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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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error :tarfile.ReadError: not a gzip file #2113

Closed 17863952296 closed 12 months ago

17863952296 commented 12 months ago

all software is installed successfully, but when I run the command :pip install anvio-7.1.tar.gz, an error occur： Processing ./anvio-7.1.tar.gz ERROR: Exception: Traceback (most recent call last): File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1645, in gzopen t = cls.taropen(name, mode, fileobj, kwargs) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1621, in taropen return cls(name, mode, fileobj, kwargs) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1484, in init self.firstmember = self.next() File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 2299, in next tarinfo = self.tarinfo.fromtarfile(self) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1092, in fromtarfile buf = tarfile.fileobj.read(BLOCKSIZE) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/gzip.py", line 276, in read return self._buffer.read(size) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/_compression.py", line 68, in readinto data = self.read(len(byte_view)) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/gzip.py", line 463, in read if not self._read_gzip_header(): File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/gzip.py", line 411, in _read_gzip_header raise OSError('Not a gzipped file (%r)' % magic) OSError: Not a gzipped file (b'\n\n')

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/cli/base_command.py", line 186, in _main status = self.run(options, args) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/commands/install.py", line 331, in run resolver.resolve(requirement_set) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 177, in resolve discovered_reqs.extend(self._resolve_one(requirement_set, req)) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 333, in _resolve_one abstract_dist = self._get_abstract_dist_for(req_to_install) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 282, in _get_abstract_dist_for abstract_dist = self.preparer.prepare_linked_requirement(req) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/operations/prepare.py", line 482, in prepare_linked_requirement hashes=hashes, File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/operations/prepare.py", line 278, in unpack_url return unpack_file_url(link, location, download_dir, hashes=hashes) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/operations/prepare.py", line 251, in unpack_file_url unpack_file(from_path, location, content_type) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/utils/unpacking.py", line 261, in unpack_file untar_file(filename, location) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/utils/unpacking.py", line 177, in untar_file tar = tarfile.open(filename, mode) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1591, in open return func(name, filemode, fileobj, kwargs) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1649, in gzopen raise ReadError("not a gzip file") tarfile.ReadError: not a gzip file (anvio-7.1) [root@localhost dengziguang]# cd /root/mambaforge/envs/anvio-7.1/lib/python3.6/ (anvio-7.1) [root@localhost python3.6]# pip install anvio-7.1.tar.gz Processing ./anvio-7.1.tar.gz ERROR: Exception: Traceback (most recent call last): File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1645, in gzopen t = cls.taropen(name, mode, fileobj, kwargs) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1621, in taropen return cls(name, mode, fileobj, **kwargs) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1484, in init self.firstmember = self.next() File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 2299, in next tarinfo = self.tarinfo.fromtarfile(self) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1092, in fromtarfile buf = tarfile.fileobj.read(BLOCKSIZE) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/gzip.py", line 276, in read return self._buffer.read(size) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/_compression.py", line 68, in readinto data = self.read(len(byte_view)) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/gzip.py", line 463, in read if not self._read_gzip_header(): File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/gzip.py", line 411, in _read_gzip_header raise OSError('Not a gzipped file (%r)' % magic) OSError: Not a gzipped file (b'\n\n')

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/cli/base_command.py", line 186, in _main status = self.run(options, args) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/commands/install.py", line 331, in run resolver.resolve(requirement_set) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 177, in resolve discovered_reqs.extend(self._resolve_one(requirement_set, req)) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 333, in _resolve_one abstract_dist = self._get_abstract_dist_for(req_to_install) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 282, in _get_abstract_dist_for abstract_dist = self.preparer.prepare_linked_requirement(req) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/operations/prepare.py", line 482, in prepare_linked_requirement hashes=hashes, File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/operations/prepare.py", line 278, in unpack_url return unpack_file_url(link, location, download_dir, hashes=hashes) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/operations/prepare.py", line 251, in unpack_file_url unpack_file(from_path, location, content_type) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/utils/unpacking.py", line 261, in unpack_file untar_file(filename, location) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/utils/unpacking.py", line 177, in untar_file tar = tarfile.open(filename, mode) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1591, in open return func(name, filemode, fileobj, kwargs) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1649, in gzopen raise ReadError("not a gzip file") tarfile.ReadError: not a gzip file (anvio-7.1) [root@localhost python3.6]# pip install ./anvio-7.1.tar.gz Processing ./anvio-7.1.tar.gz ERROR: Exception: Traceback (most recent call last): File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1645, in gzopen t = cls.taropen(name, mode, fileobj, kwargs) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1621, in taropen return cls(name, mode, fileobj, **kwargs) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1484, in init self.firstmember = self.next() File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 2299, in next tarinfo = self.tarinfo.fromtarfile(self) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1092, in fromtarfile buf = tarfile.fileobj.read(BLOCKSIZE) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/gzip.py", line 276, in read return self._buffer.read(size) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/_compression.py", line 68, in readinto data = self.read(len(byte_view)) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/gzip.py", line 463, in read if not self._read_gzip_header(): File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/gzip.py", line 411, in _read_gzip_header raise OSError('Not a gzipped file (%r)' % magic) OSError: Not a gzipped file (b'\n\n')

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/cli/base_command.py", line 186, in _main status = self.run(options, args) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/commands/install.py", line 331, in run resolver.resolve(requirement_set) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 177, in resolve discovered_reqs.extend(self._resolve_one(requirement_set, req)) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 333, in _resolve_one abstract_dist = self._get_abstract_dist_for(req_to_install) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 282, in _get_abstract_dist_for abstract_dist = self.preparer.prepare_linked_requirement(req) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/operations/prepare.py", line 482, in prepare_linked_requirement hashes=hashes, File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/operations/prepare.py", line 278, in unpack_url return unpack_file_url(link, location, download_dir, hashes=hashes) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/operations/prepare.py", line 251, in unpack_file_url unpack_file(from_path, location, content_type) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/utils/unpacking.py", line 261, in unpack_file untar_file(filename, location) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/site-packages/pip/_internal/utils/unpacking.py", line 177, in untar_file tar = tarfile.open(filename, mode) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1591, in open return func(name, filemode, fileobj, **kwargs) File "/root/mambaforge/envs/anvio-7.1/lib/python3.6/tarfile.py", line 1649, in gzopen raise ReadError("not a gzip file") tarfile.ReadError: not a gzip file

meren commented 12 months ago

Hi @17863952296, you should try to re-download the file, because it certainly is a gzip file.

By the way, I'm not sure in what environment you're working, but you should never install anvi'o (nor any other software for that matter) with root privileges.