can't install

[seaward901]

run
pip install gff3tool
Stopped
Building wheel for gff3tool (setup.py) ... -

[mpoelchau]

Hi @seaward901 ,

Can you provide the full output of the installation command? Also, what version of python are you using?

[seaward901]

Thank you python 3.8.5 [seaward]$ python3 -m pip install gff3tool Defaulting to user installation because normal site-packages is not writeable Looking in indexes: https://mirrors.aliyun.com/pypi/simple/ Collecting gff3tool &nbsp; Using cached https://mirrors.aliyun.com/pypi/packages/aa/b3/cecb768a048bf2e661f0e77bf3208ed8ef203acbd93107b1f00d7b57da1e/gff3tool-2.0.1.tar.gz (79 kB) Building wheels for collected packages: gff3tool &nbsp; Building wheel for gff3tool (setup.py) ... error &nbsp; ERROR: Command errored out with exit status 1: &nbsp; &nbsp;command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-_o7ow8rg/gff3tool/setup.py'"'"'; __file__='"'"'/tmp/pip-install-_o7ow8rg/gff3tool/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-50bjnyoc &nbsp; &nbsp; &nbsp; &nbsp;cwd: /tmp/pip-install-_o7ow8rg/gff3tool/ &nbsp; Complete output (3 lines): &nbsp; running bdist_wheel &nbsp; running build &nbsp; error: <urlopen error retrieval incomplete: got only 606208 out of 175185600 bytes&gt; &nbsp; ---------------------------------------- &nbsp; ERROR: Failed building wheel for gff3tool &nbsp; Running setup.py clean for gff3tool Failed to build gff3tool Installing collected packages: gff3tool &nbsp; &nbsp; Running setup.py install for gff3tool ... error &nbsp; &nbsp; ERROR: Command errored out with exit status 1: &nbsp; &nbsp; &nbsp;command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-_o7ow8rg/gff3tool/setup.py'"'"'; __file__='"'"'/tmp/pip-install-_o7ow8rg/gff3tool/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-ts6zm53n/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/seaward/.local/include/python3.8/gff3tool &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;cwd: /tmp/pip-install-_o7ow8rg/gff3tool/ &nbsp; &nbsp; Complete output (3 lines): &nbsp; &nbsp; running install &nbsp; &nbsp; running build &nbsp; &nbsp; error: [Errno 17] File exists: '/tmp/pip-install-_o7ow8rg/gff3tool/gff3tool/lib/ncbi-blast+' &nbsp; &nbsp; ---------------------------------------- ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-_o7ow8rg/gff3tool/setup.py'"'"'; __file__='"'"'/tmp/pip-install-_o7ow8rg/gff3tool/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-ts6zm53n/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/seaward/.local/include/python3.8/gff3tool Check the logs for full command output.

…

------------------&nbsp;原始邮件&nbsp;------------------ 发件人: "NAL-i5K/GFF3toolkit" <[email protected]&gt;; 发送时间:&nbsp;2020年11月12日(星期四) 晚上9:41 收件人:&nbsp;"NAL-i5K/GFF3toolkit"<[email protected]&gt;; 抄送:&nbsp;"陈思远"<[email protected]&gt;;"Mention"<[email protected]&gt;; 主题:&nbsp;Re: [NAL-i5K/GFF3toolkit] can't install (#108) Hi @seaward901 , Can you provide the full output of the installation command? Also, what version of python are you using? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[seaward901]

I've tried it on several operating systems，ubuntu, CentOS, Windows 10,&nbsp;The results are the same.

…

------------------&nbsp;原始邮件&nbsp;------------------ 发件人: "NAL-i5K/GFF3toolkit" <[email protected]&gt;; 发送时间:&nbsp;2020年11月12日(星期四) 晚上9:41 收件人:&nbsp;"NAL-i5K/GFF3toolkit"<[email protected]&gt;; 抄送:&nbsp;"陈思远"<[email protected]&gt;;"Mention"<[email protected]&gt;; 主题:&nbsp;Re: [NAL-i5K/GFF3toolkit] can't install (#108) Hi @seaward901 , Can you provide the full output of the installation command? Also, what version of python are you using? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[mpoelchau]

Are you installing within a virtual environment? E.g.:

#make new python environment and source it
 python3 -m venv my-newenv
source my-newenv/bin/activate
#sometimes you have to upgrade pip and install wheel:
pip install --upgrade pip
pip install wheel
#install gff3tool
pip install gff3tool

[seaward901]

