Hi im trying to install voevent-parse via pip and run into the following error:
ERROR: Could not install packages due to an OSError. Traceback (most recent call last): File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_vendor\resolvelib\resolvers.py", line 171, in _merge_into_criterion
crit = self.state.criteria[name] KeyError: 'voevent-parse'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\commands\install.py", line 316, in run
requirement_set = resolver.resolve(
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\resolution\resolvelib\resolver.py", line 121, in resolve
self._result = resolver.resolve(
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_vendor\resolvelib\resolvers.py", line 453, in resolve
state = resolution.resolve(requirements, max_rounds=max_rounds)
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_vendor\resolvelib\resolvers.py", line 318, in resolve
name, crit = self._merge_into_criterion(r, parent=None)
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_vendor\resolvelib\resolvers.py", line 173, in _merge_into_criterion
crit = Criterion.from_requirement(self._p, requirement, parent)
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_vendor\resolvelib\resolvers.py", line 82, in from_requirement
if not cands:
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_vendor\resolvelib\structs.py", line 124, in __bool__
return bool(self._sequence)
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\resolution\resolvelib\found_candidates.py", line 99, in __bool__
return any(self)
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\resolution\resolvelib\factory.py", line 237, in iter_index_candidates
candidate = self._make_candidate_from_link(
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\resolution\resolvelib\factory.py", line 165, in _make_candidate_from_link
self._link_candidate_cache[link] = LinkCandidate(
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\resolution\resolvelib\candidates.py", line 300, in __init__
super().__init__(
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\resolution\resolvelib\candidates.py", line 144, in __init__
self.dist = self._prepare()
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\resolution\resolvelib\candidates.py", line 226, in _prepare
dist = self._prepare_distribution()
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\resolution\resolvelib\candidates.py", line 311, in _prepare_distribution
return self._factory.preparer.prepare_linked_requirement(
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\operations\prepare.py", line 457, in prepare_linked_requirement
return self._prepare_linked_requirement(req, parallel_builds)
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\operations\prepare.py", line 480, in _prepare_linked_requirement
local_file = unpack_url(
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\operations\prepare.py", line 240, in unpack_url
unpack_file(file.path, location, file.content_type)
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\utils\unpacking.py", line 266, in unpack_file
untar_file(filename, location)
File "c:\users\timo\appdata\local\programs\python\python39\lib\site-packages\pip\_internal\utils\unpacking.py", line 230, in untar_file
with open(path, 'wb') as destfp:
OSError: [Errno 22] Invalid argument: 'C:\\Users\\Timo\\AppData\\Local\\Temp\\pip-install-wpb7xknq\\voevent-parse_090e9cbdcae64f31a771cb0698293f1a\\src/voeventparse/fixtures/MOA_Lensing_Event_2015-07-10T14:50:54.00.xml'
Removed build tracker: 'C:\\Users\\Timo\\AppData\\Local\\Temp\\pip-req-tracker-cmjrk9m4'
Im using the latest Windows 10 version and latest pip version
Please consider running your command line in administrator
Related
I installed python 3.10 then tried to install django but it just starts downloading by after it reaches a certain point it crashes and shows this error Exception:
Traceback (most recent call last):
File
"c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\urllib3\response.py",
line 302, in _error_catcher
yield File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\urllib3\response.py",
line 384, in read
data = self._fp.read(amt) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\cachecontrol\filewrapper.py",
line 60, in read
data = self.__fp.read(amt) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\http\client.py",
line 447, in read
n = self.readinto(b) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\http\client.py",
line 491, in readinto
n = self.fp.readinto(b) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\socket.py",
line 589, in readinto
return self._sock.recv_into(b) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\ssl.py",
line 1049, in recv_into
return self.read(nbytes, buffer) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\ssl.py",
line 908, in read
return self._sslobj.read(len, buffer) socket.timeout: The read operation timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\basecommand.py",
line 228, in main
status = self.run(options, args) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\commands\install.py",
line 291, in run
resolver.resolve(requirement_set) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\resolve.py",
line 103, in resolve
self._resolve_one(requirement_set, req) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\resolve.py",
line 257, in _resolve_one
abstract_dist = self._get_abstract_dist_for(req_to_install) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\resolve.py",
line 210, in _get_abstract_dist_for
self.require_hashes File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\operations\prepare.py",
line 310, in prepare_linked_requirement
progress_bar=self.progress_bar File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 837, in unpack_url
progress_bar=progress_bar File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 674, in unpack_http_url
progress_bar) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 898, in _download_http_url
_download_url(resp, link, content_file, hashes, progress_bar) File
"c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 618, in _download_url
hashes.check_against_chunks(downloaded_chunks) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\utils\hashes.py",
line 48, in check_against_chunks
for chunk in chunks: File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 586, in written_chunks
for chunk in chunks: File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\utils\ui.py",
line 159, in iter
for x in it: File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 575, in resp_read
decode_content=False): File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\urllib3\response.py",
line 436, in stream
data = self.read(amt=amt, decode_content=decode_content) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\urllib3\response.py",
line 401, in read
raise IncompleteRead(self._fp_bytes_read, self.length_remaining) File
"c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\contextlib.py",
line 130, in exit
self.gen.throw(type, value, traceback) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\urllib3\response.py",
line 307, in _error_catcher
raise ReadTimeoutError(self._pool, None, 'Read timed out.') pip._vendor.urllib3.exceptions.ReadTimeoutError:
HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read
timed out.
