Support Vector Machine : yes
* GNU Scientific Library : no
* GNU MPFR : no
* JSON : yes
Features
--------
* Use hash for NR Sampling : no
* C11 features : yes
* TTY colors : yes
* Float Precision(PF} : no
* Deprecation Warnings : no
Optimizations
-------------
* Auto Vectorization : yes
* Explicit SIMD Extension : yes
* Link Time Optimization : no
* POSIX Threads : yes
* OpenMP : no
Scripting Language Interfaces
-----------------------------
* Perl 5 : no
* Python 3.x : yes
* Python 2.x : yes
Documentation
-------------
* Reference Manual (PDF) : no
* Reference Manual (HTML) : no
* Tutorial (PDF) : no
* Tutorial (HTML) : no
* CLA (PDF) : no
Unit Tests
----------
* Executable Programs : yes
* C-Library : no
* Perl 5 Interface : no
* Python 3.x Interface : yes
* Python 2.x Interface : yes
MacOS X
-------
* Universal Binary : no
* Installer : no
* SDK : custom
Install Directories
-------------------
* Executables : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/00d44d36-787e-46e7-bc8f-cb0af1cb19a5/bin
* Libraries : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/00d44d36-787e-46e7-bc8f-cb0af1cb19a5/lib
* Header files : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/00d44d36-787e-46e7-bc8f-cb0af1cb19a5/include
* Extra Data : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/00d44d36-787e-46e7-bc8f-cb0af1cb19a5/share
* Man pages : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/00d44d36-787e-46e7-bc8f-cb0af1cb19a5/share/man
* Documentation : Not to be installed
(HTML) :
(PDF) :
* Perl5 Interface : Not to be installed
(binaries) :
(scripts) :
* Python 3.x Interface :
(binaries) : /Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages
(scripts) : /Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages
* Python 2.x Interface :
(binaries) : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/00d44d36-787e-46e7-bc8f-cb0af1cb19a5/lib/python2.7/site-packages
(scripts) : /private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/00d44d36-787e-46e7-bc8f-cb0af1cb19a5/lib/python2.7/site-packages
You can run 'make', 'make check', and 'make install' now!
/Library/Developer/CommandLineTools/usr/bin/make all-recursive
Making all in src
Making all in ViennaRNA
Making all in static
/Library/Developer/CommandLineTools/usr/bin/make all-am
make[5]: Nothing to be done for `all-am'.
CC plotting/alignments.lo
CC plotting/probabilities.lo
CC plotting/structures.lo
CCLD libRNA_plotting.la
CC params/io.lo
CCLD libRNA_params.la
CXXLD libRNA_conv.la
CXXLD libRNA.la
GEN libRNA.a
Making all in bin
CCLD RNAfold
CCLD RNAeval
CCLD RNAheat
CCLD RNApdist
CCLD RNAdistance
CCLD RNAinverse
CCLD RNAplot
CCLD RNAsubopt
CCLD RNALfold
CCLD RNAcofold
CCLD RNApaln
CCLD RNAduplex
CCLD RNAalifold
CCLD RNAplfold
CCLD RNAup
CCLD RNAaliduplex
CCLD RNALalifold
CCLD RNA2Dfold
CCLD RNAparconv
CCLD RNAPKplex
CCLD RNAplex
CCLD RNAsnoop
CCLD RNApvmin
CCLD RNAdos
CCLD RNAmultifold
Making all in Utils
CCLD b2ct
CCLD popt
CCLD ct2db
make[3]: Nothing to be done for `all-am'.
Making all in man
make[2]: Nothing to be done for `all'.
Making all in misc
make[2]: Nothing to be done for `all'.
Making all in doc
Making all in CLA
make[3]: Nothing to be done for `all'.
make[3]: Nothing to be done for `all-am'.
Making all in RNA-Tutorial
make[2]: Nothing to be done for `all'.
Making all in interfaces
Making all in Python
CXXLD _RNA.la
GEN RNA/_RNANone
GEN RNA/__pycache__/__init__.cpython-311.pyc
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named '_RNA'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/ViennaRNA-2.5.0/interfaces/Python/RNA/__init__.py", line 11, in <module>
from . import _RNA
ImportError: cannot import name '_RNA' from partially initialized module 'RNA' (most likely due to a circular import) (/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/ViennaRNA-2.5.0/interfaces/Python/RNA/__init__.py)
make[3]: *** [RNA/__pycache__/__init__.cpython-311.pyc] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/setup.py", line 110, in <module>
setup(
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/__init__.py", line 87, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/dist.py", line 1208, in run_command
super().run_command(command)
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/setup.py", line 107, in run
self.compile_and_install_ViennaRNA()
File "/private/var/folders/qx/w3316p_n7jz0zxwwb664g2140000gn/T/pip-install-v3ekqxq7/viennarna_83b69140d6514884a4ef8f2988664056/setup.py", line 98, in compile_and_install_ViennaRNA
subprocess.check_call('make', cwd=src_path, shell=True)
File "/Users/juyoungshin/Documents/code_repo/LinearDesign/.conda/lib/python3.11/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'make' returned non-zero exit status 2.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure
× Encountered error while trying to install package.
╰─> ViennaRNA
note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.Thanks:)
Edgeworth
commented
1 year ago I am also getting the same issue.
The main important log seems to be here (for python 3.11):
ImportError: cannot import name '_RNA' from partially initialized module 'RNA' (most likely due to a circular import) (/tmp/pip-install-87uhvbpu/viennarna_0d07ead04835461f97ab19d1df6217c4/ViennaRNA-2.5.0/interfaces/Python/RNA/__init__.py)```Please try installing again now. The problems should now have been fixed.
Edgeworth
commented
1 year ago Works for me with 2.6.2. Thanks! I guess that this can be closed for now.
Hello,
I've encountered an error of "ViennaRNA / RNAlib not installed" when I import the ViennaRNA module. But, installing it on Python3.9 works well. What can be a problem?
My system configuration is
Thanks in advance!