Thank you for your answer, I use python3.9 [seaward]$ python3.9 -m pip install --upgrade pip Defaulting to user installation because normal site-packages is not writeable Looking in indexes: https://mirrors.aliyun.com/pypi/simple/ Requirement already up-to-date: pip in /home/seaward/.local/lib/python3.9/site-packages (20.2.4) [seaward]$ python3.9 -m pip install wheel Defaulting to user installation because normal site-packages is not writeable Looking in indexes: https://mirrors.aliyun.com/pypi/simple/ Requirement already satisfied: wheel in /usr/lib/python3/dist-packages (0.34.2) [seaward]$ python3.9 -m pip install gff3tool Defaulting to user installation because normal site-packages is not writeable Looking in indexes: https://mirrors.aliyun.com/pypi/simple/ Collecting gff3tool &nbsp; Using cached https://mirrors.aliyun.com/pypi/packages/aa/b3/cecb768a048bf2e661f0e77bf3208ed8ef203acbd93107b1f00d7b57da1e/gff3tool-2.0.1.tar.gz (79 kB) Building wheels for collected packages: gff3tool &nbsp; Building wheel for gff3tool (setup.py) ... error &nbsp; ERROR: Command errored out with exit status 1: &nbsp; &nbsp;command: /usr/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-46ln5k27/gff3tool/setup.py'"'"'; __file__='"'"'/tmp/pip-install-46ln5k27/gff3tool/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-0mv9p7o9 &nbsp; &nbsp; &nbsp; &nbsp;cwd: /tmp/pip-install-46ln5k27/gff3tool/ &nbsp; Complete output (3 lines): &nbsp; running bdist_wheel &nbsp; running build &nbsp; error: <urlopen error retrieval incomplete: got only 131072 out of 175185600 bytes&gt; &nbsp; ---------------------------------------- &nbsp; ERROR: Failed building wheel for gff3tool &nbsp; Running setup.py clean for gff3tool Failed to build gff3tool Installing collected packages: gff3tool &nbsp; &nbsp; Running setup.py install for gff3tool ... error &nbsp; &nbsp; ERROR: Command errored out with exit status 1: &nbsp; &nbsp; &nbsp;command: /usr/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-46ln5k27/gff3tool/setup.py'"'"'; __file__='"'"'/tmp/pip-install-46ln5k27/gff3tool/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-nmvb99oz/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/seaward/.local/include/python3.9/gff3tool &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;cwd: /tmp/pip-install-46ln5k27/gff3tool/ &nbsp; &nbsp; Complete output (3 lines): &nbsp; &nbsp; running install &nbsp; &nbsp; running build &nbsp; &nbsp; error: [Errno 17] File exists: '/tmp/pip-install-46ln5k27/gff3tool/gff3tool/lib/ncbi-blast+' &nbsp; &nbsp; ---------------------------------------- ERROR: Command errored out with exit status 1: /usr/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-46ln5k27/gff3tool/setup.py'"'"'; __file__='"'"'/tmp/pip-install-46ln5k27/gff3tool/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-nmvb99oz/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/seaward/.local/include/python3.9/gff3tool Check the logs for full command output.

…

------------------&nbsp;原始邮件&nbsp;------------------ 发件人: "NAL-i5K/GFF3toolkit" <[email protected]&gt;; 发送时间:&nbsp;2020年11月12日(星期四) 晚上10:24 收件人:&nbsp;"NAL-i5K/GFF3toolkit"<[email protected]&gt;; 抄送:&nbsp;"陈思远"<[email protected]&gt;;"Mention"<[email protected]&gt;; 主题:&nbsp;Re: [NAL-i5K/GFF3toolkit] can't install (#108) Are you installing within a virtual environment? E.g.: #make new python environment and source it python3 -m venv my-newenv source my-newenv/bin/activate #sometimes you have to upgrade pip and install wheel: pip install --upgrade pip pip install wheel #install gff3tool pip install gff3tool — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[mpoelchau]

I'm not 100% sure what's going on. My first guess is permissions. It looks like you're not using a python virtual environment. Could you try that?

 python3 -m venv my-newenv
source my-newenv/bin/activate

Otherwise, it may be an issue with python3.9 (we've only tested up to python3.7). It will take us a while to get around to testing it in 3.9, though.

[yjx1217]

Same problem here. Python version: 3.7.6 and my python environment was set up via miniconda3.

(base) [jxyue@gpunode ~]$ ~/miniconda3/bin/pip install gff3tool
Collecting gff3tool
Using cached gff3tool-2.0.1.tar.gz (79 kB)
Building wheels for collected packages: gff3tool
Building wheel for gff3tool (setup.py) ... -

And it will take forever ...

[mpoelchau]

@yjx1217 Sorry, I'm not sure what's going on. I ran a fresh install of miniconda (Mac) and did the following:

(base) :~ $  ~/miniconda3/bin/pip install gff3tool
Collecting gff3tool
  Using cached gff3tool-2.0.1.tar.gz (79 kB)
Building wheels for collected packages: gff3tool
  Building wheel for gff3tool (setup.py) ... done
  Created wheel for gff3tool: filename=gff3tool-2.0.1-cp38-cp38-macosx_10_9_x86_64.whl size=258503026 sha256=15f261a4ddbaa9823751f68ae51e5a6695f32a901ba7260440908ea07d0c214e
  Stored in directory: ~/Library/Caches/pip/wheels/13/3e/9c/540a887846eb72db332510fdef60828b9c5eab651e91e51f13
Successfully built gff3tool
Installing collected packages: gff3tool
Successfully installed gff3tool-2.0.1
(base) : ~$ python -V
Python 3.8.5
(base) :~$ ls ~/miniconda3/bin/
2to3			gff3_sort		lzmainfo		pythonw			wish
2to3-3.8		gff3_to_fasta		lzmore			reset			wish8.6
activate		idle3			ncursesw6-config	sqlite3			xz
c_rehash		idle3.8			openssl			sqlite3_analyzer	xzcat
captoinfo		infocmp			pip			tabs			xzcmp
chardetect		infotocap		pip3			tclsh			xzdec
clear			lzcat			pydoc			tclsh8.6		xzdiff
conda			lzcmp			pydoc3			tic			xzegrep
conda-env		lzdiff			pydoc3.8		toe			xzfgrep
cph			lzegrep			python			tput			xzgrep
deactivate		lzfgrep			python.app		tqdm			xzless
easy_install		lzgrep			python3			tset			xzmore
gff3_QC			lzless			python3-config		unlzma
gff3_fix		lzma			python3.8		unxz
gff3_merge		lzmadec			python3.8-config	wheel

It took about 2 minutes for the gff3tool to build.
Can you confirm that wheel is installed and up to date in ~/miniconda3/bin/?

[yjx1217]

Hi mpoelchau,

Thanks for checking! Yes, it is a bit weird. But I managed to installed gff3tool via setup.py , so at least I can use it for my work. :-)

Best,
Jia-Xing