So I tried to replace python 3.10 with version 3.7.0 but I am still getting the same error. How do I avoid this error?
check here, probably you have bad connection to internet or the download takes too long...
Traceback (most recent call last):
File "C:\ProgramData\Anaconda3\lib\site‑packages\spyder\plugins\ipythonconsole\plugin.py", line 1223, in create_kernel_manager_and_kernel_client
kernel_manager.start_kernel(stderr=stderr_handle)
File "C:\Users\Mahima Kaushik\AppData\Roaming\Python\Python38\site‑packages\jupyter_client\manager.py", line 309, in start_kernel
kernel_cmd, kw = self.pre_start_kernel(**kw)
File "C:\Users\Mahima Kaushik\AppData\Roaming\Python\Python38\site‑packages\jupyter_client\manager.py", line 256, in pre_start_kernel
self.write_connection_file()
File "C:\Users\Mahima Kaushik\AppData\Roaming\Python\Python38\site‑packages\jupyter_client\connect.py", line 468, in write_connection_file
self.connection_file, cfg = write_connection_file(self.connection_file,
File "C:\Users\Mahima Kaushik\AppData\Roaming\Python\Python38\site‑packages\jupyter_client\connect.py", line 138, in write_connection_file
with secure_write(fname) as f:
File "C:\ProgramData\Anaconda3\lib\contextlib.py", line 113, in enter
return next(self.gen)
File "C:\Users\Mahima Kaushik\AppData\Roaming\Python\Python38\site‑packages\jupyter_core\paths.py", line 435, in secure_write
win32_restrict_file_to_user(fname)
File "C:\Users\Mahima Kaushik\AppData\Roaming\Python\Python38\site‑packages\jupyter_core\paths.py", line 361, in win32_restrict_file_to_user
import win32api
ImportError: DLL load failed while importing win32api: %1 is not a valid Win32 application.
https://github.com/spyder-ide/spyder/issues/12040#issuecomment-705033049
https://github.com/spyder-ide/spyder/issues/12040#issuecomment-705057347
I removed the following directory to fix my problem:
C:\Users\Mahima Kaushik\AppData\Roaming\Python
Any conda command returns this message
also tried reinstalling anaconda. Any help is appreciated.
Any conda command generates the same output.
