seaward901 commented 4 years ago

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

mpoelchau commented 4 years ago

Hi @seaward901 ,

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

seaward901 commented 4 years ago

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 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 Building wheel for gff3tool (setup.py) ... error ERROR: Command errored out with exit status 1: 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 cwd: /tmp/pip-install-_o7ow8rg/gff3tool/ Complete output (3 lines): running bdist_wheel running build error: <urlopen error retrieval incomplete: got only 606208 out of 175185600 bytes> ---------------------------------------- ERROR: Failed building wheel for gff3tool Running setup.py clean for gff3tool Failed to build gff3tool Installing collected packages: gff3tool Running setup.py install for gff3tool ... error ERROR: Command errored out with exit status 1: 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 cwd: /tmp/pip-install-_o7ow8rg/gff3tool/ Complete output (3 lines): running install running build error: [Errno 17] File exists: '/tmp/pip-install-_o7ow8rg/gff3tool/gff3tool/lib/ncbi-blast+' ---------------------------------------- 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.

------------------ 原始邮件 ------------------ 发件人: "NAL-i5K/GFF3toolkit" <notifications@github.com>; 发送时间: 2020年11月12日(星期四) 晚上9:41 收件人: "NAL-i5K/GFF3toolkit"<GFF3toolkit@noreply.github.com>; 抄送: "陈思远"<309204090@qq.com>;"Mention"<mention@noreply.github.com>; 主题: 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?

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seaward901 commented 4 years ago

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

------------------ 原始邮件 ------------------ 发件人: "NAL-i5K/GFF3toolkit" <notifications@github.com>; 发送时间: 2020年11月12日(星期四) 晚上9:41 收件人: "NAL-i5K/GFF3toolkit"<GFF3toolkit@noreply.github.com>; 抄送: "陈思远"<309204090@qq.com>;"Mention"<mention@noreply.github.com>; 主题: 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 commented 4 years ago

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 commented 4 years ago

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 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 Building wheel for gff3tool (setup.py) ... error ERROR: Command errored out with exit status 1: 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 cwd: /tmp/pip-install-46ln5k27/gff3tool/ Complete output (3 lines): running bdist_wheel running build error: <urlopen error retrieval incomplete: got only 131072 out of 175185600 bytes> ---------------------------------------- ERROR: Failed building wheel for gff3tool Running setup.py clean for gff3tool Failed to build gff3tool Installing collected packages: gff3tool Running setup.py install for gff3tool ... error ERROR: Command errored out with exit status 1: 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 cwd: /tmp/pip-install-46ln5k27/gff3tool/ Complete output (3 lines): running install running build error: [Errno 17] File exists: '/tmp/pip-install-46ln5k27/gff3tool/gff3tool/lib/ncbi-blast+' ---------------------------------------- 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.

------------------ 原始邮件 ------------------ 发件人: "NAL-i5K/GFF3toolkit" <notifications@github.com>; 发送时间: 2020年11月12日(星期四) 晚上10:24 收件人: "NAL-i5K/GFF3toolkit"<GFF3toolkit@noreply.github.com>; 抄送: "陈思远"<309204090@qq.com>;"Mention"<mention@noreply.github.com>; 主题: 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

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mpoelchau commented 4 years ago

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 commented 3 years ago

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 commented 3 years ago

@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 commented 3 years ago

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

NAL-i5K / GFF3toolkit

can't install #108

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