$ conda upgrade conda
Solving environment: failed
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/urllib3/contrib/pyopenssl.py", line 280, in recv_into
return self.connection.recv_into(*args, **kwargs)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/OpenSSL/SSL.py", line 1715, in recv_into
self._raise_ssl_error(self._ssl, result)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/OpenSSL/SSL.py", line 1521, in _raise_ssl_error
raise WantReadError()
OpenSSL.SSL.WantReadError
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/urllib3/contrib/pyopenssl.py", line 280, in recv_into
return self.connection.recv_into(*args, **kwargs)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/OpenSSL/SSL.py", line 1715, in recv_into
self._raise_ssl_error(self._ssl, result)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/OpenSSL/SSL.py", line 1538, in _raise_ssl_error
raise SysCallError(errno, errorcode.get(errno))
OpenSSL.SSL.SysCallError: (54, 'ECONNRESET')
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/urllib3/response.py", line 302, in _error_catcher
yield
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/urllib3/response.py", line 601, in read_chunked
chunk = self._handle_chunk(amt)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/urllib3/response.py", line 557, in _handle_chunk
value = self._fp._safe_read(amt)
File "/Users/kireto/anaconda3/lib/python3.6/http/client.py", line 612, in _safe_read
chunk = self.fp.read(min(amt, MAXAMOUNT))
File "/Users/kireto/anaconda3/lib/python3.6/socket.py", line 586, in readinto
return self._sock.recv_into(b)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/urllib3/contrib/pyopenssl.py", line 296, in recv_into
return self.recv_into(*args, **kwargs)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/urllib3/contrib/pyopenssl.py", line 285, in recv_into
raise SocketError(str(e))
OSError: (54, 'ECONNRESET')
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/requests/models.py", line 745, in generate
for chunk in self.raw.stream(chunk_size, decode_content=True):
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/urllib3/response.py", line 432, in stream
for line in self.read_chunked(amt, decode_content=decode_content):
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/urllib3/response.py", line 626, in read_chunked
self._original_response.close()
File "/Users/kireto/anaconda3/lib/python3.6/contextlib.py", line 99, in __exit__
self.gen.throw(type, value, traceback)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/urllib3/response.py", line 320, in _error_catcher
raise ProtocolError('Connection broken: %r' % e, e)
urllib3.exceptions.ProtocolError: ('Connection broken: OSError("(54, \'ECONNRESET\')",)', OSError("(54, 'ECONNRESET')",))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/conda/exceptions.py", line 789, in __call__
return func(*args, **kwargs)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/conda/cli/main.py", line 78, in _main
exit_code = do_call(args, p)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/conda/cli/conda_argparse.py", line 77, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/conda/cli/main_update.py", line 14, in execute
install(args, parser, 'update')
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/conda/cli/install.py", line 236, in install
force_reinstall=context.force,
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/conda/core/solve.py", line 504, in solve_for_transaction
force_remove, force_reinstall)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/conda/core/solve.py", line 437, in solve_for_diff
final_precs = self.solve_final_state(deps_modifier, prune, ignore_pinned, force_remove)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/conda/core/solve.py", line 178, in solve_final_state
index, r = self._prepare(prepared_specs)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/conda/core/solve.py", line 560, in _prepare
self.subdirs, prepared_specs)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/conda/core/index.py", line 213, in get_reduced_index
new_records = query_all(spec)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/conda/core/index.py", line 186, in query_all
return tuple(concat(future.result() for future in as_completed(futures)))
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/conda/core/repodata.py", line 90, in query
self.load()
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/conda/core/repodata.py", line 134, in load
_internal_state = self._load()
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/conda/core/repodata.py", line 202, in _load
mod_etag_headers.get('_mod'))
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/conda/core/repodata.py", line 402, in fetch_repodata_remote_request
timeout=timeout)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/requests/sessions.py", line 521, in get
return self.request('GET', url, **kwargs)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/requests/sessions.py", line 508, in request
resp = self.send(prep, **send_kwargs)
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/requests/sessions.py", line 658, in send
r.content
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/requests/models.py", line 823, in content
self._content = bytes().join(self.iter_content(CONTENT_CHUNK_SIZE)) or bytes()
File "/Users/kireto/anaconda3/lib/python3.6/site-packages/requests/models.py", line 748, in generate
raise ChunkedEncodingError(e)
requests.exceptions.ChunkedEncodingError: ('Connection broken: OSError("(54, \'ECONNRESET\')",)', OSError("(54, 'ECONNRESET')",))
`$ /Users/kireto/anaconda3/bin/conda upgrade conda`
environment variables:
CIO_TEST=<not set>
CONDA_ROOT=/Users/kireto/anaconda3
PATH=/Users/kireto/anaconda3/bin:/Users/kireto/anaconda3/bin:/Library/Frame
works/Python.framework/Versions/3.7/bin:/usr/local/bin:/usr/bin:/bin:/
usr/sbin:/sbin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : None
user config file : /Users/kireto/.condarc
populated config files : /Users/kireto/.condarc
conda version : 4.4.10
conda-build version : 3.4.1
python version : 3.6.4.final.0
base environment : /Users/kireto/anaconda3 (writable)
channel URLs : https://repo.continuum.io/pkgs/main/osx-64
https://repo.continuum.io/pkgs/main/noarch
https://repo.continuum.io/pkgs/free/osx-64
https://repo.continuum.io/pkgs/free/noarch
https://repo.continuum.io/pkgs/r/osx-64
https://repo.continuum.io/pkgs/r/noarch
https://repo.continuum.io/pkgs/pro/osx-64
https://repo.continuum.io/pkgs/pro/noarch
https://conda.anaconda.org/conda-forge/osx-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/bioconda/osx-64
https://conda.anaconda.org/bioconda/noarch
package cache : /Users/kireto/anaconda3/pkgs
/Users/kireto/.conda/pkgs
envs directories : /Users/kireto/anaconda3/envs
/Users/kireto/.conda/envs
platform : osx-64
user-agent : conda/4.4.10 requests/2.18.4 CPython/3.6.4 Darwin/17.7.0 OSX/10.13.6
UID:GID : 503:20
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
Upload did not complete
I tried to look at my .condarc file and even removed it but it doesn't change the outcome. Do you know what I can do to go back to a working conda?
conda version : 4.4.10
conda-build version : 3.4.1
I created a BIOM file, yyy.biom, using the functions make_biom and write_biom of the R package biomformat, version 1.2.0.
yyy.biom looks like:
"id":{},
"format":["Biological Observation Matrix 1.0.0-dev"],
"format_url":["http://biom-format.org/documentation/format_versions/biom-1.0.html"],
"type":["OTU table"],
"generated_by":["biomformat 1.2.0"],
"date":["2017-09-21 14:36:28"],
"matrix_type":["dense"],
"matrix_element_type":["int"],
"shape":[5,6],
"rows":[
{"id":["GG_OTU_1"],"metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Escherichia","s__"]},
{"id":["GG_OTU_2"],"metadata":["k__Bacteria","p__Cyanobacteria","c__Nostocophycideae","o__Nostocales","f__Nostocaceae","g__Dolichospermum","s__"]},
{"id":["GG_OTU_3"],"metadata":["k__Archaea","p__Euryarchaeota","c__Methanomicrobia","o__Methanosarcinales","f__Methanosarcinaceae","g__Methanosarcina","s__"]},
{"id":["GG_OTU_4"],"metadata":["k__Bacteria","p__Firmicutes","c__Clostridia","o__Halanaerobiales","f__Halanaerobiaceae","g__Halanaerobium","s__Halanaerobiumsaccharolyticum"]},
{"id":["GG_OTU_5"],"metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Escherichia","s__"]}
],
"columns":[
{"id":["Sample1"],"metadata":["CGCTTATCGAGA","CATGCTGCCTCCCGTAGGAGT","gut","human gut"]},
{"id":["Sample2"],"metadata":["CATACCAGTAGC","CATGCTGCCTCCCGTAGGAGT","gut","human gut"]},
{"id":["Sample3"],"metadata":["CTCTCTACCTGT","CATGCTGCCTCCCGTAGGAGT","gut","human gut"]},
{"id":["Sample4"],"metadata":["CTCTCGGCCTGT","CATGCTGCCTCCCGTAGGAGT","skin","human skin"]},
{"id":["Sample5"],"metadata":["CTCTCTACCAAT","CATGCTGCCTCCCGTAGGAGT","skin","human skin"]},
{"id":["Sample6"],"metadata":["CTAACTACCAAT","CATGCTGCCTCCCGTAGGAGT","skin","human skin"]}
],
"data": [[0,0,1,0,0,0],
[5,1,0,2,3,1],
[0,0,1,4,2,0],
[2,1,1,0,0,1],
[0,1,1,0,0,0]]
BIOM validation returns an error:
$ biom validate-table -i yyy.biom
Traceback (most recent call last):
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/bin/biom", line 6, in <module>
sys.exit(biom.cli.cli())
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 49, in validate_table
valid, report = _validate_table(input_fp, format_version, detailed_report)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 62, in _validate_table
detailed_report=detailed_report)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 113, in __call__
detailed_report=detailed_report)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 97, in run
return self._validate_json(**kwargs)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 305, in _validate_json
status_msg = method(table_json)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 496, in _valid_type
if value.lower() not in self.TableTypes:
AttributeError: 'list' object has no attribute 'lower'
I tried importing to QIIME 2 and got this error:
Traceback (most recent call last):
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/bin/qiime", line 6, in <module>
sys.exit(q2cli.__main__.qiime())
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/q2cli/tools.py", line 111, in import_data
view_type=source_format)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/qiime2/sdk/result.py", line 192, in import_data
return cls._from_view(type_, view, view_type, provenance_capture)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/qiime2/sdk/result.py", line 217, in _from_view
result = transformation(view)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/qiime2/core/transform.py", line 59, in transformation
new_view = transformer(view)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/qiime2/core/transform.py", line 207, in wrapped
file_view = transformer(view)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/q2_types/feature_table/_transformer.py", line 128, in _8
data = _parse_biom_table_v100(ff)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/q2_types/feature_table/_transformer.py", line 46, in _parse_biom_table_v100
table = biom.Table.from_json(json.load(fh))
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/table.py", line 3672, in from_json
dtype = MATRIX_ELEMENT_TYPE[json_table['matrix_element_type']]
TypeError: unhashable type: 'list'
QIIME 2 support suggested that the format 1.0.0-dev might be causing the issue. Could that be it? If so is there a way to change format?
Thanks!
I'm trying to run celery worker in OS X (Mavericks). I activated virtual environment (python 3.4) and tried to start Celery with this argument:
celery worker --app=scheduling -linfo
Where scheduling is my celery app.
But I ended up with this error: dbm.error: db type is dbm.gnu, but the module is not available
Complete stacktrace:
Traceback (most recent call last):
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/kombu/utils/__init__.py", line 320, in __get__
return obj.__dict__[self.__name__]
KeyError: 'db'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/other/PhoenixEnv/bin/celery", line 9, in <module>
load_entry_point('celery==3.1.9', 'console_scripts', 'celery')()
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/__main__.py", line 30, in main
main()
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bin/celery.py", line 80, in main
cmd.execute_from_commandline(argv)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bin/celery.py", line 768, in execute_from_commandline
super(CeleryCommand, self).execute_from_commandline(argv)))
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bin/base.py", line 308, in execute_from_commandline
return self.handle_argv(self.prog_name, argv[1:])
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bin/celery.py", line 760, in handle_argv
return self.execute(command, argv)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bin/celery.py", line 692, in execute
).run_from_argv(self.prog_name, argv[1:], command=argv[0])
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bin/worker.py", line 175, in run_from_argv
return self(*args, **options)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bin/base.py", line 271, in __call__
ret = self.run(*args, **kwargs)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bin/worker.py", line 209, in run
).start()
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/worker/__init__.py", line 100, in __init__
self.setup_instance(**self.prepare_args(**kwargs))
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/worker/__init__.py", line 141, in setup_instance
self.blueprint.apply(self, **kwargs)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bootsteps.py", line 221, in apply
step.include(parent)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bootsteps.py", line 347, in include
return self._should_include(parent)[0]
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/bootsteps.py", line 343, in _should_include
return True, self.create(parent)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/worker/components.py", line 220, in create
w._persistence = w.state.Persistent(w.state, w.state_db, w.app.clock)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/worker/state.py", line 161, in __init__
self.merge()
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/worker/state.py", line 169, in merge
self._merge_with(self.db)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/kombu/utils/__init__.py", line 322, in __get__
value = obj.__dict__[self.__name__] = self.__get(obj)
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/worker/state.py", line 238, in db
return self.open()
File "/Users/other/PhoenixEnv/lib/python3.4/site-packages/celery/worker/state.py", line 165, in open
self.filename, protocol=self.protocol, writeback=True,
File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/shelve.py", line 239, in open
return DbfilenameShelf(filename, flag, protocol, writeback)
File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/shelve.py", line 223, in __init__
Shelf.__init__(self, dbm.open(filename, flag), protocol, writeback)
File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/dbm/__init__.py", line 91, in open
"available".format(result))
dbm.error: db type is dbm.gnu, but the module is not available
Please help.
I switched to python3.5 and got the same error. On Ubuntu I could fix it with
aptitude install python3.5-gdbm
I got the same error. On Macbook I could fix it with
brew install gdb